Bulletin of the American Physical Society
APS March Meeting 2015
Volume 60, Number 1
Monday–Friday, March 2–6, 2015; San Antonio, Texas
Session D19: Invited Session: Fifty Years of Molecular Dynamics Simulations II: Past, Present and Future |
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Sponsoring Units: DCOMP DPOLY GSOFT/DBIO Chair: Rajiv Kalia, University of Southern California Room: Mission Room 103B |
Monday, March 2, 2015 2:30PM - 3:06PM |
D19.00001: A Variational Approach to Enhanced Sampling and Free Energy Calculations Invited Speaker: Michele Parrinello The presence of kinetic bottlenecks severely hampers the ability of widely used sampling methods like molecular dynamics or Monte Carlo to explore complex free energy landscapes. One of the most popular methods for addressing this problem is umbrella sampling which is based on the addition of an external bias which helps overcoming the kinetic barriers. The bias potential is usually taken to be a function of a restricted number of collective variables. However constructing the bias is not simple, especially when the number of collective variables increases. Here we introduce a functional of the bias which, when minimized, allows us to recover the free energy. We demonstrate the usefulness and the flexibility of this approach on a number of examples which include the determination of a six dimensional free energy surface. Besides the practical advantages, the existence of such a variational principle allows us to look at the enhanced sampling problem from a rather convenient vantage point. [Preview Abstract] |
Monday, March 2, 2015 3:06PM - 3:42PM |
D19.00002: Bridging scales: from atoms to coarse-grained models for soft matter systems Invited Speaker: Christine Peter Molecular simulation has extended to increasingly complex soft matter systems, and time-scale and system-size requirements have instigated the use of simulation models on multiple levels of resolution. On the classical particle-based level, a large variety of methods to develop coarse grained (CG) simulation models has emerged, an important subgroup being those scale-bridging methods where the CG model is derived from and systematically linked to an underlying atomistic description. In my talk, I will introduce a few of these methods, address the underlying concepts as well as some of the ongoing challenges that are inherent to coarse graining. A natural consequence of reducing the level of resolution in a simulation model is a loss of transferability, i.e. a decreasing ability to correctly describe a system at several thermodynamic state points. Intimately linked to this is a loss of the ability to correctly represent all structural, thermodynamic and dynamic properties of the system. Examples for these limitations are easily found in all CG simulations of multicomponent or multiphase soft matter systems -- ranging from liquid crystals, biomolecular aggregates, biomaterials to hard/soft nanocomposites. A correct representation of phase transitions, phase coexistence, environment-induced conformational transitions, or effects due to surfaces and interfaces is a severe challenge for bottom-up CG models. Addressing this challenge requires both a method of generating CG potentials as well as finding and rationalizing an appropriate reference state point to start out from. I will illustrate several of these aspects using examples from the biomolecular and (biomimetic-) materials world. [Preview Abstract] |
Monday, March 2, 2015 3:42PM - 4:18PM |
D19.00003: Polymers at Surfaces and Interfaces Invited Speaker: Mesfin Tsige Interfaces between solids, liquids, and gases play an important role in a wide range of practical applications and have been a subject of scientific interest since Poisson showed in 1831 that the order parameter of liquids near interfaces must deviate considerably from its bulk value. In particular, polymers at surfaces and interfaces have been a subject of extensive theoretical, experimental and computational studies for a long time due to their use in many diverse applications ranging from antifouling coatings to flexible electronic devices. Understanding the structure and thermodynamic properties of polymers at surfaces and interfaces is thus an area of fundamental and current technological interest. Although encouraging experimental progress has been made over the years in understanding the molecular structure of polymers in contact with various environments, selectively probing their structure and dynamics at surfaces and interfaces has been extremely difficult. Computer simulations, especially molecular dynamics (MD) simulations, have proven over the years to be an invaluable tool in providing molecular details at interfaces that are usually lacking in the experimental data. In this talk, I'll give an overview of some previous simulation efforts to understand the structure and dynamics of polymers at surfaces and buried interfaces. I will conclude by presenting our current and ongoing work on combining ab initio calculations and MD simulations with Sum Frequency Generation (SFG) Spectroscopy to study polymer surfaces. This approach demonstrates the future role of MD in surface science. [Preview Abstract] |
Monday, March 2, 2015 4:18PM - 4:54PM |
D19.00004: Systematic Coarse-graining of Molecular Dynamics Simulations Invited Speaker: Gregory Voth Coarse-grained (CG) models can provide a computationally efficient means to study biomolecular and other soft matter processes involving large numbers of atoms that are correlated over distance scales of many covalent bond lengths and at long time scales. Systematic variational coarse-graining methods based on information from molecular dynamics simulations of finer-grained (e.g., all-atom) models provide attractive tools for the systematic development of CG models. Examples include the multiscale coarse-graining (MS-CG) and relative entropy minimization methods, and results from the former theory will be presented in this talk. In addition, a new approach will be presented that is appropriate for the ``ultra coarse-grained'' (UCG) regime, e.g., at a coarse-grained resolution that is much coarser than one amino acid residue per CG particle in a protein. At this level of coarse-graining, one is faced with the possible existence of multiple metastable states ``within'' the CG sites for a given UCG model configuration. I will therefore describe newer systematic variational UCG methods specifically designed to CG entire protein domains and subdomains into single effective CG particles. This is accomplished by augmenting existing effective particle CG schemes to allow for discrete state transitions and configuration-dependent resolution. Additionally, certain aspects of this work connect back to single-state force matching and open up new avenues for method development. This general body of theory and algorithm provides a formal statistical mechanical basis for the coarse-graining of fine-grained molecular dynamics simulation data at various levels of CG resolution. Representative applications will be described as time allows. [Preview Abstract] |
(Author Not Attending)
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D19.00005: Multiscale Simulations of Membranes Invited Speaker: Michael Klein |
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