Bulletin of the American Physical Society
APS March Meeting 2015
Volume 60, Number 1
Monday–Friday, March 2–6, 2015; San Antonio, Texas
Session J51: Invited Session: Irwin Oppenheim Memorial Session: Non-Equilibrium Statistical Mechanics of Liquids, Glasses and Biomolecules |
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Sponsoring Units: GSNP GSOFT Chair: Eli Ben-Naim, Los Alamos National Laboratory Room: Grand Ballroom C1 |
Tuesday, March 3, 2015 2:30PM - 3:06PM |
J51.00001: Dynamical coarse grained models with realistic time dependence Invited Speaker: Hans Andersen Coarse grained (CG) models of molecular systems, with fewer mechanical degrees of freedom than an all-atom model, are used extensively in chemical physics. It is generally accepted that a coarse grained model that accurately describes equilibrium structural properties (as a result of having a well constructed CG potential energy function) does not necessarily exhibit appropriate dynamical behavior when simulated using conservative Hamiltonian dynamics for the CG degrees of freedom on the CG potential energy surface. Attempts to develop accurate CG dynamic models usually focus on replacing Hamiltonian motion by stochastic but Markovian dynamics on that surface, such as Langevin or Brownian dynamics. However, depending on the nature of the system and the extent of the coarse graining, a Markovian dynamics for the CG degrees of freedom may not be appropriate. We consider the problem of constructing dynamic CG models within the context of the Multi-Scale Coarse Graining (MS-CG) method of Voth and coworkers. We propose a method of converting an MS-CG model into a dynamic CG model by adding degrees of freedom to it in the form of a small number of fictitious particles that interact with the CG degrees of freedom in simple ways and that are subject to Langevin forces. The dynamic models are members of a class of nonlinear systems interacting with special heat baths that was studied by Zwanzig [R. Zwanzig, J. Stat. Phys. 9, 215 (1973)]. The dynamic models generate a non-Markovian dynamics for the CG degrees of freedom, but they can be easily simulated using standard molecular dynamics simulation programs. We present tests of this method on a series of simple examples that demonstrate that the method provides realistic dynamical CG models that have non-Markovian or close to Markovian behavior that is consistent with the actual dynamical behavior of the all-atom system used to construct the CG model. The dynamic CG models have computational requirements that are similar to those of the corresponding MS-CG model and are good candidates for CG modeling of very large systems. [Preview Abstract] |
Tuesday, March 3, 2015 3:06PM - 3:42PM |
J51.00002: Competing dynamics of vitrification and crystal coarsening Invited Speaker: David Chandler Materials undergoing glass transitions are often materials that can also crystalize. The qualities of the solid that forms depend upon the system's dynamics and experimentalist's protocols. This lecture describes some of the associated phenomena, including competition between crystal nucleation and structural relaxation, transient domains and dynamic heterogeneity, grain boundaries and polycrystallinity. A stochastic model from which all of these phenomena emerge will be presented. [Preview Abstract] |
Tuesday, March 3, 2015 3:42PM - 4:18PM |
J51.00003: Brownian motion, old and new, and Irwin's role in my academic life Invited Speaker: Katja Lindenberg Irwin Oppenheim's early work on Langevin equations, master equations, and Brownian motion was one of the earliest and strongest reasons for my change of direction from my PhD work in condensed matter theory to my later and lifelong interest in Brownian motion and, more broadly, statistical mechanics. I will talk about some of my most recent work on subdiffusion, a form of anomalous diffusion that describes random motions in crowded or disordered media where motions are hindered by the medium. On a personal note, I knew Irwin for decades, from the time before he had a family (he was a sworn bachelor...until he met his wife) until shortly before his death. For many years, first alone and then with family, Irwin would spend some portion of the cold Boston winter in warm La Jolla, and we would always get together during these visits. For a period of a number of years we decided to take advantage of these visits to write the definitive text in traditional Thermodynamics. We did not make it past about 2/3 of the project, but it was a great learning experience for me while it lasted. Irwin's knowledge and understanding of the subject were breathtaking. [Preview Abstract] |
Tuesday, March 3, 2015 4:18PM - 4:54PM |
J51.00004: Ion Atmosphere Near Nucleic Acids Invited Speaker: Udayan Mohanty We will discuss allatom structure based model that explicitly includes ionic effects, i.e., electrostatic interactions with explicit magnesium ions and implicit KCl that allow us to carry out explicit solvent molecular dynamics simulations of adenine riboswitch and SAMI riboswitch. Our predictions for the excess ions around the riboswitch, and the magnesiumRNA interaction free energy will be compared with experimental data. We will provide upper and lower bounds for preferential interaction coefficient, a statistical mechanical quantity that is a measure of excess ion atmosphere around a polyelectrolyte. We will discuss the role of surface charge density of mobile ions from added salt in determining the counterion release entropy associated with chain collapse. Finally, the Poisson's ratio of oligomeric DNA will be determined. (Work done in collaboration with R. Hayes, J. Noel, P. Whitford, S. Hennelly, J. Onuchic, and K. Sanbonmatsu.) [Preview Abstract] |
Tuesday, March 3, 2015 4:54PM - 5:30PM |
J51.00005: The Typical Lengthscale Characterizing the Glass Transition at Lower Temperatures Invited Speaker: Itamar Procaccia The existence of a static length scale that grows in accordance with the dramatic slowing down observed at the glass transition is a subject of intense interest. A recent publication compared two proposals for this length scale, one based on the point-to-set correlation technique and the other on the scale where the lowest eigenvalue of the Hessian matrix becomes sensitive to disorder. The conclusion was that both approaches lead to the same length scale, but the former is easier to measure at higher temperatures and the latter at lower temperatures. But even after using both methods together, the range of increase in the observed length scales was limited by the relaxation times reachable by standard molecular dynamics techniques (i.e. about 4-5 orders of magnitude). In this paper we therefore attempt to explore the typical scale at even lower temperatures, testing for this purpose two approaches, one based on the idea of vapor deposition and the other on a swap Monte Carlo technique. We conclude that the first approach does not help in getting to lower temperatures, but the second one does so quite effectively. We can reach a typical lengthscale that grows in accordance with at least 18 orders of magnitude increase in the relaxation time, coming close to the best experimental conditions. We conclude by discussing the relationship between the observed lengthscale and various models of the relaxation time. [Preview Abstract] |
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