Bulletin of the American Physical Society
APS March Meeting 2017
Volume 62, Number 4
Monday–Friday, March 13–17, 2017; New Orleans, Louisiana
Session K25: Advances in Molecular Dynamics Simulation: From Atomistic to Coarse-Grained Model - IVsFocus
|
Hide Abstracts |
Sponsoring Units: DCP Chair: Gregory Voth, University of Chicago Room: 288 |
Wednesday, March 15, 2017 8:00AM - 8:36AM |
K25.00001: Control of DNA-Functionalized Nanoparticle Assembly Invited Speaker: Monica Olvera De La Cruz Directed crystallization of a large variety of nanoparticles, including proteins, via DNA hybridization kinetics has led to unique materials with a broad range of crystal symmetries. The nanoparticles are functionalized with DNA chains that link neighboring functionalized units. The shape of the nanoparticle, the DNA length, the sequence of the hybridizing DNA linker and the grafting density determine the crystal symmetries and lattice spacing. By carefully selecting these parameters one can, in principle, achieve all the symmetries found for both atomic and colloidal crystals of asymmetric shapes as well as new symmetries, and drive transitions between them. A scale-accurate coarse-grained model with explicit DNA chains provides the design parameters, including degree of hybridization, to achieve specific crystal structures. The model also provides surface energy values to determine the shape of defect-free single crystals with macroscopic anisotropic properties, as well as the parameters to develop colloidal models that reproduce both the shape of single crystals and their growth kinetics. [Preview Abstract] |
Wednesday, March 15, 2017 8:36AM - 8:48AM |
K25.00002: Functional specificity and universal scaling in an analytical coarse-graining of protein dynamics. Jeremy Copperman, Marina Guenza Biology demands specificy in protein motions, which we describe in the dynamical modes of the Langevin Equation for Protein Dynamics (LE4PD). The LE4PD is a coarse-grained description at the level of a single site per amino acid tracing the protein backbone. Theoretical predictions are shown to quantitatively agree with experiment across picosecond to millisecond timescales, and provide insight into protein functions such as ligand binding and multi-protein assembly. We have discovered that underlying this dynamical specificity is a hierarchical scaling at the free energy level, constraining protein domains as a class. Microscopic critical stability maps the origin of the shared properties to the Kardar-Parisi-Zhang universality class. [Preview Abstract] |
Wednesday, March 15, 2017 8:48AM - 9:00AM |
K25.00003: Development of Coarse Grained Models for Long Chain Alkanes Gaurav Gyawali, Samuel Sternfield, In Chul Hwang, Steven Rick, Revati Kumar Modeling aggregation in aqueous solution is a challenge for molecular simulations as it involves long time scales, a range of length scales, and the correct balance of hydrophobic and hydrophilic interactions. We have developed a coarse-grained model fast enough for the rapid testing of molecular structures for their aggregation properties. This model, using the Stillinger-Weber potential, achieves efficiency through a reduction in the number of interaction sites and the use of short-ranged interactions. The model can be two to three orders of magnitude more efficient than conventional all atom simulations, yet through a careful parameterization process and the use of many-body interactions can be remarkably accurate. We have developed models for long chain alkanes in water that reproduce the thermodynamics and structure of water-alkane and liquid alkane systems. [Preview Abstract] |
Wednesday, March 15, 2017 9:00AM - 9:36AM |
K25.00004: All-atom molecular dynamics simulation of lipid bilayers: Recent successes and current challenges Invited Speaker: Edward Lyman About twenty years ago, the first molecular dynamics simulations of lipid bilayers revealed dynamics and structure on timescales of a few tens of picoseconds and lengthscales of a few nanometers. In the intervening years, ever increasing computational power has enabled ever more stringent tests of the models. The current generation of models obtains quantitative agreement with experiments for many \textit{thermodynamic} observables for \textit{simple} bilayers --- quantities like NMR order parameters, area per lipid, and elastic constants. In this talk I will highlight three challenges that must be met in order for MD simulation to approach the complexity of cell membranes: bilayer asymmetry, lipidomic complexity, and translational dynamics. I will use our own recent work simulating complex lipid mixtures on the Anton computer to highlight two unexpected features of lipidomically complex membranes: Lateral subdiffusion on timescales up to milliseconds, and non-additive curvature energetics of lipid mixtures. [Preview Abstract] |
Wednesday, March 15, 2017 9:36AM - 9:48AM |
K25.00005: Many-body effects in systematic coarse graining Christoph Scherer, Denis Andrienko Particle based coarse-graining (CG) is a systematic way of reduction of the number of degrees of freedom describing a physical system. It involves three steps: choice of the CG degrees of freedom, identification of a merit function which quantifies the difference between the fine- and coarse-grained representations, and determination of the CG potential energy surface (PES). The entire procedure is sensitive to the number and types of basis-functions employed in the CG representations: for example, the incorporation of nonbonded three-body interactions in a coarse-grained water model helps to reproduce both thermodynamic and structural properties [1,2]. In this work, we investigate the effect of extending the basis set to three-body interactions for several organic solvents and formulate clear criteria for when these many-body terms are required. The coarse-graining scheme is implemented in the VOTCA-CSG toolkit [3]. [1] V. Molinero, E. B. Moore, J. Phys. Chem. B, 113, 4008 (2009) [2] L. Larini, L. Lu, G.A. Voth, J. Chem. Phys. 132, 164107 (2010) [3] V. Rühle, C. Junghans, A. Lukyanov, K. Kremer, D. Andrienko, J. Chem. Theory. Comput. 5, 3211 (2009) [Preview Abstract] |
Wednesday, March 15, 2017 9:48AM - 10:00AM |
K25.00006: Consistent integration of experimental and ab initio data into molecular and coarse-grained models Lukas Vlcek As computer simulations are increasingly used to complement or replace experiments, highly accurate descriptions of physical systems at different time and length scales are required to achieve realistic predictions. The questions of how to objectively measure model quality in relation to reference experimental or ab initio data, and how to transition seamlessly between different levels of resolution are therefore of prime interest. To address these issues, we use the concept of statistical distance to define a measure of similarity between statistical mechanical systems, i.e., a model and its target, and show that its minimization leads to general convergence of the systems' measurable properties. Through systematic coarse-graining, we arrive at appropriate expressions for optimization loss functions consistently incorporating microscopic ab initio data as well as macroscopic experimental data. The design of coarse-grained and multiscale models is then based on factoring the model system partition function into terms describing the system at different resolution levels. The optimization algorithm takes advantage of thermodynamic perturbation expressions for fast exploration of the model parameter space, enabling us to scan millions of parameter combinations per hour on a single CPU. The robustness and generality of the new model optimization framework and its efficient implementation are illustrated on selected examples including aqueous solutions, magnetic systems, and metal alloys. [Preview Abstract] |
Wednesday, March 15, 2017 10:00AM - 10:36AM |
K25.00007: Thermodynamic forces in coarse-grained simulations Invited Speaker: William Noid Atomically detailed molecular dynamics simulations have profoundly advanced our understanding of the structure and interactions in soft condensed phases. Nevertheless, despite dramatic advances in the methodology and resources for simulating atomically detailed models, low-resolution coarse-grained (CG) models play a central and rapidly growing role in science. CG models not only empower researchers to investigate phenomena beyond the scope of atomically detailed simulations, but also to precisely tailor models for specific phenomena. However, in contrast to atomically detailed simulations, which evolve on a potential energy surface, CG simulations should evolve on a free energy surface. Therefore, the forces in CG models should reflect the thermodynamic information that has been eliminated from the CG configuration space. As a consequence of these thermodynamic forces, CG models often demonstrate limited transferability and, moreover, rarely provide an accurate description of both structural and thermodynamic properties. In this talk, I will present a framework that clarifies the origin and impact of these thermodynamic forces. Additionally, I will present computational methods for quantifying these forces and incorporating their effects into CG MD simulations. As time allows, I will demonstrate applications of this framework for liquids, polymers, and interfaces. [Preview Abstract] |
Wednesday, March 15, 2017 10:36AM - 10:48AM |
K25.00008: Ultra-coarse-grained (UCG) models for biomolecular simulations John Grime, Gregory Voth Computational molecular dynamics (MD) is a well-established complement to traditional experimental techniques and can provide information at very high spatial and temporal resolutions. Traditional MD has typically used atomic-level molecular representations, but the use of "coarse-grained" models (which require fewer degrees of freedom) can provide access to significantly larger time and length scales. The use of coarse-grained models at very large scales can introduce unique challenges that require novel theoretical approaches and software algorithms to overcome. In this talk, recent successes in the application of "ultra-coarse-grained" (UCG) models will also be described in the context of a medically relevant viral system: self-assembly of the capsid protein of type 1 Human Immunodeficiency Virus (HIV-1). [Preview Abstract] |
Wednesday, March 15, 2017 10:48AM - 11:00AM |
K25.00009: Transferability of structure, thermodynamics, and dynamics in coarse-grained macromolecular liquids Mohammadhasan Dinpajooh, Marina Guenza The Integral Equation Coarse-Graining (IECG) approach is an analytically solved theory of coarse-graining for the structure, thermodynamics, and dynamics of macromolecular liquid, either in equilibrium or out of equilibrium. We present here a brief overview of the method and recent developments that optimizes computational efficiency, as well as applications of the IECG to liquids of macromolecules and their mixtures. [Preview Abstract] |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700