Bulletin of the American Physical Society
APS March Meeting 2014
Volume 59, Number 1
Monday–Friday, March 3–7, 2014; Denver, Colorado
Session Y26: Focus Session: Modeling of Rare Events |
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Sponsoring Units: DCOMP Chair: Amit Samanta, Princeton University Room: 502 |
Friday, March 7, 2014 8:00AM - 8:36AM |
Y26.00001: Computer Simulation of Membrane Permeation by Milestoning Invited Speaker: Ron Elber Atomically detailed molecular dynamics trajectories in conjunction with Milestoning are used to analyze the different contributions of coarse variables to the permeation process of a small peptide (N-acetyl-L-tryptophanamide, NATA) through a 1,2-dioleoyl-\textit{sn}-glycero-3-phosphocholine (DOPC) membrane. Milestoning is a theory and algorithm that exploits the use of short trajectories between interfaces in phase space (milestones) to compute equilibrium and long time behavior. The permeation process takes hours, which makes it appropriate for a Milestoning study. Reasonable agreement between experiment and simulation is obtained. The peptide reverses its overall orientation as it permeates through the biological bilayer. The large change in orientation is investigated explicitly but is shown to impact the free energy landscape and permeation time only moderately. [Preview Abstract] |
Friday, March 7, 2014 8:36AM - 9:12AM |
Y26.00002: ABSTRACT WITHDRAWN |
Friday, March 7, 2014 9:12AM - 9:48AM |
Y26.00003: ABSTRACT WITHDRAWN |
Friday, March 7, 2014 9:48AM - 10:24AM |
Y26.00004: Computing Rates of Small Molecule Diffusion Through Protein Channels Using Markovian Milestoning Invited Speaker: Cameron Abrams Measuring diffusion rates of ligands plays a key role in understanding the kinetic processes inside proteins. For example, although many molecular simulation studies have reported free energy barriers to infer rates for CO diffusion in myoglobin (Mb), they typically do not include direct calculation of diffusion rates because of the long simulation times needed to infer these rates with statistical accuracy. We show in this talk how to apply Markovian milestoning along minimum free-energy pathways to calculate diffusion rates of CO inside Mb. In Markovian milestoning, one partitions a suitable reaction coordinate space into regions and performs restrained molecular dynamics in each region to accumulate kinetic statistics that, when assembled across regions, provides an estimate of the mean first-passage time between states. The mean escape time for CO directly from the so-called distal pocket (DP) through the histidine gate (HG) is estimated at about 24 ns, confirming the importance of this portal for CO. But Mb is known to contain several internal cavities, and cavity-to-cavity diffusion rates are also computed and used to build a complete kinetic network as a Markov state model. Within this framework, the effective mean time of escape to the solvent through HG increases to 30 ns. Our results suggest that carrier protein structure may have evolved under pressure to modulate dissolved gas release rates using a network of ligand-accessible cavities. [Preview Abstract] |
Friday, March 7, 2014 10:24AM - 10:36AM |
Y26.00005: Study of methane hydrate nucleation by accelerated molecular simulation Yuanfei Bi, Tianshu Li Recently clathrate hydrates have gained increasing attention due to their significance in energy, environment, safety, and gas transportation. The formation of such important compounds remains elusive, as a molecular level understanding of the nucleation mechanism is still missing. To gain such understanding, we combined forward flux sampling method with molecular dynamics, to simulate the nucleation process of methane hydrate. In particular, we have developed an effective order parameter that allows calculating hydrate nucleation rate explicitly for the first time. The order parameter is constructed based on the topological analysis of the tetrahedral network, and is capable of efficiently distinguishing hydrate from ice and liquid water. Employing this approach, we conducted molecular simulation under different thermodynamics conditions. Ensembles of nucleation pathways, containing both crystalline and amorphous hydrate nuclei, were obtained and analyzed under different conditions. In particular, pressure was found to significantly affect hydrate nucleation rate and pathways. [Preview Abstract] |
Friday, March 7, 2014 10:36AM - 10:48AM |
Y26.00006: Sampling saddle points on the free energy surface Amit Samanta |
Friday, March 7, 2014 10:48AM - 11:00AM |
Y26.00007: Three-Dimensional self-learning kinetic Monte Carlo model for arbitrary surfaces Andreas Latz, Lothar Brendel, Dietrich E. Wolf The self-learning kinetic Monte Carlo (SLKMC) method combines the calculation of transition rates from a realistic potential with the efficiency of a rate catalog, using a pattern recognition scheme. Originally limited to twodimensional systems with one specific surface orientation, we recently extended the method to three dimensions and arbitrarily shaped surfaces. We showed that by setting up an initial database, the concomitant huge increase of rate calculations on the fly can be decreased significantly. The model is applied to the homoepitaxial growth of Ag on Ag(111) at low temperatures and the drift of voids and islands due to electromigration. [Preview Abstract] |
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