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Additional newsletters available at http://www.ima.umn.edu/newsletters
IMA Newsletter #387
January 2009
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.
IMA Events
IMA Tutorial
Fundamentals of Chemical Dynamics Simulations
January 11, 2009
Speakers: Peter Deuflhard (Zuse Institute Berlin (ZIB)), David J. Tannor (Weizmann Institute of Science), Stefan Teufel (Eberhard-Karls-Universität Tübingen)IMA Annual Program Year Workshop
Chemical Dynamics: Challenges and Approaches
January 12-16, 2009
Organizers: Bill Hase (Texas Tech University), Christian Lubich (Eberhard-Karls-Universität Tübingen), Maurizio Persico (Università di Pisa)Public Lecture
Robert Ghrist - Mathematics Making Sense of Sensors
January 22, 2009
Speakers: Robert Ghrist (University of Pennsylvania)
Schedule
Thursday, January 1
| All Day | New Years Day. The IMA is closed. |
Monday, January 5
| 10:45am-11:15am | Coffee break | Lind Hall 400 |
Tuesday, January 6
| 10:45am-11:15am | Coffee break | Lind Hall 400 | ||
| 11:15am-12:15pm | Interpolation with sparsity assumptions: From syphilis testing to sparse Fourier transforms | Mark Iwen (University of Minnesota) | Lind Hall 305 | PS |
Wednesday, January 7
| 10:45am-11:15am | Coffee break | Lind Hall 400 |
Thursday, January 8
| 10:45am-11:15am | Coffee break | Lind Hall 400 |
Friday, January 9
| 10:45am-11:15am | Coffee break | Lind Hall 400 |
Sunday, January 11
| 8:15am-8:45am | Coffee and registration | EE/CS 3-176 | T1.11.09 | |
| 8:45am-9:00am | Welcome to the IMA | Fadil Santosa (University of Minnesota) | EE/CS 3-180 | T1.11.09 |
| 9:00am-10:00am | Potential energy surfaces, nonadiabatic transitions, and surface crossings | Maurizio Persico (Università di Pisa) | EE/CS 3-180 | T1.11.09 |
| 10:00am-10:30am | Break | EE/CS 3-176 | T1.11.09 | |
| 10:30am-11:30am | Mixed quantum-classical dynamics | Maurizio Persico (Università di Pisa) | EE/CS 3-180 | T1.11.09 |
| 11:30am-12:30pm | Adiabatic decoupling and the partial classical limit | Stefan Teufel (Eberhard-Karls-Universität Tübingen) | EE/CS 3-180 | T1.11.09 |
| 12:30pm-2:00pm | Lunch | T1.11.09 | ||
| 2:00pm-3:00pm | Adiabatic decoupling and the partial classical limit (continued) | Stefan Teufel (Eberhard-Karls-Universität Tübingen) | EE/CS 3-180 | T1.11.09 |
| 3:00pm-3:30pm | Break | EE/CS 3-176 | T1.11.09 | |
| 3:30pm-5:30pm | Tutorial on time-dependent quantum mechanics | David J. Tannor (Weizmann Institute of Science) | EE/CS 3-180 | T1.11.09 |
Monday, January 12
| All Day | Morning Session Topic – "Integrating Trajectories and Interpolating Potential Energy Surfaces for Direct Dynamics Simulations" Chair – William L. Hase (Texas Tech University)
Afternoon Session Topic – "Quantum Dynamics" | W1.12-16.09 | ||
| 8:00am-8:45am | Registration and coffee | EE/CS 3-176 | W1.12-16.09 | |
| 8:45am-9:00am | Welcome to the IMA | Fadil Santosa (University of Minnesota) | EE/CS 3-180 | W1.12-16.09 |
| 9:00am-9:45am | Overview talk on potential energy surfaces | Joel M. Bowman (Emory University) | EE/CS 3-180 | W1.12-16.09 |
| 9:45am-10:00am | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 10:00am-10:30am | Fourier grid QM/MM simulations of the hydrated electron | John M. Herbert (Ohio State University) | EE/CS 3-180 | W1.12-16.09 |
| 10:30am-10:40am | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 10:40am-11:10am | Coffee | EE/CS 3-176 | W1.12-16.09 | |
| 11:10am-11:40am | Automatic construction of ab initio potential energy surfaces | Donald L. Thompson (University of Missouri) | EE/CS 3-180 | W1.12-16.09 |
| 11:40am-11:50pm | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 11:50am-12:30pm | Concluding discussion | Bill Poirier (Texas Tech University) | EE/CS 3-180 | W1.12-16.09 |
| 12:30pm-2:00pm | Lunch | W1.12-16.09 | ||
| 2:00pm-2:45pm | Using Diffusion Monte Carlo to investigate molecules that undergo large amplitude vibrational motions | Anne B. McCoy (Ohio State University) | EE/CS 3-180 | W1.12-16.09 |
| 2:45pm-3:00pm | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 3:00pm-3:30pm | Bohmian mechanics with complex action: An exact formulation of quantum mechanics with complex trajectories | David J. Tannor (Weizmann Institute of Science) | EE/CS 3-180 | W1.12-16.09 |
| 3:30pm-3:40pm | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 3:40pm-3:50pm | Group Photo | W1.12-16.09 | ||
| 3:50pm-4:20pm | Coffee | EE/CS 3-176 | W1.12-16.09 | |
| 4:20pm-4:50pm | Geometric integrators for the Schrödinger equation: Splitting and Magnus integrators | Sergio Blanes (Polytechnical University of Valencia) | EE/CS 3-180 | W1.12-16.09 |
| 4:50pm-5:00pm | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 5:00pm-5:30pm | A fast path integral method for liquid water | David E. Manolopoulos (University of Oxford) | EE/CS 3-180 | W1.12-16.09 |
| 5:30pm-5:40pm | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 5:40pm-7:00pm | Reception and Poster Session
Poster submissions welcome from all participants | Lind Hall 400 | W1.12-16.09 | |
| Coherent and optimal control of adiabatic motion of ions in a trap | Dmitri Babikov (Marquette University) | |||
| Analysis of structured populations in aquaculture | József Z. Farkas (University of Stirling) | |||
| Tunneling dynamics in a double well within the approximate quantum trajectories framework | Sophya Garashchuk (University of South Carolina) | |||
| Quantum transition state theory applied to collinear reactions | Roman Schubert (University of Bristol) Arseni Goussev (University of Bristol) | |||
| Non–adiabatic scattering wave functions in a simple Born–Oppenheimer model | George A. Hagedorn (Virginia Polytechnic Institute and State University) | |||
| Born-Oppenheimer corrections near a Renner-Teller intersection | Mark S. Herman (University of Minnesota) | |||
| Mechanistic simulation of the autocatalytic isopeptide bond formation in pili with QM/MM minimum free energy path method | Xiangqian Hu (Duke University) | |||
| Solvation dynamics in supercritical fluoroform | Francesca Ingrosso (Université de Nancy I (Henri Poincaré)) | |||
| A self-consistent, polarizable, electron-water potential for use in hydrated-electron simulations | Leif David Jacobson (Ohio State University) | |||
| Many-body theory of surface-enhanced Raman scattering | David J. Masiello (Northwestern University) | |||
| Partial differential equations in chemical dynamics with finite elements | Craig Michoski (University of Texas) | |||
| Memory, hysteresis and oscillation induced by multiple covalent modifications and its application to circadian rhythm of Cyanobacteria | Isamu Ohnishi (Hiroshima University) | |||
| Azobenzene in solution: excited state dynamics simulation | Maurizio Persico (Università di Pisa) | |||
| A model for the photo-orientation of a molecular sample irradiated with polarized light | Maurizio Persico (Università di Pisa) | |||
| Symmetry-broken independent-particle models in Born-Oppenheimer molecular dynamics of chemical bond dissociation | Igor V. Schweigert (Naval Research Laboratory) | |||
| A quantum chemist’s view of molecular conduction via the reduced density matrix | Joseph Eli Subotnik (Tel Aviv University) | |||
| Infrared spectroscopy and dynamics of the Zundel cation | Oriol Vendrell-Romagosa (Ruprecht-Karls-Universität Heidelberg) | |||
| Improved united-atom models for perfluorinated self-assembled monolayers | Saulo A. Vázquez (University of Santiago de Compostela) | |||
| Calculating solution redox free energies with Ab initio QM/MM minimum free energy path method | Xiancheng Zeng (Duke University) |
Tuesday, January 13
| All Day | Morning Session Topic - "Quantum Dynamics" Chair – Reinhard Schinke (Max-Planck-Institut für Dynamik und Selbstorganisation)
Afternoon Session Topic – "Conformational Dynamics, Reaction
Paths, Transition States, and Rare Events for Complex Many-Atom
Systems" | W1.12-16.09 | ||
| 8:00am-8:30am | Coffee | EE/CS 3-176 | W1.12-16.09 | |
| 8:30am-9:00am | Quantum dynamics of complex-forming reactions | Hua Guo (University of New Mexico) | EE/CS 3-180 | W1.12-16.09 |
| 9:00am-9:10am | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 9:10am-9:40am | Quantum molecular dynamics of complex systems studied with MCTDH: Dynamics and IR-spectroscopy of the protonated water dimer H5O2+ and its isotopologues | Hans-Dieter Meyer (Ruprecht-Karls-Universität Heidelberg) | EE/CS 3-180 | W1.12-16.09 |
| 9:40am-9:50am | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 9:50am-10:40am | Coffee | EE/CS 3-176 | W1.12-16.09 | |
| 10:40am-11:10am | Reduced vs. full system-bath quantum dynamics: Vibrational excitation and relaxation of adsorbates at surfaces | Peter Saalfrank (Universität Potsdam) | EE/CS 3-180 | W1.12-16.09 |
| 11:10am-11:20am | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 11:20am-12:20pm | Concluding discussion | Dmitri Babikov (Marquette University) | EE/CS 3-180 | W1.12-16.09 |
| 12:20pm-2:00pm | Lunch | W1.12-16.09 | ||
| 2:00pm-2:45pm | Overview talk: Advanced computing platforms offer a "microscope" for [simulating] conformational changes | Tamar Schlick (New York University) | EE/CS 3-180 | W1.12-16.09 |
| 2:45pm-3:00pm | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 3:00pm-3:30pm | Single-sweep methods for free energy calculations | Eric Vanden-Eijnden (New York University) | EE/CS 3-180 | W1.12-16.09 |
| 3:30pm-3:40pm | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 3:40pm-4:30pm | Coffee | EE/CS 3-176 | W1.12-16.09 | |
| 4:30pm-5:00pm | Rare event statistics in molecular dynamics | Christof Schütte (Freie Universität Berlin) | EE/CS 3-180 | W1.12-16.09 |
| 5:00pm-5:10pm | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 5:10pm-5:40pm | Recent progress in conformational analysis | Marcus Weber (Konrad-Zuse-Zentrum für Informationstechnik (ZIB)) | EE/CS 3-180 | W1.12-16.09 |
| 5:40pm-5:50pm | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 5:50pm-6:15pm | Concluding discussion | Mark E. Tuckerman (New York University) | EE/CS 3-180 | W1.12-16.09 |
| 6:15pm-7:15pm | Reception | Lind Hall 400 | W1.12-16.09 |
Wednesday, January 14
| All Day | Morning Session Topic - "Non-Adiabatic Dynamics" Chair – Jack Simons (University of Utah)
Afternoon Session Topic – "Semi-empirical and QM/MM Electronic
Structure Theories for Direct Dynamics" | W1.12-16.09 | ||
| 8:00am-8:30am | Coffee | EE/CS 3-176 | W1.12-16.09 | |
| 8:30am-9:15am | Trajectory studies of gas/liquid reactions | George C. Schatz (Northwestern University) | EE/CS 3-180 | W1.12-16.09 |
| 9:15am-9:30am | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 9:30am-10:00am | Nuclear-electronic orbital approach: Electron-proton correlation, multicomponent density functional theory, and tunneling splittings | Sharon Hammes-Schiffer (Pennsylvania State University) | EE/CS 3-180 | W1.12-16.09 |
| 10:00am-10:10am | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 10:10am-11:00am | Coffee | EE/CS 3-176 | W1.12-16.09 | |
| 11:00am-11:30am | Path integral and semiclassical methods for quantum dynamics | Nancy Makri (University of Illinois at Urbana-Champaign) | EE/CS 3-180 | W1.12-16.09 |
| 11:30am-11:40am | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 11:40am-12:15pm | Concluding discussion | Millard Alexander (University of Maryland) | EE/CS 3-180 | W1.12-16.09 |
| 12:15pm-2:00pm | Lunch | W1.12-16.09 | ||
| 2:00pm-2:45pm | Overview talk: Free energies of chemical reactions in solution and in enzymes with Ab initio quantum mechanics/molecular mechanics methods | Weitao Yang (Duke University) | EE/CS 3-180 | W1.12-16.09 |
| 2:45pm-3:00pm | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 3:00pm-3:30pm | Surface hopping dynamics with direct semiempirical solution of the electronic problem | Maurizio Persico (Università di Pisa) | EE/CS 3-180 | W1.12-16.09 |
| 3:30pm-3:40pm | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 3:40pm-4:30pm | Coffee | EE/CS 3-176 | W1.12-16.09 | |
| 4:30pm-5:00pm | Self consistent polarization electronic structure | Gregory K. Schenter (Pacific Northwest National Laboratory) | EE/CS 3-180 | W1.12-16.09 |
| 5:00pm-5:10pm | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 5:10pm-6:10pm | Concluding discussion | Gilles H. Peslherbe (Concordia University) | EE/CS 3-180 | W1.12-16.09 |
Thursday, January 15
| All Day | Session Topic - "Condensed Phase and Macromolecule Chemical Dynamics" Morning Chair: Roi Baer (Hebrew University) Afternoon Chair – Donald G. Truhlar (University of Minnesota) | W1.12-16.09 | ||
| 8:00am-8:30am | Coffee | EE/CS 3-176 | W1.12-16.09 | |
| 8:30am-9:15am | Dynamics on the nanoscale: Time-domain ab initio studies of quantum dots and carbon nanotubes | Oleg Prezhdo (University of Washington) | EE/CS 3-180 | W1.12-16.09 |
| 9:15am-9:30am | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 9:30am-10:00am | Optimizing efficiency in replica-exchange molecular dynamics and avoiding the traps of Langevin dynamics | Adrian E. Roitberg (University of Florida) | EE/CS 3-180 | W1.12-16.09 |
| 10:00am-10:10am | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 10:10am-11:00am | Coffee | EE/CS 3-176 | W1.12-16.09 | |
| 11:00am-11:30am | Multilayer multiconfiguration time-dependent Hartree theory | Haobin Wang (New Mexico State University) | EE/CS 3-180 | W1.12-16.09 |
| 11:30am-11:40am | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 11:40am-12:10pm | Dogmatic and pragmatic spirits in time-dependent density functional theory | Roi Baer (Hebrew University) | EE/CS 3-180 | W1.12-16.09 |
| 12:10pm-12:20pm | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 12:20pm-2:00pm | Lunch | W1.12-16.09 | ||
| 2:00pm-2:30pm | The X-Pol potential: an explicit polarization quantum mechanical force field for condensed phase and protein dynamics | Jiali Gao (University of Minnesota) | EE/CS 3-180 | W1.12-16.09 |
| 2:30pm-2:40pm | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 2:40pm-3:10pm | Quantum dynamics of photoinduced processes in extended molecular systems | Irene Burghardt (École Normale Supérieure) | EE/CS 3-180 | W1.12-16.09 |
| 3:10pm-3:20pm | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 3:20pm-4:10pm | Coffee | EE/CS 3-176 | W1.12-16.09 | |
| 4:10pm-4:40pm | Hybrid ab initio valence bond / molecular mechanics (VB/MM), a new method for calculating biochemical systems | Avital Shurki (Hebrew University) | EE/CS 3-180 | W1.12-16.09 |
| 4:40pm-4:50pm | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 4:50pm-5:50pm | Concluding discussion | Greg Scholes (University of Toronto) | EE/CS 3-180 | W1.12-16.09 |
| 6:30pm-8:30pm | Workshop dinner at Pagoda | Pagoda Restaurant 1417 4th St. SE Minneapolis, MN 612-378-4710 |
W1.12-16.09 |
Friday, January 16
| All Day | Session Topic - "Semi-Classical and Mixed Classical/Quantum Dynamics" Chair – Ahren Jasper (Sandia National Laboratories) | W1.12-16.09 | ||
| 8:00am-8:30am | Coffee | EE/CS 3-176 | W1.12-16.09 | |
| 8:30am-9:15am | Adiabatic perturbation theory and the time-dependent Born-Oppenheimer approximation | Stefan Teufel (Eberhard-Karls-Universität Tübingen) | EE/CS 3-180 | W1.12-16.09 |
| 9:15am-9:30am | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 9:30am-10:00am | Stable long-time semiclassical description of zero-point energy in high-dimensional molecular systems | Vitaly Rassolov (University of South Carolina) | EE/CS 3-180 | W1.12-16.09 |
| 10:00am-10:10am | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 10:10am-11:00am | Coffee | EE/CS 3-176 | W1.12-16.09 | |
| 11:00am-11:30am | The time-dependent Born-Oppenheimer approximation, crossings, and avoided crossings | George A. Hagedorn (Virginia Polytechnic Institute and State University) | EE/CS 3-180 | W1.12-16.09 |
| 11:30am-11:40am | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 11:40am-12:10pm | Well defined and accurate semiclassical surface hopping propagators and wave functions | Michael F. Herman (Tulane University) | EE/CS 3-180 | W1.12-16.09 |
| 12:10pm-12:20pm | Discussion | EE/CS 3-180 | W1.12-16.09 | |
| 12:20pm-1:20pm | Concluding discussion | David F. Coker (Boston University) | EE/CS 3-180 | W1.12-16.09 |
Monday, January 19
| All Day | Martin Luther King holiday. The IMA is closed. |
Tuesday, January 20
| 10:45am-11:15am | Coffee break | Lind Hall 400 | ||
| 11:15am-12:15pm | Multi-scale approach in chemotaxis models | Zhian Wang (University of Minnesota) | Lind Hall 305 | PS |
| 12:15pm-1:30pm | Postdoc lunch meeting | Lind Hall 409 | ||
| 3:00pm-4:00pm | Reading group for Professor Ridgway Scott's book "Digital Biology" | L. Ridgway Scott (University of Chicago) | Lind Hall 401 |
Wednesday, January 21
| 10:45am-11:15am | Coffee break | Lind Hall 400 | ||
| 2:30pm-3:30pm | A short course on fast multipole method | Jingfang Huang (University of North Carolina) | Lind Hall 305 | FMM |
Thursday, January 22
| 10:45am-11:15am | Coffee break | Lind Hall 400 | ||
| 5:00pm-6:30pm | Math Matters Public Lecture Reception | Lind Hall 400 | PUB1.22.09 | |
| 7:00pm-8:30pm | Math Matters Public Lecture: Mathematics Making Sense of Sensors | Robert Ghrist (University of Pennsylvania) | Willey Hall 125 | PUB1.22.09 |
Friday, January 23
| 10:45am-11:15am | Coffee break | Lind Hall 400 | ||
| 1:30pm-3:00pm | The DE Shaw group recruiting event. Contact Person: Elie Yuan Elisheva.Yuan@deshaw.com | Lind Hall 305 | IPS |
Monday, January 26
| 10:45am-11:15am | Coffee break | Lind Hall 400 | ||
| 2:30pm-3:30pm | A short course on fast multipole method | Jingfang Huang (University of North Carolina) | Lind Hall 305 | FMM |
Tuesday, January 27
| 10:45am-11:15am | Coffee break | Lind Hall 400 | ||
| 11:15am-12:15pm | Analysis of structured populations in aquaculture | József Z. Farkas (University of Stirling) | Lind Hall 305 | PS |
Wednesday, January 28
| 10:45am-11:15am | Coffee break | Lind Hall 400 | ||
| 1:00pm-2:00pm | Computational strategy options in tackling a problem of molecular excited state dynamics | Maurizio Persico (Università di Pisa) | Lind Hall 305 | SMC |
| 2:30pm-3:30pm | A short course on fast multipole method | Jingfang Huang (University of North Carolina) | Lind Hall 305 | FMM |
Thursday, January 29
| 10:45am-11:15am | Coffee break | Lind Hall 400 | ||
| 1:00pm-2:00pm | Reading group for Professor Ridgway Scott's book "Digital Biology" | L. Ridgway Scott (University of Chicago) | Lind Hall 401 |
Friday, January 30
| 10:45am-11:15am | Coffee break | Lind Hall 400 |
Event Legend: |
|
| FMM | A Short Course on Fast Multipole Method |
| IPS | Industrial Problems Seminar |
| PS | IMA Postdoc Seminar |
| PUB1.22.09 | Robert Ghrist - Mathematics Making Sense of Sensors |
| SMC | IMA Seminar on Mathematics and Chemistry |
| T1.11.09 | Fundamentals of Chemical Dynamics Simulations |
| W1.12-16.09 | Chemical Dynamics: Challenges and Approaches |
Abstracts
| Millard Alexander (University of Maryland) | Concluding discussion |
| Abstract: No Abstract | |
| Dmitri Babikov (Marquette University) | Concluding discussion |
| Abstract: No Abstract | |
| Dmitri Babikov (Marquette University) | Coherent and optimal control of adiabatic motion of ions in a trap |
| Abstract: Vibrational motion of ions in a linear trap can be efficiently controlled by creating small anharmonicity of the trapping potential and using optimally shaped MHz pulses to induce the desired states-to-state transitions. In this work the motional quantum states of ions in an anharmonic trap were calculated numerically using expansion over the basis set of Hermit polynomials. The Optimal Control Theory is employed in order to optimize shaped pulses for the major quantum gates, such as NOT, CNOT, Pi-rotation and the Hadamard transform. | |
| Roi Baer (Hebrew University) | Dogmatic and pragmatic spirits in time-dependent density functional theory |
| Abstract: On the dogmatic spirit we discuss the issue applicability of adiabatic functional also in strong high frequency laser-fields. On the pragmatic side we explain the necessity of using a TUNED range-separated time-dependent and time independent density functional theory for difficult systems. For DFT we bring examples for symmetric cationic radicals, such as H2+, He2+, Ne2+, (H2O)2+ and (C6H6)2+ and for TDDFT we discuss charge transfer excitations as examples. A tuned range parameter theory is also capable of treating a variety of solids. Co-Authors in various parts of this work: Dr. Helen Eisenberg, Dr. Ester Livshits, Tamar Stein (Institute of Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem) Professor Leeor Kronik (Weizmann Institute of Science) Professor Anna Krylov (University of California). | |
| Sergio Blanes (Polytechnical University of Valencia) | Geometric integrators for the Schrödinger equation: Splitting and Magnus integrators |
| Abstract: The time-dependent Schrödinger equation plays an essential role to understand non-relativistic atomic and molecular processes. This is a linear partial differential equation with a very particular structure. A good model for a problem is usually given by a Hamiltonian operator, which suffices to describe the evolution of the system (for given initial conditions) while preserving many qualitative properties (energy, unitarity, etc.). Unfortunately, in general, analytical solutions for the equations are unknown, even for most simple models, and numerical methods are required. Some techniques frequently used are spectral decomposition or spatial discretisation. In general, one has to solve a system of linear ordinary differential equations. Standard numerical methods do not preserve the qualitative properties mentioned and usually have a significant error propagation along the integration. Then, to get accurate and reliable results can be computationally very expensive. Geometric numerical integration has been developed during the last years and it intends to build numerical methods which preserve most qualitative properties of the exact solution. Some of these methods are developed for problems with similar structure to the Schrödinger equation leading in many cases to improved qualitative and quantitative results. In this talk we review two families of methods: Magnus integrators [1] (for non-autonomous problems) and splitting methods [2] (for systems which are separable in solvable parts). [1] S. Blanes, F. Casas, J.A. Oteo and J. Ros, The Magnus and expansion and some of its applications. Physics Reports. In Press. [2] S. Blanes, F. Casas, and A. Murua, Splitting and composition methods in the numerical integration of differential equations, (arXiv:0812.0377v1). | |
| Joel M. Bowman (Emory University) | Overview talk on potential energy surfaces |
| Abstract: Joint work with Bastiaan J. Braams and Yimin Wang (Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, GA 30322). The currently exists a variety of methods to represent potential energy surfaces for high dimensional systems, and these will be reviewed after a short, selective, historical introduction to the topic. I will describe the progress we have made. The central aspect of progress is to perform standard least-squares fits of the order of 104 "scattered" electronic energies using a polynomial basis that is invariant with respect to all permutations of like atoms. Some of the technical details of this approach will be given followed by several case studies with a focus on recent work on the water dimer and trimer. I will conclude with a review of some related fitting strategies, which are quite different from full-dimensional fitting approaches, which are know as "n-mode representation of the potential," the "high dimensional model representation" and the "potfit." Financial support from the National Science Foundation, the Department of Energy, and the Office of Naval Research is gratefully acknowledged. | |
| Irene Burghardt (École Normale Supérieure) | Quantum dynamics of photoinduced processes in extended molecular systems |
| Abstract: The photophysics of extended systems like conjugated polymers or molecular aggregates is characterized on the one hand by the properties of the molecular building blocks and on the other hand by the delocalized nature of the electronic excitations, i.e., the formation of excitonic states. The dynamical phenomena induced by photoexcitation therefore involve an interplay of site-site interactions entailing excitation energy transfer, and vibronic (electron-phonon) coupling which typically leads to ultrafast internal conversion processes. We propose here a molecular-level, quantum-dynamical approach as exemplified by our recent study of exciton dissociation at interfaces of semiconducting polymer phases (so-called heterojunctions) [1]. This study combines a vibronic coupling model parametrized for the three most relevant electronic states and 20-30 phonon modes, with accurate multiconfigurational quantum dynamics calculations using the MCTDH method and a Gaussian-based variant thereof (G-MCTDH) [2]. In addition, we employ recently developed transformation techniques [1,3] by which a relevant set of effective modes is constructed which account for the short-time dynamics in high-dimensional systems involving conical intersection topologies. For the semiconducting polymer systems under study, which typically involve high- vs. low-frequency phonon bands, this analysis leads to a mechanistic picture showing that the dynamical interplay between the two types of phonon modes is crucial for the ultrafast dissociation of the photogenerated exciton state. A perspective is given on the effect of averaging over ensembles of interface structures, on the role of coherence, and on the extension of the analysis to finite temperatures. [1] H. Tamura, J. G. S. Ramon, E. R. Bittner, and I. Burghardt, Phys. Rev. Lett. 100, 107402 (2008), J. Phys. Chem. B, 112, 495 (2008). [2] G. A. Worth, H.-D. Meyer, H. Koeppel, L. S. Cederbaum, and I. Burghardt, Int. Rev. Phys. Chem., 27, 569 (2008); I. Burghardt, K. Giri, and G. A. Worth, J. Chem. Phys., 129, 174104 (2008). [3] L. S. Cederbaum, E. Gindensperger and I. Burghardt, Phys. Rev. Lett., 94, 113003 (2005). | |
| David F. Coker (Boston University) | Concluding discussion |
| Abstract: No Abstract | |
| József Z. Farkas (University of Stirling) | Analysis of structured populations in aquaculture |
| Abstract: Farmed and wild salmonid fish are subject to parasitism from a number of copepod parasites of the family Caligidae. These sea lice are damaging, causing reduced growth and appetite, wounding and susceptability to secondary infections. Economic losses due to this type of parasites are high, with a value in excess of US $100 million globally. The life history of the parasite involves a succession of ten distinct developmental stages from egg to adult. In the present talk I will focus on the mathematical analysis of a nonlinear partial differential equation model with distributed states-at-birth, which type of model is intended to desribe the dynamics at the first chalimus stage of the parasite. | |
| József Z. Farkas (University of Stirling) | Analysis of structured populations in aquaculture |
| Abstract: Farmed and wild salmonid fish are subject to parasitism from a number of copepod parasites of the family Caligidae. These sea lice are damaging, causing reduced growth and appetite, wounding and susceptability to secondary infections. Economic losses due to this type of parasites are high, with a value in excess of US $100 million globally. The life history of the parasite involves a succession of 10 distinct developmental stages from egg to adult. In the present talk I will focus on the mathematical analysis of a nonlinear partial differential equation model with distributed states-at-birth, which type of model is intended to desribe the dynamics at the first chalimus stage of the parasite. | |
| Jiali Gao (University of Minnesota) | The X-Pol potential: an explicit polarization quantum mechanical force field for condensed phase and protein dynamics |
| Abstract: Molecular dynamics simulation has become a powerful tool for studying biochemical properties. At the heart of these calculations is the potential energy function that describes intermolecular interactions in the system, and often it is the accuracy of the potential energy surface that determines the reliability of simulation results. The current generation of force fields was essentially established in the 1960s; while the accuracy has been improved tremendously by systematic parameterization, little has changed in the formalism. The explicit polarization (X-Pol) potential is an electronic structure-based polarization force field, designed for molecular dynamics simulations and modeling of biopolymers. In this approach, molecular polarization and charge transfer effects are explicitly treated by a combined quantum mechanical and molecular mechanical (QM/MM) scheme, and the wave function of the entire system is variationally optimized by a double self-consistent field (DSCF) method. We illustrate the possibility of parametrizing the X-Pol potential to achieve the desired accuracy as that from MM force fields, and demonstrate the feasibility of carrying out molecular dynamics (MD) simulation of solvated proteins. We use a system consisting of 14281 atoms and about 30,000 basis functions, including the protein bovine pancreatic trypsin inhibitor (BPTI) in water with periodic boundary conditions, to show the efficiency of an electronic structure-based force field in atomistic simulations. In this model, an approximate electronic wave function for the entire system is variationally optimized to yield the minimum Born-Oppenheimer energy at every MD step; this allows the efficient evaluation of the required analytic forces for the dynamics. Intramolecular and intermolecular polarization and intramolecular charge transfer effects are examined and are found to be significant. The new-generation X-POL force field permits the inclusion of time-dependent quantum mechanical polarization and charge transfer effects in much larger systems than was previously possible. | |
| Sophya Garashchuk (University of South Carolina) | Tunneling dynamics in a double well within the approximate quantum trajectories framework |
| Abstract: Quantum-mechanical (QM) effects in molecular dynamics – zero-point energy, tunneling and nonadiabatic dynamics – are essential for accurate description and understanding of reactions in complex molecular systems. Since the exact solution of the Schrödinger equation for such systems in full dimension is neither feasible nor necessary, the trajectory-based approaches have special appeal: classical description is often appropriate for dynamics of heavy particles such as nuclei, and cheap – methods of molecular mechanics are routinely applied to high-dimensional systems of hundreds of atoms. The challenge is to include quantum effects on dynamics of the trajectories. We use the de Broglie-Bohm formulation of the Schrodinger equation to formulate a semiclassical trajectory method. QM effects are included through the quantum force due to localization of the trajectory ensemble, acting on the trajectories in addition to the classical forces. A cheap approximation to the quantum potential makes the method practical in many dimensions and captures dominant quantum effects in semiclassical systems. The latest development is a description of the double well dynamics – a prototype of the proton transfer reactions – which exhibits "hard" quantum effect of tunneling. This is achieved by combining the approximate quantum trajectory dynamics with the population amplitudes in the reactant and product wells. The trajectories are driven by the asymptotic classical potentials, while the population amplitudes are described in a small basis. The method is exact if these reactant/product potentials are harmonic and the basis size is sufficiently large. In the semiclassical regime trajectory dynamics is approximate, and the basis size can be as small as two functions. The approach is fully compatible with the trajectory description of multidimensional systems capturing quantum tunneling along the reactive coordinate and ZPE flow among all degrees of freedom. | |
| Robert Ghrist (University of Pennsylvania) | Math Matters Public Lecture: Mathematics Making Sense of Sensors |
| Abstract: Sensor networks are poised to impact society in fundamental ways analogous to the impact of the networked personal computers. The rapid development of small-scale sensors coupled with wireless ad hoc networking capability foreshadows a day when our physical surroundings will wake up with sensory data, assuming it does not drown in the data first. In this lecture, Professor Ghrist will describe a recent calculus for sensor network data, whose origins lie in the century-old theory of algebraic topology. Sums and simplices, holes and homologies, counting and calculus, all converge to a tool for helping the walls to wake up. | |
| Arseni Goussev (University of Bristol), Roman Schubert (University of Bristol) | Quantum transition state theory applied to collinear reactions |
| Abstract: We apply a recently developed quantum version of Transition State Theory based on Quantum Normal Forms (QNF) to simple collinear reactions. We find that the normal form converges quickly for molecules which are not too light. | |
| Hua Guo (University of New Mexico) | Quantum dynamics of complex-forming reactions |
| Abstract: We will discuss some recent advances in quantum dynamic studies of several complex-forming reactions, such as H + O2 → OH + O and O + H2 → OH + H. Calculated differential and integral cross sections shed much light on mechanisms of these reactions. We will address important dynamic issues such as non-adiabatic transitions and statistical nature of the reactions. | |
| George A. Hagedorn (Virginia Polytechnic Institute and State University) | The time-dependent Born-Oppenheimer approximation, crossings, and avoided crossings |
| Abstract: We review mathematical results concerning the time-dependent Born-Oppenheimer approximation. We then turn attention to some results concerning molecular propagation through level crossings and avoided crossings with small gaps. | |
| George A. Hagedorn (Virginia Polytechnic Institute and State University) | Non–adiabatic scattering wave functions in a simple Born–Oppenheimer model |
| Abstract: No Abstract | |
| Sharon Hammes-Schiffer (Pennsylvania State University) | Nuclear-electronic orbital approach: Electron-proton correlation, multicomponent density functional theory, and tunneling splittings |
| Abstract: Recent advances in the development of the nuclear-electronic orbital (NEO) approach will be presented. In the NEO approach, selected nuclei are treated quantum mechanically on the same level as the electrons with molecular orbital techniques. For hydrogen transfer and hydrogen bonding systems, typically the hydrogen nuclei and all electrons are treated quantum mechanically. Electron-proton dynamical correlation is highly significant because of the attractive electrostatic interaction between the electron and the proton. An explicitly correlated Hartree-Fock scheme has been formulated to include explicit electron-proton correlation directly into the nuclear-electronic orbital self-consistent-field framework with Gaussian-type geminal functions. A multicomponent density functional theory has also been formulated, and electron-proton functionals have been developed based on the explicitly correlated electron-proton pair density. Initial applications illustrate that these new methods provide accurate nuclear densities, thereby enabling calculations of a wide range of molecular properties. Recently the NEO method has been combined with vibronic coupling theory to calculate hydrogen tunneling splittings in polyatomic molecules. In this NEO-vibronic coupling approach, the transferring proton and all electrons are treated quantum mechanically at the NEO level, and the other nuclei are treated quantum mechanically using vibronic coupling theory. This approach is computationally practical and efficient for relatively large molecules. The calculated tunneling splitting for malonaldehyde is in excellent agreement with the experimental value. Furthermore, this approach enables the identification of the dominant modes coupled to the transferring hydrogen motion and provides insight into their roles in the hydrogen tunneling process. | |
| John M. Herbert (Ohio State University) | Fourier grid QM/MM simulations of the hydrated electron |
| Abstract: This talk will discuss recent developments in one-electron model Hamiltonians for the hydrated electron, and their application to both anionic water clusters and bulk aqueous electrons. Our group has recently developed a new hydrated-electron model that combines the polarizable AMOEBA water model with a "static exchange" treatment of the electron-water interaction, parameterized from electronic structure calculations. Efficient, grid-based QM/MM algorithms have also been developed, in which the QM wave function and the MM water molecules polarize one another in a fully self-consistent fashion. Comparison to electronic structure benchmarks indicates that the new model is substantially more accurate than existing models based on non-polarizable water potentials. What role, if any, the polarization plays in establishing the structure of anionic water clusters will be discussed, along with preliminary results from bulk simulations. | |
| Mark S. Herman (University of Minnesota) | Born-Oppenheimer corrections near a Renner-Teller intersection |
| Abstract: We perform a rigorous mathematical analysis of the bending modes of a linear triatomic molecule that exhibits the Renner-Teller effect. Assuming the potentials are smooth, we prove that the wave functions and energy levels have asymptotic expansions in powers of epsilon, where the fourth power of epsilon is the ratio of an electron mass to the mass of a nucleus. To prove the validity of the expansion, we must prove various properties of the leading order equations and their solutions. The leading order eigenvalue problem is analyzed in terms of a parameter b, which is equivalent to the parameter originally used by Renner. Perturbation theory and finite difference calculations suggest that there is a crossing involving the ground bending vibrational state near b=0.925. The crossing involves two states with different degeneracy. | |
| Michael F. Herman (Tulane University) | Well defined and accurate semiclassical surface hopping propagators and wave functions |
| Abstract: The form of accurate semiclassical surface hopping propagators and wave functions for processes involving more than one electronic quantum state is discussed. It is shown that conditions, which define the required non-classical events along trajectories, can be derived from the Schrödinger equation. These conditions also uniquely specify the direction of the momentum change accompanying the energy conserving hops between electronic energy surfaces and the amplitudes associated with these hops. Transition probabilities obtained from surface hopping calculations on model systems are presented for classically allowed and classically forbidden transitions, and these results are compared with exact quantum calculations. | |
| Xiangqian Hu (Duke University) | Mechanistic simulation of the autocatalytic isopeptide bond formation in pili with QM/MM minimum free energy path method |
| Abstract: We studied the detailed reaction mechanism of autocatalytic intramolecular isopeptide bond formations in pili of Gram-negative bacteria with the recently developed QM/MM minimum free-energy path (QM/MM-MFEP) method. The scrutinized reaction mechanism consists of at least three steps in which proton transfers occur prior to and after the formation of the intramolecular isopeptide bond. Preliminary results revealed crucial roles of an active-site Glu residue in both the proton transfer reactions and the formation of the intramolecular isopeptide bond. Our results will provide important information for identifying and designing new vaccine candidates that can be applied to the bacterial pilus. | |
| Francesca Ingrosso (Université de Nancy I (Henri Poincaré)) | Solvation dynamics in supercritical fluoroform |
| Abstract: We present a molecular dynamics simulation study of solvation and collective polarizability dynamics supercritical fluoroform at a series of densities at constant temperature, slightly above the critical temperature, T_c. Our solvation dynamics studies were designed to represent the time-dependent frourescence Stokes shift for the chromophore coumarin 153. The equilibrium and nonequilibrium solvation responses were calculated. We found strong density dependence of solvation time correlations, with slower decay at lower densities and more pronounced for the excited-state than for the ground-state response. As for the nonequilibrium response, we showed that the inclusion of the interaction between the solute charge density and solvent induced dipoles improves the agreement with available experimental data. Preliminary results of an investigation of collective polarizability anisotropy relaxation in pure supercritical fluoroform are also presented. We focus on the nuclear response observable in optical Kerr effect and show that the results at higher densities are sensitive to the model used for the interaction-induced polarizability. | |
| Mark Iwen (University of Minnesota) | Interpolation with sparsity assumptions: From syphilis testing to sparse Fourier transforms |
| Abstract: I will discuss the application of group testing techniques to compressed sensing problems and sparse signal recovery. From this general framework I will narrow focus down to the specific problem of recovering a periodic function that is well approximated by the sum of a small number of sinusoids using as few function samples as possible. We will see that these considerations lead to sublinear-time Fourier algorithms capable of quickly recovering sparse superpositions using a smaller number of samples than required by straightforward application of the Nyquist/Shannon sampling theorem. Finally, we will conclude with a brief discussion of other compressed sensing applications to function learning/interpolation with sparsity assumptions. | |
| Leif David Jacobson (Ohio State University) | A self-consistent, polarizable, electron-water potential for use in hydrated-electron simulations |
| Abstract: Previously Turi and Borgis have parameterized an electron-water interaction potential in the static exchange approximation to yield a one-electron pseudopotential that has been applied to the study of anionic water clusters and the bulk hydrated electron. This potential has been used solely in conjunction with the Simple Point Charge (SPC) water model which is known to yield poor results for neutral water clusters. We re-parameterize the pseudopotential to be used with the polarizable AMOEBA water model to yield a potential in which the one-electron density polarizes the water molecules and vice versa in a fully self-consistent manner. The resulting model Hamiltonian is considerably more accurate for reproducing vertical electron binding energies (VEBEs), cluster geometries, and relative isomer energies when compared to ab initio results. The role of self-consistent polarization is particularly pronounced in clusters where the excess electron is bound in the interior of the cluster. | |
| Nancy Makri (University of Illinois at Urbana-Champaign) | Path integral and semiclassical methods for quantum dynamics |
| Abstract: Recent developments in semiclassical and path integral methods for quantum dynamics will be presented.
Forward-backward semiclassical dynamics (FBSD) is a rigorous and efficient methodology for capturing quantum mechanical effects in the time evolution of condensed phase systems through classical trajectory information. Combined with a discretized path integral representation of the Boltzmann operator, this methodology has enabled the simulation of the dynamics of such fluids as para-hydrogen and helium across the normal-to-superfluid transition. The results of these calculations are in very good agreement with experimental results on diffusion coefficients and dynamic structure factors probed by neutron scattering. The FBSD simulations provide novel insights into the separate roles of quantum mechanical and quantum statistical effects on the dynamics of these fluids.
Accurate, fully quantum mechanical results for the short-time behavior of complex-time correlation functions of low-temperature fluids have been obtained using the pair product approximation to evaluate the complex-time propagator in a single step. These results provide useful benchmarks for assessing the accuracy of approximate propagation methods.
Finally, an iterative Monte Carlo (IMC) methodology appears to overcome the sign problem associated with path integral calculations. By evaluating the discretized path integral expression iteratively on a grid selected by a Monte Carlo procedure. Both the grid points and the summations performed in each iteration utilize importance sampling, leading to favorable scaling with the number of particles, while the stepwise evaluation of the integrals circumvents the exponential growth of statistical error with time. |
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| David E. Manolopoulos (University of Oxford) | A fast path integral method for liquid water |
| Abstract: We have recently shown how path integral simulations can be streamlined by decomposing the potential into a sum of rapidly varying short-range and slowly varying long-range contributions. In this talk, I will describe an efficient way to perform this decomposition for systems with electrostatic interactions, and illustrate the method with an application to a flexible water model. In the limit of large system size, where the calculation of long-range forces dominates, the present method enables path integral (and ring polymer molecular dynamics) simulations of liquid water to be performed with less than twice the computational effort of classical molecular dynamics simulations [1,2]. [1] T. E. Markland and D. E. Manolopoulos, J. Chem. Phys.129, 024105 (2008). [2] T. E. Markland and D. E. Manolopoulos, Chem. Phys. Lett. 464, 256 (2008). | |
| David J. Masiello (Northwestern University) | Many-body theory of surface-enhanced Raman scattering |
| Abstract: Joint work with George C. Schatz. A many-body Green's function approach to the microscopic theory of surface-enhanced Raman scattering is presented. Interaction ects between a general molecular system and a spatially anisotropic metal particle supporting plasmon excitations in the presence of an external radiation field are systematically included through many-body perturbation theory. Reduction of the exact ects of molecular-electronic correlation to the level of Hartree-Fock mean-field theory is made for practical initial implementation, while description of collective oscillations of conduction electrons in the metal is reduced to that of a classical plasma density; extension of the former to a Kohn-Sham density-functional or second-order Møller-Plesset perturbation theory is discussed; further specialization of the latter to the random-phase approximation allows for several salient features of the formalism to be highlighted without need for numerical computation. Scattering and linear-response properties of the coupled system subjected to an external perturbing electric field in the electric-dipole interaction approximation are investigated. Both damping and finite-lifetime ects of molecular-electronic excitations as well as the characteristic fourth-power enhancement of the molecular Raman scattering intensity are elucidated from first principles. It is demonstrated that the presented theory reduces to previous models of surface-enhanced Raman scattering and leads naturally to a semiclassical picture of the response of a quantum-mechanical molecular system interacting with a spatially anisotropic classical metal particle with electronic polarization approximated by a discretized collection of electric dipoles. | |
| Anne B. McCoy (Ohio State University) | Using Diffusion Monte Carlo to investigate molecules that undergo large amplitude vibrational motions |
| Abstract: This talk will highlight recent work in our group in which we use Diffusion Monte Carlo approaches to study molecular vibrations of several fluxional systems. The molecular systems that will be the focus of the talk will be CH5+ and ion-water complexes. For these studies, we focus on two approaches. The first involves a fixed-node treatment of rotationally and vibrationally excited states. This approach enables us to evaluate the "zero-order bright state" associated with a particular molecular vibration. The results of these calculations include the frequency of the state of interest as well as the associated probability amplitude. A second approach will be described in which we re-express the excited state energy as an expectation value over the ground-state wave function. The results of these approaches are promising. | |
| Hans-Dieter Meyer (Ruprecht-Karls-Universität Heidelberg) | Quantum molecular dynamics of complex systems studied with MCTDH: Dynamics and IR-spectroscopy of the protonated water dimer H5O2+ and its isotopologues |
| Abstract: In this presentation we discuss a full (15D) quantum simulation of the infrared absorption spectrum and dynamics of the protonated water dimer (H5O2+) by the multiconfiguration time-dependent Hartree (MCTDH) method. The main features of the IR spectrum are explained an assigned, in particular a complicated doublet structure at about 1000 cm-1 related to the proton transfer motion, which was not understood. Also the couplings of various fundamental motions which shape the spectrum between 800 and 2000 cm-1 are explained and assigned. A picture of the cation arises in which the central proton motion determines the dynamics of various other modes, mostly water bending and water pyramidalization. We show that a full quantum-dynamical description of such a complex molecular system can be achieved, providing explicative and predictive power and a very good agreement to available experimental data. This success is largely due to the use of the MCTDH method, a powerful algorithm for propagating wavepackets. The basics of the MCTDH algorithm are briefly discussed. To account for the interatomic potential and the interaction with the radiation we make use of the potential energy surface and dipole-moment surfaces recently developed by Bowman and collaborators, which constitute the most accurate ab initio surfaces available to date for this system. | |
| Craig Michoski (University of Texas) | Partial differential equations in chemical dynamics with finite elements |
| Abstract: We introduce some mathematical analysis in the form of existence and uniqueness results for chemically miscible compressible classical systems of equations. Then we show some extensions to chemical reactor systems, where chemical kinetics and intermolecular diffusion is taken into consideration, and applied to atmospheric chemistry. Finally we show an extension to quantum hydrodynamic systems of equations, used to model chemical reactions. | |
| Isamu Ohnishi (Hiroshima University) | Memory, hysteresis and oscillation induced by multiple covalent modifications and its application to circadian rhythm of Cyanobacteria |
| Abstract: No transcription-translation feedback system of circadian clock by KaiC protein's phosphorylation is very interesting and also significant as a kind of core cycle of the circadian rhythm in Cyanobacteria. In order to understand the oscillation phenomena, we pay attention to a function of memory in a cell level. A standard structure of such a binary digit of memory is presented by use of multiple covalent modifications in this presentation. A key idea is bistability of covalent modification states which creates hysterecally and digitally switching mechanism between them. By use of this kind of memory, we see the circadian oscillation be realized. In fact, by deterministic simulations as well as by stochastic simulation, it is shown that the system obtains stable circadian oscillations, and shown that multiplicity of modification sites reinforces the stability of memory in several senses. Moreover, it is reported that this model explains well several molecular biologically experimental facts about period's change by use of mutants of Kai proteins in the circadian rhythm of Cyanobacteria. | |
| Maurizio Persico (Università di Pisa) | Surface hopping dynamics with direct semiempirical solution of the electronic problem |
| Abstract: We present a strategy for the simulation of nonadiabatic excited state dynamics by surface hopping, with direct calculation of the electronic wavefunctions and energies. The electronic problem is solved by a semiempirical NDO method, especially modified to deal with excited states, bond breaking and orbital degeneracies. A reparameterization of the semiempirical hamiltonian is needed to obtain accurate PESs. For large systems, a QM/MM variant is available. The focus of the talk will be on open problems and future perspectives. | |
| Maurizio Persico (Università di Pisa) | Potential energy surfaces, nonadiabatic transitions, and surface crossings |
| Abstract: Adiabatic states and nonadiabatic couplings. Electronic excitation and decay. Curve crossings and the breakdown of the Born-Oppenheimer approximation. The non-crossing rule. The diabatic representation. The conical intersections | |
| Maurizio Persico (Università di Pisa) | Mixed quantum-classical dynamics |
| Abstract: The nuclear coordinates as parameters in the time-dependent Schroedinger equation. Mean-field and surface hopping methods. Tully's fewest switches algorithm. Quantum decoherence corrections. The selection of initial conditions. | |
| Maurizio Persico (Università di Pisa) | Azobenzene in solution: excited state dynamics simulation |
| Abstract: We present a set of surface hopping simulations of the excited state decay and photoisomerization of azobenzene, in vacuo and in two solvents of different viscosity, methanol and ethylene glycol. We are able to reproduce the experimental quantum yields and the fluorescence transients (both intensity and anisotropy). We bring out the effects of solvation on the photodynamics and propose a new interpretation of recent experiments. | |
| Maurizio Persico (Università di Pisa) | A model for the photo-orientation of a molecular sample irradiated with polarized light |
| Abstract: Molecules irradiated by polarized light have a maximum excitation probability when their transition dipole vector is parallel to the light polarization. An excited molecule, because of its internal motions and of the interactions with the chemical environment, will change its orientation. As a consequence, a molecular sample gets oriented when irradiated, but the spontaneous rotational diffusion tends to restore the isotropic conditions. We have set up a stochastic model to represent the photo-induced anisotropy and its development in time. The calculation uses as input the results of single chromophore surface hopping simulations. The method is tested on azobenzene and shows the interplay of photo-orientation, rotational diffusion, and photoisomerization. | |
| Maurizio Persico (Università di Pisa) | Computational strategy options in tackling a problem of molecular excited state dynamics |
| Abstract: We shall briefly introduce a particular (but typical) problem concerning the photophysical and photochemical behaviour of a class of compounds, namely azobenzene and its derivatives. We shall also motivate the goal of running computer simulations of such processes, mainly consisting in the interplay with very refined experiments and with proposals of new applications. We shall examine the computational tools currently available and we shall motivate our choices, namely, direct trajectory methods with semiempirical electronic energies and wavefunctions. We shall conclude by underlying strong and weak points of the computational approach, and by discussing the proposal of a Molecular Dynamics method based on a time-dependent force-field for excited states. | |
| Gilles H. Peslherbe (Concordia University) | Concluding discussion |
| Abstract: No Abstract | |
| Bill Poirier (Texas Tech University) | Concluding discussion |
| Abstract: No Abstract | |
| Oleg Prezhdo (University of Washington) | Dynamics on the nanoscale: Time-domain ab initio studies of quantum dots and carbon nanotubes |
| Abstract: Device miniaturization requires an understanding of the dynamical response of materials on the nanometer scale. A great deal of experimental and theoretical work has been devoted to characterizing the excitation, charge, spin, and vibrational dynamics in a variety of novel materials, including carbon nanotubes, quantum dots, conducting polymers, inorganic semiconductors and molecular chromophores. We have developed state-of-the-art non-adiabatic molecular dynamics techniques and implemented them within time-dependent density functional theory in order to model the ultrafast photoinduced processes in these materials at the atomistic level, and in real time. Quantum dots (QD) are quasi-zero dimensional structures with a unique combination of molecular and bulk properties. As a result, QDs exhibit new physical properties such as carrier multiplication, which has the potential to greatly increase the efficiency of solar cells. The electron-phonon and Auger relaxation in QDs compete with carrier multiplication. Our detailed studies of the competing processes in PbSe QDs rationalize why carrier multiplication was first observed in this material. The electron-phonon interactions in carbon nanotubes (CNT) determine the response times of optical switches and logic gates, the extent of heating and energy loss in CNT wires and field-effect transistors, and even a superconductivity mechanism. Our ab initio studies of CNTs directly mimic the experimental data and reveal a number of unexpected features, including the fast intrinsic intraband relaxation and electron-hole recombination, the importance of defects, the dependence of the relaxation rate on the excitation energy and intensity, and a detailed understanding of the role of active phonon modes. O. V. Prezhdo, W. R. Duncan, V. V. Prezhdo, “Dynamics of the photoexcited electron at the chromophore-semiconductor interface”, Acc. Chem. Res., 41, 339 (2008). O. V. Prezhdo, “Multiple excitons and electron-phonon bottleneck in semiconductor quantum dots: Insights from ab initio studies”, Chem. Phys. Lett. – Frontier Article, 460, 1-9, (2008) B. F. Habenicht, O. V. Prezhdo, “Nonradiative quenching of fluorescence in a semiconducting carbon nanotube: a time-domain ab initio study”, Phys. Rev. Lett., 100, 197402 (2008). | |
| Vitaly Rassolov (University of South Carolina) | Stable long-time semiclassical description of zero-point energy in high-dimensional molecular systems |
| Abstract: Joint work with Sophya Garashchuk (Universit of South Carolina). Semiclassical implementation of the quantum trajectory formalism [J. Chem. Phys. 120, 1181 (2004)] is further developed to give stable long-time description of zero-point energy in anharmonic systems of high dimensionality. The method is based on a numerically cheap linearized quantum force approach; stabilizing terms compensating for the linearization errors are added into the time evolution equations for the classical and nonclassical components of the momentum operator. The wavefunction normalization and energy are rigorously conserved. Numerical tests are performed for model systems of up to 40 degrees of freedom. | |
| Adrian E. Roitberg (University of Florida) | Optimizing efficiency in replica-exchange molecular dynamics and avoiding the traps of Langevin dynamics |
| Abstract: I will present two different half-talks. In the first section, I will focus on the ideas behind replica exchange molecular dynamics, with an emphasis on improving efficiency by optimizing the time between attempted exchanges in Monte Carlo. In the second half, I will present a peculiarity of Langevin thermostats, which could cause substantially wrong dynamical behavior if care is not taken in the choice of random seeds. | |
| Peter Saalfrank (Universität Potsdam) | Reduced vs. full system-bath quantum dynamics: Vibrational excitation and relaxation of adsorbates at surfaces |
| Abstract: Vibrationally excited adsorbates at surfaces have been suggested to be useful precursors in a number of applications, ranging from spectroscopy over quantum computing, to vibrationally mediated, bond-selective chemistry. To selectively excite adsorbate vibrations, tailored infrared laser pulses can be used, which are, however, perturbed by ultrafast vibrational relaxation. In this talk we shall present approaches of how to calculate vibrational lifetimes, and the laser-driven excitation and quantum dynamics of adsorbates at semiconductor (H/Si(100)) or at metal surfaces (CO/Cu(100) and H/Ru(0001)). For this purpose a reduced description of this system (molecule) / bath (surface) problem is chosen by applying Markovian or non-Markovian open-system density matrix theory, often with relaxation rates determined from perturbation theory. For H/Si, where vibrational relaxation is due to vibration-phonon coupling, in addition a `full' approach is adopted in which a multi-dimensional nuclear Schrödinger equation of the system-bath type is solved by using efficient schemes based on single- or multi-configurational time-dependent Hartree methods. | |
| George C. Schatz (Northwestern University) | Trajectory studies of gas/liquid reactions |
| Abstract: This talk will describe recent work in my group by Brian Radak, Scott Yockel and Dongwook Kim concerned with modeling the dynamics of reactions at the gas/liquid interface using a QM/MM approach. The reactions involve atomic oxygen and atomic fluorine collisions with liquid squalane, which is a hydrocarbon polymer, at hyperthermal energies (0.5-5.0 eV). The QM/MM model involves use of the MSINDO semiempirical Hamiltonian for the QM part, and the OPLS empirical force field for the MM part, with QM/MM calculations being done within the framework of the ONIOM model. In all studies, we have calibrated the accuracy of the electronic structure model by comparison with coupled-cluster results for similar gas phase reactions, and we have in some cases done direct dynamics studies of the gas phase reaction dynamics for reference. Detailed comparison with beam/surface measurements are provided. These studies provide new insights about the role of liquid interfaces in governing reactive collisions. They also demonstrate how dynamical processes may be described for condensed phase systems in which several bonds may be broken or formed in a series of chemical reactions all within a single simulation. | |
| Gregory K. Schenter (Pacific Northwest National Laboratory) | Self consistent polarization electronic structure |
| Abstract: I will describe our efforts to enhance efficient electronic structure methods such as NDDO semiempirical theory and density functional theory (DFT) by adding self consistent polarization (SCP). This approach enhances the polarization response of an efficient electronic structure method while providing a consistent representation of the dispersive interaction that is based on second-order perturbation theory. The first application of this method resulted in the effective parameterization of the interaction of water clusters to reproduce the accurate MP2/CBS estimates of small water cluster binding energies as well as the intramolecular frequency shifts as a function of cluster size. Preliminary efforts to extend this approach to DFT electronic structure will be described in terms of Argon and water systems. | |
| Tamar Schlick (New York University) | Overview talk: Advanced computing platforms offer a "microscope" for [simulating] conformational changes |
| Abstract: Solving challenging conformational dynamics problems requires advanced tools from chemistry, mathematics, physics, biology, engineering and scientific computing. In recent years, an enormous range of methods has been proposed for exploring conformational space, deducing mechanistic information, computing free energy profiles, and estimating reaction rates. Methods range from simple stochastic approaches to various spectral-based methods, to coarse-graining approaches, to rigorous mathematical approaches that manipulate by divide and conquer strategies the energy function an simulation protocol. A flavor of this enormous range of innovative approaches will be presented through selected examples and applications. Applications to DNA polymerases fidelity mechanisms by transition path sampling, molecular dynamics, and quantum/classical hybrid simulations will also be described. | |
| Greg Scholes (University of Toronto) | Concluding discussion |
| Abstract: No Abstract | |
| Igor V. Schweigert (Naval Research Laboratory) | Symmetry-broken independent-particle models in Born-Oppenheimer molecular dynamics of chemical bond dissociation |
| Abstract: Joint work with Brett I. Dunlap. Simulating chemical bond dissociation dynamics requires electronic structure methods to seamlessly describe the transition from the initial closed-shell configuration to an open-shell intermediate. Direct-dynamic simulations of the RO-NO2 bond dissociation in nitric esters are presented to demonstrate the importance of using unrestricted single-determinant methods and spin-symmetry-broken orbitals. Challenges in locating the symmetry-broken electronic potential energy surface in the course of a reactive trajectory are discussed. The second derivative of the unrestricted energy with respect to nuclear displacement is shown to be discontinuous at the onset of symmetry breaking, in analogy with the discontinuous specific heat in the Landau theory of second-order phase transitions. | |
| Christof Schütte (Freie Universität Berlin) | Rare event statistics in molecular dynamics |
| Abstract: The efficient determination of reliable rare event statistics is one of the grand challenges in molecular dynamics. For example, direct accurate computation of folding rates requires very long simulations, in many cases infeasibly long ones. The question of how the exploration of such transition statistics can be sped up has attracted much attention recently. The talk will present some new approaches to this problem. In these approaches the energy landscape of a molecular system is appropriately coarse grained into a discrete transition network. Simultaneously, the associated transition rates are computed from parallel molecular dynamics simulations until accuracy requirements are met. Total simulation lengths will be shown to be much shorter than those required by direct simulation approaches. | |
| Avital Shurki (Hebrew University) | Hybrid ab initio valence bond / molecular mechanics (VB/MM), a new method for calculating biochemical systems |
| Abstract: The growing demand for realistic methods that would calculate chemical reactions in biological systems resulted with the development of hybrid quantum mechanical (QM) molecular mechanical (MM) schemes. Recent years have proven schemes that are based on concepts from valence bond (VB) methodology, to be beneficial for the description of enzyme catalysis and reactivity. The development of a new hybrid (QM/MM) method where the QM part is treated by ab-initio Valence Bond (VB) theory will be presented. This VB/MM method has the advantages of Empirical VB (EVB) methodology but does not rely on empirical parameterization for the quantum part. The method utilizes various approximations that will be explained. Furthermore, examination of these approximations which was based on a recent extension of the method justifies their use. The validity of the method will be shown to be successful in several examples. | |
| Joseph Eli Subotnik (Tel Aviv University) | A quantum chemist’s view of molecular conduction via the reduced density matrix |
| Abstract: We present a very simple model for numerically describing the steady state dynamics of a system interacting with continua of states representing a bath. Our model can be applied to equilibrium and non-equilibrium problems. For a one-state system coupled to two free electron reservoirs, our results match the Landauer formula for current traveling through a molecule. More significantly, we can also predict the non- equilibrium steady state population on a molecule between two out-of-equilibrium contacts. While the method presented here is for one-electron Hamiltonians, we outline how this model may be extended to include electron-electron interactions and correlations, an approach which suggests a connection between the conduction problem and the electronic structure problem. | |
| David J. Tannor (Weizmann Institute of Science) | Bohmian mechanics with complex action: An exact formulation of quantum mechanics with complex trajectories |
| Abstract: Ever since the advent of Quantum Mechanics, there has been a quest for a trajectory based formulation of quantum theory that is exact. In the 1950’s, David Bohm, building on earlier work of Madelung and de Broglie, developed an exact formulation of quantum mechanics in which trajectories evolve in the presence of the usual Newtonian force plus an additional quantum force. In recent years, there has been a resurgence of interest in Bohmian Mechanics (BM) as a numerical tool because of its apparently local dynamics, which could lead to significant computational advantages for the simulation of large quantum systems. However, closer inspection of the Bohmian formulation reveals that the nonlocality of quantum mechanics has not disappeared — it has simply been swept under the rug into the quantum force. In this work, we present a new formulation of Bohmian mechanics in which the quantum action, S, is taken to be complex. This requires the propagation of complex trajectories, but with the reward of a significantly higher degree of localization. For example, using strictly localized trajectories (no communication with their neighbors) we obtain extremely accurate quantum mechanical tunneling probabilities down to 10-7. We have recently extended the formulation to include interference effects, which has been one of the major obstacles in conventional Bohmian mechanics. Applications to one- and two-dimensional tunneling, thermal rate constants in one and two dimensions, and the calculation of eigenvalues will be provided. A variation on the method allows for the calculation of thermal rate constants and eigenvalues using just one or two zero-velocity trajectories. On the formal side, the approach is shown to be a rigorous extension of generalized Gaussian wavepacket methods to give exact quantum mechanics, and has intriguing implications for fundamental quantum mechanics. | |
| David J. Tannor (Weizmann Institute of Science) | Tutorial on time-dependent quantum mechanics |
| Abstract: Many people find time-dependent quantum mechanics the most interesting and understandable part of quantum mechanics. However, standard courses in quantum mechanics devote little attention to this perspective, and its relationship to the rest of the syllabus is disjointed. Yet it is possible to develop quantum mechanics from beginning to end from a time-dependent perspective, using a small set of conceptual building blocks. The tutorial will have two parts. In the first part I will present the basic building blocks. I will begin with several animations that highlight the visual appeal of time-dependent quantum mechanics and its relationship with classical mechanics. Next, I will introduce the concept of a wavepacket time-correlation function and show how it is related to a spectrum via Fourier transform. I will then discuss the reciprocity of wavepackets and eigenstates — just as a wavepacket is a superposition of eigenstates, an eigenstate is a superposition of wavepackets. Finally, I will return to wavepacket time-correlation functions and show how they can be used to calculate reflection/transmission probabilities, emphasizing that barrier scattering and spectroscopy are two sides of the same coin. In the second part of the tutorial I will show that the time-dependent perspective provides a simple and unified interpretation of many of the frontier experiments in modern Chemical Physics — from femtochemistry to resonance Raman spectroscopy, from coherent control to photodissociation to reactive scattering — using the same small set of conceptual building blocks described in the first part. | |
| Stefan Teufel (Eberhard-Karls-Universität Tübingen) | Adiabatic perturbation theory and the time-dependent Born-Oppenheimer approximation |
| Abstract: Adiabatic perturbation theory is a general scheme that allows for the mathematically rigorous derivation of effective equations in quantum mechanical slow-fast systems. In this lecture I explain how to justify and compute corrections to the time-dependent Born-Oppenheimer approximation. In the second part I present some recent results (jointly with Volker Betz) on computing the dynamics of exponentially small non-adiabatic transitions between different electronic energy surfaces. | |
| Stefan Teufel (Eberhard-Karls-Universität Tübingen) | Adiabatic decoupling and the partial classical limit |
| Abstract: In many physical systems it is believed that one can describe parts of the system by classical and parts of the system by quantum mechanics. In this lecture I explain how to rigorously derive such effective "mixed quantum-classical" descriptions from the underlying quantum mechanics for the whole system. The important mechanism is adiabatic decoupling and the method adiabatic perturbation theory. As the paradigmatic example I will discuss the time-dependent Born-Oppenheimer approximation. | |
| Donald L. Thompson (University of Missouri) | Automatic construction of ab initio potential energy surfaces |
| Abstract: A highly accurate and efficient method for molecular global potential energy surface (PES) construction and fitting is demonstrated. An interpolating moving least-squares (IMLS) method using low-density ab initio potential, gradient, or Hessian values to compute PES parameters is shown to lead to an accurate and efficient PES representation. The method is automated and flexible so that a PES can be optimally generated for classical trajectories, spectroscopy, or other applications. Two main drivers for the fitting method have been developed thus far. The first is a PES generator designed primarily for spectroscopy applications. Using this method, the configuration space defined by a specified energy range is automatically fit to a predefined accuracy. A second approach is based on trajectory methods for computing reaction rates. In this approach, the configuration space that is dynamically accessible to a particular ensemble of trajectories is fit "on the fly." Results that are indicative of the accuracy, efficiency, and scalability will be presented. | |
| Mark E. Tuckerman (New York University) | Concluding discussion |
| Abstract: No Abstract | |
| Eric Vanden-Eijnden (New York University) | Single-sweep methods for free energy calculations |
| Abstract: Free energy (or potential of mean force) calculations are a central issue in biophysics. Molecular dynamics (MD) simulations provide a tool for performing such calculations on a computer in a way which is potentially both precise and inexpensive. Since a free energy associated with some collective variables is proportional to the logarithm of the probability density function of these variables, it can in principle be calculated by histogram methods based on the binning of an MD trajectory. This direct approach, however, turns out to be unpractical in general because the time scale required for the trajectory to explore all the relevant regions of configuration space is prohibitively long. The standard way around this difficulty is to use umbrella sampling methods such as the weighted histogram analysis method (WHAM), but this technique is restricted to calculations of free energies in low dimension, i.e. when the number of collective variables is small (typically, 1 or 2). An alternative approach, however, is to calculate the gradient of the free energy (i.e. the mean force) locally, and use these data to reconstruct the free energy globally. In this talk, I will present a new method based on this idea which can be used to map free energy landscapes in multidimensions. The method uses radial-basis functions to represent the free energy and a variational approach to reconstruct the free energy globally from the local data on the mean force. The method will be illustrated on the several examples and compared with existing techniques based on histogram methods such as WHAM or metadynamics. | |
| Oriol Vendrell-Romagosa (Ruprecht-Karls-Universität Heidelberg) | Infrared spectroscopy and dynamics of the Zundel cation |
| Abstract: Results are presented on the dynamics and IR spectroscopy of the Zundel (H5O2+) cation. The full-dimensional (15D) quantum simulations are performed with the multiconfiguration time-dependent Hartree (MCTDH) method. We investigate the IR spectroscopy of H5O2+ and various of its isotopomers, namely D5O2+, HD4O2+ and DH4O2+ isotopomers, and provide a comparison to recent experiments on these systems. Dramatic changes in the dynamics and spectroscopy of the clusters are observed upon isotopic substitution. Accurate measurements of IR spectra of protonated water clusters prepared in the gas phase has become possible in recent years. The aim of our theoretical studies is to sheed light on interpretation of these complex spectra, provide useful physical insight in the dynamics of the hydrated proton, and last but not least, to advance in the description of complex molecular systems and clusters by full quantum methods. | |
| Saulo A. Vázquez (University of Santiago de Compostela) | Improved united-atom models for perfluorinated self-assembled monolayers |
| Abstract: Several united-atom (UA) force fields for perfluorinated self-assembled monolayer (FSAM) surfaces are proposed. These UA models of FSAM are based on a preceding force field, and the modifications done in this work involved the type of potential function and parameters used to represent the nonbonded interactions among the united atoms of the FSAM chains, which have been shown to play a key role in the energy transfer that takes place in collisions of gases with self-assembled monolayers. | |
| Haobin Wang (New Mexico State University) | Multilayer multiconfiguration time-dependent Hartree theory |
| Abstract: The multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) theory is a rigorous and powerful method to simulate quantum dynamics in complex many-body problems. This approach extends the regular MCTDH theory of Meyer, Manthe, and Cederbaum to include several dynamically contracted layers whose equations of motion are determined from variational principle. In this talk I will discuss the general derivation of the theory, the scaling of the method, and the application of the theory to simulate dynamics of electron transfer reactions in the condensed phase. Furthermore, a new generalization of the theory, the ML-MCTDH theory with second quantization (ML-MCTDH/SQ) will be presented to treat many-body identical particle (fermion or boson) systems. | |
| Zhian Wang (University of Minnesota) | Multi-scale approach in chemotaxis models |
| Abstract: This talk is focused on two questions of chemotaxis modeling. One is how to connect the macroscopic model with the microscopic mode. The other is how information in the microscopic model is passed onto the macroscopic model. For the first question, I use a non-perturbative approach to derive the parabolic limits of microscopic model and quickly get the desired macroscopic model. This approach has many advantages compared with conventional perturbation method. For the second question, I investigate the traveling waves of both microscopic and macroscopic models from which we can see how traveling waves in the microscopic model are retained, lost or created during the transition from the microscopic to macroscopic models. Biological implications will be discussed based on these result. | |
| Marcus Weber (Konrad-Zuse-Zentrum für Informationstechnik (ZIB)) | Recent progress in conformational analysis |
| Abstract: Conformation dynamics aims at an identification of dynamically metastable subsets of the position space of molecular systems. A time-discretized molecular simulation of such a system leads to a Markov operator. A space discretization of this operator leads to a stochastic transition matrix. In the talk, a cluster algorithm is presented which identifies metastable subsets of the position space by a spectral analysis of the transition matrix. This analysis was originally valid for reversible Markov chains, but can be extended to the non-reversible case. | |
| Weitao Yang (Duke University) | Overview talk: Free energies of chemical reactions in solution and in enzymes with Ab initio quantum mechanics/molecular mechanics methods |
| Abstract: Combined quantum mechanics/molecular mechanics (QM/MM) methods provide an accurate and efficient energetic description of complex chemical and biological systems, leading to significant advances in the understanding of chemical reactions in solution and in enzymes. Here we review progress in QM/MM methodology and applications, focusing on ab initio QM-based approaches. Ab initio QM/MM methods capitalize on the accuracy and reliability of the associated quantum-mechanical approaches, however, at a much higher computational cost compared with semiempirical quantum-mechanical approaches. Thus reaction-path and activation free-energy calculations based on ab initio QM/MM methods encounter unique challenges in simulation timescales and phase-space sampling. This review features recent developments overcoming these challenges and enabling accurate free-energy determination for reaction processes in solution and in enzymes, along with applications. (Reference: Hao. Hu and Weitao Yang, Annual Review of Physical Chemistry, 59,. 573–601, 2008). | |
| Xiancheng Zeng (Duke University) | Calculating solution redox free energies with Ab initio QM/MM minimum free energy path method |
| Abstract: A quantum mechanical/molecularmechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force (PMF) surface of the solute degrees of freedom. The MD sampling is only carried out with the QM subsystem fixed. It thus avoids "on-the-fly" QM calculations and overcomes the high computational cost of the direct ab initio QM/MM molecular dynamics (MD) needed for sampling. The enhanced efficiency and uncompromised accuracy of this approach are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions. | |
Visitors in Residence
| James Haley Adler | University of Colorado | 1/11/2009 - 1/17/2009 |
| Millard Alexander | University of Maryland | 1/11/2009 - 1/14/2009 |
| Donald G. Aronson | University of Minnesota | 9/1/2002 - 8/31/2009 |
| Dmitri Babikov | Marquette University | 1/10/2009 - 1/17/2009 |
| Roi Baer | Hebrew University | 1/10/2009 - 1/17/2009 |
| George L. Barnes | Texas Tech University | 1/10/2009 - 1/16/2009 |
| Sergio Blanes | Polytechnical University of Valencia | 1/11/2009 - 1/18/2009 |
| Sara Bonella | Università di Roma "La Sapienza" | 1/11/2009 - 1/16/2009 |
| Joel M. Bowman | Emory University | 1/11/2009 - 1/16/2009 |
| Bastiaan J. Braams | Emory University | 1/12/2009 - 1/16/2009 |
| Peter Brune | University of Chicago | 9/8/2008 - 6/30/2009 |
| Irene Burghardt | École Normale Supérieure | 1/11/2009 - 1/17/2009 |
| Maria-Carme T. Calderer | University of Minnesota | 9/1/2008 - 6/30/2009 |
| Hannah Callender | University of Minnesota | 9/1/2007 - 8/31/2009 |
| Alessandro Cembran | University of Minnesota | 1/12/2009 - 1/16/2009 |
| Santanu Chaudhuri | Washington State University | 1/10/2009 - 1/16/2009 |
| Xianjin Chen | University of Minnesota | 9/1/2008 - 8/31/2010 |
| David F. Coker | Boston University | 1/11/2009 - 1/16/2009 |
| Ludovica Cecilia Cotta-Ramusino | University of Minnesota | 1/12/2009 - 2/13/2009 |
| Daniel Dix | University of South Carolina | 1/1/2009 - 6/30/2009 |
| Olivier Dubois | University of Minnesota | 9/3/2007 - 8/31/2009 |
| József Z. Farkas | University of Stirling | 1/8/2009 - 2/8/2009 |
| Christopher Fraser | University of Chicago | 8/27/2008 - 6/30/2009 |
| Laura Gagliardi | University of Minnesota | 1/1/2009 - 2/28/2009 |
| Jiali Gao | University of Minnesota | 1/12/2009 - 1/15/2009 |
| Sophya Garashchuk | University of South Carolina | 1/11/2009 - 1/16/2009 |
| Robert Ghrist | University of Pennsylvania | 1/21/2009 - 1/23/2009 |
| Jay Gopalakrishnan | University of Florida | 9/1/2008 - 2/28/2009 |
| Arseni Goussev | University of Bristol | 1/10/2009 - 1/17/2009 |
| Vasile Catrinel Gradinaru | Eidgenössische TH Zürich-Zentrum | 1/10/2009 - 1/18/2009 |
| Francesca Guerra | University of Minnesota | 1/12/2009 - 1/16/2009 |
| Hua Guo | University of New Mexico | 1/12/2009 - 1/16/2009 |
| George A. Hagedorn | Virginia Polytechnic Institute and State University | 1/11/2009 - 1/17/2009 |
| Sharon Hammes-Schiffer | Pennsylvania State University | 1/11/2009 - 1/16/2009 |
| Jaebeom Han | University of Minnesota | 1/12/2009 - 1/16/2009 |
| Bill Hase | Texas Tech University | 1/11/2009 - 1/16/2009 |
| John M. Herbert | Ohio State University | 1/11/2009 - 1/16/2009 |
| Mark S. Herman | University of Minnesota | 9/1/2008 - 8/31/2010 |
| Michael F. Herman | Tulane University | 1/11/2009 - 1/16/2009 |
| Peter Hinow | University of Minnesota | 9/1/2007 - 8/31/2009 |
| Hao Hu | Duke University | 1/11/2009 - 1/16/2009 |
| Xiangqian Hu | Duke University | 1/11/2009 - 1/16/2009 |
| Jingfang Huang | University of North Carolina | 12/30/2008 - 5/31/2009 |
| Yunkyong Hyon | University of Minnesota | 9/1/2008 - 8/31/2010 |
| Francesca Ingrosso | Université de Nancy I (Henri Poincaré) | 1/10/2009 - 1/16/2009 |
| Mark Iwen | University of Minnesota | 9/1/2008 - 8/31/2010 |
| Alexander Izzo | Bowling Green State University | 9/1/2008 - 6/30/2009 |
| Leif David Jacobson | Ohio State University | 1/11/2009 - 1/16/2009 |
| Ahren Jasper | Sandia National Laboratories | 1/11/2009 - 1/16/2009 |
| Srividhya Jeyaraman | University of Minnesota | 9/1/2008 - 8/31/2010 |
| Lijian Jiang | University of Minnesota | 9/1/2008 - 8/31/2010 |
| Markus Keel | University of Minnesota | 7/21/2008 - 6/30/2009 |
| Claude Le Bris | CERMICS | 9/11/2008 - 5/30/2009 |
| Chiun-Chang Lee | National Taiwan University | 8/26/2008 - 7/31/2009 |
| Yongfeng Li | University of Minnesota | 9/1/2008 - 8/31/2010 |
| Pinsker Lin | University of Minnesota | 1/12/2009 - 1/16/2009 |
| Tai-Chia Lin | National Taiwan University | 8/23/2008 - 7/31/2009 |
| Chun Liu | University of Minnesota | 9/1/2008 - 8/31/2010 |
| Christian Lubich | Eberhard-Karls-Universität Tübingen | 1/11/2009 - 1/17/2009 |
| Russell Luke | University of Delaware | 1/11/2009 - 1/16/2009 |
| Daniel James Lundberg | Gallaudet University | 1/11/2009 - 1/16/2009 |
| Mitchell Luskin | University of Minnesota | 9/1/2008 - 6/30/2009 |
| Nancy Makri | University of Illinois at Urbana-Champaign | 1/12/2009 - 1/14/2009 |
| Bhabani Shankar Mallik | University of Minnesota | 1/11/2009 - 1/14/2009 |
| David E. Manolopoulos | University of Oxford | 1/11/2009 - 1/19/2009 |
| Vasileios Maroulas | University of Minnesota | 9/1/2008 - 8/31/2010 |
| David J. Masiello | Northwestern University | 1/11/2009 - 1/16/2009 |
| Anne B. McCoy | Ohio State University | 1/11/2009 - 1/16/2009 |
| Kevin W. Mclaughlin | University of Wisconsin - River Falls | 1/6/2009 - 6/30/2009 |
| Hans-Dieter Meyer | Ruprecht-Karls-Universität Heidelberg | 1/11/2009 - 1/17/2009 |
| Craig Michoski | University of Texas | 1/11/2009 - 1/17/2009 |
| Steven L. Mielke | University of Minnesota | 1/12/2009 - 1/16/2009 |
| Jorge Alberto Morales | Texas Tech University | 1/11/2009 - 1/16/2009 |
| Junalyn Navarra-Madsen | Texas Woman's University | 1/10/2009 - 1/16/2009 |
| Isamu Ohnishi | Hiroshima University | 11/1/2008 - 1/17/2009 |
| Maurizio Persico | Università di Pisa | 1/5/2009 - 2/6/2009 |
| Gilles H. Peslherbe | Concordia University | 1/11/2009 - 1/16/2009 |
| Bill Poirier | Texas Tech University | 1/11/2009 - 1/16/2009 |
| Oleg Prezhdo | University of Washington | 1/13/2009 - 1/16/2009 |
| Neeraj Rai | University of Minnesota | 1/11/2009 - 1/16/2009 |
| Vitaly Rassolov | University of South Carolina | 1/11/2009 - 1/16/2009 |
| Melissa Reeves | Tuskegee University | 1/11/2009 - 1/16/2009 |
| Adrian E. Roitberg | University of Florida | 1/11/2009 - 1/16/2009 |
| Peter Saalfrank | Universität Potsdam | 1/11/2009 - 1/16/2009 |
| Fadil Santosa | University of Minnesota | 7/1/2008 - 6/30/2010 |
| George C. Schatz | Northwestern University | 1/12/2009 - 1/14/2009 |
| Arnd Scheel | University of Minnesota | 9/1/2008 - 6/30/2009 |
| Gregory K. Schenter | Pacific Northwest National Laboratory | 1/11/2009 - 1/16/2009 |
| Reinhard Schinke | Max-Planck-Institut für Dynamik und Selbstorganisation | 1/11/2009 - 1/16/2009 |
| Tamar Schlick | New York University | 1/10/2009 - 1/15/2009 |
| Greg Scholes | University of Toronto | 1/11/2009 - 1/16/2009 |
| Roman Schubert | University of Bristol | 1/6/2009 - 1/24/2009 |
| Christof Schütte | Freie Universität Berlin | 1/11/2009 - 1/14/2009 |
| Igor V. Schweigert | Naval Research Laboratory | 1/11/2009 - 1/16/2009 |
| L. 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 |
| Jing Shi | Wayne State University | 1/1/2009 - 5/31/2009 |
| Avital Shurki | Hebrew University | 1/11/2009 - 1/16/2009 |
| Heinz Siedentop | Ludwig-Maximilians-Universität München | 1/14/2009 - 4/21/2009 |
| Jack Simons | University of Utah | 1/11/2009 - 1/15/2009 |
| Andrew M. Stein | University of Minnesota | 9/1/2007 - 8/31/2009 |
| Joseph Eli Subotnik | Tel Aviv University | 1/11/2009 - 1/16/2009 |
| David J. Tannor | Weizmann Institute of Science | 1/11/2009 - 1/14/2009 |
| Andrew G Taube | Sandia National Laboratories | 1/11/2009 - 1/16/2009 |
| Stefan Teufel | Eberhard-Karls-Universität Tübingen | 1/10/2009 - 1/17/2009 |
| Donald L. Thompson | University of Missouri | 1/10/2009 - 1/16/2009 |
| Sana Tishchenko | University of Minnesota | 1/12/2009 - 1/16/2009 |
| Saber Trabelsi | Universität Wien | 1/11/2009 - 1/23/2009 |
| Donald G. Truhlar | University of Minnesota | 9/1/2008 - 6/30/2009 |
| Mark E. Tuckerman | New York University | 1/10/2009 - 1/14/2009 |
| Erkan Tüzel | University of Minnesota | 9/1/2007 - 8/31/2009 |
| Rosendo Valero | University of Minnesota | 1/12/2009 - 1/16/2009 |
| Steven M. Valone | Los Alamos National Laboratory | 1/10/2009 - 1/31/2009 |
| Eric Vanden-Eijnden | New York University | 1/12/2009 - 1/14/2009 |
| Oriol Vendrell-Romagosa | Ruprecht-Karls-Universität Heidelberg | 1/11/2009 - 1/16/2009 |
| Haobin Wang | New Mexico State University | 1/11/2009 - 1/17/2009 |
| Zhian Wang | University of Minnesota | 9/1/2007 - 8/31/2009 |
| Marcus Weber | Konrad-Zuse-Zentrum für Informationstechnik (ZIB) | 1/10/2009 - 1/17/2009 |
| Stephen Wiggins | University of Bristol | 1/10/2009 - 6/30/2009 |
| Kin-Yiu Wong | University of Minnesota | 1/11/2009 - 1/16/2009 |
| Dexuan Xie | University of Wisconsin | 9/1/2008 - 1/15/2009 |
| Wei Xiong | University of Minnesota | 9/1/2008 - 8/31/2010 |
| Xiang Xu | Pennsylvania State University | 1/26/2009 - 6/1/2009 |
| Weitao Yang | Duke University | 1/12/2009 - 1/15/2009 |
| Yuncheng You | University of South Florida | 1/10/2009 - 1/17/2009 |
| Xiancheng Zeng | Duke University | 1/11/2009 - 1/16/2009 |
| Lei Zhang | Pennsylvania State University | 1/11/2009 - 1/16/2009 |
| Weigang Zhong | University of Minnesota | 9/1/2008 - 8/31/2010 |
| Yu Zhuang | Texas Tech University | 1/10/2009 - 1/17/2009 |
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 Cincinnati, 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