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IMA Newsletter #386

December 2008

2008-2009 Program

Mathematics and Chemistry

See http://www.ima.umn.edu/2008-2009 for a full description of the 2008-2009 program on Mathematics and Chemistry.

News and Notes

Annual thematic program on Simulating our complex world: Modeling, computation and analysis approved by IMA Board of Governors for 2010–2011

See http://www.ima.umn.edu/2010-2011/ for the preliminary program description.

Dr. Juan Meza Awarded Blackwell-Tapia Prize

Dr. Juan Meza, department head of the High Performance Computing Research Department at Lawrence Berkeley National Laboratory, was awarded the Blackwell-Tapia Prize November 14, 2008. The prize is named after David Blackwell and Richard Tapia, two influential figures who inspired a generation of African-American, Native American and Latino/Latina students to pursue careers in mathematics.  The award recognizes a mathematical scientist who has contributed significantly to research and who has served as a role model for mathematical scientists and students from under-represented minority groups.

Dr. Meza received the award as a result of his exceptionally distinguished record as a mathematical scientist, an accomplished and effective head of a large department doing cutting-edge explorations in the computational sciences, computational mathematics, and future technologies, and a role model and active advocate for others from groups under-represented in the mathematical sciences.

Dr. Meza served on the IMA Board of Governors from January 1999 to December 2001.  He has also provided scientific leadership to the IMA by organizing workshops, most recently, the September 2008 workshop on Electronic Structures.

For more information on the 2008 Blackwell-Tapia Conference, go to: http://www.samsi.info.

Margaret Wright was awarded an honorary PhD degree by the Royal Institute of Technology (KTH) in Stockholm

Margaret Wright, a member of the IMA Board of Governors since 2005, was awarded an honorary PhD degree by the Royal Institute of Technology (KTH) in Stockholm on November 21. A Professor at New York University, Wright has made major contributions to applied mathematics, especially in the fields of optimization and scientific computing. She has also worked to include more women in the mathematical sciences.

The Board of Governors consists of 15 distinguished mathematical scientists from academia, industry, and government laboratories. It provides oversight and direction for all major aspects of the organization.

Wright is a member of the National Academy of Sciences. She completed her doctoral degree in computer science at Stanford University in 1976 and stayed here until 1988. Between 1988 and 2000, she worked at Bell Laboratories and then moved on to the Courant Institute of Mathematical Sciences at New York University in 2001 as Professor and Chair of the Computer Science Department.

IMA Events

IMA Tutorial

Theories of solvation within quantum chemistry

December 7, 2008

Organizers: Jiali Gao (University of Minnesota Twin Cities), Benedetta Mennucci (Università di Pisa)

IMA Annual Program Year Workshop


December 8-12, 2008

Organizers: Michael J. Holst (University of California), Benedetta Mennucci (Università di Pisa), B. Montgomery Pettitt (University of Houston), Ridgway Scott (University of Chicago)

Monday, December 1

10:45am-11:15amCoffee breakLind Hall 400
2:30pm-3:30pmMath 8994: Topics in classical and quantum mechanics
Electronic structure calculations and molecular simulation: A mathematical initiation
Eric Cances (CERMICS)
Claude Le Bris (CERMICS)
Lind Hall 305

Tuesday, December 2

10:45am-11:15amCoffee breakLind Hall 400
11:15am-12:15pmMaximum dissipation principle for numerical methods in complex fluidsYunkyong Hyon (University of Minnesota)Lind Hall 305 PS
3:00pm-4:00pmReading group for Professor Ridgway Scott's book "Digital Biology"Ridgway Scott (University of Chicago)Lind Hall 401

Wednesday, December 3

10:45am-11:15amCoffee breakLind Hall 400
1:15pm-2:15pmStability of traveling waves in quasi-linear hyperbolic systems with relaxation and diffusionTong Li (University of Iowa)Lind Hall 305 SMC
2:30pm-3:30pmMath 8994: Topics in classical and quantum mechanics
Electronic structure calculations and molecular simulation: A mathematical initiation
Eric Cances (CERMICS)
Claude Le Bris (CERMICS)
Lind Hall 305

Thursday, December 4

10:45am-11:15amCoffee breakLind Hall 400
11:15am-12:15pmPolynomial extension operators in Sobolev spaces Jay Gopalakrishnan (University of Florida)Vincent Hall 570 AMS

Friday, December 5

10:45am-11:15amCoffee breakLind Hall 400

Sunday, December 7

8:15am-8:45amRegistration and coffeeEE/CS 3-176 T12.7.08
8:45am-9:00amWelcome to the IMAFadil Santosa (University of Minnesota)EE/CS 3-180 T12.7.08
9:00am-9:40amSimulations of solvent effects using combined QM/MM methods Jiali Gao (University of Minnesota)EE/CS 3-180 T12.7.08
9:40am-10:20amAn introduction to quantum mechanical continuum solvation modelsBenedetta Mennucci (Università di Pisa)EE/CS 3-180 T12.7.08
10:20am-10:50amCoffeeEE/CS 3-176 T12.7.08
10:50am-11:30amAb initio molecular dynamics via the Car-Parrinello method: Basic ideas, theory, and algorithmsMark E. Tuckerman (New York University)EE/CS 3-180 T12.7.08
11:30am-12:30pmDiscussionEE/CS 3-180 T12.7.08
12:30pm-2:30pmLunch T12.7.08
2:30pm-3:10pmApplications of combined QM/MM methodsJiali Gao (University of Minnesota)EE/CS 3-180 T12.7.08
3:10pm-3:50pmApplications of quantum mechanical continuum solvation models to the study of molecular properties and spectroscopic features of molecular solutes in different environmentsBenedetta Mennucci (Università di Pisa)EE/CS 3-180 T12.7.08
3:50pm-4:20pmCoffeeEE/CS 3-176 T12.7.08
4:20pm-5:00pmAb initio path-integrals and specific applications of the Car-Parrinello approach to problems of aqueous ion solvation and transportMark E. Tuckerman (New York University)EE/CS 3-180 T12.7.08
5:00pm-5:30pmDiscussionEE/CS 3-180 T12.7.08

Monday, December 8

All DaySession (Protein Solvation)
Chair: Benedetta Mennucci (Università di Pisa)
8:15am-9:00amRegistration and coffeeEE/CS 3-176 W12.8-12.08
9:00am-9:20amWelcome to the IMAFadil Santosa (University of Minnesota)EE/CS 3-180 W12.8-12.08
9:20am-10:00amSolvation and the energetics of protein foldingRobert L. Baldwin (Stanford University)EE/CS 3-180 W12.8-12.08
10:00am-10:40amIntricate role of water molecules in protein dynamicsDonald Hamelberg (Georgia State University)EE/CS 3-180 W12.8-12.08
10:40am-11:10amCoffeeEE/CS 3-176 W12.8-12.08
11:10am-11:50amSolubility profiles of amyloidogenic molecular structures. Theory and experiment Florin Despa (University of California, Davis)EE/CS 3-180 W12.8-12.08
11:50am-12:30pmProbing the prion hydration by Molecular dynamics simulations: from native via misfolded to amyloid conformationsAlfonso De Simone (University of Cambridge)EE/CS 3-180 W12.8-12.08
12:30pm-2:30pmLunch W12.8-12.08
2:30pm-3:10pmSecond chancesRidgway Scott (University of Chicago)EE/CS 3-180 W12.8-12.08
3:10pm-3:25pmGroup photo W12.8-12.08
3:30pm-5:30pmPoster Session and Reception
Poster submissions welcome from all participants
Lind Hall 400 W12.8-12.08
Solvation and the energetics of protein folding (poster)Robert L. Baldwin (Stanford University)
Competition of steric repulsion and electrostatic attraction determines the selectivity of calcium channelsDezső Boda (University of Pannonia)
On the Vibrational effective polarizabilities calculation from continuum solvation modelsRoberto Cammi (Università di Parma, e-mail: roberto.cammi@unipr.it)
Modeling environment effects on electronic energy transfer Carles Curutchet (University of Toronto)
Aurora Muñoz (Università di Pisa)
An adaptive fast multipole algorithm for electrostatic interactions in biomolecular systemJingfang Huang (University of North Carolina)
Optimization of transition pathways using interpolated parameters from swarms of trajectoriesDmitry A. Kondrashov (University of Wisconsin)
Slip boundary conditions in nanofluidics from the molecular theory of solvationAndriy Kovalenko (National Institute for Nanotechnology)
3D molecular theory of solvation in multiscale modeling of chemical nanostructures in solutionAndriy Kovalenko (National Institute for Nanotechnology)
Novel stochastic methods in biochemical electrostaticsMichael Mascagni (Florida State University)
Cross sections and photoelectron angular distributions in photodetachment from negative ions using EOM-CCSD Dyson orbitalsC. Melania Oana (University of Southern California)
Macroscopic pattern formation of liquid crystal in kappa-carrageenan gelIsamu Ohnishi (Hiroshima University)
Optimization of a hybrid implicit/explicit solvation modelJason A. Wagoner (Stanford University)

Tuesday, December 9

All DaySession (QM/MM & Cont)
Morning Chair: B. Montgomery Pettitt (University of Houston)
Afternoon Chair: Jingfang Huang (University of North Carolina)
8:30am-9:00amCoffeeEE/CS 3-176 W12.8-12.08
9:00am-9:40amQM or MM? Development of a next-generation force field for chemical and biomolecular simulationsJiali Gao (University of Minnesota)EE/CS 3-180 W12.8-12.08
9:40am-10:20amAn overview of the non linearity in Quantum Chemical continuum solvation modelsRoberto Cammi (Università di Parma, e-mail: roberto.cammi@unipr.it)EE/CS 3-180 W12.8-12.08
10:20am-10:50amCoffeeEE/CS 3-176 W12.8-12.08
10:50am-11:30amQuantum chemical modelling of molecules at dielectric surfaces and interfacesLuca Frediani (University of Tromsø)EE/CS 3-180 W12.8-12.08
11:30am-2:20pmLunch W12.8-12.08
2:20pm-3:00pmBiomolecular solvation: from molecular to continuum modelsNathan A. Baker (Washington University School of Medicine)EE/CS 3-180 W12.8-12.08
3:00pm-3:40pmCoupling the level-set method with variational implicit-solvent models for molecular solvationBo Li (University of California, San Diego)EE/CS 3-180 W12.8-12.08
3:40pm-4:10pmCoffeeEE/CS 3-176 W12.8-12.08
4:10pm-5:00pmSecond chancesMark E. Tuckerman (New York University)EE/CS 3-180 W12.8-12.08

Wednesday, December 10

All DayMorning session (Sim-MD)
Chair: Nina Singhal Hinrichs (University of Chicago)

Afternoon session: TBA

8:30am-9:00amCoffeeEE/CS 3-176 W12.8-12.08
9:00am-9:40amHydration from organic molecules to protein-ligand complexesWilliam L. Jorgensen (Yale University)EE/CS 3-180 W12.8-12.08
9:40am-10:20amSolvation and hydration at different scalesBernard R. Brooks (National Institutes of Health)EE/CS 3-180 W12.8-12.08
10:20am-10:50amCoffeeEE/CS 3-176 W12.8-12.08
10:50am-11:30amCalculation of small molecule solvation free energy by molecular dynamics and Monte Carlo simulations.Yuqing Deng (Zymeworks Inc.)EE/CS 3-180 W12.8-12.08
11:30am-12:10pmClassical molecular dynamics simulations of the liquid water-gold interfaceStefano Corni (Consiglio Nazionale delle Ricerche (CNR))EE/CS 3-180 W12.8-12.08
12:10pm-2:20pmLunch W12.8-12.08
2:20pm-3:00pmFirst-principles simulation of electrochemical systems Eric Cances (CERMICS)EE/CS 3-180 W12.8-12.08
3:00pm-3:40pmFast algorithms for integral equationsCarl Timothy Kelley (North Carolina State University)EE/CS 3-180 W12.8-12.08
3:40pm-4:10pmCoffeeEE/CS 3-176 W12.8-12.08
4:10pm-5:00pmSecond chancesMichael J. Holst (University of California, San Diego)EE/CS 3-180 W12.8-12.08

Thursday, December 11

All DaySession (Poisson-Boltzmann (PB))
Morning Chair: Robert D. Skeel (Purdue University)
Afternoon Chair: Stephen Bond (University of Illinois at Urbana-Champaign)
8:30am-9:00amCoffeeEE/CS 3-176 W12.8-12.08
9:00am-9:40amA fast N-body solver for the Poisson(-Boltzmann) equationRobert D. Skeel (Purdue University)EE/CS 3-180 W12.8-12.08
9:40am-10:20amThe membrane potential and its representation in computer simulationsBenoit Roux (University of Chicago)EE/CS 3-180 W12.8-12.08
10:20am-10:50amCoffeeEE/CS 3-176 W12.8-12.08
10:50am-11:30amSelf-organized models of selectivity in Ca and Na channelsRobert S. Eisenberg (Rush University Medical Center)EE/CS 3-180 W12.8-12.08
11:30am-12:10pmMolecular recognition in life phenomena probed with the statistical mechanics of liquidsFumio Hirata (National Institutes of Natural Sciences)EE/CS 3-180 W12.8-12.08
12:10pm-2:20pmLunch W12.8-12.08
2:20pm-3:00pmEstimating electrostatic contributions to solvation via boundary-integral equation theoryJaydeep P. Bardhan (Argonne National Laboratory)EE/CS 3-180 W12.8-12.08
3:00pm-3:40pmTBAMarcia O. Fenley (Florida State University)EE/CS 3-180 W12.8-12.08
3:40pm-4:10pmCoffeeEE/CS 3-176 W12.8-12.08
4:10pm-5:00pmSecond chancesMatthew Gregg Knepley (Argonne National Laboratory)EE/CS 3-180 W12.8-12.08
6:30pm-8:00pmWorkshop dinner at PagodaPagoda Restaurant
1417 4th St. SE
Minneapolis, MN

Friday, December 12

All DaySession (Statistics)
Chair: Carlos J. Garcia-Cervera (University of California, Santa Barbara)
8:30am-9:40amCoffeeEE/CS 3-176 W12.8-12.08
9:40am-10:20amClassical density functional theory approach to solvation in polar solventsDaniel Jean Borgis (École Normale Supérieure)EE/CS 3-180 W12.8-12.08
10:20am-10:50amCoffeeEE/CS 3-176 W12.8-12.08
10:50am-11:30amDimerization of formamideModesto Orozco (Institute for Research in Biomedicine (IRB Barcelona))EE/CS 3-180 W12.8-12.08
11:30am-12:00pmSecond chancesEE/CS 3-180 W12.8-12.08
12:00pm-12:10pmClosureEE/CS 3-180 W12.8-12.08

Monday, December 15

10:45am-11:15amCoffee breakLind Hall 400

Tuesday, December 16

10:45am-11:15amCoffee breakLind Hall 400
11:15am-12:15pmTime lags in signaling cascadesSrividhya Jeyaraman (University of Minnesota)Lind Hall 305 PS
1:00pm-3:00pmIMA Holiday Potluck LuncheonLind Hall 400

Wednesday, December 17

10:45am-11:15amCoffee breakLind Hall 400

Thursday, December 18

10:45am-11:15amCoffee breakLind Hall 400
3:00pm-4:00pmReading group for Professor Ridgway Scott's book "Digital Biology"Ridgway Scott (University of Chicago)Lind Hall 401

Friday, December 19

10:15am-11:15amCoffee breakLind Hall 400

Thursday, December 25

All DayChristmas Day. The IMA is closed.

Friday, December 26

All DayFloating holiday. The IMA is closed.
Second chances
Abstract: No Abstract
IMA Holiday Potluck Luncheon
Abstract: Please join us for the annual IMA Holiday Potluck Luncheon, December 16, 2008 from 1:00-3:00pm in 400 Lind Hall. We would like you to share a prepared traditional recipe that means something to you (appetizer, salad, entree, dessert, etc.) If your cooking skills are not something you feel should be shared with the rest of us, Lund's/Byerly's, Whole Foods, and Kowalski's are always willing to cover for you. The IMA will provide the beverages. There is a sign-up sheet located on the 4th floor, at the break treats table. It is going to be a ton of fun! We hope you can join us! -IMA Staff
Nathan A. Baker (Washington University School of Medicine) Biomolecular solvation: from molecular to continuum models
Abstract: Continuum electrostatics methods have become increasingly popular due to their ability to provide approximate descriptions of solvation energies and forces without the expensive sampling required by all-atom solvent models. In particular, the Poisson–Boltzmann equation (PBE) provides electrostatic potentials, solvation energies, and forces by modeling the solvent as a featureless dielectric material and the mobile ions as a continuous distribution of charge. Polar solvation forces and energies obtained from the PBE are often supplemented with simple solvent-accessible surface area (SASA) models of nonpolar solvation. However, while polar and nonpolar continuum models have been assessed on their ability to reproduce global properties, such as solvation free energies, their ability to provide accurate representations of local solvation properties such as forces has not previously been adequately studied. We have developed efficient software for describing polar biomolecular solvation by solving the Poisson-Boltzmann equation using multigrid and adaptive finite element methods. Additionally, we have implemented new models to describe nonpolar solvation phenomena. These models have been used to study solvation forces for protein, RNA, and alkane systems. In particular, we have performed comparisons of continuum and all-atom representations of solvation forces for these very different molecular systems in order to assess the performance of continuum models in the presence of widely varying charge densities. The results of these comparisons show that current implementations of the PBE are capable of generating polar solvation forces that correlate well with explicit solvent forces for protein systems but provide significantly less accurate representations of polar solvation forces for RNA systems. Conversely, SASA-based nonpolar forces are found to have no significant correlation with nonpolar explicit solvent forces for either protein or RNA molecules. Good correlation between explicit and continuum nonpolar forces is only obtained when area, volume, and attractive dispersion forces are included in the continuum model. We discuss the implications of these studies in the context of molecular simulation as well as the impact of this work on basic models for understanding experimental observations of biomolecular binding and folding.
Robert L. Baldwin (Stanford University) Solvation and the energetics of protein folding
Abstract: Solvation makes major contributions to the energetics of protein folding. In an unfolded protein the free energy of solvating nonpolar side chains is unfavorable while solvating polar peptide groups is favorable. The classical model for the energetics of burying nonpolar side chains through folding is Kauzmann's 1959 proposal to use transfer data for model hydrocarbons from water to an organic solvent. The simple picture is that 50 square angstroms of water-accessible surface area (ASA) per average side chain is buried via folding and -25 cal mol-1 is gained per square angstrom or -1.25 kcal mol-1 per residue. Today this model is regarded as seriously over-simplified and side chain burial is modeled by a 2-step process. (1) First remove the nonpolar side chain from water, using liquid to gas phase transfer data; (2) pack the folded protein side chains using the Lennard-Jones potential and protein structural coordinates to find the packing energy. A major unsolved problem is the highly approximate proportionality between solvation free energy and ASA. Model compound data give a huge value for the solvation enthalpy of the peptide group (-14.2 kcal/mol, Makhatadze & Privalov, 1993), more than 10 times larger than the free energy change per residue for burying nonpolar side chains. Its size shows that more work is badly needed on determining accurate energetics for peptide solvation and forming peptide H-bonds. Recent work shows that the principle of group additivity is not valid for the polar peptide group.
Robert L. Baldwin (Stanford University) Solvation and the energetics of protein folding (poster)
Abstract: Two classes of protein groups in an unfolded protein interact strongly with water and make major contributions to the energetics of folding. Nonpolar side chains interact unfavorably with water and become buried in the protein interior during folding. Polar peptide groups interact favorably and very strongly with water, and as the protein folds the peptide groups become desolvated and form hydrogen bonds (H-bonds) with each other. Two models are used currently to represent desolvation of nonpolar side chains during folding. Kauzmann’s model (1959) treats the protein interior as an organic liquid and uses liquid-liquid transfer data to estimate the enerrgetics. The packing-desolvation model (Privalov and Gill, 1988) treats the protein interior as a semi-crystalline solid and uses gas to liquid transfer data to estimate desolvation while using the Lennard-Jones potential and the protein structural coordinates to estimate the packing energetics. Solvation energetics of the peptide group are based on calorimetric data for the solvation enthalpy of dipeptide analogs and mono-amides together with electrostatic calculations of solvation energetics for longer peptides. These results indicate that, contrary to the longstanding assumption that group additivity is valid, it is in fact entirely invalid for the polar peptide groups. These new results may explain the 2-fold discrepancy between the 1995 simulations of folding energetics by Lazaridis, Archontis and Karplus versus the calorimetric results of Makhatadze and Privalov.
Jaydeep P. Bardhan (Argonne National Laboratory) Estimating electrostatic contributions to solvation via boundary-integral equation theory
Abstract: Implicit-solvent models commonly decompose the molecular solvation free energy into a sum of electrostatic and non-polar terms, with separate theoretical and numerical procedures employed for each component. In this talk I will describe a new method for estimating the electrostatic free energy of solvation, called BIBEE (boundary-integral-based electrostatics estimation). The BIBEE method rapidly approximates the solution of the apparent-surface-charge (ASC) or polarizable-continuum-model (PCM) integral equation formulation of the mixed-dielectric continuum electrostatics problem that is often solved using finite-element or finite-difference methods. The method draws inspiration from the surface-generalized Born model, but avoids the unphysical interpolations inherent to generalized-Born method. As a result, BIBEE methods more accurately reproduce solvent-screened interactions between charges. Furthermore, it is straightforward to show that variants of the BIBEE method can generate rigorous upper and lower bounds for the actual electrostatic free energy of solvation.
Dezső Boda (University of Pannonia) Competition of steric repulsion and electrostatic attraction determines the selectivity of calcium channels
Abstract: Calcium channels conduct Na ions in the absence of Ca, but they selectively conduct Ca ions when Ca ions are present at physiological concentrations. In an experiment when Ca is added to NaCl gradually, even a micromolar amount of Ca ions effectively blocks Na current. In our model of the selectivity filter of Ca channels, the terminal groups of the side chains of amino acids—four glutamates--in the selectivity filter are represented as mobile ions that are restricted so they move inside the filter These structural ions form a liquid-like self-adjusting environment for the passing ions so that the system assumes minimum free energy. They also fill part of the pore so the counterions have to compete for space in the crowded selectivity filter (charge/space competition (CSC) mechanism). In this picture electrostatic attraction and repulsive entropic excluded volume effects compete with each other to determine which ions can enter the selectivity filter. We argue that this competition is crucial in explaining the selectivity mechanism of Ca channels. We show grand canonical Monte Carlo simulation results for competition between ions of different valence and diameter. We couple our Monte Carlo simulations to the integrated Nernst-Planck equation to compute current from equilibrium profiles. Our results are in good agreement with experimental data.
Daniel Jean Borgis (École Normale Supérieure) Classical density functional theory approach to solvation in polar solvents
Abstract: We draw a comparison between the quantum density functional theory for electronic structure calculations and the ''classical'' density functional theory of molecular liquids and we show how, borrowing ideas and techniques from electronic DFT, classical DFT can be used as a useful chemist's tool to provide, at a microscopic level, the solvation properties of complex molecules in polar solvents. This includes the determination of absolute solvation free-energies, as well as three-dimensional microscopic solvation structures. The proposed strategy is as follows: we first compute the homogeneous-fluid, position and angle-dependent, direct correlation function, the c-function. To this end, we carry out extensive MD simulations of the pure solvent, and compute this way the position and angle-dependent pair distribution function (the h-function). We invert subsequently the so-called Ornstein-Zernike equation to go from the h-function to the c-function. This direct correlation can then be used as the definition of the –unknown– excess free-energy in the expression of the free-energy functional. In the presence of a given molecular solute, which provides the external potential, this functional can be minimized with respect to the position and angle-dependent density, using a 3D cartesian grid for positions and a Gauss-Legendre angular grid for orientations, to obtain, at the minimum, the absolute solvation free-energy of the solute and the equilibrium solvent density profile around it. The DFT results can be compared to direct MD simulations of the solute/solvent system or experimental data The procedure is shown to be efficient and accurate for polar solvents such as acetonitrile. [1] Rosa Ramirez, Ralph Gebauer, Michel Mareschal, and Daniel Borgis, Phys. Rev. E, 66, 031206 (2002). [2] Rosa Ramirez and Daniel Borgis, J. Phys. Chem B 109, 6754 (2005). [3] Rosa Ramirez, Michel Mareschal, and Daniel Borgis, Chem. Phys. 319, 261 (2005). [4] Lionel Gendre, PhD Thesis, Université d'Evry, July 2008. Manuscript in preparation.
Bernard R. Brooks (National Institutes of Health) Solvation and hydration at different scales
Abstract: No Abstract
Roberto Cammi (Università di Parma, e-mail: roberto.cammi@unipr.it) An overview of the non linearity in Quantum Chemical continuum solvation models
Abstract: Quantum chemistry computational tools coupled with a continuum description of the solvent offer an effective approach to study molecular properties and processes in condensed phase due to modest increase of the computational effort with respect a QM calculation of isolated molecules [1]. However, this coupling is by no meas free of problems. The QM continuum models are characterized by the use of a non-linear Hamiltonian, being the solute Hamiltonian term representing by the solute-solvent interaction dependent on the wave-function of the solute it selves. As a consequence all the conventional Quantum Chemical models to be able to describe in a coherent way the effects of the solute-solvent interaction have to be reconsidered from their basic principles and suitably modified to take into account of this non linearity. The neglecting of this effects may lead to a systematic errors in the numerical outcome of the QM solvation models. In this talk we will give an overview of the systematic work done within the Polarizable Continuum Model group to introduce the non-linearity effects into the Quantum Chemical methods. The emphasis will be given on the basic principles and problems involved. In particular we will focus on the definition of a new basic energetic functional [2] , different, from that used for isolated molecules, which has to be taken as a starting point to develop QM methods for continuum solvation models. A wide sample of QM-solvation methods will be also discussed, ranging from the ab-initio time independent methods (Hartree-Fock, MC-SCF, Moeller Plesset) to the corresponding time-dependent response function formalisms, and from the the Density Functional Theory to the Time dependent DFT approach to the excited states of solvated chromophores. Final remarks will regards some still open issues in the coupling of QM methods with continuum solvation models. [1] Tomasi J., B. Mennucci, Cammi, R. "Quantum Mechanical Continuum Solvations Models", Chem. Rev., 2005, 105, 2999. [2] Cammi, R., Tomasi, J. J. Comp. Chem. 16, 1449, 1994
Roberto Cammi (Università di Parma, e-mail: roberto.cammi@unipr.it) On the Vibrational effective polarizabilities calculation from continuum solvation models
Abstract: The increasing efforts devoted to study linear and non linear optical properties (NLO) of solvated molecules have followed the success of modern quantum mechanical (QM) methods in the forecast of the NLO properties of isolated systems. The approaches adopted uses the same QM methodology developed for the isolated systems with the additional introduction of the features due to the solute-solvent interactions. However, even when all the solvent effects are included in the solvation model the computed NLO quantities are still microscopic in nature and cannot be directly compared with their macroscopic manifestation, i.e. the macroscopic scusceptibility. In recent years we have introduced an effective framework to treat local field effects in linear and non-linear NLO properties in solution within the quantum mechanical Polarizable Continuum Model [1,2]. In this framework effective polarizabilities are defined to include the effect due to the difference between the local field acting on the solute molecules and the macroscopic field in the medium (Maxwell field). In this poster we will focus on the vibrational components of the effective polarizabilities within the quantum mechanical Polarizable Continuum Model framework. In particular, we will give a detailed overview of the method for the calculation of the vibrational effective polarizabilities in the double harmonic approximation [3] . As will be show, the double harmonic procedure can be reformulated within the PCM so as to obtain the effective vibrational polarizabilities in terms of the derivatives with respect to normal coordinates of effective electronic molecular properties [4]. We will also discuss the connection between the PCM formulation of the vibrational effective polarizabilities and the parallel approach given within the framework of semiclassical Onsager-Wortmann-Bishop method [5]. [1] R. Cammi, B. Mennucci, and J. Tomasi, J. Phys. Chem. A, 102(1998)870.
[2] R. Cammi, B. Mennucci, and J. Tomasi, J. Phys. Chem. A, 104(2000)4690.
[3] J. Tomasi, B. Mennucci and R. Cammi, Chem. Rev., 105(2005)2999.
[4] R. Cammi, B. Mennucci, and J. Tomasi, in M.G. Papadopulos (ed.), Nonlinear Optical Response of Molecules Solids and Liquids: Methods and Applications, Research Signpost, Kerala, India, 2003, p.113.
[5] R. Wortmann and D. Bishop, J. Chem. Phys., 108(1998)1001.
Eric Cances (CERMICS), Claude Le Bris (CERMICS) Math 8994: Topics in classical and quantum mechanics
Electronic structure calculations and molecular simulation: A mathematical initiation
Abstract: Meeting time: Mondays and Wednesdays 2:30 ‐ 3:30 pm Room 305 Lind Hall. The course will present the basics of the quantum theory commonly used in computational chemistry for electronic structure calculations, and the basics of molecular dynamics simulations. The perspective is definitely mathematical. After the presentation of the models, the mathematical properties will be examined. The state of the art of the mathematical knowledge will be mentioned. Numerical analysis and scientific computing questions will also be thoroughly investigated. The course is intended for students and researchers with a solid mathematical background in mathematical analysis and numerical analysis. Familiarity with the models in molecular simulation in the broad sense is not needed. The purpose of the course to introduce the audience to the field. This is a 1‐3 credit course offered through the School of Mathematics. Non‐student participants are welcome to audit without registering. Note that no particular knowledge of quantum mechanics or classical mechanics will be necessary: the basic elements will be presented. For additional information and course registration, please contact: Markus Keel (keel@math.umn.edu).
Eric Cances (CERMICS) First-principles simulation of electrochemical systems
Abstract: Understanding the electrical response of electrochemical convertors, such as fuel cells or batteries, involves elucidating the effect of the macroscopic voltage on the microscopic charge distribution at the electrode-electrolyte interface. I will present a quantum/classical model which couples a quantum molecular description of the electrode-electrolyte interface with a polarizable-continuum representation of the long-range effects of the ionic solvent. I will mainly focus on the mathematical and numerical aspects. In the last part of my talk, I will present numerical calculations of the vibrational Stark effect for chemisorbed CO, which demonstrate the efficiency of this approach. This is a joint work with I. Dabo, Y. Li and N. Marzari.
Stefano Corni (Consiglio Nazionale delle Ricerche (CNR)) Classical molecular dynamics simulations of the liquid water-gold interface
Abstract: Several phenomena take place at the interface between liquid water and the gold (111) surface. For example, it is a widespread system for controlled electrochemical investigations, for the study of molecular conduction and of the interaction between proteins and the solid surfaces in water. Despite this great and interdisciplinary importance, the wettability properties of the gold surface are microscopically not well understood. For example, the contact angle between water and clean gold is zero, thus the gold surface is considered hydrophilic [1]. On the other hand, computational DFT studies on single molecules (or model monolayers) on the gold surface pointed out that the gold-water interaction is very small [2]. The term hydrophobic is often used in this context to classify Au(111). To shed light on the microscopic structure of the water-Au(111) interface, we performed classical molecular dynamics simulations of water on a gold (111) surface. These simulations are based on a force field for gold-water and gold-protein interactions that we have recently developed [3]. It is based on available experimental results and quantum mechanical (DFT and MP2) calculations. Gold polarization effects are also taken into account. In this talk I will discuss the developed force field and the results of our simulations for a neutral gold surface, with particular emphasis on the microscopic nature of the water-gold interface [1] K.W. Bewing, and W. A. Zisman, J. Phys. Chem 69, 4238 (1965).
[2] A. Michaelides et al., Phys. Rev. Lett. 90, 216102 (2003).
[3] F. Iori, and S. Corni J. Comp. Chem. 29, 1656 (2008); F. Iori et al. J. Comp. Chem. in press.
Carles Curutchet (University of Toronto), Aurora Muñoz (Università di Pisa) Modeling environment effects on electronic energy transfer
Abstract: Understanding solvent effects, which cause line broadening and screen electronic interactions, is fundamentally important because of its central role in the control of EET dynamics. Recent work has furthermore shown that simple models for solvation may not be sufficient to explain effects that go beyond Förster theory, such as coherent contribution to energy transfer.[1] Here results obtained from novel quantum-mechanical methodologies will be reported as a starting point for an atomistic description of the interplay between solvation and electronic energy transfer. First, we will present results obtained with a quantum-mechanical method that accounts for the actual shape of the molecules inside the dielectric environment through the Polarizable Continuum Model (PCM), thus overcoming the point-dipole assumption of Förster theory. This model predicts an exponential distance-dependent attenuation of the solvent screening in chromophore pairs taken from light harvesting antenna proteins,[2] thus indicating a substantial underestimation of EET rates by Förster theory at separations less than about 20 Å. As a further step towards a realistic model of solvation in EET, we will present a combined quantum mechanics/molecular mechanics (QM/MM) method that adopts an atomistic description of the solvent, thus going beyond the continuum dielectric approximation. [1] (a) Jang, S.; Newton, M. D.; Silbey, R. J. Phys. Rev. Lett. 2004, 92, 218301. (b) Engel, G. S.; Calhoun, T. R.; Read, E. L.; Ahn, T.-K.; Mancal, T.; Cheng, Y.-C.; Blankenship, R. E.; Fleming, G. R. Nature 2007, 446, 782.
[2] (a) Scholes, G. D.; Curutchet, C.; Mennucci, B.; Cammi, R.; Tomasi, J. J. Phys. Chem. B 2007, 111, 6978. (b) Curutchet, C.; Scholes, G. D.; Mennucci, B.; Cammi, R. J. Phys. Chem. B 2007, 111, 13253.
Alfonso De Simone (University of Cambridge) Probing the prion hydration by Molecular dynamics simulations: from native via misfolded to amyloid conformations
Abstract: Water at the surface of proteins plays a crucial biological role. The study of hydration is therefore fundamental for achieving a complete description of key factors determining the protein biology. In this framework, Molecular Dynamics simulations have provided precious tools for elucidating the structure and dynamics of waters in the protein hydration shell. We employed Molecular Dynamics to address on the hydration properties of the Prion Protein, whose misfolding and aggregation is associated to Transmissible Spongiform Encephalopathies. The investigations focused on different states along a likely aggregation pathway specifically analyzing native state, misfolded state and amyloid-like state. The presentation will discuss on the influence that water exerts on protein structural stability [1, 2], intermolecular interactions [3], misfolding [4] and self-assembly [5, 6]. References
1. PNAS (2005) 102:7535-7540.
2. FEBS Letters (2006) 580:2488-2494.
3. Biophysical Journal (2006) 90:3052-61.
4. Biophysical Journal (2007) 93:1284-1292.
5. Proteins (2008) 70:863-872.
6. BBRC (2008) 366:800-806.
Yuqing Deng (Zymeworks Inc.) Calculation of small molecule solvation free energy by molecular dynamics and Monte Carlo simulations.
Abstract: Solvation free energy determines the thermostability of molecules in solution. Accurate prediction of solvation free energy from atomistic simulations have great impact on the understanding of many biologically important processes. What makes the simulation of the solvation free energy difficult is that it consists of competing effects from opposing interactions at a molecular level. To accelerate convergence, separations of the competing forces are necessary. Traditionally formulation of solvation free energy separates van der Waals and electrostatics. We find that further separation of the attractive and repulsive forces within the van der Waals interactions is also necessary. Test calculations with constant pressure molecular dynamics (MD) in water show that the seemingly small nonpolar solvation free energy is made up of relatively large unfavorable contribution from repulsive forces and a canceling favorable contribution from the attractive forces. Our results show good agreement with experimental solvation free energies and those of other computational studies. Alternative to the constant pressure simulation with a fluctuating volume, the same results can be generated with fixed volume but fluctuating number of water molecules --- grand canonical ensemble. With the grand canonical Monte Carlo (GCMC) moves on solvent water, we are able to obtain accurate solvation free energy as well. The GCMC/MD method is shown to yielded accurate results for ligand binding in cytochrome p450, in which case water displacement from a confined binding pocket can not be account for in typical MD simulation time.
Florin Despa (University of California, Davis) Solubility profiles of amyloidogenic molecular structures. Theory and experiment
Abstract: Hydration shells of normal proteins display both structured and bulk- like waters. Isomers with considerable bulk-like hydration tend to aggregate. In my talk, I will present both theoretical and experimental data showing that different morphological states of aggregated isomers differ by hydration distribution profiles and water magnetic resonance (MR) signals. The results help explain the MR contrast patterns of amyloids, a subject of long controversy, and suggest a new approach for identifying unusual protein aggregation related to disease. As an example, I will present MRI data and cell toxicity measurements revealing the relationship between the structural conformations of several amyloidogenic peptides and the mechanisms of cellular dysfunction.
Robert S. Eisenberg (Rush University Medical Center) Self-organized models of selectivity in Ca and Na channels
Abstract: Selectivity is one of the most important properties of living systems. One of the founders of molecular biology (Nobel Laureate Aaron Klug) recently said (with some hyperbole I suspect) "There is only one word that matters in biology and that is specificity." My collaborators and I study selectivity in ion channels. Ion channels are proteins with a hole down their middle that are the (nano nearly pico)valves of life. Ion channels control an enormous range of biological function in health and disease. A large amount of data is available about selectivity in many channels. Selectivity in ion channels occurs without structural change of the channel protein (on the biological time scale of 10-5 sec or longer) and does not involve changes in covalent bonds (i.e., changes in shape of electron orbitals). Selectivity in channels involves only electrodiffusion—usually of charged hard spheres. Thus, physical analysis of selectivity in ion channels is easier than analysis of specificity in enzymes or many other proteins while being at least as important biologically. A simple pillbox model with two adjustable parameters accounts for the selectivity of both DEEA Ca channels (Aspartate Glutamate Glutamate Alanine) and DEKA Na channels (Aspartate Glutamate Lysine Alanine) in many ionic solutions of different composition and concentration. The predicted properties of the Na and Ca channels are very different even though 'Pauling' crystal radii are used for ions and all parameters are the same for both channels in all solutions. Only the side chains are different in the model of the Ca and Na channels. No information from crystal structures is used in the model. Side chains of the channel protein are grossly approximated as spheres. How can such a simple model give such powerful results when chemical intuition says that selectivity depends on the precise relation of ions and side chains? We use Monte Carlo simulations of this model that determine the most stable-lowest free energy-structure of the ions and side chains. Structure is the computed consequence of the forces in this model and so is different in different conditions. The relationship of ions and side chains vary with ionic solution and are very different in simulations of the Na and Ca channels. Selectivity is a consequence of the 'induced fit' of side chains to ions and depends on the flexibility (entropy) of the side chains as well as their location. The induced fit depends on the concentrations of ions in the surrounding solutions in a complex way. Thus, calculations in a single set of conditions are of limited use. In particular, calculations of 'free energy of binding' in infinitely dilute or ideal solutions are not likely to give useful estimates of binding in physiological solutions. Physiological solutions are typically ~ 200 mM, far from dilute. The self-organized induced-fit model captures the relation of side chains and ions well enough to account for selectivity of both Na channels and Ca channels in the wide range of conditions measured in experiments, even though the components of the model are grossly oversimplified. Perhaps the simplified model works because the structures in both the model and the real channel are the most stable, self-organized, and at their free energy minimum, different in different conditions. It seems that an important biological function can be understood by an oversimplified model if the model calculates the 'most stable' structure as it changes from solution to solution, and mutation to mutation.
Luca Frediani (University of Tromsø) Quantum chemical modelling of molecules at dielectric surfaces and interfaces
Abstract: The study of chromophores located at surfaces and interfaces is important both in material science and in biological chemistry: coated materials, sensors, nanoparticles, cell membranes, micelles are systems where the interface is not a mere boundary between different bulk regions but the central part of the investigated system. Chromophores are often employed to probe and investigate the surface by making use of surface-specific techniques as second harmonic generation (SHG) and sum-frequency generation (SFG). It is therefore important to develop the theoretical tools necessary to model chromophores in such a peculiar environment in order to interpret and understand the spectroscopic findings. Continuum solvation models have in recent years been extended to surfaces and interfaces. A brief account of the challenges faced and the theoretical developments needed to achieve the goal will here be given. Recent results making use of the developed theoretical models will also be presented.
Jiali Gao (University of Minnesota) QM or MM? Development of a next-generation force field for chemical and biomolecular simulations
Abstract: Traditionally, molecular dynamics and Monte Carlo simulations of condensed phase systems including biopolymers are carried out using molecular mechanics or force fields that describe intermolecular interactions. In fact, the formalism of these force fields for biomolecular simulatiosn was established in the 1960s. Although the computational accuracy has increased enormously through parameterization, little has changed in the functional terms used in the force fields. In this talk, I will describe an explicit polarization (X-Pol) method based on quantum mechanics for developing force fields in condensed phase simulations. The theory, algorithm and application of this approach will be illustrated and its feasibility is demonstrated.
Jiali Gao (University of Minnesota) Simulations of solvent effects using combined QM/MM methods
Abstract: There are two main advantages of using a combined quantum mechanical and molecular mechanical (QM/MM) potential in molecular dynamics and Monte Carlo simulations. First, since only a small portion of the condensed phase system is treated by an explicit electronic structure method, combined QM/MM methods can be applied to large molecular systems along with extensive configurational sampling. Secondly, the accuracy of the QM model representing the solute molecule can be systematically improved by using larger basis sets and by including better treatment of electron correlation. Parallel to the QM treatment, the quality of the MM approximation for the solvent system can also be improved by including polarization terms to account for the mutual solute (QM) and solvent (MM) charge polarization. In this talk, I will summarize early studies and highlight some recent developments including the use of mixed molecular orbital and valence bond (MOVB) models and the incorporation of solvent polarization in combined QM/MM simulations.
Jiali Gao (University of Minnesota) Applications of combined QM/MM methods
Abstract: In this tutorial, I will present a few specific applications in which the need for an explicit treatment of the electronic structure of the solute is particularly important and cannot be conveniently circumvented by developing a problem-specific force field. The examples include the computation of the pKa of organic acid in the electronically excited state, the solvatochormic shifts of an organic chromophore from steam vapor to ambient water, the vibrational energy relaxation of a ligand in the enzyme active site, and the kinetic isotope effects in a proton transfer reaction in water using Feynman path integrals.
Donald Hamelberg (Georgia State University) Intricate role of water molecules in protein dynamics
Abstract: Water molecules are ubiquitous in living organisms and have therefore been viewed more as an environment for biomolecules rather than as a collection of interacting molecules. Water molecules make up an integral part of protein structures, while assisting in catalysis, providing stability and controlling the plasticity of binding sites. In order to realistically mimic the environment of biomolecules, molecular dynamics simulations are routinely done in explicit water. Unfortunately, most of the computational resources go into computing the interactions between these water molecules. Therefore, many implicit solvation models pursued over the years have only viewed the presence of water as a continuum dielectric. However, critical questions do arise about the inherent faster dynamics that are usually obtained with implicit solvation models. We show that explicit water does not only slow down protein dynamics by increasing the frictional drag, but also by increasing the local energetic roughness of the energy landscape by as much as 1.0 kcal/mol, an effect which is lacking in typical implicit solvation models. The possible implications of this effect in catalysis will also be discussed.
Fumio Hirata (National Institutes of Natural Sciences) Molecular recognition in life phenomena probed with the statistical mechanics of liquids
Abstract: Few years ago, we have succeeded to “probe” water molecules bound in a cavity of a protein by means of the statistical mechanics of molecular liquids, or the RISM/3D-RISM theory. This is the first finding in the history of the statistical mechanics to show that the theory is applicable to such fluids in an extremely inhomogeneous field in atomic scale. On the other hand, the finding implies that we got a powerful machinery in our hand to clarify the “molecular recognition” which is the most fundamental process in living cells. It will become a “bridgehead” in our theoretical challenge on life phenomena. In the succeeding applications of the method, we have focused on a variety of molecular processes in bio-systems, in which the molecular recognition plays an essential role: the selective ion-binding by protein, an enzymatic reaction, water channels (aquaporin), the preferential binding of inert gas by protein, and the pressure denaturation of protein. In the talk, I will present our recent studies on the chemical processes concerned with the molecular recognition, focusing especially on the possibility of ion permeation through aquaporins. The talk will include also prospects of the theory to be extended to the temporal fluctuation of protein structure coupled with the solvent dynamics.
Michael J. Holst (University of California, San Diego) Second chances
Abstract: No Abstract
Jingfang Huang (University of North Carolina) An adaptive fast multipole algorithm for electrostatic interactions in biomolecular system
Abstract: Poisson-Boltzmann (PB) electrostatics is a well established model in biophysics, however its application to the study of large scale biosystem dynamics such as the protein-protein encounter is still limited by the efficiency and memory constraints of existing numerical techniques. In this poster, we present an efficient and accurate scheme which incorporates recently developed novel numerical techniques to further enhance the present computational ability. In particular, a boundary integral equation approach is applied to discretize the linearized Poisson-Boltzmann (LPB) equation; the resulting integral formulas are well conditioned and are extended to systems with arbitrary number of biomolecules; the solution process is accelerated by the Krylov subspace methods and an adaptive new version of fast multipole method (FMM); and in addition to the full electrostatic interaction energy, the forces and torques are computed in the post-processing procedure using interpolation. The Adaptive Fast Multipole Poisson-Boltzmann (AFMPB) solver will be released under open source license agreement.
Yunkyong Hyon (University of Minnesota) Maximum dissipation principle for numerical methods in complex fluids
Abstract: We discuss the general energetic variational approaches for hydrodynamic systems of complex fluids. In these energetic variational approaches, the least action principle (LAP) with action functional gives the Hamiltonian parts (conservative force) of the hydrodynamic systems, and the maximum/minimum dissipation principle (MDP), i.e., Onsager's principle, gives the dissipative parts (dissipative force) of the systems. When we combine the two systems derived from the two different principles, we obtain a whole coupled nonlinear system of equations satisfying the dissipative energy laws. We will discuss the important roles of MDP in designing numerical method for computations of hydrodynamic system in complex fluids. We will reformulate the dissipation in energy equation in terms of a rate in time by using an appropriate evolution equations, then the MDP is employed in the reformulated dissipation to obtain the dissipative force for the hydrodynamic system. The systems are consistent with the Hamiltonian parts which are derived from LAP. This procedure allows the usage of lower order element (a continuous $C^0$ finite element) in numerical method to solve the system rather than high order elements, and at the same time preserves the dissipative energy law.
Srividhya Jeyaraman (University of Minnesota) Time lags in signaling cascades
Abstract: Biochemical Signaling cascades are the primary source of information transfer in cellular mechanisms. Cell signaling is predominantly achieved by Phosphorylation-Dephosphorylation (PD) reactions knit in a cascade like fashion. These cascades respond to a stimulus and conduct the information that regulates several key events within the cell. Mathematical models of these cascades predict a phenomenon called "Zero-order Ultrasensitivity" which corresponds to an unusually increased sensitivity to conduct the signals across the cascades. This has been confirmed experimentally. However, experiments have also observed a certain time lag in the response of these cascades. In this talk I will discuss the effect of time lag in some of the mathematical models to see what effect they may bring in. A small amount of time lag brings in the capability of sustained signal transduction even when the stimulus strength is very weak. This suggests that PD cascades coupled with time lags may be one of the fundamental mechanisms of signal transduction in cellular processes under weak stimuluses.
William L. Jorgensen (Yale University) Hydration from organic molecules to protein-ligand complexes
Abstract: No Abstract
Carl Timothy Kelley (North Carolina State University) Fast algorithms for integral equations
Abstract: We will discuss a class of fast algorithms for linear and nonlinear integral equations. These are two-level algorithms based on the classic Atkinson-Brakhage method from the 1970s. We will present more efficient approach which uses a matrix-free Newton-Krylov iteration on the coarse mesh and does the fine-to-coarse intergrid transfer with an average. We will then apply the approach to the Ornstein-Zernike (OZ) equations for atomic fluids and some extensions of the OZ equations for molecular fluids.
Dmitry A. Kondrashov (University of Wisconsin) Optimization of transition pathways using interpolated parameters from swarms of trajectories
Abstract: Joint work with A.C. Pan and B. Roux. Understanding the mechanism of conformational changes in macromolecules requires the knowledge of the intermediate states. A version of the string method, which uses multiple short dynamics trajectories to propagate the pathway, was recently developed by Pan et al. We use data from swarms of trajectories calculated at discrete points in phase space to interpolate the average displacement and variance of the system at arbitrary points. This is tested on model potentials using statistics from actual swarms of trajectories. We use the interpolated parameters to compute the Markovian propagators from one point on the transition path to the next. We use them to obtain a time-dependent action of a path, which can be optimized to produce the highest probability pathway. We describe the optimization protocol and demonstrate that in artificial flat potentials the existing string method cannot correct problems such as loops in the initial path, while the new method produces the correct pathway. The method will be tested by applying it to protein conformational transitions, such as the KcsA potassium channel, and comparing its performance to existing transition pathway methods.
Andriy Kovalenko (National Institute for Nanotechnology) Slip boundary conditions in nanofluidics from the molecular theory of solvation
Abstract: Joint work with Alexander E. Kobryn (National Institute for Nanotechnology, National Research Council of Canada). Motivated by the fundamental questions raised by the most recent experimental achievements in nanofluidics, we propose the first-ever derivation and calculation of the hydrodynamic slip length from the first principles of statistical mechanics, based on a combination of linear response theory and equilibrium molecular theory of solvation. The slip length obtained is independent of the type of flow and is related to the fluid organization near the solid surface, as governed by the solid-liquid interaction. In the wide range of shear rates and surface-liquid interactions, the slip length is expressed in terms of the Green-Kubo-Nakano relations as a function of the anisotropic inhomogeneous time correlation function of density fluctuations of the liquid in contact with the surface. The time dependence of the correlation function is factored out by treating it in the hydrodynamic limit. And the spatially inhomogeneous two-body correlation function is represented in the Kirkwood-like approximation as a product of the three-dimensional density distributions of interaction sites of the liquid near the surface and the site-site pair correlations of the bulk liquid. The presented treatment generalizes the phenomenological definition of the friction coefficient (as well as the slip length) to a tensor quantity, which reflects an anisotropic nature of an ordered crystalline surface. This enables theoretical prediction of friction forces acting aslant to the liquid flow direction for such surfaces. We derive generic analytical expressions for the liquid-surface friction coefficient (and slip length) for an arbitrary surface-liquid interaction potential. We further illustrate it by numerical calculations for the case of a laminar flow of acetonitrile, benzene, ethanol, ethanolamine, dimethylsulfoxide, glycerol, methanol, tert-butyl alcohol, and water, at ambient conditions in contact with the (100) FCC surface of gold, copper and nickel modeled by using all-atom or united-atom models for liquids and the Steele potential for crystalline surfaces. The obtained values for slip length range from few to hundreds of nanometers and are consistent with experimental measurements. We complement calculations by obtaining pressure and temperature dependence of the slip length for water in wide range of these thermodynamic parameters.
Andriy Kovalenko (National Institute for Nanotechnology) 3D molecular theory of solvation in multiscale modeling of chemical nanostructures in solution
Abstract: A salient feature of nanoscale objects and phenomena is that they are very different from the atomic constituents as well as from those described by the conventional, macroscopic laws of continuous media. The behavior of nanostructures can be changed in a wide range, which constitutes the promise of nanoscience on control over properties of materials. Examples are self-assembly of synthetic organic supramolecular nanoarchitectures in solution, nanocatalysis, and electrochemistry in disordered nanoporous electrodes. Modeling of nanosystems should operate at length scale from one to hundreds nanometers and time scale up to microseconds and more, and yet derive their properties from the chemical functionalities of the constituents. Explicit molecular modeling of such nanosystems involves long-time description of millions of molecules which is by far not feasible with ab initio methods, very problematic for molecular simulations, and thus requires multiple-scale approaches. Statistical-mechanical, molecular theory of solvation, a.k.a. three-dimensional reference interaction site model (3D-RISM), predicts from the first principles the molecular structure and thermodynamics of nanosystems, with proper account of their chemical functionalities [1]. The theory operates with 3D distributions of species averaged over the statistical ensemble rather than with trajectories of individual molecules, and yields the thermodynamics and volumetrics of solvation analytically. It represents both long-range electrostatic and short-range steric features of the solvation structure of chemical specificities, such as hydrogen bonding, hydrophobicity, and electrochemical effects. The 3D-RISM theory can be regarded as a molecular extension to the Poisson-Boltzmann solvation electrostatics. This presentation describes the 3D-RISM methodology for the solvation structure and thermodynamics, and its self-consistent combination with ab initio quantum chemical methods in multiscale theory of electronic structure in solution. The methodology is illustrated with applications to solvation of different molecules and chemical reactions in solution [2], self-assembly and conformational stability of synthetic organic supramolecular nanoarchitectures [3], and supercapacitor and electrosorption cell devices with nanoporous carbon electrodes [4]. References [1] A. Kovalenko, Three-dimensional RISM theory for molecular liquids and solid-liquid interfaces, in: Molecular Theory of Solvation, F. Hirata (Ed.) Series: Understanding Chemical Reactivity, P. G. Mezey (Ed.), vol.24, (Kluwer Academic Publishers, Dordrecht, 2003, 360 p.) pp.169-275. [2] S. Gusarov, T. Ziegler, A. Kovalenko, Self-Consistent Combination of the Three-Dimensional RISM Theory of Molecular Solvation with Analytical Gradients and the Amsterdam Density Functional Package, J. Phys. Chem. A, 110, 6083 (2006); D. Casanova, S. Gusarov, A. Kovalenko, T. Ziegler, Evaluation of the SCF Combination of KS-DFT and 3D-RISM-KH; Solvation Effect on Conformational Equilibria, Tautomerization Energies, and Activation Barriers, J. Chem. Theory Comput., 3, 458 (2007). [3] R.S. Johnson, T. Yamazaki, A. Kovalenko, H. Fenniri, Molecular Basis for Water-Promoted Supramolecular Chirality Inversion in Helical Rosette Nanotubes, J. Am. Chem. Soc., 129, 5735 (2007); J.G. Moralez, J. Raez, T. Yamazaki, R.K. Motkuri, A. Kovalenko, H.Fenniri, Helical Rosette Nanotubes with Tunable Stability and Hierarchy, J. Am. Chem. Soc. Communications, 127, 8307 (2005). [4] A. Kovalenko, Molecular description of electrosorption in a nanoporous carbon electrode, J. Comput. Theor. Nanosci., 1, 398 (2004); A. Tanimura, A. Kovalenko, F. Hirata, A molecular theory of a double layer formed by aqueous electrolyte solution sorbed in a carbonized polyvinylidene chloride nanoporous electrode, Chem. Phys. Lett., 378, 638 (2003).
Bo Li (University of California, San Diego) Coupling the level-set method with variational implicit-solvent models for molecular solvation
Abstract: Recent studies have questioned the consistency and applicability of the existing implicit-solvent models in which solvent accessible surfaces (SAS) or solvent excluded surfaces (SES) are pre-defined, and used for the calculation of solvation free energies. As an emerging concept and theory, the variational implicit solvation determines equilibrium solute-solvent interfaces and solvation free energies by minimizing a mean-field free-energy functional. This free energy couples the surface energy, dispersive interaction, and electrostatic contribution. It can also incorporate molecular mechanical interactions. A level-set method is developed to numerically relax an initial interface of high free energy to an equilibrium in the direction of steepest descent. Numerical results demonstrate the initial success of the coupling of the level-set method with the variational theory of solvation, particularly in capturing the hydrophobic interaction. Such interactions are crucial to biomolecular structuring and dynamics, but are not well accounted for by SAS/SES implicit-solvent models. This is joint work with Li-Tien Cheng, Zhongming Wang, Yang Xie, Jianwei Che, Joachim Dzubiella, and J. Andrew McCammon.
Tong Li (University of Iowa) Stability of traveling waves in quasi-linear hyperbolic systems with relaxation and diffusion
Abstract: We establish the existence and the stability of traveling wave solutions of quasi-linear hyperbolic systems with both relaxation and diffusion. The traveling wave solutions are shown to be asymptotically stable against small perturbations provided that the diffusion coefficient is bounded by a constant multiple of the relaxation time. The result provides an important first step toward the understanding of the transition from stability to instability as the diffusion coefficient increases.
Michael Mascagni (Florida State University) Novel stochastic methods in biochemical electrostatics
Abstract: We present a novel Monte Carlo method for solving partial differential equation (PDE) boundary-value problems (BVPs) involving the Poisson-Boltzmann equation (PBE). Such BVPs arise in many situations where the calculation of electrostatic properties of solvated large molecules is desired. These techniques are very accurate, and are fundamentally different than their deterministic counterparts. They are based on using the Feynman-Kac formula to solve the Poisson and the linearized PBE, as well as the introduction of a stochastic method to enforce the boundary conditions on the surface of the molecule. In addition, we present an algorithm for computing the electrostatic free energy for all salt concentrations of interest, simultaneously. This, coupled with the naturally parallel nature of Monte Carlo methods, makes these techniques very appealing for studying solvation-based effects.
Benedetta Mennucci (Università di Pisa) An introduction to quantum mechanical continuum solvation models
Abstract: Continuum solvation models have a quite long history which goes back to the first versions by Onsager (1936) and Kirkwood (1934), however only recently (starting since the 90’s) they have become one of the most used computational techniques in the field of molecular modelling. This has been made possible by two factors which will be presented and discussed in the present talk, namely the increase in the realism of the model on the one hand, and the coupling with quantum-mechanical approaches on the other hand. In particular, the talk will focus on a specific class of continuum solvation models, namely those using as a descriptor for the solvent polarization an apparent surface charge (ASC) spreading on the molecular cavity which contains the solute.
Benedetta Mennucci (Università di Pisa) Applications of quantum mechanical continuum solvation models to the study of molecular properties and spectroscopic features of molecular solutes in different environments
Abstract: Examples of application of QM continuum models to the study of solvent effects on molecular properties and spectroscopies are presented and discussed together with their generalizations to hybrid continuum/discrete approaches in which the presence of specific interactions (e.g. solute-solvents H-bonds) is explicitly taken into account by including some solvent molecules strongly interacting with the solute.
C. Melania Oana (University of Southern California) Cross sections and photoelectron angular distributions in photodetachment from negative ions using EOM-CCSD Dyson orbitals
Abstract: Joint work with Anna I. Krylov. Experimental photoelectron angular distributions (PADs) contain information about the excited states of less stable compounds and their dissociation mechanism, but the interpretation of the results is difficult for molecules with complex electronic structure, e.g. NO dimer, CS2 photodissociation. Ionization cross-sections and PADs can be calculated from the corresponding electronic transition dipole matrix elements. The wavefunction of the leaving electron is given by Dyson orbitals, which are the overlap between an N electron molecular wavefunction and the N-1/N+1 electron wavefunction of the corresponding cation/anion. Our implementation of the Dyson orbitals calculation within the high level ab initio EOM-IP/EA-CCSD method, allows the calculation of these terms for the ionization of electronically excited states and open-shell species, when correlation effects become important. As a first approximation, the states of the ionized electron are described by plane waves expressed in the bases of spherical waves, |E, l, m>. Currently, the calculation of photodetachment cross-sections and anisotropies is benchmarked on atoms, and small molecules. Calculated PADs for NO dimer photodissociation allow qualitative comparison with experimental distributions. In the case of larger, anisotropic molecules, the development of better approximations for the description of the ionized electron is necessary.
Isamu Ohnishi (Hiroshima University) Macroscopic pattern formation of liquid crystal in kappa-carrageenan gel
Abstract: A macroscopic pattern consisting of liquid crystal layers in hydorgel is self-organized. The pattern forms when potassium ion diffuses into a kappa-carrageenan solution from one end of the glass capillary that contains the kappa-carrageenan solution. Both the distance between two adjacent liquidcrystalline layers (spacing, xn+1 −xn,) and thickness of liquid crystalline layers (width, wn) depend linearly on the distance from the diffusing end of the potassium ion xn. The time prior to the formation of the nth liquid crystalline layer tn depends linearly on x2 n. In addition, the spacing coefficient p is inversely proportional to the concentration of potassium ions. These results are in good agreement with the Liesegang henomenon. In this system the kappa-carrageenan solution behaves as a supporting medium for the spatial pattern, as well as the pattern forming substance. The lower values of p, rather than the common Liesegang pattern, in this system could be attributed to the large molecular weight of the kappa-carrageenan–potassium complex. The pattern consisted of discrete liquid crystal phases must be formed due to the much larger diffusion constant of potassium ion (diffusant) than that of kappa-carrageenan (product).
Modesto Orozco (Institute for Research in Biomedicine (IRB Barcelona)) Dimerization of formamide
Abstract: No Abstract
Benoit Roux (University of Chicago) The membrane potential and its representation in computer simulations
Abstract: A modified Poisson-Boltzmann equation is developed from statistical mechanical considerations to describe the influence of the transmembrane potential on macromolecular systems [1]. Using a Green's function formalism, the electrostatic free energy of a protein associated with the membrane is expressed as the sum of three terms: a contribution from the energy required to charge the system's capacitance, a contribution corresponding to the interaction of the protein charges with the membrane potential, and a contribution corresponding to a voltage-independent reaction field free energy. The membrane potential, which is due to the polarization interface, is calculated in the absence of the protein charges, whereas the reaction field is calculated in the absence of transmembrane potential. Then, a theoretical framework is elaborated to account for the effect of a transmembrane potential in computer simulations with explicit solvent. It is shown that a simulation with a constant external electric field applied in the direction normal to the membrane is equivalent to the influence of surrounding infinite baths maintained to a voltage difference via ion-exchanging electrodes connected to an electromotive force [2]. It is also shown that the linearly-weighted displacement charge within the simulation system tracks the net flow of charge through the external circuit comprising the electromotive force and the electrodes. Using a statistical mechanical reduction of the degrees of freedom of the external system, three distinct theoretical routes are formulated and examined for the purpose of characterizing the free energy of a protein embedded in a membrane that is submitted to a voltage difference. The two methods are compared and applied to the voltage-gated potassium channel. 1. Roux, B. 1997. Influence of the membrane potential on the free energy of an intrinsic protein. Biophysical J. 73:2980-2989. 2. Roux, B. 2008. The membrane potential and its representation by a constant electric field in computer simulations. Biophys J. 95:4205-4216.
Ridgway Scott (University of Chicago) Second chances
Abstract: No Abstract
Robert D. Skeel (Purdue University) A fast N-body solver for the Poisson(-Boltzmann) equation
Abstract: Descriptions of implicit solvent models like the Poisson-Boltzmann equation express the electrostatic potential as the solution of an elliptic PDE with delta function source terms. These equations are particularly good fits with iterative solvers that use a fast N-body solver as a preconditioner. Also, modern architectures favor such algorithms due to their high ratio of floating-point operations to memory references. Two types of N-body solvers can be distinguished: hierarchical-clustering algorithms, such as the celebrated fast multipole method, and kernel-splitting algorithms, such as the popular particle--mesh Ewald method. By formulating the problem as that of computing a matrix--vector product, the basic structure of these algorithms is elucidated. Additionally, evidence is presented indicating that kernel-splitting algorithms are much to be preferred for molecular simulations and that the virtually unknown multilevel summation method of Brandt and Lubrecht is the best among these. This method uses hierarchical interpolation of interaction potentials on nested grids to calculate energies and forces in linear time for both periodic and nonperiodic boundary conditions. This is joint work with David Hardy. Its application to the Poisson(-Boltzmann) equation is being pursued in a collaboration with Stephen Bond.
Mark E. Tuckerman (New York University) Second chances
Abstract: No Abstract
Mark E. Tuckerman (New York University) Ab initio molecular dynamics via the Car-Parrinello method: Basic ideas, theory, and algorithms
Abstract: In an ab initio molecular dynamics calculation, the finite-temperature dynamics of a system is generated using forces obtained directly from electronic structure calculations performed ``on the fly'' as the simulation proceeds. Within this approach, manybody forces, electronic polarization, and chemical bond-breaking and forming evnets are treated explicitly, thereby allowing chemical processes in condensed phases to be studied efficiently and with reasonable accuracy. The method of Car and Parrinello, first introduced in 1985, allows such calculations to be performed within the elegant framework of an extended Lagrangian and has become an immensely popular approach for performing ab initio molecular dynamics simulations. The aim of this tutorial is to develop the basic theory of ab initio molecular dynamics and its implementation via the Car-Parrinello method. Questions of how ab initio molecular dynamics is derived from the Schroedinger equation, adiabatic dynamics and the justification of the Car-Parrinello approach, and several algorithmic issues including basis sets and pseudopotentials will be addressed.
Mark E. Tuckerman (New York University) Ab initio path-integrals and specific applications of the Car-Parrinello approach to problems of aqueous ion solvation and transport
Abstract: In this tutorial, we will show how to incorporate nuclear quantum effects into an ab initio molecular dynamics calculation via the Feynman path-integral formulation of quantum statistical mechanics. Important algorithmic advances needed to accelerate the convergence of the calculations will be discussed as well as approximation dynamical path-integral schemes. Finally, an application of the ab initio molecular dynamics and ab initio path-integral approaches to the problem of the solvation and transport of topological charged defects in water will be discussed.
Jason A. Wagoner (Stanford University) Optimization of a hybrid implicit/explicit solvation model
Abstract: Hybrid solvation models can be used in molecular dynamics simulations to extract the salient features of both explicit and implicit solvent methods, maintaining the atomic detail of solvent near regions of interest while removing such degrees of freedom elsewhere. We present such a hybrid solvation model that, in the spirit of previous methods, decomposes the simulation domain into explicit and bulk regions separated by an energetic barrier. The use of a Grand Canonical Monte Carlo scheme at the boundary is used to represent particle exchange with the bulk reservoir and extends the applicability of this model by allowing the use of a dynamic explicit domain. Current testing of this model is aimed at obtaining thermodynamic quantities within the explicit region with a focus on removing boundary artifacts for bulk liquid simulations.
Visitors in Residence
Donald G. Aronson University of Minnesota 9/1/2002 - 8/31/2009
Nathan A. Baker Washington University School of Medicine 12/9/2008 - 12/12/2008
Robert L. Baldwin Stanford University 12/7/2008 - 12/11/2008
Jaydeep P. Bardhan Argonne National Laboratory 12/7/2008 - 12/12/2008
Dezső Boda University of Pannonia 12/7/2008 - 12/12/2008
Stephen Bond University of Illinois at Urbana-Champaign 12/8/2008 - 12/13/2008
Daniel Jean Borgis École Normale Supérieure 12/7/2008 - 12/12/2008
Bernard R. Brooks National Institutes of Health 12/7/2008 - 12/11/2008
Peter Brune University of Chicago 9/8/2008 - 6/30/2009
Maria-Carme T. Calderer University of Minnesota 9/1/2008 - 6/30/2009
Hannah Callender University of Minnesota 9/1/2007 - 8/31/2009
Roberto Cammi Università di Parma, e-mail: roberto.cammi@unipr.it 11/14/2008 - 12/20/2008
Eric Cances CERMICS 9/1/2008 - 12/23/2008
Chiara Cappelli Università di Pisa 12/6/2008 - 12/13/2008
Alessandro Cembran University of Minnesota 12/7/2008 - 12/12/2008
Xianjin Chen University of Minnesota 9/1/2008 - 8/31/2010
Daniel M. Chipman University of Notre Dame 9/14/2008 - 12/14/2008
Stefano Corni Consiglio Nazionale delle Ricerche (CNR) 12/7/2008 - 12/13/2008
Ludovica Cecilia Cotta-Ramusino University of Minnesota 10/1/2007 - 12/12/2008
Carles Curutchet University of Toronto 12/6/2008 - 12/12/2008
Allison Cuttler University of California, San Diego 12/6/2008 - 12/11/2008
Ismaila Dabo Massachusetts Institute of Technology 12/7/2008 - 12/14/2008
Yuqing Deng Zymeworks Inc. 12/7/2008 - 12/12/2008
Alfonso De Simone University of Cambridge 12/3/2008 - 12/12/2008
Florin Despa University of California, Davis 12/7/2008 - 12/12/2008
Olivier Dubois University of Minnesota 9/3/2007 - 8/31/2009
Robert S. Eisenberg Rush University Medical Center 12/4/2008 - 12/12/2008
Jorge Estevez University of Minnesota 12/7/2008 - 12/12/2008
Marcia O. Fenley Florida State University 12/7/2008 - 12/12/2008
Daniel Flath Macalester College 8/27/2008 - 12/20/2008
James Fonseca Rush University Medical Center 12/6/2008 - 12/12/2008
Christopher Fraser University of Chicago 8/27/2008 - 6/30/2009
Luca Frediani University of Tromsø 12/7/2008 - 12/13/2008
Jiali Gao University of Minnesota 12/7/2008 - 12/12/2008
Weiguo Gao Fudan University 9/27/2008 - 12/8/2008
Carlos J. Garcia-Cervera University of California, Santa Barbara 9/2/2008 - 12/12/2008
Janhavi Giri Rush University Medical Center 12/6/2008 - 12/12/2008
Jay Gopalakrishnan University of Florida 9/1/2008 - 2/28/2009
Donald Hamelberg Georgia State University 12/7/2008 - 12/12/2008
Jaeboem Han University of Minnesota 12/7/2008 - 12/12/2008
Timothy F. Havel Massachusetts Institute of Technology 10/31/2008 - 12/12/2008
Mark S. Herman University of Minnesota 9/1/2008 - 8/31/2010
Masahiro Higashi University of Minnesota 12/8/2008 - 12/12/2008
Peter Hinow University of Minnesota 9/1/2007 - 8/31/2009
Nina Singhal Hinrichs University of Chicago 12/7/2008 - 12/12/2008
Fumio Hirata National Institutes of Natural Sciences 12/7/2008 - 12/12/2008
Michael J. Holst University of California, San Diego 12/7/2008 - 12/12/2008
Jingfang Huang University of North Carolina 12/30/2008 - 5/31/2009
Jingfang Huang University of North Carolina 12/7/2008 - 12/13/2008
Yunkyong Hyon University of Minnesota 9/1/2008 - 8/31/2010
Mark Iwen University of Minnesota 9/1/2008 - 8/31/2010
Alexander Izzo Bowling Green State University 9/1/2008 - 6/30/2009
Lasse Jensen Pennsylvania State University 12/7/2008 - 12/12/2008
Srividhya Jeyaraman University of Minnesota 9/1/2008 - 8/31/2010
Lijian Jiang University of Minnesota 9/1/2008 - 8/31/2010
William L. Jorgensen Yale University 12/8/2008 - 12/10/2008
Hiqmet Kamberaj University of Minnesota 12/7/2008 - 12/12/2008
Markus Keel University of Minnesota 7/21/2008 - 6/30/2009
Carl Timothy Kelley North Carolina State University 12/7/2008 - 12/12/2008
Yongho Kim University of Minnesota 12/7/2008 - 12/12/2008
Matthew Gregg Knepley Argonne National Laboratory 12/7/2008 - 12/13/2008
Dmitry A. Kondrashov University of Chicago 12/8/2008 - 12/13/2008
Andriy Kovalenko National Institute for Nanotechnology 12/6/2008 - 12/13/2008
Anna Krylov University of Southern California 9/25/2008 - 12/20/2008
Claude Le Bris CERMICS 9/11/2008 - 5/30/2009
Chiun-Chang Lee National Taiwan University 8/26/2008 - 7/31/2009
Hijin Lee Korea Advanced Institute of Science and Technology (KAIST) 12/8/2008 - 12/12/2008
Bo Li University of California, San Diego 12/7/2008 - 12/11/2008
Tong Li University of Iowa 11/2/2008 - 12/10/2008
Yongfeng Li University of Minnesota 9/1/2008 - 8/31/2010
Pinsker Lin University of Minnesota 12/7/2008 - 12/12/2008
Tai-Chia Lin National Taiwan University 8/23/2008 - 7/31/2009
Chun Liu University of Minnesota 9/1/2008 - 8/31/2010
Mitchell Luskin University of Minnesota 9/1/2008 - 6/30/2009
Vasileios Maroulas University of Minnesota 9/1/2008 - 8/31/2010
Marcelo Marucho Washington University School of Medicine 12/7/2008 - 12/12/2008
Michael Mascagni Florida State University 12/6/2008 - 12/12/2008
Benedetta Mennucci Università di Pisa 12/6/2008 - 12/13/2008
Aurora Muñoz Università di Pisa 12/6/2008 - 12/13/2008
C. Melania Oana University of Southern California 12/4/2008 - 12/20/2008
Isamu Ohnishi Hiroshima University 11/1/2008 - 1/17/2009
Modesto Orozco Institute for Research in Biomedicine (IRB Barcelona) 12/7/2008 - 12/12/2008
B. Montgomery Pettitt University of Houston 12/7/2008 - 12/12/2008
Benoit Roux University of Chicago 12/10/2008 - 12/12/2008
Fadil Santosa University of Minnesota 7/1/2008 - 6/30/2010
Arnd Scheel University of Minnesota 9/1/2008 - 6/30/2009
Ridgway Scott University of Chicago 9/1/2008 - 6/30/2009
Tsvetanka Sendova University of Minnesota 9/1/2008 - 8/31/2010
Yuk Sham University of Minnesota 9/1/2008 - 6/30/2009
Tei Shi University of Minnesota 12/7/2008 - 12/12/2008
Heinz Siedentop Ludwig-Maximilians-Universität München 9/22/2008 - 12/19/2008
Robert D. Skeel Purdue University 12/8/2008 - 12/11/2008
Lingchun Song University of Minnesota 12/7/2008 - 12/12/2008
Andrew M. Stein University of Minnesota 9/1/2007 - 8/31/2009
Andrij Trokhymchuk Institute for condensed matter physics 12/6/2008 - 12/14/2008
Donald G. Truhlar University of Minnesota 9/1/2008 - 6/30/2009
Mark E. Tuckerman New York University 12/6/2008 - 12/15/2008
Erkan Tüzel University of Minnesota 9/1/2007 - 8/31/2009
Sinisa Vukovic University of Toronto 12/6/2008 - 12/13/2008
Jason A. Wagoner Stanford University 12/7/2008 - 12/12/2008
Zhian Wang University of Minnesota 9/1/2007 - 8/31/2009
Zhongming Wang University of California, San Diego 12/7/2008 - 12/12/2008
Guowei Wei Michigan State University 12/7/2008 - 12/11/2008
Kin-Yiu Wong University of Minnesota 12/7/2008 - 12/12/2008
Dexuan Xie University of Wisconsin 9/1/2008 - 1/15/2009
Wei Xiong University of Minnesota 9/1/2008 - 8/31/2010
Ke Yang University of Minnesota 12/7/2008 - 12/12/2008
Dmytro S. Yershov University of Illinois at Urbana-Champaign 12/8/2008 - 12/13/2008
Norio Yoshida National Institutes of Natural Sciences 12/7/2008 - 12/12/2008
Weigang Zhong University of Minnesota 9/1/2008 - 8/31/2010
Yongcheng Zhou University of California, San Diego 12/7/2008 - 12/12/2008
Legend: Postdoc or Industrial Postdoc Long-term Visitor

IMA Affiliates:
Arizona State University, Boeing, Corning, ExxonMobil, Ford, General Motors, Georgia Institute of Technology, Honeywell, IBM, Indiana University, Iowa State University, Kent State University, Lawrence Livermore National Laboratory, Lockheed Martin, Los Alamos National Laboratory, Medtronic, Michigan State University, Michigan Technological University, Microsoft Research, Mississippi State University, Motorola, Northern Illinois University, Ohio State University, Pennsylvania State University, Purdue University, Rice University, Rutgers University, Sandia National Laboratories, Schlumberger Cambridge Research Laboratories, Schlumberger-Doll, Seoul National University, Siemens, Telcordia, Texas A & M University, University of Central Florida, University of Chicago, University of Delaware, University of Houston, University of Illinois at Urbana-Champaign, University of Iowa, University of Kentucky, University of Maryland, University of Michigan, University of Minnesota, University of Notre Dame, University of Pittsburgh, University of Tennessee, University of Wisconsin, University of Wyoming, US Air Force Research Laboratory, Wayne State University, Worcester Polytechnic Institute