Bulletin of the American Physical Society
APS March Meeting 2013
Volume 58, Number 1
Monday–Friday, March 18–22, 2013; Baltimore, Maryland
Session F42: Focus Session: Multiscale Modeling--Coarse-graining in Space and Time III |
Hide Abstracts |
Sponsoring Units: DCP Chair: William Noid, Pennsylvania State University Room: Hilton Baltimore Holiday Ballroom 3 |
Tuesday, March 19, 2013 8:00AM - 8:36AM |
F42.00001: Adaptive Resolution Simulations: Applications and New Developments towards Open Systems MD Invited Speaker: Kurt Kremer The relation between atomistic structure, architecture, molecular weight and material properties is a basic concern of modern soft matter science. A typical additional focus is on surface interface aspects or the relation between structure and function in nanoscopic molecular assemblies. Here computer simulations on different levels of resolution play an increasingly important role. To progress further adaptive schemes are being developed, which allow for a free exchange of particles (atoms, molecules) between the different levels of resolution. The lecture will concentrate on these methods, however will also include first approaches to connect particle based simulations to continuum as well as to include quantum effects. Furthermore the extension to open systems MD as well as new recent methodology advances will be explained. A general review on the first part can be found in M. Praprotnik et al. Ann. Rev. Phys. Chem. 59, 2008 and recent advances in S. Fritsch et al. PRL 108, 170602 (2012) [Preview Abstract] |
Tuesday, March 19, 2013 8:36AM - 9:12AM |
F42.00002: Ions without Charges, Hydrogen-Bonds without Hydrogen: Coarse-Grained Models with Short-Range, Anisotropic Interactions Invited Speaker: Valeria Molinero Water, ions, hydrophilic and hydrophobic moieties are the building blocks of materials and biomolecules. Modeling of the hydrogen-bonded structure of water is particularly challenging for coarse-grained simulations. Nevertheless, reproducing the hydrogen-bonded order of water is necessary not only to reproduce the anomalous thermodynamics, structure and dynamics of liquid water, but also its properties as solvent of ions and hydrophobes, and water-driven interactions. In this talk I will discuss a strategy for the development of coarse-grained models based on short-range anisotropic interactions, and their application for the development of accurate and efficient coarse-grained models of water, solvated ions and DNA, methane and hydrophobic nanoparticles and cavities. These models are 100 to 1000 times computationally more efficient than atomistic models while having quite high fidelity in the description of the structure and -with some caveats- their thermodynamics. I will discuss the level of agreement of the coarse-grained simulations with experimental or atomistic results, and highlight some of their applications. [Preview Abstract] |
Tuesday, March 19, 2013 9:12AM - 9:24AM |
F42.00003: Solving Multiscale Polymer Field Theory Simulations with Lattice Boltzmann Equation Hsieh Chen, YongJoo Kim, Alfredo Alexander-Katz A new Lattice Boltzmann (LB) approach is introduced to solve for the modified diffusion equations in polymer field theory. This method bridges two desired properties from different numerical techniques, namely: (i) it is robust and stable as the pseudo-spectral method, and (ii) it is flexible and allows for grid refinement and arbitrary boundary conditions. While the LB method is not as accurate as the pseudo-spectral method, full self-consistent field theoretic (SCFT) simulations of block copolymers on graphoepitaxial templates yield indistinguishable results from pseudo-spectral calculations. Furthermore, we were able to achieve speedups of about 100x compared to single CPU core implementations by using graphics processing units (GPUs). We expect this method to be very useful in truly multi-scale studies where small length scale details have to be resolved, such as in strongly segregating block copolymer blends, nanoparticle-polymer interfaces, or polymer wetting phenomena. [Preview Abstract] |
Tuesday, March 19, 2013 9:24AM - 9:36AM |
F42.00004: Model path-integral dynamics for nonadiabatic reactions in the condensed phase Nandini Ananth, Artur Menzeleev, Thomas Miller We introduce mapping-variable ring polymer molecular dynamics (MV-RPMD), a direct, real-time dynamic technique for the atomistic simulation of nonadiabatic reactions. The dynamics are based on the recently derived exact path-integral Stock-Thoss (PI-ST)representation for the quantum Boltzmann operator that has been previously used to calculate equilibrium properties for N-level systems, and as a way to initialize semiclassical trajectories for the calculation of thermal correlation functions. Both these methods use the Stock-Thoss (ST) mapping protocol to map from a discrete electronic states basis to a continuous Cartesian variables basis, providing the even-handed treatment of electrons and nuclei required to accurately describe their dynamically coupled motions and to describe resonance energy transfer. Like the existing RPMD approach, this method can be used to generate statistically meaningful ensembles of reactive trajectories but, unlike RPMD, it is applicable to photochemical reactions and reactions where proper electronic state quantization is essential. We present the results of simulations using MV-RPMD to calculate correlation functions for a series of model N-level systems over a wide range of nonadiabatic coupling strengths. [Preview Abstract] |
Tuesday, March 19, 2013 9:36AM - 9:48AM |
F42.00005: Coarse-Grained Simulation of Solvated Cellulose Ib Microfibril Bingxin Fan, Janna Maranas We construct a coarse-grained (CG) model of cellulose microfibrils in water. The force field is derived from atomistic simulation of a 40 glucose-unit-long microfibril by requiring consistency between the chain configuration, intermolecular packing and hydrogen bonding of the two levels of modeling. Intermolecular interactions such as hydrogen bonding are added sequentially until the force field holds the microfibril crystal structure. This stepwise process enables us to evaluate the importance of each potential and provides insight to ordered and disordered regions. We simulate cellulose microfibrils with 100 to 400 residues, comparable to the smallest observed microfibrils. Microfibrils longer than 100nm would form a bending region along their longitudinal direction. Multiple bends are observed in the microfibril containing 400 residues. Although the cause is not clear, the bending regions may provide us insights about the periodicity and the behavior of the disordered regions in the microfibril. [Preview Abstract] |
Tuesday, March 19, 2013 9:48AM - 10:24AM |
F42.00006: Development and application of coarse-grained models for lipids Invited Speaker: Qiang Cui I'll discuss a number of topics that represent our efforts in developing reliable molecular models for describing chemical and physical processes involving biomembranes. This is an exciting yet challenging research area because of the multiple length and time scales that are present in the relevant problems. Accordingly, we attempt to (1) understand the value and limitation of popular coarse-grained (CG) models for lipid membranes with either a particle or continuum representation; (2) develop new CG models that are appropriate for the particular problem of interest. As specific examples, I'll discuss (1) a comparison of atomistic, MARTINI (a particle based CG model) and continuum descriptions of a membrane fusion pore; (2) the development of a modified MARTINI model (BMW-MARTINI) that features a reliable description of membrane/water interfacial electrostatics and its application to cell-penetration peptides and membrane-bending proteins. Motivated specifically by the recent studies of Wong and co-workers, we compare the self-assembly behaviors of lipids with cationic peptides that include either Arg residues or a combination of Lys and hydrophobic residues; in particular, we attempt to reveal factors that stabilize the cubic ``double diamond" Pn3m phase over the inverted hexagonal H$_{II}$ phase. For example, to explicitly test the importance of the bidentate hydrogen-bonding capability of Arg to the stabilization of negative Gaussian curvature, we also compare results using variants of the BMW-MARTINI model that treat the side chain of Arg with different levels of details. Collectively, the results suggest that both the bidentate feature of Arg and the overall electrostatic properties of cationic peptides are important to the self-assembly behavior of these peptides with lipids. The results are expected to have general implications to the mechanism of peptides and proteins that stimulate pore formation in biomembranes. [Preview Abstract] |
Tuesday, March 19, 2013 10:24AM - 11:00AM |
F42.00007: Coarse-Grained Molecular Simulation of Lipid Self-Assembly Invited Speaker: Wataru Shinoda The talk will review our recent work on understanding the behavior of lipid self-assembly using a coarse-grained (CG) force field model developed recently [1]. The CG model is designed to reproduce experimental surface/interfacial properties as well as distribution functions from all-atom (AA) molecular dynamics (MD) simulations. A series of MD simulations has elucidated that the CG model reproduces the phase diagram reasonably and produces the membranes with reasonable elastic moduli, surface and line tensions. With a help of technical development of free energy computation, we have evaluated the stability of liposome. [2] A comparison of CG-MD and a simple continuum theory for the free energy barrier to the vesicle-to-bicelle transformation reveals that the internal structural relaxation in the bilayer membrane plays an important role in lowering the free energy barrier in case of a small unilamellar vesicle. [2] The effects of lipid components and additives are also discussed in this talk. Especially the effect of fullerenes on the membrane properties will be discussed in details.[3] The behavior of fullerenes in the bilayer membrane and the resultant membrane properties depend on the size of fullerene and bilayer thickness quite sensitively. To discuss these details, we need a chemically accurate CG model constructed based on extensive AA-MD results.\\[4pt] [1] W. Shinoda, R. DeVane, M. L. Klein, Mol Simul 33, 27 (2007); ibid, Soft Matter 4, 2454 (2008); ibid, J. Phys. Chem. B 114, 6836 (2010); ibid, Soft Matter, 7, 6178 (2011).\\[0pt] [2] W. Shinoda, T. Nakamura, S. O. Nielsen, Soft Matter, 7, 9012(2011).; T. Nakamura, W. Shinoda, T. Ikeshoji, J. Chem. Phys. 135, 094106 (2011).\\[0pt] [3] R. DeVane et al. J. Phys. Chem. B, 114, 6386 (2010); C. Chiu et al. J. Phys. Chem. B 114, 6394 (2010). R. DeVane et al. J. Phys. Chem. B, 114, 16364 (2010); A. Jusufi et al. Soft Matter 7, 1139 (2011); C. Chiu et al. Soft Matter, 8 9610(2012). [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