Institute for Mathematics and its Applications University of Minnesota 114 Lind Hall 207 Church Street SE Minneapolis, MN 55455 
We are delighted to announce that Fadil Santosa has been appointed the next director of the Institute for Mathematics and its Applications (IMA), beginning in summer 2008. Please see the press release for more information.
Solicitation of Proposals for IMA Participating Institutions Conferences: All faculty members of the Participating Institutions of the Institute for Mathematics and its Applications are invited to submit proposals for the 20082009 IMA Participating Institution conferences. Deadline: November 15, 2007. Please see Solicitation of Proposals for more information.
All Day  Independence Day. The IMA is closed. 
11:15a12:15p  Tim Hardy, Wayne State College Real algebraic geometry tutorial: Distance matrices  Lind Hall 409  RAG 
All Day  Themes for Birds of a Feather Sessions will be specified on Day 1.  SP7.238.3.07  
8:30a9:15a  Registration and coffee  EE/CS 3176  SP7.238.3.07  
9:15a9:30a  Welcome and introduction  Douglas N. Arnold (University of Minnesota Twin Cities)  EE/CS 3180  SP7.238.3.07 
9:30a10:30a  Introduction to molecular dynamics  Robert D. Skeel (Purdue University)  EE/CS 3180  SP7.238.3.07 
10:30a11:00a  Coffee  EE/CS 3176  SP7.238.3.07  
11:00a12:00p  Statistical mechanics and molecular dynamics  Mark E. Tuckerman (New York University)  EE/CS 3180  SP7.238.3.07 
12:00p2:00p  Lunch  SP7.238.3.07  
2:00p3:00p  Dynamical equations and numerical integrators  Benedict Leimkuhler (University of Edinburgh)  EE/CS 3180  SP7.238.3.07 
3:00p3:30p  Coffee  SP7.238.3.07  
3:30p5:30p  Handson computer session on MD simulation (parallel session)  Eric Barth (Kalamazoo College) Stephen Bond (University of Illinois at UrbanaChampaign) Robert D. Skeel (Purdue University) Chris R. Sweet (University of Notre Dame)  EE/CS 3180 handson computer session EE/CS 3230 parallel session 
SP7.238.3.07 
3:30p4:00p  Integrators for highly oscillatory Hamiltonian systems: an homogenization approach  Frederic Legoll (École Nationale des PontsetChaussées)  EE/CS 3230  SP7.238.3.07 
4:00p4:30p  Analysis and computational studies of the ergodicity of the NoseHoover thermostat  Mitchell Luskin (University of Minnesota Twin Cities)  EE/CS 3230  SP7.238.3.07 
9:00a9:30a  Coffee  EE/CS 3176  SP7.238.3.07  
9:30a10:30a  Free energy calculations and the potential of mean force  Mark E. Tuckerman (New York University)  EE/CS 3180  SP7.238.3.07 
10:30a11:00a  Coffee  EE/CS 3176  SP7.238.3.07  
11:00a12:00p  Molecular sampling  Robert D. Skeel (Purdue University)  EE/CS 3180  SP7.238.3.07 
12:00p2:00p  Lunch  SP7.238.3.07  
2:00p3:00p  Constraints and coarse graining  Giovanni Ciccotti (Università di Roma "La Sapienza")  EE/CS 3180  SP7.238.3.07 
3:00p3:30p  Coffee  EE/CS 3176  SP7.238.3.07  
3:30p5:00p  Handson computer session (parallel session)  Eric Barth (Kalamazoo College) Stephen Bond (University of Illinois at UrbanaChampaign) Robert D. Skeel (Purdue University) Chris R. Sweet (University of Notre Dame)  EE/CS 3180 handson computer session EE/CS 3230 parallel session 
SP7.238.3.07 
3:30p4:00p  Towards a mathematical justification of kinetic theory  Florian Theil (University of Warwick)  EE/CS 3230  SP7.238.3.07 
4:00p4:30p  Analysis of a lattice model for phase transitions and derivation of kinetic relations  Johannes Zimmer (University of Bath)  EE/CS 3230  SP7.238.3.07 
5:00p6:30p  Reception and Poster Session  Lind Hall 400  SP7.238.3.07  
Molecular modelling the structure and dynamics of alginate oligosaccharides  Hoda AbdelAal Bettley (University of Manchester)  
Method for determination of Hubbard model phase diagram from optical lattice experiments by two parameter scaling  Vivaldo L. Campo (University of Minnesota Twin Cities)  
Absolute entropy and free energy of free and bound states of a mobile loop of alphaamylase using the hypothetical scanning method  Srinath Cheluvaraja (University of Pittsburgh)  
A comparison of maximum likelihood and weighted residual approximations to the potential of mean force  Eric C. Cyr (University of Illinois at UrbanaChampaign)  
Objective structures and their applications  Kaushik Dayal (University of Minnesota Twin Cities)  
Modelling of local defects in crystals  Amélie Deleurence (École Nationale des PontsetChaussées (ENPC))  
A systematic method to explore possible silicon tip structures used in AFM  SeyedAlireza Ghasemi (Universität Basel)  
Multilevel summation method for Coulomb interactions  David J. Hardy (University of Illinois at UrbanaChampaign)  
Conformational reinvestigation of two cyclic pentapeptides: to a generic approach in drug development  Pieter Hendrickx (University of Ghent (UG))  
An ab initio molecular dynamics simulation of solid CL20: mechanism and kinetics of thermal decomposition  Olexandr Isayev (Jackson State University)  
Numerical method for solving stochastic differential equations with nonGaussian noise  Changho Kim (Korea Advanced Institute of Science and Technology (KAIST))  
ParticleScaling function (P3S) algorithm for electrostatic problems in free boundary conditions  Alexey Neelov (Universität Basel)  
Temperatureregulated microcanonical dynamics  Emad Noorizadeh (University of Edinburgh)  
A BellEvansPolanyi principle for molecular dynamics trajectories and its implications for global optimization  Shantanu Roy (Universität Basel)  
Uniqueness of the densitytopotential mapping in excitedstate densityfunctional theory  Prasanjit Samal (University of Minnesota Twin Cities)  
Precision problems in density functional development for better molecular modeling  Michael Teter (Cornell University)  
Mesoscopic model for the fluctuating hydrodynamics of binary and ternary mixtures  Erkan Tüzel (North Dakota State University)  
New numerical algorithms and software for minimizing biomolecular potential energy functions  Dexuan Xie (University of Wisconsin) 
9:00a9:30a  Coffee  EE/CS 3176  SP7.238.3.07  
9:30a10:30a  Transition pathways of rare events  Eric VandenEijnden (New York University)  EE/CS 3180  SP7.238.3.07 
10:30a11:00a  Coffee  EE/CS 3176  SP7.238.3.07  
11:00a12:00p  Rate constants  Giovanni Ciccotti (Università di Roma "La Sapienza") Mark E. Tuckerman (New York University)  EE/CS 3180  SP7.238.3.07 
12:15p2:00p  Lunch  SP7.238.3.07  
2:00p3:00p  Adaptive methods for free energy computation and coarsegraining strategies  Eric Felix Darve (Stanford University)  EE/CS 3180  SP7.238.3.07 
3:00p3:30p  Coffee  EE/CS 3176  SP7.238.3.07  
3:30p4:25p  "Birds of a feather" sessions:
Data Abstractions
Coarse Graining  EECS 3180 EECS 3111 
SP7.238.3.07  
4:35p5:30p  "Birds of a feather" sessions:
Thermostatting
Collective Variables  EECS 3180 EECS 3111 
SP7.238.3.07 
8:45a9:15a  Coffee  EE/CS 3176  SP7.238.3.07  
9:15a9:55a  Milestoning, extending time scale of molecular simulations  Ron Elber (University of Texas)  EE/CS 3180  SP7.238.3.07 
9:55a10:35a  Nanomechanics of biomolecules  Christof Schuette (Freie Universität Berlin)  EE/CS 3180  SP7.238.3.07 
10:35a11:00a  Coffee  EE/CS 3176  SP7.238.3.07  
11:00a11:20a  A reduced stochastic model for shock and detonation waves  Gabriel Stoltz (École Nationale des PontsetChaussées (ENPC))  EE/CS 3180  SP7.238.3.07 
11:40a12:00p  Efficient implementation of adaptively biased molecular dynamics  Celeste Sagui (North Carolina State University)  EE/CS 3180  SP7.238.3.07 
12:00p12:15p  Group Photo  SP7.238.3.07  
12:15p2:00p  Lunch  SP7.238.3.07  
2:00p2:40p  Hybrid Monte Carlo methods  Jesus A. Izaguirre (University of Notre Dame)  EE/CS 3180  SP7.238.3.07 
2:40p3:00p  Normal mode partitioning of Langevin dynamics for the simulation of biomolecules  Chris R. Sweet (University of Notre Dame)  EE/CS 3180  SP7.238.3.07 
3:00p3:30p  Coffee  EE/CS 3176  SP7.238.3.07  
3:30p3:50p  Efficient modeling of solvent environments  Michael Feig (Michigan State University)  EE/CS 3180  SP7.238.3.07 
3:50p4:10p  Cluster optimization in protein docking  Julie C. Mitchell (University of Wisconsin)  EE/CS 3180  SP7.238.3.07 
4:10p4:30p  Umbrella sampling for nonequilibrium processes  Aaron Dinner (University of Chicago)  EE/CS 3180  SP7.238.3.07 
4:30p5:00p  Second Chances  EE/CS 3180  SP7.238.3.07  
6:30p8:30p  Group dinner at Kikugawa  Kikugawa at Riverplace
43 Main St. SE. Minneapolis, MN (612) 3783006 
SP7.238.3.07 
8:45a9:15a  Coffee  EE/CS 3176  SP7.238.3.07  
9:15a9:55a  Coarsegraining the free energy of atomistic systems: a mathematical approach  Claude Le Bris (École Nationale des PontsetChaussées (ENPC))  EE/CS 3180  SP7.238.3.07 
9:55a10:15a  Estimating accuracy in classical molecular simulation  Stephen Bond (University of Illinois at UrbanaChampaign)  EE/CS 3180  SP7.238.3.07 
10:15a10:35a  Adaptive methods for molecular dynamics  Tony Lelievre (Ecole Nationale des Ponts et Chaussees)  EE/CS 3180  SP7.238.3.07 
10:35a11:00a  Coffee  EE/CS 3176  SP7.238.3.07  
11:00a11:20a  Boundary conditions for nonequilibrium molecular dynamics simulation  Xiantao Li (Pennsylvania State University)  EE/CS 3180  SP7.238.3.07 
11:20a11:40a  Quantum reaction rates  Raymond Kapral (University of Toronto)  EE/CS 3180  SP7.238.3.07 
11:40a2:00p  Lunch  SP7.238.3.07  
2:00p2:40p  Accelerated molecular dynamics methods  Arthur F. Voter (Los Alamos National Laboratory)  SP7.238.3.07  
2:40p3:00p  Coffee  EE/CS 3176  SP7.238.3.07  
3:00p3:20p  MD modelling of primary damage production in displacement cascades  Roman Voskoboynikov (University of Cambridge)  EE/CS 3180  SP7.238.3.07 
3:20p3:40p  Thermal boundary conditions for molecular dynamics simulations  Simon Gill (University of Leicester)  EE/CS 3180  SP7.238.3.07 
3:40p4:00p  Protein materials balance strength, energy dissipation and robustness by selecting nanopatterned, hierarchical features  Markus J. Buehler (Massachusetts Institute of Technology)  EE/CS 3180  SP7.238.3.07 
4:00p4:30p  Second Chances  EE/CS 3180  SP7.238.3.07 
8:30a9:00a  Coffee  EE/CS 3176  SP7.238.3.07  
9:00a9:40a  Quantum Drude models : A complete description of polarization and dispersion  Glenn Martyna (IBM Corporation)  EE/CS 3180  SP7.238.3.07 
9:40a10:00a  Effective normal modes from finite temperature molecular dynamics simulations  Rodolphe Vuilleumier (Université de Paris VI (Pierre et Marie Curie))  EE/CS 3180  SP7.238.3.07 
10:00a10:20a  Direct calculation of interfacial free energy using molecular simulation  Brian Laird (University of Kansas)  EE/CS 3180  SP7.238.3.07 
10:20a11:00a  Coffee  EE/CS 3176  SP7.238.3.07  
11:00a11:20a  Aspects of nonautonomous molecular dynamics  Michel Cuendet (Swiss Institute of Bioinformatics)  EE/CS 3180  SP7.238.3.07 
11:20a12:00p  Second chances and closing remarks  EE/CS 3180  SP7.238.3.07 
All Day  No activity scheduled.  SP7.238.3.07 
9:00a9:30a  Coffee  EE/CS 3176  SP7.238.3.07  
9:30a10:45a  Introduction to quantum chemistry and ab initio calculations of interatomic potentials  Eric Cances (Centre d'Enseignement et de Recherche en Mathématiques et Calcul Scientifique (CERMICS))  EE/CS 3180  SP7.238.3.07 
10:45a11:15a  Coffee  EE/CS 3176  SP7.238.3.07  
11:15a12:30p  Numerical algorithms for density functional theory  Yousef Saad (University of Minnesota Twin Cities)  EE/CS 3180  SP7.238.3.07 
12:30p2:30a  Lunch  SP7.238.3.07  
2:30p3:30p  Density functional theory for periodic systems  Eric Cances (Centre d'Enseignement et de Recherche en Mathématiques et Calcul Scientifique (CERMICS))  EE/CS 3180  SP7.238.3.07 
3:30p4:00p  Coffee  EE/CS 3176  SP7.238.3.07  
4:00p5:00p  Numerical algorithms for density functional theory (continued)  Yousef Saad (University of Minnesota Twin Cities)  EE/CS 3180  SP7.238.3.07 
9:00a9:30a  Coffee  EE/CS 3176  SP7.238.3.07  
9:30a10:45a  Densityfunctional practice  Nicola Marzari (Massachusetts Institute of Technology)  EE/CS 3180  SP7.238.3.07 
10:45a11:15a  Coffee  EE/CS 3176  SP7.238.3.07  
11:15a12:30p  Electronic correlations and Hubbard approaches  Matteo Cococcioni (University of Minnesota Twin Cities)  EE/CS 3180  SP7.238.3.07 
12:30p2:30a  Lunch  SP7.238.3.07  
2:30p3:30p  Tutorial on static calculations  Matteo Cococcioni (University of Minnesota Twin Cities) Ismaila Dabo (Massachusetts Institute of Technology)  EE/CS 3180  SP7.238.3.07 
3:30p4:00p  Coffee  EE/CS 3176  SP7.238.3.07  
4:00p5:30p  Tutorial on CarParrinello molecular dynamics  Nicola Marzari (Massachusetts Institute of Technology) Arash A. Mostofi (University of Cambridge)  EE/CS 3180  SP7.238.3.07 
8:30a9:00a  Coffee  EE/CS 3176  SP7.238.3.07  
9:00a10:00a  Wavelets for electronic structure calculations and electrostatic problems  Stefan Goedecker (Universität Basel)  EE/CS 3180  SP7.238.3.07 
10:00a10:15a  Coffee  EE/CS 3176  SP7.238.3.07  
10:15a11:15a  Exchange and correlation in electronic systems: the hole story  Axel D. Becke (Dalhousie University)  EE/CS 3180  SP7.238.3.07 
11:15a11:30a  Coffee  EE/CS 3176  SP7.238.3.07  
11:30a12:00p  Efficient KohnSham density functional calculations using the Gaussian and plane waves approach  Jürg Hutter (Universität Zürich)  EE/CS 3180  SP7.238.3.07 
12:00p12:30p  TBA  David Langreth (Rutgers University)  EE/CS 3180  SP7.238.3.07 
12:30p2:30p  Lunch  SP7.238.3.07  
2:30p3:00p  Linearscaling densityfunctional calculations with planewaves  Arash A. Mostofi (University of Cambridge)  EE/CS 3180  SP7.238.3.07 
3:00p3:30p  A Linearscaling AObased MP2 method for large molecules by rigorous integral estimates  Christian Ochsenfeld (EberhardKarlsUniversität Tübingen)  EE/CS 3180  SP7.238.3.07 
3:30p4:00p  Coffee  EE/CS 3176  SP7.238.3.07  
4:00p5:30p  Second Chances session on fast algorithms  EE/CS 3180  SP7.238.3.07  
6:30p8:30p  Group dinner at Caspian Bistro  Caspian Bistro
2418 University Ave SE
Minneapolis, MN 55414
(612) 6231113 
SP7.238.3.07 
8:30a9:00a  Coffee  EE/CS 3176  SP7.238.3.07  
9:00a9:30a  Dealing with spatial regions  Andreas Savin (Université de Paris VI (Pierre et Marie Curie))  EE/CS 3180  SP7.238.3.07 
9:30a10:00a  KohnSham methods for implicit density functionals  Viktor N. Staroverov (University of Western Ontario)  EE/CS 3180  SP7.238.3.07 
10:00a10:30a  QM/MM studies on enzymes  Walter Thiel ( MaxPlanckInstitut für Kohlenforschung)  EE/CS 3180  SP7.238.3.07 
10:30a11:00a  Coffee  EE/CS 3176  SP7.238.3.07  
11:00a11:30a  TBA  Donald Truhlar (University of Minnesota Twin Cities)  EE/CS 3180  SP7.238.3.07 
11:30a12:00p  TBA  Y. Alexander Wang (University of British Columbia)  EE/CS 3180  SP7.238.3.07 
12:00p12:30p  TBA  Renata Wentzcovitch (University of Minnesota Twin Cities)  EE/CS 3180  SP7.238.3.07 
12:30p2:30a  Lunch  SP7.238.3.07  
2:30p3:00p  Orbitalfree embedding potential: properties, approximations, and the use in computer simulations to couple quantum chemical and classical levels of description  Tomasz A. Wesolowski (Université de Genève)  EE/CS 3176  SP7.238.3.07 
3:00p4:30p  Second Chances session on DFT  EE/CS 3180  SP7.238.3.07 
All Day  Workshop Outline: Posing of problems by the 6 industry mentors. Halfhour introductory talks in the morning followed by a welcoming lunch. In the afternoon, the teams work with the mentors. The goal at the end of the day is to get the students to start working on the projects.  EE/CS 3180  MM8.817.07  
9:00a9:30a  Coffee and Registration  EE/CS 3176  MM8.817.07  
9:30a9:40a  Welcome and Introduction  Douglas N. Arnold (University of Minnesota Twin Cities) Richard J. Braun (University of Delaware) Fernando Reitich (University of Minnesota Twin Cities) Arnd Scheel (University of Minnesota Twin Cities)  EE/CS 3180  MM8.817.07 
9:40a10:00a  Team 1: Supersonic design  Natalia Alexandrov (NASA Langley Research Center)  EE/CS 3180  MM8.817.07 
10:00a10:20a  Team 2: 802.11 WLAN MAC layer modeling  Radu V. Balan (Siemens Corporate Research, Inc.)  EE/CS 3180  MM8.817.07 
10:20a10:40a  Team 3: Associating earthorbiting objects detected by astronomical telescopes  Gary B. Green (The Aerospace Corporation)  EE/CS 3180  MM8.817.07 
10:40a11:00a  Break  EE/CS 3176  MM8.817.07  
11:00a11:20a  Team 4: High dimensional, nonlinear, nonconvex optimization problems in the area of aircraft and vehicle design  John R. Hoffman (Lockheed Martin Missiles and Space Company, Inc.)  EE/CS 3180  MM8.817.07 
11:20a11:40a  Team 5: Size and shape comparisons from noisy, unlabeled, incomplete configurations of landmarks in threedimensional space  Mark A. Stuff (General Dynamics Advanced Information Systems)  EE/CS 3180  MM8.817.07 
11:40a12:00p  Team 6: Wavelength assignment and conversion in optical networking  Lisa Zhang (Lucent Technologies Bell Laboratories)  EE/CS 3180  MM8.817.07 
12:00p1:30p  Lunch  Lind Hall 400  MM8.817.07  
1:30p4:30p  afternoon  start work on projects  Breakout Rooms  MM8.817.07 
All Day  Students work on the projects. Mentors guide their groups through the modeling process, leading discussion sessions, suggesting references, and assigning work.  Breakout Rooms  MM8.817.07 
All Day  Students work on the projects. Mentors guide their groups through the modeling process, leading discussion sessions, suggesting references, and assigning work.  Breakout Rooms  MM8.817.07 
Event Legend: 

MM8.817.07  Mathematical Modeling in Industry XI  A Workshop for Graduate Students 
RAG  Weekly Tutorial: Real Algebraic Geometry 
SP7.238.3.07  Classical and Quantum Approaches in Molecular Modeling 
Tim Hardy, Wayne State College Real algebraic geometry tutorial: Distance matrices 

Abstract: "distance matrix" is a matrix containing the distances, taken pairwise, of a set of points. I shall trace the history of distance matrices during the last 150 years. I shall develop distance matrices from an inner product. I shall present some applications and at least one generalization.  
Hoda AbdelAal Bettley (University of Manchester)  Molecular modelling the structure and dynamics of alginate oligosaccharides  
Abstract: Joint work with Richard A. Bryce. Alginate copolymers are a key component of the extracellular polymeric substances (EPS) matrix of bacterial microorganisms such as P. aeruginosa, and occur in high abundance in nature. Alginate heteropolysaccharides comprise alternating blocks of alpha(1>4)linked Lguluronate and beta(1>4)linked Dmannuronate. To understand the microscopic behaviour and interactions of these flexible acidic sugars within the EPS matrix, a suitable molecularlevel model is required. We derive a molecular mechanical force field for the two uronic acids, with validation against available experimental data. We then construct a detailed study of the structure and dynamics of alginate chains. We explore alginate models of increasing complexity, from disaccharides to single and doublestranded oligomer helices, employing the techniques of molecular dynamics and replicaexchange molecular dynamics. The condensed phase behaviour of these systems is discussed, including the role of counterions and the implications for interaction with other constituents of the EPS matrix.  
Hoda AbdelAal Bettley (University of Manchester)  Molecular modelling the structure and dynamics of alginate oligosaccharides  
Abstract: Same abstract as the 7/24 poster session.  
Natalia Alexandrov (NASA Langley Research Center)  Team 1: Supersonic design  
Abstract: Designing affordable, efficient, quiet supersonic passenger
aircraft has been under investigation for many years.
Obstacles to designing such aircraft are also many, both in
fundamental physics and in computational science and
engineering. The problem of design is multidisciplinary in its
nature and the goals of the constituent disciplines that govern
the behavior of an aircraft are often at odds. In particular,
aircraft that yields low sonic boom may not be attractive
aerodynamically, while aerodynamically optimized aircraft may
produce unacceptable sonic boom. One of the essential
difficulties in using direct optimization methods to design for
low boom and low drag is in modeling the design problem. For
instance, it is not clear what objective functions to use.
This project will use simple aerodynamic and sonic boom models to examine modeling of the design problem itself. We will attempt to establish a meaningful direct functional dependence between the shape of the aircraft and aerodynamic and noise quantities of interest by studying the sensitivity of these quantities to changes in shape. We will experiment with several direct multiobjective optimization problem formulations. References:
Prerequisites: Required: Scientific computing skills (Matlab or Fortran 90/95 or C), 1 semester in nonlinear optimization Desired: Some background in statistical modeling, numerical analysis, multiobjective optimization Keywords: multidisciplinary optimization, supersonic design, low boom, aerodynamic optimization 

Paul W. Ayers (McMaster University)  Densityfunctional theory and its generalizations: legendre transform, constrained search, open problems  
Abstract: The quantum manyelectron problem is easy in principle (solve the Nelectron Schrödinger equation) and hard in practice (because the cost of numerical methods typically grows exponentially with the number of variables). However, there are simplifying features. First, the dimensionality can be reduced because electronic Hamiltonians contain only 1body and 2body terms. (This leads to reduced densitymatrix methods.) Second, the dimensionality can be reduced because electrons are identical particles: if you know everything about one electron, then you know everything about all of the electrons. (This leads to electronpropagator theory and densityfunctional theory.) There is a “catch.” Reducing the number of dimensions leads to other problems associated with approximating the energy functional and/or associated with restricting the domain of the variational procedure. Two powerful techniques for resolving these difficulties are the Legendre transform and constrainedsearch formulations of density functional theory. This talk will discuss these formulations, and show how they can be extended to define "generalized" densityfunctional theories. I'll conclude with some of my favorite open problems in densityfunctional theory.  
Radu V. Balan (Siemens Corporate Research, Inc.)  Team 2: 802.11 WLAN MAC layer modeling  
Abstract: 802.11 Wireless Local Area Networks (WLANs) have become as
ubiquitous as Internet access for personal computers. The basic
unit of a WLAN is composed of one Access Point (AP), and
several mobile stations (STAs), all forming a Basic Service Set
(BSS). A typical WLAN setup is depicted in Figure 1.
Figure 1: A typical Basic Service Set (BSS), with one AP, and several mobile stations. The IEEE Standard governing WLANs describes two modes of operation: Distributed Coordination Function (DCF), and Point Coordination Function (PCF). By and large, chipset manufacturers implement only the DCF mode, and compatibility testing is done for this mode exclusively. The DCF is a contentionbased mechanism where each wireless device (AP, or STA) competes for air time. More specifically, the 802.11 standard is implemented as follows:
Description of the problem Basically there are two distinct regimes, completely opposite from one another:
The goal of this research group is to address one or more of the issues above. Ideally, students should have:  familiarity with basic stochastic modeling concepts (such as Markov chains) Figure 2: A Markov Chain Model for a WLAN device. Bibliography [1] G.Bianchi, Performance Analysis of the IEEE 802.11 Distributed Coordination Function, IEEE Journal on Selected Areas of Communications, 18 (3), 2000, 535547. [2] P.E.Engelstad and O.N.Osterbo, NonSaturation and Saturation Analysis of IEEE 802.11e EDCA with Starvation Prediction, MSWiM.05: Proceedings of the 8th ACM international symposium on Modeling, analysis and simulation of wireless and mobile systems, Montreal, Canada, 2005. 

Axel D. Becke (Dalhousie University)  Exchange and correlation in electronic systems: the hole story  
Abstract: Exchange and correlation effects in electronic systems are rigorously related to a twoelectron function called the exchangecorrelation "hole". Modelling of the hole in real space is a powerful route to development and refinement of exchange and correlation functionals in DFT. We have developed realspace models of all correlation types of importance in chemical physics (dynamical, nondynamical, and dispersion) and these will be reviewed.  
Stephen Bond (University of Illinois at UrbanaChampaign)  Estimating accuracy in classical molecular simulation  
Abstract: In classical molecular dynamics, the accuracy of numerical methods should be measured with respect to statistical averages, due to the lack of a meaningful exact trajectory. In this talk I will survey some results from backward error analysis and show how (under certain assumptions) these results can be applied to compute estimates of the error in averages from molecular dynamics simulations. Results from several test problems will be explored including examples from constant temperature molecular dynamics using a Nosé thermostat.  
Markus J. Buehler (Massachusetts Institute of Technology)  Protein materials balance strength, energy dissipation and robustness by selecting nanopatterned, hierarchical features  
Abstract: Deformation and fracture are fundamental phenomena with major implications on the stability and reliability of machines, buildings and biological systems. All deformation processes begin with erratic motion of individual atoms around flaws or defects that quickly evolve into formation of macroscopic fractures as chemical bonds rupture rapidly, eventually compromising the integrity of the entire structure. However, most existing theories of fracture treat matter as a continuum, neglecting the existence of atoms or nanoscopic features. Clearly, such a description is questionable. Here we discuss an atomistic approach to describe such processes using ultra largescale molecular dynamics (MD) simulation implemented supercomputers. MD provides unparalleled insight into the complex atomicscale deformation processes, linking nano to macro, without relying on empirical input, since all atomic interaction parameters can be derived from fundamental quantum chemical theories. We demonstrate how MD can be used within a multiscale simulation framework to predict the elastic and fracture properties of hierarchical protein materials, marvelous examples of structural designs that balance a multitude of tasks, representing some of the most sustainable material solutions that integrate structure and function across the scales. Breaking the material into its building blocks enables us to perform systematic studies of how microscopic design features influence the mechanical behavior at larger scales. We review studies of collagen – Nature’s superglue, spider silk – a natural fiber that can reach the strength of a steel cable, as well as intermediate filaments – an important class of structural proteins responsible for the mechanical integrity of cells, which, if flawed, can cause serious diseases such as the rapid aging disease progeria. The common ground of these examples is the significance of the material properties at large deformation, its alteration under stress, presence of defects or the effect of variation of environmental conditions. Our studies elucidate intriguing material concepts that enable to balance strength, energy dissipation and robustness by selecting nanopatterned, hierarchical features.  
Vivaldo L. Campo (University of Minnesota Twin Cities)  Method for determination of Hubbard model phase diagram from optical lattice experiments by two parameter scaling  
Abstract: We propose[1] an experimental scheme to obtain the phase diagram of the Hubbard model using cold atoms in optical lattices.[2] The scheme is based on measuring the total energy for a sequence of trapping potentials with diﬀerent proﬁle and is independent of di mensionality. Its essential ingredient is a twoparameter scaling pro cedure that combines a variant of the familiar ﬁnitesize scaling with a nontrivial additional ’ﬁnitecurvature scaling’ necessary to reach the homogeneous limit. We illustrate the viability of the scheme in the onedimensional case, using simulations based on the Bethe Ansatz localdensity approximation as a substitute for experimental data, and show that the ﬁlling corresponding to the Mott transition can be determined with better than 3% accuracy.  
Vivaldo L. Campo (University of Minnesota Twin Cities)  ethod for determination of Hubbard model phase diagram from optical lattice experiments by two parameter scaling  
Abstract: Same abstract as the 7/24 poster session.  
Eric Cances (Centre d'Enseignement et de Recherche en Mathématiques et Calcul Scientifique (CERMICS))  Introduction to quantum chemistry and ab initio calculations of interatomic potentials  
Abstract: Quantum Chemistry aims at understanding the properties of matter through the modelling of its behaviour at a subatomic scale, where matter is described as an assembly of nuclei and electrons. At this scale, the equation that rules the interactions between these constitutive elements is the Schrdinger equation. It can be considered (except in few special cases notably those involving relativistic phenomena or nuclear reactions) as a universal model for at least three reasons. First it contains all the physical information of the system under consideration so that any of the properties of this system can be deduced in theory from the Schrdinger equation associated to it. Second, the Schrdinger equation does not involve any empirical parameter, except some fundamental constants of Physics (the Planck constant, the mass and charge of the electron, ...); it can thus be written for any kind of molecular system provided its chemical composition, in terms of natures of nuclei and number of electrons, is known. Third, this model enjoys remarkable predictive capabilities, as confirmed by comparisons with a large amount of experimental data of various types. Unfortunately, the Schrdinger equation cannot be directly simulated, except for very small chemical systems. It indeed reads as a timedependent 3(M+N)dimensional partial differential equation, where M is the number of nuclei and N the number of the electrons in the system under consideration. On the basis of asymptotic and semiclassical limit arguments, it is however often possible to approximate the Schrdinger dynamics by the socalled BornOppenheimer dynamics, in which nuclei behave as classical pointlike particles. The internuclei (or interatomic) potential can be computed ab initio, by solving the timeindependent electronic Schrdinger equation. The latter equation is a 3Ndimensional partial differential equation (it is in fact a spectral problem), for which several approximation methods are available. The main of them are the wavefunction methods and the Density Functional Theory (DFT). They lead in particular to the HartreeFock model and to the KohnSham model, respectively. In this introductory lecture, I will first present the electronic Schrdinger equation, and show how to derive from this equation the HartreeFock and KohnSham models. Although obtained from totally different approaches, these models have similar mathematical structures. They read as constrained optimization problems, whose EulerLagrange equations are nonlinear eigenvalue problems. In the second part of the lecture, I will introduce the Linear Combination of Atomic Orbitals (LCAO) discretization method, and briefly discuss two important numerical issues: ensuring selfconsistent field (SCF) convergence, and reducing computational scaling.  
Eric Cances (Centre d'Enseignement et de Recherche en Mathématiques et Calcul Scientifique (CERMICS))  Density functional theory for periodic systems  
Abstract: By means of thermodynamic limit arguments, the KohnSham model can be extended to the case when the nuclear configuration is periodic. The resulting periodic KohnSham model is very useful to understand the electronic structure of perfect crystals, but also to simulate the condensed phase by means of artificial periodic boundary conditions. In the latter case, the periodic cell may contain a very large number of nuclei and electrons. In the first part of the lecture, I will present the Bloch theory of periodic Schrdinger operators, and recall how the band structure of their spectrum can be related to the insulating or conducting character of the underlying material. I will also present the concept of Wannier functions, which is of growing importance in various applications (computation of dielectric and magnetic properties, local correlation methods, electronic structure of crystals with defects, ...). In the second part of the lecture, I will focus on the discretization of the periodic KohnSham model in planewave (PW) basis sets.  
James R. Chelikowsky (University of Texas)  Real space pseudopotentials applied to nanoscale systems  
Abstract: One of the most challenging issues in materials physics is to predict the properties of matter at the nanoscale. In this size regime, new structural and electronic properties exist that resemble neither the atomic, nor solid state. These altered properties can have profound technological implications. Theoretical methods to address such issues face formidable challenges. Nanoscale systems may contain thousands of electrons and atoms, and often possess little symmetry. I will illustrate some recent advances in this area based on new computational methods and apply these techniques to systems ranging from clusters of a few dozen atoms to quantum dots containing thousands of atoms. Recent publications: Y. Zhou, Y. Saad, M.L. Tiago, and J.R. Chelikowsky: "Parallel SelfConsistentField Calculations via ChebyshevFiltered Subspace Acceleration,'' Phys. Rev. E 74, 066704 (2006). M.L. Tiago, Y. Zhou, M.M.G. Alemany, Y. Saad, J.R. Chelikowsky: "The Evolution of Magnetism in Iron from the Atom to the Bulk,'' Phys. Rev. Lett. 97, 147201 (2006). M. Lopez del Puerto, M.L. Tiago, and J.R. Chelikowsky: "Excitonic effects and optical properties of passivated CdSe clusters,'' Phys. Rev. Lett. 97, 096401 (2006).  
Srinath Cheluvaraja (University of Pittsburgh)  Absolute entropy and free energy of free and bound states of a mobile loop of alphaamylase using the hypothetical scanning method  
Abstract: A new simulation method is studied which is capable of calculating the absolute entropy and free energy of a microstate. The method is based on calculating the probability of a member in the statistical ensemble by growing the configuration in a stepbystep manner and expressing it as a product of conditional probabilities, each of which is calculated by performing simulations at every step. This is a potentially exact method with the errors arising only from inadequate sampling. The method is applied to a small protein loop in implicit solvent and the results obtained agree quite well with those obtained from other (approximate) methods. Unlike other methods, all long range interactions are taken into account in the reconstruction procedure.  
Giovanni Ciccotti (Università di Roma "La Sapienza")  Constraints and coarse graining  
Abstract: Holonomic constraints as coarse graining of (large) molecules. The dynamical evolution of a system subjected to holonomic constraints (SHAKE and beyond): Lagrange & Hamilton eq.s of first type; the standard (unstable) solution; Shake , i.e. an evolution satisfying exactly the constraints at every time step. The statistical measure and its associated evolution equation (Liouville equation) for mechanical systems with holonomic constraints: nonhamiltonian systems and their statistical behavior; the eq.s of motions of a mechanical systems subjected to constraints as a nonhamiltonian system; generalized Liouville eq. and statistical equilibrium probability.  
Giovanni Ciccotti (Università di Roma "La Sapienza"), Mark E. Tuckerman (New York University)  Rate constants  
Abstract: The linear response theory formulation of a rate constan as a suitable time correlation function; its representation via the transition state theory (TST) term and the transmission coefficient. Calculation of the TST term via the bluemoon approach. i.e. impose a reaction coordinate as a constraint, compute its associated free energy and, by exponentiation, compute the associated probability. Use the unbiased constrained ensemble to generate a proper ensemble of reactive trajectories and compute the transmission coeffcient. The product of the TST term times the transmission coefficient provides the rate constant.  
Matteo Cococcioni (University of Minnesota Twin Cities)  Electronic correlations and Hubbard approaches  
Abstract: Electronic correlation play a very important role in the physical properties of many materials characterized by very localized electronic states (as transitionmetals or rareearths compounds). Unfortunately, standard approximations to Density Functional Theory (like the Local Density Approximation or the Generalized Gradient Approximation) are not accurate enough to give a proper description of correlation effects. While multiconfigurational QuantumChemistry methods are too expensive for most systems but very small molecules, several corrections to DFT have been introduced to give a better description of correlated states without giving up the relatively low computational cost of DFT calculations. After a general introduction on electronic correlation, one of the simplest corrective approaches, named LDA+U, will be described along with its implementation in a planewave pseudopotential DFT code.  
Matteo Cococcioni (University of Minnesota Twin Cities), Ismaila Dabo (Massachusetts Institute of Technology)  Tutorial on static calculations  
Abstract: A handson tutorial on DFT total energy and force calculations will cover optimization of input parameters through convergence tests, electronic relaxation and structural optimization. The simulations will be performed using the planewave pseudopotential implementation of DFT contained in the QuantumESPRESSO package.  
Matteo Cococcioni (University of Minnesota Twin Cities)  A consistent, linearresponse approach to LDA+U  
Abstract: Hubbard Ucorrected DFT functionals have been very successful in describing several stronglycorrelated systems for which "standard" approximations to DFT fail. Unfortunately no explicit expression exists for the effective electronic interaction parameter (the Hubbard U) contained in the corrective ("+U") functional and semiempirical estimates have been often used to determine its value. In this talk, after a general introduction to the LDA+U method, I will present our linear response approach to the evaluation of the Hubbard U [1]. Within this approach the onsite electronic coupling is computed from the response of the considered system to a shift in the potential acting on its correlated atomic states. Specifically, it is evaluated as the difference between the inverse of the bare and fully interacting response matrices. The U we obtain thus corresponds to the effective (atomically averaged) interaction between electrons that are located on the same site. In this way the strength of the "+U" correction is consistently evaluated from the same DFT scheme we aim to correct; the LDA+U is transformed in a completely abinitio method with no need for any empirical evaluation of the effective coupling. The results are also largely independent on the choice of the localized orbitals: the same occupation matrix that enters the expression of the "+U" correction is consistently used to compute the effective interaction parameter. With this approach we successfully studied the structural, electronic, chemical and electrochemical properties of several transition metals compounds. Examples of applications will include minerals in the Earth's interior [1], cathode materials for nextgeneration lithiumion batteries [2] and catalysis reactions on molecules [3]. [1] M. Cococcioni and S. de Gironcoli, PRB (2005). [2] F. Zhou, M. Cococcioni, A. C. Marianetti, D. Morgan and G. Ceder, PRB (2004). [3] H. J. Kulik, M. Cococcioni, D. Scherlis and N. Marzari, PRL (2007).  
Michel Cuendet (Swiss Institute of Bioinformatics)  Aspects of nonautonomous molecular dynamics  
Abstract: Performing constant temperature (and pressure) molecular dynamics simulation requires adequate thermostating (and barostating) algorithms, which couple additional degrees of freedom to the physical phase space variables. Thermostating is particularly important when external work is performed on the system in order to induce a nonequilibrium transition between two states. It appeared recently that nonequilibrium statistical mechanical relations such as the Jarzynski identity and the Crooks theorem naturally emerge as a property of nonautonomous thermostated dynamical systems. This however imposes an additional condition on the form of the thermostating dynamics, which is not required in the equilibrium case and is not fulfilled by all stateoftheart thermostats.  
Eric C. Cyr (University of Illinois at UrbanaChampaign)  A comparison of maximum likelihood and weighted residual approximations to the potential of mean force  
Abstract: The potential of mean force (PMF) describes the change in free energy along a reaction coordinate and determines the strength and likelihood of association in molecular systems. Current methods, like Thermodynamic Integration (TI) and WHAM, use piecewise linear and piecewise constant approximations of the PMF. We propose two methods that allow the use of arbitrary basis functions, one based on maximum likelihood estimation and another on the method of weighted residuals. Numerical comparisons with TI and WHAM are performed.  
Ismaila Dabo (Massachusetts Institute of Technology)  Realspace corrections for electrostatic interactions in periodic boundary conditions  
Abstract: Joint work with Boris Kozinsky (Department of Physics, MIT), Nicholas E. SinghMiller, and Nicola Marzari (Department of Materials Science and Engineering, MIT). We address periodicimage errors arising from the use of periodic boundary conditions to describe systems that do not exhibit full three dimensional periodicity. We show that the difference between the periodic potential, straightforwardly obtained from a Fourier transform, and the exact potential can be characterized analytically. In light of this observation, we present an efficient realspace method to correct periodicimage errors, demonstrating that exponential convergence of the energy with respect to cell size can be achieved in practical periodic boundarycondition calculations. Comparing the method with existing schemes, we find that it is particularly advantageous for studying charged systems and systems exhibiting partial periodicity.  
Eric Felix Darve (Stanford University)  Adaptive methods for free energy computation and coarsegraining strategies  
Abstract: Free energy computation is one of the main goals of molecular dynamics simulations. Numerically, these calculations are made difficult by the presence of free energy barriers separating metastable basins. Several methods have been developed to address this issue such as the adaptive biasing force (ABF), in which an external force is progressively adapted. Upon convergence, the reaction coordinate along which the free energy is computed exhibits a diffusive behavior in a flat free energy profile, leading to a rapid convergence of the computed averages and a rapid reduction of statistical errors. Such methods can serve as the starting point for computing coarse grained models of large proteins in which the number of degree of freedom is greatly reduced. We will show the role the free energy plays in formulating these models. In this case as well, ABF can be applied to yield faster convergence.  
Ernest R. Davidson (University of Washington)  Theoretical description of electrons in singloe molecule magnets  
Abstract: Single molecule magnets are usually based on transition metals with partially filled d shells. When several metal centers are involved this leads to molecules with many single occupied orbitals coupled into an intermediate spin state. Conventional methods of quantum chemistry are not able to deal with this situation, so the Heisenberg model hamiltonian is often used with parameters estimated from DFT calculations. Practical as well as logical problems with this approach will be discussed. Some of the difficulties with treating exchange in DFT for open shell systems will be presented.  
Kaushik Dayal (University of Minnesota Twin Cities)  Objective structures and their applications  
Abstract: Objective structures [1] are a recent classification of atomic and molecular structures that includes numerous systems of current interest. Examples are nanotubes and biological virus components. While these structures are not crystalline, there are many strong analogies to crystals. These analogies can be exploited to generalize computational techniques developed in the context of crystals to these new systems. Further, they may provide strategies for selfassembly and structure determination. Some examples of current work exploiting these ideas will be presented. These include finding the normal modes of these structures (in analogy with phonons), Objective Molecular Dynamics in analogy with conventional MD, and DFT and other firstprinciples techniques in the Objective setting. Recent work on finding all possible objective structures will be described. [1] R. D. James, Objective Structures, J. Mech. Phys. Solids, 54, 23542390 (2006).  
Kaushik Dayal (University of Minnesota Twin Cities)  Objective structures and their applications  
Abstract: Same abstract as the 7/24 poster session.  
Amélie Deleurence (École Nationale des PontsetChaussées (ENPC))  Modelling of local defects in crystals  
Abstract: Work in collaboration with Eric Cancès (CERMICSENPC, France) and Mathieu Lewin (Department of Mathematics, Université de Cergy, France) We present mathematical results obtained for a new meanfield model dedicated to the description of interacting electrons in crystals with local defects. We work with a reduced HartreeFock model, obtained from the usual HartreeFock model by neglecting the exchange term. Then we deduce a new variational model for computing the perturbation in a basis of precomputed maximally localized Wannier functions of the reference perfect crystal. Finally we show some numerical results in which we have applied the variational approximation and used a onedimensional model with Yukawa interaction potential.  
Amélie Deleurence (École Nationale des PontsetChaussées (ENPC))  Modelling of local defects in crystals  
Abstract: Same abstract as the 7/24 poster session.  
Aaron Dinner (University of Chicago)  Umbrella sampling for nonequilibrium processes  
Abstract: Many systems of significant fundamental and applied interest are irreversible. These include, but are not limited to, living systems, chemical reactors, systems with driven flows of matter and energy, and photoactivated systems. For theoretical studies of such nonequilibrium processes, the steadystate distribution is of central importance because it enables calculation of static averages of observables for comparison to experimental measurements. For systems at equilibrium, low probability states can be explored efficiently in simulations with umbrella sampling methods, in which biasing potentials that are functions of one or more order parameters are used to enhance sampling of selected regions of phase space. What complicates extending umbrella sampling to simulations of nonequilibrium processes is that, by definition, they do not obey detailed balance (microscopic reversibility). As such, one must account for the fact that the steadystate probability of observing particular values of the order parameters can be determined by a balance of flows in phase space through different possible transitions. In this talk, I will describe the first algorithm for enforcing equal sampling of different regions of phase space in an ergodic system arbitrarily far from equilibrium, which enables its steadystate probability distribution to be determined with high accuracy. The efficiency of the algorithm will be demonstrated by applying it to a model of a genetic toggle switch which evolves irreversibly according to a continuous time Monte Carlo procedure.  
Ron Elber (University of Texas)  Milestoning, extending time scale of molecular simulations  
Abstract: A new computational algorithm to extend time scales of atomically detailed simulations is illustrated. The algorithm (Milestoning) is based on partitioning the dynamics to a sequence of trajectories between “milestones” and constructing a nonMarkovian model for the motion along a reaction coordinate. Besides "toy" models, two molecular systems are discussed: (i) The kinetics of a conformational transition in a blocked alanine is computed and shown to be accurate, more efficient than straightforward Molecular Dynamics by a factor of about 9, and nonexponential. (ii) The allosteric conformational transition in Scapharca hemoglobin is calculated. The results for the rate (about 10+/9 microseconds) are in accord with experiment and are obtained about 1,000 times faster than straightforward Molecular Dynamics. No assumption of an activated process or states separated by significant barrier is made. A general scaling argument predicts linear speedup with the number of milestones for diffusive processes, and exponential speedup for transitions over barriers. The algorithm is also trivial to parallelize. As a side result Milestoning also produces the free energy profile along the reaction coordinate, and is able to describe nonequilibrium motions along one (or a few) degrees of freedom.  
JeanLuc Fattebert (Lawrence Livermore National Laboratory)  Realspace finite difference method for O(N) firstprinciples molecular dynamics with plane waves accuracy  
Abstract: Representing the electronic structure in Density Functional Theory (DFT)
by a set of localized wave functions discretized on a realspace mesh
essentially leads to a linear scaling of the computational cost with
the size of the physical system.
This can be achieved by formulating the DFT energy functional
in terms of general nonorthogonal orbitals which are then optimized
under localization constraints (spatial confinement).
Multigrid preconditioning and a block version of Anderson's
extrapolation scheme are used to accelerate convergence towards the
ground state.
For localization regions  constraints  large enough,
one can reduce truncation error to a value smaller than discretization
error and achieve the level of accuracy of a Plane Waves calculation.
Accuracy is improved by allowing for flexible localization regions that
can adapt to the system.
This also reduces problems with local minima and enables energy
conserving BornOppenheimer molecular dynamics simulations.
Our implementation of this approach scales on hundreds of processors and
becomes competitive with Plane Waves codes around 500 atoms.
References: [1] J.L. Fattebert and F. Gygi, Phys. Rev. B 73, 115124 (2006) [2] J.L. Fattebert and F. Gygi, Comput. Phys. Comm. 162, 24 (2004) This work was performed under the auspices of the U.S. Department of Energy by University of California Lawrence Livermore National Laboratory under contract No. W7405Eng48. 

Michael Feig (Michigan State University)  Efficient modeling of solvent environments  
Abstract: The accurate representation of the solvent environment is an essential but also very costly component of biomolecular simulations. As a computationally less expensive alternative, implicit solvent models based on continuum electrostatic theory have become attractive alternatives to the standard explicit solvent models. Examples of biomolecular simulations with implicit aqueous solvent and implicit biological membranes are presented along with remaining mathematical challenges to fully take advantage of the much reduced model complexity.  
SeyedAlireza Ghasemi (Universität Basel)  A systematic method to explore possible silicon tip structures used in AFM  
Abstract: Same abstract as the 7/24 poster session.  
SeyedAlireza Ghasemi (Universität Basel)  A systematic method to explore possible silicon tip structures used in AFM  
Abstract: We present a systematic way to construct silicon tips by using the minima hopping method(MHM) with limited temperature. In Molecular Dynamics part of the MHM we limit the temperature to some value used in experiments. We used TightBinding scheme to evaluate energy and forces of silicon and hydrogen atoms in MHM. Structures with lowest energy obtained with this method are used in AFM simulation and force between tip and surface is calculated in terms of distance and some of obtained results are presented in this poster.  
Simon Gill (University of Leicester)  Thermal boundary conditions for molecular dynamics simulations  
Abstract: A method for applying transient thermal boundary conditions to a molecular dynamics simulation is presented. The Kapitza effect at the boundaries is avoided by a diffuse feedbackcontrolled buffer zone. It is shown that this technique can be extended to provide a simple interface for coupling between concurrent atomistic and continuum simulations for ballistic heat transport.  
Stefan Goedecker (Universität Basel)  Wavelets for electronic structure calculations and electrostatic problems  
Abstract: Wavelets are a systematic localized basis set that is well suited for representing KohnSham orbitals. I will explain the algorithms that we are using in our new ABINIT wavelet program and show perfomance results. In the second part I will show how scaling functions can be used to solve electrostatic problems both for continuous and discrete charge distributions under various boundary conditions.  
Gary B. Green (The Aerospace Corporation)  Team 3: Associating earthorbiting objects detected by astronomical telescopes  
Abstract: Project description:
Astronomical telescopes detect the passage of an earthorbiting
object as a streak in an image. Over a period of months, it is
possible that many objects will pass through the field of view,
some appearing more than once. There are estimates of 100,000
objects in orbit that might be detected by high resolution
telescopes. A large field of view telescope may see 100
streaks a night. Most of these objects are space debris that
pose a hazard to operational satellites. There is keen interest
within the space community to discover and track all these
objects.
If the telescope sensor is properly instrumented, it is possible to obtain timetagged pairs of angles that relate the space object position to the sensor. With enough angle pairs, it is possible to estimate the position and velocity (the state) of the object, along with estimates of the uncertainties of these parameters. The workshop problem is to develop techniques to identify all the streaks made by each object. Streaks created by an object must somehow be associated with one another and disassociated from those made by other objects. One solution approach treats the state data as vectors in R6 and uses statistical clustering techniques for the association. A variation on this approach addresses physical properties of the orbits, sorting according to those least likely to change with small state variations. Regardless of the approach, there are several interesting aspects to the problem. Automatic streak detection is required, with transform techniques of interest. Orbit mechanics are essential to effective state estimation as well as clustering techniques. In addition, traditional clustering techniques are computationally taxing. A related problem is identification of asteroids that might pose a hazard to planet earth. References: Vallado, David A., Fundamentals of Astrodynamics and Applications, Edition 2, Microsoft Press, 2004; Milani, Andrea, "Three Short Lectures on Identifications and Orbit Determination," http://copernico.dm.unipi.it/~milani/preprints/preprint.html, 2006; Kaufman, L. and Rousseeuw, P., Finding Groups in Data  An Introduction to Cluster Analysis. Wiley Interscience 2005 Prerequisites: Required: computing proficiency demonstrated by knowledge of at least one compiler, one semester differential equations, one semester statistics Desired: one semester numerical analysis, familiarity with orbit mechanics and estimation theory. Keywords: orbit mechanics, astronomical telescopes, statistical clustering The Panstarrs telescope on Mount Haleakela in Hawaii will be used, among other tasks, to search for asteroids. However, using its 1.4 billion pixel sensor, it will also detect earthorbiting objects. 

David J. Hardy (University of Illinois at UrbanaChampaign)  Multilevel summation method for Coulomb interactions  
Abstract: The multilevel summation method (MSM) computes an approximation to the pairwise interaction potential and its gradient with an amount of work that scales linearly as the size of the system. The potential is smoothly split into a sum of partial potentials of increasing range and decreasing variability with the longestrange parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate for dynamical simulations, because it can produce continuous forces for both nonperiodic and periodic boundary conditions. A small correction to the gridbased force approximation can be used to conserve both energy and momentum.  
Nicholas M. Harrison (Imperial College London)  Novel materials for quantum computing  
Abstract: The controlled transport of spin polarised electrons on a 1 nanometre length scale is a realistic prospect and could be the basis for new multifunctional devices with a component density an order of magnitude higher than current VLSI technology. The fundamental materials chemistry challenge is to produce a nanostructured semiconductor that is ferromagnetic at room temperature. Ideally the electronic and magnetic properties need to be robust but tunable through control of composition and structure. The results of recent high quality theoretical calculations on a number of pure carbon materials will be presented. A novel mechanism for long range magnetic coupling in extended pibonded systems will be discussed and documented with explicit calculations on graphene ribbons and defective graphene sheets. A putative ordered defect phase which gives rise to a semiconducting ground state that is ferromagnetic at room temperature will be presented. It will also be shown that the band gap and magnetic coupling may be controlled by varying the defect density.  
Pieter Hendrickx (University of Ghent (UG))  Conformational reinvestigation of two cyclic pentapeptides: to a generic approach in drug development  
Abstract: Same abstract as the 7/24 poster session.  
Pieter Hendrickx (University of Ghent (UG))  Conformational reinvestigation of two cyclic pentapeptides: to a generic approach in drug development  
Abstract: Joint work with I. Van den Eynde^{2}, J.C. Martins^{1} and D. Tourwé^{2} As part of a bigger research effort which consists of the development of a generic approach for drug development, two cyclic peptides based on the active sequence of somatostatin were characterized using nuclear magnetic resonance spectroscopy (NMR). In order to obtain the 3D conformation of these molecules, conformational relevant parameters (eg. nOe, scalar couplings and amide temperature coefficients) were recorded. A simulated annealing protocol using distance restraints was used to obtain a set of conformations which were validated by analysis of the hydrogen bridges present and by recalculating the measured scalar couplings. Future efforts will consist of generating mathematical descriptions (templates) of this kind of small peptide chains as well as creating templates of nonpeptidic small molecules. This must allow for an intelligent choice for drug templates upon positive screening results of the small peptide molecules. ^{1}NMR and Structure Analysis Unit, Department of Organic Chemistry, Ghent University, Krijgslaan 281 S4 B9000 Gent, Belgium ^{2}Unit for Organic Studies, Department of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2 9G616 B1050 Elsene, Belgium  
John R. Hoffman (Lockheed Martin Missiles and Space Company, Inc.)  Team 4: High dimensional, nonlinear, nonconvex optimization problems in the area of aircraft and vehicle design  
Abstract: Presently, when a physics motivated vehicle designer explores
vehicle
designs for a new concept, he is often faced with an enormous
range of
choices and constraints. For an example, an aircraft designer
has
Aircraft shape, fuel type, and engine as his main free
variables. While
his main constraints are dictated by the laws of physics
(weight, size,
power, lift, and stall). Additionally, he has his objective
which is
typically some combination/subset of acceleration,
maneuverability,
range, endurance, payload capacity (size, weight and power),
max and min
speeds, manufacturing cost, maintainability, reliability,
development
cost, takeoff length, landing length, noise footprint and other
items.
I am interested in examining the following problem: Given a set of performance objectives, how does one determine the space of designs available to the designer and find the optimal designs? How does the designer best visualize this space of options? Because he doesn't want just "the" answer, he wants to understand many aspects of the answer. While I'm interested in the general vehicle design problem, we will focus on aircraft design using a baseline tool that is to be determined as a concrete example with which we can test our ideas. 

Jürg Hutter (Universität Zürich)  Efficient KohnSham density functional calculations using the Gaussian and plane waves approach  
Abstract: The Gaussian and plane waves (GPW) approach combines the description of the KohnSham orbitals as a linear combination of Gaussian functions with a representation of the electron density in plane waves. The unique properties of Gaussian functions allow for a fast and accurate calculation of the density in the plane wave basis. The plane wave representation of the density leads to an easy solution of Poisson's equation and thereby a representation of the electrostatic potential. Matrix elements of this potential can be calculated using the same methods. The auxiliary representation of the density is further used in the calculation of the exchangecorrelation energy and potential. The resulting approach scales O(N log N) in the number of electrons and has many additional interesting features, namely, a small prefactor, early onset of linear scaling, and a nominal quadratic scaling in the basis set size for fixed system size. The GPW method is combined with a direct optimization of the subspace of occupied KohnSham orbitals using an orbital transformation (OT) method. A variation of this method has recently been implemented that only requires matrix multiplications. The method combines a small prefactor with efficient implementation on parallel computers, thereby shifting the break even point with linear scaling algorithms to much larger systems. A strategy to combine the OT method with sparse linear algebra will be outlined.  
Olexandr Isayev (Jackson State University)  An ab initio molecular dynamics simulation of solid CL20: mechanism and kinetics of thermal decomposition  
Abstract: Joint work with Leonid Gorb,^{(1
and 2)} Mo. Qasim,^{(2)} and
Jerzy Leszczynski. ^{(1)}
CL20
(Octahydro1,3,4,7,8,10hexanitro5,2,6(iminomethenimino)1Himidazo[4,5b]pyrazin)
is one of the most important high energetic nitramines which
are used as explosives and propellants. The decomposition of
CL20 is very complicated and involves hundreds of elementary
reactions. Accurate knowledge of these reactions and
predictions of their kinetic parameters are important for
modeling these complex processes in combustion and explosion.
However, due to the energetic nature of these materials and the
rapid rates of the intermediate reactions, it is difficult to
monitor these individual reactions experimentally. Recent
advances in first principles modeling have led to enormous
progress toward understanding complex condensed phase chemical
phenomena. Theoretical methods, especially accurate ab initio
molecular dynamics method, provide a viable alternative to
study the dynamics of these reactions. Electronic properties
and the dynamics of the initial thermal decomposition step of
gas, and ecrystal phases of CL20 are investigated using the
CarParrinello molecular dynamics (CPMD) approach. The
difference in the reaction pathways between gas and crystal
phases has been accounted for the strong intermolecular
interaction into crystal lattice. The thermal rate constants
have been also estimated.
^{1)} Computational Center of Molecular Structure and Interactions,
Jackson State University, Jackson, MS 39217 ^{2)} US Army ERDC, Vicksburg, MS, 39180. 

Olexandr Isayev (Jackson State University)  An ab initio molecular dynamics simulation of solid CL20: mechanism and kinetics of thermal decomposition  
Abstract: Same abstract as the 7/24 poster session.  
Jesus A. Izaguirre (University of Notre Dame)  Hybrid Monte Carlo methods  
Abstract: Hybrid Monte Carlo, introduced in quantum chromodynamics, is a rigorous sampling method that eliminates the bias due to time step discretization of molecular dynamics (MD). I will discuss the method, give some example of its application, and show some recent improvements to its efficiency, particularly by discussing the Shadow Hybrid Monte Carlo method.  
Raymond Kapral (University of Toronto)  Quantum reaction rates  
Abstract: The calculation of quantum reaction rates in condensed phase systems from the perspective of quantumclassical Liouville dynamics will be described. The rate problem will be cast in a form that involves quantum equilibrium sampling combined with quantumclassical dynamics for the evolution. Application to proton transfer in the condensed phase and polar molecule nanoclusters will be described. The results of simulations of nonadiabatic reaction rates using a surfacehopping scheme based on quantumclassical Liouville dynamics will be presented. The dynamic and structural factors that influence the rate and reaction mechanism will be discussed.  
Changho Kim (Korea Advanced Institute of Science and Technology (KAIST))  Numerical method for solving stochastic differential equations with nonGaussian noise  
Abstract: We propose numerical integration schemes to solve stochastic differential equations driven by two important nonGaussian noises – dichotomous Markov noise and Poissonian white shot noise. Our formula, which is based on an integral equation, which is equivalent to the stochastic differential equation, utilizes a discrete time approximation with fixed integration time step. We show that our integration formula approaches the Euler formula if these noises approach the Gaussian white noise. We further propose a simplified weak scheme that significantly reduces the computation time, while still satisfying the moment properties up to the required order. Our approach is readily applicable to dynamical systems driven by arbitrary types of noise, provided there exists a way to describe the random increment of the noise accumulated during each integration time step. The accuracy and efficiency of the proposed algorithms are numerically examined.  
Changho Kim (Korea Advanced Institute of Science and Technology (KAIST))  Numerical method for solving stochastic differential equations with nonGaussian noise  
Abstract: Same abstract as the 7/24 poster session.  
Brian Laird (University of Kansas)  Direct calculation of interfacial free energy using molecular simulation  
Abstract: The interfacial free energy is the work required to reversibly form a unit area of interface between two materials and is a principal quantity governing crystal growth kinetics and morphology, nucleation and wetting phenomena. In this talk I will review our recent work on the direct calculation of the interfacial free energy for a number of model systems including crystal/fluid, wallfluid and wallcrystal systems. For the crystalmelt interface, our method of cleaving walls, based on thermodynamic integration [Phys. Rev. Lett, 85, 4751 (2000)], is of sufficient precision to resolve the often small anisotropy in the interfacial free energy, which is crucial in determining the kinetics and morpholgy of dendritic growth. Our calculations are motivated by the enormous difficulty in obtaining precise interfacial free energies by experiment. We report values of the crystalmelt interfacial free energy for the hardsphere and LennardJones systems, as well as recent results on the series of inversepower potentials. In addition, recent work extending the method to wallfluid and wallcrystal systems is discussed and applied to a recent controversy regarding surfaceinduced prefreezing in hardspheres.  
Claude Le Bris (École Nationale des PontsetChaussées (ENPC))  Coarsegraining the free energy of atomistic systems: a mathematical approach  
Abstract: We present a possible approach for the computation of free energies and ensemble averages in the context of onedimensional coarsegrained models in materials science. The approach is based upon a thermodynamic limit process, and makes use of ergodic type theorems and large deviation theory. In addition to providing a possible efficient computational strategy for ensemble averages, the approach in particular allows for assessing the validity and the accuracy of some basic assumptions of the finitetemperature quasicontinuum method. This is joint work with X. Blanc (Univ. Paris 6), F. Legoll (ENPC Paris), C. Patz (WIAS Berlin).  
Frederic Legoll (École Nationale des PontsetChaussées)  Integrators for highly oscillatory Hamiltonian systems: an homogenization approach  
Abstract: We introduce a systematic way to construct symplectic schemes for the numerical integration of a large class of highly oscillatory Hamiltonian systems. The bottom line of our construction is to consider the HamiltonJacobi form of the Newton equations of motion, and to perform a twoscale expansion of the solution, for small times and high frequencies. Several options for the derivation are presented. The various integrators obtained are tested and compared to several existing algorithms. The numerical results demonstrate their efficiency. This is joint work with C. Le Bris (ENPC Paris).  
Benedict Leimkuhler (University of Edinburgh)  Dynamical equations and numerical integrators  
Abstract: This lecture will introduce the basic types of dynamical models arising in molecular dynamics, and the formulation of structurepreserving numerical methods for integrating the equations of motion. Topics to be covered include: multiple timescale modelling, the use of constraints, the computation of averages, the role of symplecticness and timereversal symmetry, the properties of appropriate numerical methods, splitting methods, and SHAKE and RATTLE discretizations. The talk will conclude with a discussion of the use of backward error analysis to correct the numerical bias introduced in dynamical thermostatting methods.  
Tony Lelievre (Ecole Nationale des Ponts et Chaussees)  Adaptive methods for molecular dynamics  
Abstract: Stochastic dynamics to compute free energy differences are widely used in computational chemistry and biology. Many recent methods rely on complex Markov processes (nonhomogeneous or nonlinear processes). Examples of such methods are exponential reweighting of nonequilibrium paths (Jarzynski equality) and Adaptive Biasing Force (ABF) techniques. A unifying presentation of adaptive methods is proposed. We also prove the convergence of a certain class of adaptive methods. Finally, we present an efficient implementation of adaptive dynamics using an interacting particle system with birth death processes.  
Xiantao Li (Pennsylvania State University)  Boundary conditions for nonequilibrium molecular dynamics simulation  
Abstract: Nonequilibrium molecular dynamics simulations, such as crack propagaion in solids, requires realistic boundary conditions to guarantee the accuracy of the computation. In this talk, exact boundary conditions will be derived using a dimension reduction technique. I will also discuss practical implementations under this framework.  
Mitchell Luskin (University of Minnesota Twin Cities)  Analysis and computational studies of the ergodicity of the NoseHoover thermostat  
Abstract: The NoseHoover thermostat is a deterministic dynamical system designed for computing phase space integrals for the canonical Gibbs distribution. Newton's equations are modified by coupling an additional reservoir variable to the physical variables. The correct sampling of the phase space according to the Gibbs measure is dependent on the NoseHoover dynamics being ergodic. Hoover presented numerical experiments that show the NoseHoover dynamics to be nonergodic when applied to the harmonic oscillator. We have proven that the NoseHoover thermostat does not give an ergodic dynamics for the onedimensional harmonic oscillator when the "mass" of the reservoir is large. Our proof of nonergodicity uses KAM theory to demonstrate the existence of invariant tori for the NoseHoover dynamical system that separate phase space into invariant regions. We present numerical experiments motivated by our analysis that seem to show that the dynamics is not ergodic even for a moderate thermostat mass. We also give numerical experiments of the NoseHoover chain (proposed by Martyna, Klein, and Tuckerman) with two thermostats applied to the onedimensional harmonic oscillator. These experiments seem to support the nonergodicity of the dynamics if the masses of the reservoirs are large enough and are consistent with ergodicity for more moderate masses. Joint work with Frederic Legoll and Richard Moeckel.  
Glenn Martyna (IBM Corporation)  Quantum Drude models : A complete description of polarization and dispersion  
Abstract: Present empirical molecular force fields ignore polarization, that is the rearrangement of charge distribution due to environment, and only treat dispersion or vanderWaals forces at the pair level. The former approximation limits the ability of empirical models to describe the properties of materials at surface/interfaces. For example, the solvation shell of a chlorine ion in water can only be predicted by properly accounting for the polarizability of the water molecules. The latter approximation is equally problematic at surfaces, yielding large errors in surfaces tensions which leads to errors in acouning for hydrophobic solvation. Although ab initio calculations could in principle restore manybody polarization and manybody dispersion, in fact, the present level of theory that is sufficiently computational efficient to employ in studies of large systems, Gradient Corrected Density Functional Theory, does not treat dispersion even at the pair level. Since the goal of present theoretical research is to describe the complex interfacial phenomena that drive processes such as protein folding and transport of materials through membranes, it is critical to develop novel, linear scale methods, that can treat both manybody polarization and dispersion. Here, the applied mathematics that underlies the Drude method including a new path integral scheme that not only models manybody polarization and dispersion efficient and accurately, but goes beyond the standard dipole approximation to include all multipole interactions without requiring an explicit multipole expansion is presented.  
Nicola Marzari (Massachusetts Institute of Technology)  Densityfunctional practice  
Abstract: Electronicstructure modeling based on densityfunctional theory has become a popular, successful, and reasonably accurate technnique to characterize and predict material properties. The successful outcome of a calculations is nevertheless linked to a comprehensive understanding of the underlying structure of a modern electronicstructure code, and on the most important parameters that insure accuracy of the calculation, without sacrificing speed. We'll overview the basics of the totalenergy planewave pseudopotential method, including issues related to basis set completeness, Brillouin zone sampling, longrange electrostatic interactions, exchangecorrelation functionals, and minimization techniques.  
Nicola Marzari (Massachusetts Institute of Technology), Arash A. Mostofi (University of Cambridge)  Tutorial on CarParrinello molecular dynamics  
Abstract: A handson tutorial on firstprinciples molecular dynamics, using either CarParrinello or BornOppenheimer approaches, as implemented in the CP package of the QuantumESPRESSO distribution.  
Julie C. Mitchell (University of Wisconsin)  Cluster optimization in protein docking  
Abstract: Recent progress in obtaining docked protein complexes will be discussed. The combination of exhaustive search, clustering and localized global optimization can reliably find energy minima to highly nonconvex biomolecular energy functions. Using an energy function that adds desolvation and screened electrostatics to classical molecular mechanics potentials, the global minimum is found very near to the observed native state. This is demonstrated across a large number of benchmark examples.  
Arash A. Mostofi (University of Cambridge)  Linearscaling densityfunctional calculations with planewaves  
Abstract: A number of reasons have resulted in planewaves becoming one of the basis sets of choice for simulations based on densityfunctional theory, for example: the kinetic energy operator is diagonal in momentum space; quantities are switched efficiently between real space and momentum space using fastFourier transforms; the atomic forces are calculated by straightforward application of the HellmannFeynman theorem; the completeness of the basis is controlled systematically with a single parameter. The resulting simulations require a computational effort which scales as the cube of the systemsize, which makes the cost of largescale calculations prohibitive. For this reason there has been much interest in developing methods whose computational cost scales only linearly with systemsize and hence bringing to bear the predictive power of densityfunctional calculations on nanoscale systems. At first sight the extended nature of planewaves makes them unsuitable for representing the localised orbitals of linear scaling methods. In spite of this, we have developed ONETEP (OrderN Electronic Total Energy Package), a linearscaling method based on planewaves which overcomes the above difficulty and which is able to achieve the same accuracy and convergence rate as traditional cubicscaling planewave calculations.  
Alexey Neelov (Universität Basel)  ParticleScaling function (P3S) algorithm for electrostatic problems in free boundary conditions  
Abstract: A simple algorithm for fast calculation of the Coulombic forces and energies of point particles with free boundary conditions will be presented. Its calculation time scales as N log N for N particles. This novel method has lower crossover point with the full O(N^2) direct summation than the Fast Multipole Method. The forces obtained by our algorithm are analytical derivatives of the energy which guarantees energy conservation during a molecular dynamics simulation. Our method is based on the Poisson solver [2] for continuous charge distribution that uses the DeslaurierDubuc (interpolating) wavelets. [1] L. Genovese, T. Deutsch, A. Neelov, S. Goedecker, and G. Beylkin, Efficient solution of Poisson's equation with free boundary conditions, J. Chem. Phys. 125, 007415 (2006). [2] A. Neelov, S. A. Ghasemi, S. Goedecker, ParticleParticle, ParticleScaling function (P3S) algorithm for electrostatic problems in free boundary conditions, J. Chem. Phys., 2007 (to appear)  
Alexey Neelov (Universität Basel)  ParticleScaling function (P3S) algorithm for electrostatic problems in free boundary conditions  
Abstract: Same abstract as the 7/24 poster session.  
Emad Noorizadeh (University of Edinburgh)  Temperatureregulated microcanonical dynamics  
Abstract: Joint work with Ben Leimkuhler (School of Mathematics, University of Edinburgh) and Frederic Legoll (LAMI, Ecole Nationale des Ponts et Chaussees, France). We describe a new dynamical technique for the equilibration of molecular dynamics. Temperature is moderated by a control law and an additional variable, as in Nose dynamics, but whose influence on the system decreases as the system approaches equilibrium. This device enables approximation of microcanonical averages and autocorrelation functions consistent with given target temperature. Moreover, we demonstrate that the suggested technique is effective for the regulation of heat production in a nonequilibrium setting.  
Christian Ochsenfeld (EberhardKarlsUniversität Tübingen)  A Linearscaling AObased MP2 method for large molecules by rigorous integral estimates  
Abstract: Describing electron correlation effects for large molecules is a major challenge for quantum chemistry due to the strong increase of the computational effort with molecular size. In order to overcome this limitation, we present a rigorous method based on an AOformulation of MP2 theory, which allows to avoid the conventional fifthpower scaling of MOMP2 theory and to reduce the scaling to linear without sacrificing accuracy. The key feature of our method are multipolebased integral estimates (MBIE), which account for the 1/R coupling in twoelectron integrals and allow to rigorously preselect integral products in AOMP2 theory. Here, the magnitude of products decays at least with 1/R**4, so that a linearscaling behavior can be achieved by numerical thresholding without sacrificing any accuracy. The linearscaling increase of the computational effort is reached much earlier than for HF or DFT approaches: e.g. the exact behavior of products indicates a scaling of N**1.0 from one to two DNA basepairs for a 631G* basis. The number of significant elements in the pseudodensity matrices and of shell pairs hints to a very similar linearscaling behavior for larger basis sets studied up to ccpVQZ. First results of a preliminary implementation show that an early crossover to conventional MP2 schemes below two DNA base pairs is observed, while already for a system with four DNA base pairs wins are at least a factor of 16.  
Shantanu Roy (Universität Basel)  A BellEvansPolanyi principle for molecular dynamics trajectories and its implications for global optimization  
Abstract: Joint work with Waldemar Hellmann and Stefan Goedecker (Institute of Physics, University of Basel). The BellEvansPolanyi principle that is valid for a chemical reaction that proceeds along the reaction coordinate over the transition state is extended to molecular dynamics trajectories that in general do not cross the dividing surface between the initial and the final local minimum at the exact transition state. Our molecular dynamics BellEvansPolanyi principle states that low energy molecular dynamics trajectories are more likely to lead into the basin of attraction of a low energy local minimum than high energy trajectories. In the context of global optimization schemes based on molecular dynamics our molecular dynamics BellEvansPolanyi principle implies that using low energy trajectories one needs to visit a smaller number of distinguishable local minima before finding the global minimum than when using high energy trajectories.  
Shantanu Roy (Universität Basel)  A BellEvansPolanyi principle for molecular dynamics trajectories and its implications for global optimization  
Abstract: Same abstract as the 7/24 poster session.  
Yousef Saad (University of Minnesota Twin Cities)  Numerical algorithms for density functional theory  
Abstract: Density Functional Theory (DFT) is a successful technique used to determine the electronic structure of matter which is based on a number of approximations that convert the original nparticle problem into an effective oneelectron system. The endproblem is essentially a nonlinear eigenvalue problem which is solved iteratively. The challenge comes from the large number of eigenfunctions to be computed for realistic systems with, say, hundreds or thousands of electrons. We will discuss techniques for diagonalization, and for dealing with the nonlinearity. It is important consider the problem as one of computing an invariant subspace in the nonlinear context of the KohnSham equations. This viewpoint leads to considerable savings as it deemphasizes the accurate computation of individual eigenvectors and focuses instead on the subspace which they span. We will also discuss other algorithmic issues encountered in DFT and will offer some thoughts on diagonalizationfree techniques.  
Celeste Sagui (North Carolina State University)  Efficient implementation of adaptively biased molecular dynamics  
Abstract: Joint work with Volodymyr Babin and Christopher Roland (Department of Physics, North Carolina State University, Raleigh, NC 276958202). The Adaptively Biased Molecular Dynamics (ABMD) method presented here corresponds to the general class of nonequilibrium dynamics methods that use the history of the sampling process to bias the dynamics, thereby effectively flattening the free energy surface of the chosen order parameter(s). These adaptive methods, are a generalization of umbrella sampling with a timedependent potential, and include the WangLandau approach, the adaptive biasing force method, and nonequilibrium metadynamics (MTD). Recently, we implemented a variation of MTD in the AMBER package [V. Babin, C. Roland, T.A. Darden and C. Sagui, J. Chem. Phys. 125, 204909 (2006)]. In spite of the efficient implementation, MTD still has a square dependence on the sampling time t, i.e., scales as O(t^{2}) , which can be a significant problem in large systems with nonnegligible entropy. In addition, the large number of parameters in MTD influences the output in an entangled way. In the present work, we seek to cure these problems by carrying out an efficient implementation of ABMD. The method has only two parameters and scales linearly with time, i.e., it is O(t). Comparative results for the folding of small peptides are presented.  
Prasanjit Samal (University of Minnesota Twin Cities)  Uniqueness of the densitytopotential mapping in excitedstate densityfunctional theory  
Abstract: Jont work with Manoj K. Harbola (Department of Physics, Indian Institute of Technology, Kanpur 208016, India).
The question of whether there exists a mapping from
an excitedstate density to a potential is central to performing densityfunctional calculation for excited states. The motivation of the present work is to establish a unique way of selecting a system (potential) for a given excitedstate density. The issue of density – to – potential mapping has been addressed in a series of work by Sahni et al [1], Harbola [2] and Gaudoin et al [3]. In the work of [1] and [2], it was shown that ground or excitedstate density can be generated by configuration of one’s choice. In the work [3], they have shown that even with a fixed configuration, one could reproduce same excitedstate density from more than one potentials as shown in Fig.1. This implies in addition to the excitedstate density one requires some extra information to establish such a unique mapping. This has been done by comparison of ground state densities in LevyNagy [4] theory. Following the earlier attempts we have further explored the densitytopotential mapping based on the work of LevyNagy [4] and Gorling [5] for excitedstates [6]. We have proposed a new criterion [7], which uniquely establishes such mapping.
Fig.1: Two potentials (middle panel) giving the same excitedstate density (upper panel)
along with their corresponding groundstate densities (lower panel) for an excitedstate
of the three electron 1D infinitely deep well model system.
References: [1] V. Sahni, L. Massa, R. Singh and M. Slamet, Phys. Rev. Lett. 87, 113002 (2001). [2] M. K. Harbola, Phys. Rev. A 69, 042512 (2004). [3] R. Gaudoin and K. Burke, Phys. Rev. Lett. 93, 173001 (2004). [4] M. Levy and A. Nagy, Phys. Rev. Lett. 83, 4361 (1999). [5] A. Gorling, Phys. Rev. A 59, 3359 (1999). [6] P. Samal, M. K. Harbola and A. Holas, Chem. Phys. Lett. 419, 217 (2006) [7] P. Samal and M. K. Harbola, J. Phys. B 39, 4065 (2006). 

Prasanjit Samal (University of Minnesota Twin Cities)  Uniqueness of the densitytopotential mapping in excitedstate densityfunctional theory  
Abstract: Same abstract as the 7/24 poster session.  
Andreas Savin (Université de Paris VI (Pierre et Marie Curie))  Dealing with spatial regions  
Abstract: Chemists are used to see molecules in three dimensions, and think of the molecular properties often related to specific regions of space. This is a good source of inspiration for theoretical methods, but efficient algorithms for a mathematical treatment of models needing, e.g., integration in arbitrary, flexible regions in 3D are still needed.  
Christof Schuette (Freie Universität Berlin)  Nanomechanics of biomolecules  
Abstract: The talk will demonstrate how to extract nanomechanical properties like stiffnesses and friction parameters of biomolecules from molecular dynamics simulations. The aim is to construct optimal sets of parameters from molecular dynamics time series for all important conformations of a biomolecule under investigation. Parameter optimality will be measured in a maximal likelihood estimation sense, i.e., such parameters are optimal for which the probability that the observed time series is an output of equations of motions with these parameters is the highest possible. It will be demonstrated how to derive the equation for the optimal parameter set, how these can be implemented efficiently, and how the resulting algorithm perform for moderately sized examples (12alanine with implicit water and some BDNA 16mer with explicit water).  
Robert D. Skeel (Purdue University)  Introduction to molecular dynamics  
Abstract: Computer simulations of molecular dynamics find many applications in physical chemistry, materials science, biophysics, and structural biology. The basic idea is to simulate the motion of a set of atoms, typically (but not necessarily) in full atomic detail. For this, Newton's equations of motion are used with the forces defined by gradients of a potential energy function that is a rough approximation to that defined by quantum mechanics. A remarkably effective numerical integrator is the simple leapfrog/Stormer/Verlet method. Modeling the boundary of the simulation domain is problematic. Typically, periodicity is assumed, though spherical restraints are sometimes used. The boundary may or may not permit the exchange of energy, momentum, or mass. For the canonical ensemble, only energy is permitted to be exchanged across the boundary. This can be modeled by stochastic boundary conditions. The micro(scopic) state of a system is largely unknown, so initial conditions are chosen at random from a stationary probability distribution of the dynamics. Such a distribution can be obtained for the canonical ensemble by equilibration using Langevin dynamics. Indeed, most quantities of interest are defined only in terms of a stationary distribution and the purpose of the dynamics is to sample configuration space. In some cases, kinetic quantities are of interest and realistic Newtonian dynamics must be used. The practicalities of doing such calculations involves three steps: structure building, simulation, analysis.  
Robert D. Skeel (Purdue University)  Molecular sampling  
Abstract: Perhaps the greatest computational challenge of molecular dynamics is to generate molecular configurations at random from a prescribed probability distribution, for example, the BoltzmannGibbs distribution. Markov chain Monte Carlo methods provide a rigorous solution to this problem, but designing efficient trial moves is challenging. Two systematic approaches are presented: one based on Brownian dynamics, the other on molecular dynamics. The extra computational expense of rejected moves can be avoided by using dynamics instead, the drawback being the introduction of a bias due to the finite stepsize of the integrator. Either deterministic or stochastic dynamics may be used. To achieve reasonable performance, the basic sampling scheme must be combined with more advanced techniques, such as replica exchange and WangLandau Monte Carlo.  
Viktor N. Staroverov (University of Western Ontario)  KohnSham methods for implicit density functionals  
Abstract: Density functional theory calculations with a certain class of approximations to the KohnSham exchangecorrelation energy require an indirect evaluation of the functional derivative of an implicit functional. Although the formal prescription for obtaining this derivative is known, there are fundamental pitfalls in its practical implementation using discrete basis set representations of the operators. We discuss several pragmatic solutions to this problem and compare their advantages in various applications.  
Gabriel Stoltz (École Nationale des PontsetChaussées (ENPC))  A reduced stochastic model for shock and detonation waves  
Abstract: (work in collaboration with J.B. Maillet and L. Soulard (CEA/DAM, Bruyeres le Chatel, France)) I present a model of mesoparticles, in the Dissipative Particle Dynamics spirit, in which a molecule is replaced by a particle with an internal thermodynamic degree of freedom (temperature or energy). The corresponding dynamics, named DPDE and idependently derived by Avalos and Mackie and by Espanol, is energy conserving and Galilean invariant. This model is shown to give quantitatively accurate results for the simulation of shock waves in a crystalline polymer. I also present an extension to detonation waves, which are shock waves triggering exothermic chemical reactions. In this case, an additional variable per mesoparticle is introduced, namely a progress variable describing the chemical reaction, and some reversible second order kinetics depending on the internal energies of the particles is postulated.  
Gabriel Stoltz (École Nationale des PontsetChaussées (ENPC))  Local exchange potentials: A mathematical viewpoint  
Abstract: Work in collaboration with Eric Cancès (CERMICS), Ernest R. Davidson (Department of Chemistry, University of Washington), Artur F. Izmaylov, Gustavo Scuseria and Viktor N. Staroverov (Department of Chemistry, Rice University). This work reviews and presents in a unified fashion several wellknown local exchange potentials, such as the Slater potential, Optimized Effective Potentials and their approximations (KLI, CEDA local potentials) and the recently proposed Effective Local Potential. We provide alternative derivations of some of these wellknown potentials, mainly based on variational arguments (the local exchange potential being defined as the best approximation of the nonlocal HartreeFock operator in some least square sense). The remaining potentials are approximate solutions of the socalled OEP integral equation, and can be recovered through convenient approximations of the resolvent of the Hamiltonian operator.  
Mark A. Stuff (General Dynamics Advanced Information Systems)  Team 5: Size and shape comparisons from noisy, unlabeled, incomplete configurations of landmarks in threedimensional space  
Abstract: Traditional noninvasive sensing technologies have generated information about only one or two dimensional projections of objects of interest. But the use of arrays of sensor components, and opportunities to rapidly move such arrays around objects of interest are enabling the practical generation of many forms of threedimensional data. For example, in acoustics there has been steady progression from onedimensional echo trains, to twodimensional acoustic images, to modern threedimensional reconstructions, on scales from ultrasound wavelengths to global seismic surveys. Similarly, threedimensional tomographic reconstructions from xrays are now commonly used to resolve ambiguities in traditional twodimensional xray images.
As more threedimensional data becomes available, the value of automatic tools for utilizing such data increases. Several desired applications need methods by which to automate the finding of correspondences between threedimensional data sets. These threedimensional data sets frequently share many geometric characteristics, but also have significant differences, due to differences in data collection geometries, changes in sensor capabilities, temporal changes in the object of interest, and noise in the data. One approach to finding unknown coordinate transformations, which are needed to align multidimensional data sets, is to require an expert to examine each set and label certain common landmarks. If sufficient landmarks, having the same unique labels can be found in both sets, the threedimensional coordinates of the landmarks enable the coordinate transformation to be estimated. This is like aligning images of faces, by first extracting the coordinates the tips of the noses, the left corners of the mouths, the bases of the right earlobes, etc. But when no prior expertise is available, we need methods of estimating the transformation from set of automatically generated coordinates of 'interesting' locations (unlabeled landmarks). We expect that a significant subset of corresponding unlabeled landmarks may exist somewhere in the data set to which we need to compare. To solve our alignment problems, we need to devise automated methods to robustly find a pair of large subsets from a pair of sets of unlabeled landmarks, such that the subsets have similar geometric characteristics.
Does there exist a rigid motion mapping the configuration of red points onto a subset of the blue points? If so, what is the blue subset, and what is the rigid motion? If not, how much deformation of the red configuration is needed to make it so? In principle, these problems can be solved by exhaustively comparing every possibility, but the level of effort grows exponentially fast with the number of landmarks. Our goal will be to find and test new approaches to this problem, seeking to devise algorithms which are robust and far more efficient. References:
Prerequisites: Basics of linear algebra and matrix theory, basic computer programming skills, elementary Euclidean geometry Desired: Ability to bring relevant ideas from one or more of geometry, invariant theory, optimization theory, graph theory, combinatorics, or something else. 

Chris R. Sweet (University of Notre Dame)  Normal mode partitioning of Langevin dynamics for the simulation of biomolecules  
Abstract: A novel NormalModePartitioned Langevin dynamics integrator is proposed. The aim is to approximate the kinetics or thermodynamics of a biomolecule by a reduced model based on a normal mode decomposition of the dynamical space. The basis set uses the eigenvectors of a mass reweighted Hessian matrix calculated with a biomolecular force field. This particular choice has the advantage of an ordering according to the eigenvalues, which has a physical meaning (squareroot of the mode frequency). Low frequency eigenvalues correspond to more collective motions, whereas the highest frequency eigenvalues are the limiting factor for the stability of the integrator. The higher frequency modes are overdamped and relaxed near to their energy minimum while respecting the subspace of low frequency dynamical modes. Numerical results confirm that both sampling and rates are conserved for an implicitly solvated alanine dipeptide model, with only 30% of the modes propagated, when compared to the full model. For implicitly solvated systems the method can be shown to give improvements in efficiency more than 2 times even for sampling a small 22 atom (alanine dipeptide) model and in excess of an order of magnitude for sampling an 882 atom (bovine pancreatic trypsin inhibitor, or BPTI) model, with good scaling with system size subject to the number of modes propagated.  
Michael Teter (Cornell University)  Precision problems in density functional development for better molecular modeling  
Abstract: Classical modeling depends upon Density Functional Theory (DFT) for its potential parameters, and quantum modeling usually uses DFT directly. The only significant improvement in DFT in the last 40 years has been the gradient corrections by Perdew et al., and they only improved the gross energy errors without improving molecular geometries or forces. Indeed, many of the talks in the second week address this problem. If we are to get better modeling, we need DFT functional development. The primary problem with DFT functional development is that the total energy errors are quadratic in electron density errors while the force errors are linear, so that further improvements must get the electron densities right. The differences between the electron densities predicted by the various theories is at the 12% level. So, in order to get the differences right, one must actually have a numerical method which resolves the density to 1/10% or the energies to a part per million. Easytouse methods which can achieve this accuracy regularly do not exist, hence my work.  
Michael Teter (Cornell University)  Precision problems in density functional development for better molecular modeling  
Abstract: Same abstract as the 7/24 poster session.  
Florian Theil (University of Warwick)  Towards a mathematical justification of kinetic theory  
Abstract: No Abstract  
Walter Thiel ( MaxPlanckInstitut für Kohlenforschung)  QM/MM studies on enzymes  
Abstract: The lecture will report on recent progress in combined quantum
mechanical / molecular mechanical (QM/MM) approaches for
modeling
chemical reactions in large biomolecules. After a brief outline
of
the theoretical background and the chosen strategy [1], we
address
freeenergy QM/MM calculations as well as the use of accurate
correlated ab initio QM methods in QM/MM work. Case studies are
presented for biocatalysis by phydroxybenzoate hydroxylase
[2,3]
and cytochrome P450cam [4,5].
[1] H. M. Senn, W. Thiel, Top. Curr. Chem. 2007, 268,
173290. [2] H. M. Senn, S. Thiel, W. Thiel, J. Chem. Theory Comput. 2005, 1, 494505. [3] F. Claeyssens, J. N. Harvey, F. R. Manby, R. Mata, A. J. Mulholland, K. E. Ranaghan, M. Schuetz, S. Thiel, W. Thiel, H.J. Werner, Angew. Chem. Int. Ed. 2006, 45, 68566859. [4] J. C. Schoeneboom, F. Neese, W. Thiel, J. Am. Chem. Soc. 2005, 127, 58405853. [5] A. Altun, V. Guallar, R. A. Friesner, S. Shaik, W. Thiel, J. Am. Chem. Soc. 2006, 128, 39243925. 

Mark E. Tuckerman (New York University)  Statistical mechanics and molecular dynamics  
Abstract: Statistical mechanics provides the connection between the microscopic description of a system and the macroscopic properties that can be observed in experiments. In this lecture, the classical statistical mechanics principles that allow us to extract macroscopic observables from microscopic simulations will be discussed. Statistical mechanical techniques for analyzing microscopic equations of motion in terms of the phasespace distributions they generate will be covered. The first part of the lecture will focus on static equilibrium properties. In the last part of the lecture, timedependent statistical mechanics and the calculation of dynamical observables from time correlation functions will be discussed.  
Mark E. Tuckerman (New York University)  Free energy calculations and the potential of mean force  
Abstract: The free energy plays a central role in statistical mechanics and is a key quantity of experimental interest. The free energy is equal to the reversible work needed to effect a thermodynamic process and is the generator of other thermodynamic properties in a given statistical ensemble. Free energies are directly related to equilibrium constants (for example, the efficacy of a drug is measured by an equilibrium constant known as the inhibition constant, which is related to the binding free energy between an inhibitor and its target enzyme) and chemical potentials, and can be used to estimate rate constants. Obtaining accurate free energies is challenging because of the inability of straightforward simulation techniques to sample phase space sufficiently. In this lecture, we will introduce the concept of free energy and discuss a number of stateoftheart techniques for enhancing phasespace sampling, particularly when the sampling is hindered by socalled rare events.  
Erkan Tüzel (North Dakota State University)  Mesoscopic model for the fluctuating hydrodynamics of binary and ternary mixtures  
Abstract: Joint work with Guoai Pan (National Institute for Nanotechnology, Canada), Thomas Ihle and Daniel M. Kroll (Department of Physics, North Dakota State University). A recently introduced particlebased model for fluid dynamics with continuous velocities is generalized to model immiscible binary mixtures. Excluded volume interactions between the two components are modeled by stochastic multiparticle collisions which depend on the local velocities and densities. Momentum and energy are conserved locally, and entropically driven phase separation occurs for high collision rates. An explicit expression for the equation of state is derived, and the concentration dependence of the bulk free energy is shown to be the same as that of the WidomRowlinson model. Analytic results for the phase diagram are in excellent agreement with simulation data. Results for the line tension obtained from the analysis of the capillary wave spectrum of a droplet agree with measurements based on the Laplace's equation. The dispersion relation for the capillary waves is derived and compared with the numerical measurements of the time correlations of the radial fluctuations in the damped and overdamped limits. The introduction of "amphiphilic" dimers makes it possible to model the phase behavior of ternary surfactant mixtures.  
Erkan Tüzel (North Dakota State University)  Mesoscopic model for the fluctuating hydrodynamics of binary and ternary mixtures  
Abstract: Same abstract as the 7/24 poster session.  
Eric VandenEijnden (New York University)  Transition pathways of rare events  
Abstract: Many processes in nature occur in the form of rare but important events. Well known examples of such events include conformation changes of biomolecules, chemical reactions, and nucleation events during phase transformation. Rare events do not happen very often on the internal clock of the system (which makes their simulation very challenging), but this clock can be very fast and this leaves plenty of room for the appearance of rare events in our daily life. We will review classical theories like Transition State Theory for the description of rare events, recent theoretical developments such as Transition Path Theory, and we will discuss how to compute the pathway and rate of rare events efficiently using the String Method.  
Roman Voskoboynikov (University of Cambridge)  MD modelling of primary damage production in displacement cascades  
Abstract: Displacement cascades are the primary source of radiation damage of reactor structural materials exposed to fastneutron irradiation. They are formed by the recoil of primary knockon atoms with a kinetic energy of more than ~1 keV. The cascade process is characterized by lengths and times of the order of nm and ps, respectively, and it can be modelled by the method of molecular dynamics. At a time in the early stage of a cascade, only a small proportion of atoms recoil with high velocity while the rest satisfy the equilibrium velocity distribution for the ambient temperature. Because the convergent integration timestep is determined by the velocity of the fastest atom, conventional techniques that use fixed stepsize integration over the entire ensemble are impractical at that stage. To obtain reasonable computational efficiency we decomposed the ensemble into evolving subsets of ‘cold’ and ‘hot’ atoms and conducted integration of the equations of motion using variable timestep. Four different techniques were applied to identify point defects and point defect clusters created in displacement cascades and determine the size of clusters and their morphology.  
Arthur F. Voter (Los Alamos National Laboratory)  Accelerated molecular dynamics methods  
Abstract: A significant problem in the atomistic simulation of materials is that molecular dynamics simulations are limited to nanoseconds, while important reactions and diffusive events often occur on time scales of microseconds and longer. Although rate constants for slow events can be computed directly using transition state theory (with dynamical corrections, if desired, to give exact rates), this requires first knowing the transition state. Often, however, we cannot even guess what events will occur. For example, in vapordeposited metallic surface growth, surprisingly complicated exchange events are pervasive. I will discuss our accelerated molecular dynamics approach for treating this problem of complex, infrequentevent processes. The idea is to directly accelerate the dynamics to achieve longer times without prior knowledge of the available reaction paths. With these methods, we can often achieve accurate dynamical evolution on time scales exceeding that available to direct molecular dynamics by many orders of magnitude. Time permitting, I will also discuss some of our most recent method developments.  
Rodolphe Vuilleumier (Université de Paris VI (Pierre et Marie Curie))  Effective normal modes from finite temperature molecular dynamics simulations  
Abstract: Ab initio Molecular Dynamics has been recognized lately as a powerful tool to compute infrared spectra of a variety of systems. The main advantage of this approach with respect to the usual normal mode analysis approach at the optimized geometry is the explicit treatment of temperature and environmental effects, without need for an harmonic approxiamation. However, the interpretation of the simulated spectra in temrs of atomic motions, phonons or vibrational modes is still a challenge. Here, a general method for obtaining effective normal modes from Molecular Dynamics simulations is presented. The method is based on a localization criterion for the fourier transformed velocity timecorrelation functions (FTVCF) of the effective modes. For a given choice of the localization function used, the method becomes equivalent to the principal mode analysis (PMA) based on covariance matrix diagonalization. On the other hand, proper choice of the localization function leads to a novel method with strong analogy with the usual normal mode analysis of equilibrium structures, where the system's Hessian at the minimum energy structure is replaced by the thermal averaged Hessian, although the Hessian itself is never actually calculated. This method does not introduce any extra numerical cost during the simulation and bears the same simplicity as PMA itself. It can thus be readily applied to ab initio Molecular Dynamics simulations. Some examples will be given here.  
Tomasz A. Wesolowski (Université de Genève)  Orbitalfree embedding potential: properties, approximations, and the use in computer simulations to couple quantum chemical and classical levels of description  
Abstract: Practical applications of oneelectron equations for embedded orbitals (Eqs. 2021 in Ref. [1])
hinge on the availability of explicit density functionals to approximate adequately the exchangecorrelation energy and the nonadditive kinetic energy. The former quantity is defined as in the KohnSham formulation
of density functional theory, whereas the latter one arises from the use of orbitals (/embedded orbitals/) for only
a selected component of the total electron density in the applied formal framework. The quality of the /shifts /of the electronic properties of a chemical species due to its condensed phase
environment calculated by means of Eqs. 2021 of Ref. [1] is determined by the kineticenergyfunctional
dependent component of the total effective potential.
In this work, our recent works concerning the development and testing of systemindependent
approximations this component of the embedding potential. and selected representative applications
to study details of the electronic structure of embedded systems in condensed phase [2,3] are reviewed.
[1] T.A. Wesolowski & A. Warshel, /J. Phys. Chem./ *97* (1993), 8050.
[2] M. Zbiri, C. Daul, and T.A. Wesolowski, /Journal of Chemical Theory and Computation / *2* (2006) 1106. [3] J. Neugebauer, C.R. Jacob, T.A. Wesolowski, E.J. Baerends, /J. Phys. Chem. A./ *109* (2005) 7805. 

Dexuan Xie (University of Wisconsin)  New numerical algorithms and software for minimizing biomolecular potential energy functions  
Abstract: This poster reports some progresses we made recently in developing numerical algorithms and program packages for minimizing large scale biomolecular potential energy functions, which is one of the fundamental tasks in biomolecular simulations. The new algorithms are designed from a sparse incomplete Hessian matrix constructed by a spherical cutoff strategy according to the problem size and computer capability. They are called the incomplete Hessian Newton method (IHN), the truncatedIHN method (TIHN), and the refined TIHN method (RTIHN), respectively. The program package of RTIHN for solving the biomolecular potential energy minimization problem is developed based on a widelyused biomolecular simulation packages, CHARMM. This poster will give RTIHN a detailed description, and present its numerical performances for some large scale protein systems. In theory, these new algorithms are defined and analyzed for a general unconstrained minimization problem with a target function having a dense Hessian matrix. They are proved to be convergent globally. While IHN and TIHN are shown to have a linear rate of convergence, RTIHN is proved to have a superlinear rate of convergence. Hence, these new algorithms can be applied to other large scale scientific and engineering applications. For this purpose, we develop a general program package of RTIHN in C++ based on the optimization program package TAO (http://wwwunix.mcs.anl.gov/tao/index.html), and apply it to solve the chemical database optimal projection mapping problem. This is the joint work with Mazen G. Zarrouk and Jun Wang.  
Dexuan Xie (University of Wisconsin)  New numerical algorithms and software for minimizing biomolecular potential energy functions  
Abstract: Same abstract as the 7/24 poster session.  
Lisa Zhang (Lucent Technologies Bell Laboratories)  Team 6: Wavelength assignment and conversion in optical networking  
Abstract: Today's optical telecommunication networks carry audio, video
and data
traffic over fiber optics at extremely high bit rates. The
design of
such networks encompasses a range of challenging combinatorial
optimization problems. Typically, these problems are
computationally
hard even for restricted special cases. In this project we
study how to
assign wavelengths and place equipment so as to carry a set of
traffic
demands in large scale optical networks.
Our design problems are motivated by a popular optical technology called Wavelength Division Multiplexing (WDM). In this setting each fiber is partitioned into a fixed number of wavelengths and demands sharing a common fiber must be transported on distinct wavelengths. A demand stays on the same wavelength along its routing path as much as possible. When this is infeasible, we can either deploy an extra fiber for the demand to continue on the same wavelength; or place a wavelength converter for the demand to continue on a different wavelength. Both options incur cost. One objective is to assign wavelengths and place converters in an advantageous way so as to minimize the total cost. In this project we explore algorithms and heuristics for assigning wavelengths and placing converters. The goals include studying the tradeoff between optimality and complexity and understanding the gap between theoretical bounds and practical performance. References: [1] Matthew Andrews and Lisa Zhang, Complexity of Wavelength Assignment in Optical Network Optimization. (Please see Section VI.) Proceedings of IEEE INFOCOM 2006. Barcelona, Spain, April 2006. http://cm.belllabs.com/~ylz/2006.coloring4.pdf [2] C. Chekuri, et al. Design Tools for Transparent Optical Networks. Bell Labs Technical Journal. Vol. 11, No. 2, pp. 129143, 2006. Prerequisite: Required: One semester of algorithms; One semester of theory of computing; One semester of programming. Desired: Knowledge of Python and CPLEX. Keywords: Analysis of algorithms, combinatorial optimization, implementation of heuristics 

Johannes Zimmer (University of Bath)  Analysis of a lattice model for phase transitions and derivation of kinetic relations  
Abstract: A short overview over solidsolid phase transitions ("martensitic transformations") will be given, and a onedimensional lattice model will be analysed. The equations of motions are given by Newton's law, where the force is given by the interaction of neighbouring atoms. The challenge is that the interaction potential is nonconvex, to model phase transitions. The existence of subsonic travelling waves can be proved. We will explain how this information can be used to derive socalled kinetic relations, which relate the velocity of the phase boundary to a driving force. The interest in kinetic relations can be explained by their relevance for a continuum modelling of phase transitions; this will be briefly sketched. This is joint work with Hartmut Schwetlick (Bath). 
Hoda AbdelAal Bettley  University of Manchester  7/22/2007  8/3/2007 
Nikhil Chandra Admal  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
Jungha An  University of Minnesota Twin Cities  9/1/2005  8/31/2007 
Douglas N. Arnold  University of Minnesota Twin Cities  7/15/2001  8/31/2008 
Donald G. Aronson  University of Minnesota Twin Cities  9/1/2002  8/31/2007 
Nii AttohOkine  University of Delaware  7/22/2007  8/3/2007 
Paul W. Ayers  McMaster University  7/29/2007  8/3/2007 
Eric Barth  Kalamazoo College  7/22/2007  8/3/2007 
Daniel J. Bates  University of Minnesota Twin Cities  9/1/2006  8/31/2008 
Axel D. Becke  Dalhousie University  7/31/2007  8/4/2007 
Guy Bencteux  Électricité de France  7/22/2007  8/3/2007 
Yermal Sujeet Bhat  University of Minnesota Twin Cities  9/1/2006  8/31/2008 
Dan Bolintineanu  University of Minnesota Twin Cities  7/24/2007  8/3/2007 
Stephen Bond  University of Illinois at UrbanaChampaign  7/22/2007  8/3/2007 
Sarah Bonella  Scuola Normale Superiore  7/22/2007  8/3/2007 
Sebastien Boyaval  Ecole Nationale des Ponts et Chaussees  7/22/2007  8/4/2007 
Markus J. Buehler  Massachusetts Institute of Technology  7/26/2007  7/28/2007 
Leslie Button  Corning  7/22/2007  8/3/2007 
Vivaldo L. Campo  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
Eric Cances  Centre d'Enseignement et de Recherche en Mathématiques et Calcul Scientifique (CERMICS)  7/22/2007  8/4/2007 
Matt Challacombe  Los Alamos National Laboratory  7/29/2007  8/3/2007 
Adam Chamberlin  University of Minnesota Twin Cities  7/24/2007  8/3/2007 
James R. Chelikowsky  University of Texas  7/29/2007  8/3/2007 
Srinath Cheluvaraja  University of Pittsburgh  7/22/2007  7/29/2007 
TingLan Chin  University of Minnesota Twin Cities  7/25/2007  8/3/2007 
Jun Kyung Chung  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
Giovanni Ciccotti  Università di Roma "La Sapienza"  7/22/2007  8/3/2007 
Matteo Cococcioni  University of Minnesota Twin Cities  7/31/2007  8/3/2007 
Christopher J. Cramer  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
Michel Cuendet  Swiss Institute of Bioinformatics  7/22/2007  7/28/2007 
Eric C. Cyr  University of Illinois at UrbanaChampaign  7/22/2007  7/28/2007 
Ismaila Dabo  Massachusetts Institute of Technology  7/27/2007  8/3/2007 
Eric Felix Darve  Stanford University  7/24/2007  7/28/2007 
Bonhommeau Andre David  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
Ernest R. Davidson  University of Washington  7/31/2007  8/4/2007 
Kaushik Dayal  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
Amélie Deleurence  École Nationale des PontsetChaussées (ENPC)  7/22/2007  8/4/2007 
Aaron Dinner  University of Chicago  7/22/2007  7/28/2007 
Kenneth R. Driessel  Iowa State University  9/1/2006  8/3/2007 
Ron Elber  University of Texas  7/22/2007  7/28/2007 
JeanLuc Fattebert  Lawrence Livermore National Laboratory  7/31/2007  8/3/2007 
Olalla Nieto Faza  University of Minnesota Twin Cities  7/24/2007  8/3/2007 
Michael Feig  Michigan State University  7/22/2007  7/28/2007 
Laura Gagliardi  Université de Genève  7/22/2007  8/3/2007 
Timur Gatanov  Harvard University  7/22/2007  8/3/2007 
SeyedAlireza Ghasemi  Universität Basel  7/22/2007  8/4/2007 
Manik Ghosh  Kyungpook National University  7/22/2007  8/3/2007 
Simon Gill  University of Leicester  7/22/2007  7/27/2007 
Stefan Goedecker  Universität Basel  7/31/2007  8/4/2007 
Jason E. Gower  University of Minnesota Twin Cities  9/1/2006  8/31/2008 
Sergei Grudinin  Forschungszentrum Jülich  7/22/2007  8/3/2007 
Venkata Suresh Reddy Guthikonda  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
Woods Halley  University of Minnesota Twin Cities  7/24/2007  8/3/2007 
David J. Hardy  University of Illinois at UrbanaChampaign  7/22/2007  7/26/2007 
Nicholas M. Harrison  Imperial College London  7/29/2007  8/2/2007 
Carsten Hartmann  Free University of Berlin  7/25/2007  8/3/2007 
Pieter Hendrickx  University of Ghent (UG)  7/21/2007  8/5/2007 
Milena Hering  University of Minnesota Twin Cities  9/1/2006  8/31/2008 
Andres Heyden  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
Tony Hill  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
Benjamin J. Howard  University of Minnesota Twin Cities  9/1/2006  8/21/2007 
Jürg Hutter  Universität Zürich  7/31/2007  8/4/2007 
Olexandr Isayev  Jackson State University  7/22/2007  8/4/2007 
Jesus A. Izaguirre  University of Notre Dame  7/22/2007  7/28/2007 
Alexander Izzo  Bowling Green State University  7/22/2007  8/4/2007 
Richard D. James  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
Raymond Kapral  University of Toronto  7/22/2007  7/28/2007 
Dan Karls  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
Abdelouahab Kenoufi  Universität Basel  7/28/2007  8/4/2007 
Changho Kim  Korea Advanced Institute of Science and Technology (KAIST)  7/22/2007  8/4/2007 
Hyungjun Kim  California Institute of Technology  7/22/2007  8/4/2007 
SiJo Kim  Andong National University  7/23/2007  8/3/2007 
Daniel Kroll  North Dakota State University  7/23/2007  7/27/2007 
Leeor Kronik  Weizmann Institute of Science  7/22/2007  8/3/2007 
SongHwa Kwon  University of Minnesota Twin Cities  8/30/2005  8/31/2007 
Brian Laird  University of Kansas  7/24/2007  7/28/2007 
David Langreth  Rutgers University  7/31/2007  8/3/2007 
Niels Lauritzen  Aarhus University  8/28/2006  7/10/2007 
Claude Le Bris  École Nationale des PontsetChaussées (ENPC)  7/22/2007  8/4/2007 
Chang Hyeong Lee  Worcester Polytechnic Institute  7/21/2007  7/30/2007 
Frederic Legoll  École Nationale des PontsetChaussées  7/22/2007  8/4/2007 
Benedict Leimkuhler  University of Edinburgh  7/21/2007  7/28/2007 
Tony Lelievre  Ecole Nationale des Ponts et Chaussees  7/22/2007  7/29/2007 
Anton Leykin  University of Minnesota Twin Cities  8/16/2006  8/15/2008 
Qizhen Li  University of Nevada  7/22/2007  8/4/2007 
Xiantao Li  Pennsylvania State University  7/23/2007  8/3/2007 
Hstau Y Liao  University of Minnesota Twin Cities  9/2/2005  8/31/2007 
Florence J. Lin  University of Southern California  7/25/2007  8/3/2007 
Liping Liu  California Institute of Technology  7/22/2007  8/3/2007 
Xinlian Liu  Hood College  7/22/2007  8/3/2007 
Marie Lopez del Puerto  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
Jianfeng Lu  Princeton University  7/21/2007  8/3/2007 
Laura Lurati  University of Minnesota Twin Cities  9/1/2006  8/31/2008 
Mitchell Luskin  University of Minnesota Twin Cities  7/23/2007  7/28/2007 
Hannah Markwig  University of Minnesota Twin Cities  9/1/2006  8/31/2007 
Glenn Martyna  IBM Corporation  7/22/2007  8/3/2007 
Nicola Marzari  Massachusetts Institute of Technology  7/29/2007  8/1/2007 
Julie C. Mitchell  University of Wisconsin  7/22/2007  8/3/2007 
Michal Mlejnek  Corning  7/22/2007  8/3/2007 
Robert Molt Jr  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
Arash A. Mostofi  University of Cambridge  7/30/2007  8/3/2007 
Alexey Neelov  Universität Basel  7/22/2007  8/4/2007 
Jiawang Nie  University of Minnesota Twin Cities  9/1/2006  8/31/2007 
Emad Noorizadeh  University of Edinburgh  7/22/2007  7/28/2007 
Christian Ochsenfeld  EberhardKarlsUniversität Tübingen  7/30/2007  8/3/2007 
Holly Pinkerton  University of Minnesota Twin Cities  7/18/2007  7/18/2007 
Keith Promislow  Michigan State University  7/23/2007  7/31/2007 
Aravind Rammohan  Corning  7/22/2007  8/3/2007 
Andres Reyes  Universidad Nacional de Colombia  7/22/2007  8/4/2007 
Shantanu Roy  Universität Basel  7/22/2007  8/4/2007 
Qing Ruan  Pennsylvania State University  7/22/2007  7/31/2007 
Yousef Saad  University of Minnesota Twin Cities  7/30/2007  8/3/2007 
Celeste Sagui  North Carolina State University  7/23/2007  7/27/2007 
Prasanjit Samal  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
Julien Saur  École Nationale des PontsetChaussées (ENPC)  7/22/2007  8/4/2007 
Andreas Savin  Université de Paris VI (Pierre et Marie Curie)  7/29/2007  8/3/2007 
Abdallah SayyedAhmad  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
Arnd Scheel  University of Minnesota Twin Cities  7/15/2004  8/31/2007 
Christof Schuette  Freie Universität Berlin  7/22/2007  7/27/2007 
Gustavo E. Scuseria  Rice University  7/29/2007  8/3/2007 
Chehrzad Shakiban  University of Minnesota Twin Cities  9/1/2006  8/31/2008 
Juanfang Shen  Purdue University  7/22/2007  7/29/2007 
Robert D. Skeel  Purdue University  7/22/2007  7/28/2007 
Viktor N. Staroverov  University of Western Ontario  7/29/2007  8/3/2007 
Gabriel Stoltz  École Nationale des PontsetChaussées (ENPC)  7/22/2007  8/4/2007 
Chris R. Sweet  University of Notre Dame  7/22/2007  7/28/2007 
Stephen Taylor  University of Auckland  7/21/2007  8/6/2007 
Michael Teter  Cornell University  7/22/2007  8/4/2007 
Florian Theil  University of Warwick  7/22/2007  7/28/2007 
Walter Thiel  MaxPlanckInstitut für Kohlenforschung  7/29/2007  8/3/2007 
Carl Toews  University of Minnesota Twin Cities  9/1/2005  8/31/2007 
Donald Truhlar  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
Igor Tsukerman  University of Akron  7/22/2007  8/3/2007 
Mark E. Tuckerman  New York University  7/22/2007  8/3/2007 
Erkan Tüzel  North Dakota State University  7/22/2007  8/3/2007 
Paolo Valentini  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
Eric VandenEijnden  New York University  7/24/2007  7/26/2007 
Kochuparambil Vargheese  Corning  7/22/2007  8/3/2007 
Sorkin Viacheslav  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
John Voight  University of Minnesota Twin Cities  8/15/2006  8/31/2007 
Roman Voskoboynikov  University of Cambridge  7/22/2007  8/5/2007 
Arthur F. Voter  Los Alamos National Laboratory  7/22/2007  7/28/2007 
Rodolphe Vuilleumier  Université de Paris VI (Pierre et Marie Curie)  7/27/2007  8/2/2007 
Sinisa Vukovic  University of Toronto  7/22/2007  8/3/2007 
Feng Wang  Kent State University  7/22/2007  8/3/2007 
Renata Wentzcovitch  University of Minnesota Twin Cities  7/31/2007  8/3/2007 
Tomasz A. Wesolowski  Université de Genève  7/29/2007  8/5/2007 
Di Wu  Western Kentucky University  7/21/2007  7/28/2007 
Seongho Wu  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
Zhijun Wu  Iowa State University  7/22/2007  7/27/2007 
Dexuan Xie  University of Wisconsin  7/22/2007  8/4/2007 
Xiangrong Xin  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
Hongchao Zhang  University of Minnesota Twin Cities  9/1/2006  8/31/2008 
Peter Zhang  Medtronic  7/23/2007  7/25/2007 
Yan Zhaw  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
Jingjing Zheng  University of Minnesota Twin Cities  7/23/2007  8/3/2007 
Yunkai Zhou  Southern Methodist University  7/22/2007  8/4/2007 
Johannes Zimmer  University of Bath  7/22/2007  8/4/2007 