Bulletin of the American Physical Society
APS March Meeting 2013
Volume 58, Number 1
Monday–Friday, March 18–22, 2013; Baltimore, Maryland
Session A43: Focus Session: Multiscale modeling--Coarse-graining in Space and Time I |
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Sponsoring Units: DCP Chair: William Noid, Pennsylvania State University Room: Hilton Baltimore Holiday Ballroom 2 |
Monday, March 18, 2013 8:00AM - 8:36AM |
A43.00001: The Theory of Ultra Coarse-graining Invited Speaker: Gregory Voth Coarse-grained (CG) models provide a computationally efficient means to study biomolecular and other soft matter processes involving large numbers of atoms correlated over distance scales of many covalent bond lengths and long time scales. Variational methods based on information from simulations of finer-grained (e.g., all-atom) models, for example the multiscale coarse-graining (MS-CG) and relative entropy minimization methods, provide attractive tools for the systematic development of CG models. However, these methods have important drawbacks when used in the ``ultra coarse-grained'' (UCG) regime, e.g., at a resolution level coarser or much coarser than one amino acid residue per effective CG particle in proteins. This is due to the possible existece of multiple metastable states ``within'' the CG sites for a given UCG model configuration. In this talk I will describe 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 conclusions of this work connect back to single-state force matching and open up new avenues for method development in that area. These results provide a formal statistical mechanical basis for UCG methods related to force matching and relative entropy CG methods and suggest practical algorithms for constructing optimal approximate UCG models from fine-grained simulation data. [Preview Abstract] |
Monday, March 18, 2013 8:36AM - 9:12AM |
A43.00002: Coarse-graining with information theory and the relative entropy Invited Speaker: M. Scott Shell There remain many both fundamental and practical/methodological questions regarding how coarse-grained models should be developed. Are there theoretically intuitive and numerically robust strategies for turning small-scale all-atom simulations into coarse models suitable for large-scale modeling? How can we identify what atomic details are unnecessary and can be discarded? Are there systematic ways to detect emergent physics? Here we discuss a fundamentally new approach to this problem. We propose that a natural way of viewing the coarse-graining problem is in terms of information theory. A quantity called the relative entropy measures the information lost upon coarse graining and hence the (inverse) fitness of a particular coarse-grained model. Minimization of the relative entropy thus provides a sort-of universal variational principle for coarse-graining, and a way to ``automatically'' discover and generate coarse models of many systems. We show that this new approach enables us to develop very simple but surprisingly accurate models of water, hydrophobic interactions, self-assembling peptides, and proteins that enable new physical insights as well as simulations of large-scale interactions. We discuss both theoretical and numerical aspects of this approach, in particular highlighting a new coarse-graining algorithm that efficiently optimizes coarse-grained models with even thousands of free parameters. We also discuss how the relative entropy approach suggests novel strategies for predicting the errors of coarse models, for identifying relevant degrees of freedom to retain, and for understanding the relationships among other coarse-graining methodologies. [Preview Abstract] |
Monday, March 18, 2013 9:12AM - 9:48AM |
A43.00003: A Top Down Approach to Multiscale Modeling of Structured Materials Invited Speaker: Juan de Pablo There is considerable interest in developing multiscale modeling approaches capable of describing both the structure and dynamics of inhomogeneous materials having characteristic features ranging from a few to a several hundred nanometers. Examples include block polymers, which exhibit an array of ordered morphologies with characteristic dimensions in the tens of nanometers, or liquid crystalline materials, where ordered domains and defects can also span tens of nanometers. This presentation will describe a relatively new class of particle-based methods that rely on established continuum models to describe thermodynamic properties, but that adopt a molecular representation to describe molecular structure and mesoscale morphology. While these methods can describe mesoscale structure quantitatively, they can also be augmented to describe the dynamics of complex fluids, including entangled polymers, composites, and nanoparticle dispersed in structured fluids, over dynamic ranges that in some cases span multiple orders of magnitude. [Preview Abstract] |
Monday, March 18, 2013 9:48AM - 10:00AM |
A43.00004: Coarse graining approach to First principles modeling of structural materials Khorgolkhuu Odbadrakh, Don Nicholson, Aurelian Rusanu, German Samolyuk, Yang Wang, Roger Stoller, Xiaoguang Zhang, George Stocks Classical Molecular Dynamic (MD) simulations characterizing extended defects typically require millions of atoms. First principles calculations employed to understand these defect systems at an electronic level cannot, and should not deal with such large numbers of atoms. We present an efficient coarse graining (CG) approach to calculate local electronic properties of large MD-generated structures from the first principles. We used the Locally Self-consistent Multiple Scattering (LSMS) method for two types of iron defect structures 1) screw-dislocation dipoles and 2) radiation cascades. The multiple scattering equations are solved at fewer sites using the CG. The atomic positions were determined by MD with an embedded atom force field. The local moments in the neighborhood of the defect cores are calculated with first-principles based on full local structure information, while atoms in the rest of the system are modeled by representative atoms with approximated properties. This CG approach reduces computational costs significantly and makes large-scale structures amenable to first principles study. Work is sponsored by the USDoE, Office of Basic Energy Sciences, ``Center for Defect Physics,'' an Energy Frontier Research Center. This research used resources of the Oak Ridge Leadership Computing Facility at the ORNL, which is supported by the Office of Science of the USDoE under Contract No. DE-AC05-00OR22725. [Preview Abstract] |
Monday, March 18, 2013 10:00AM - 10:12AM |
A43.00005: Construction of interaction models of dissipative particle dynamics by coarse-graining Lennard-Jones fluids: Evaluation of non-Markovian formulation Yuta Yoshimoto, Toshiki Mima, Akinori Fukushima, Ikuya Kinefuchi, Takashi Tokumasu, Shu Takagi, Yoichiro Matsumoto The application of molecular dynamics (MD) simulation to mesoscale (10-100 nm) flow analysis is computationally expensive at present. Dissipative particle dynamics (DPD) simulation is a powerful candidate for the alternative method because the DPD interaction, which has a soft potential between mesoscopic particles, enables larger space and longer time simulation. In the present study, we develop the method of bottom-up construction of non-Markovian DPD (NMDPD) models by means of MD simulations. We focus on the center of mass of the cluster containing Lennard-Jones particles, and extract the effective forces exerted on the clusters. Moreover, we sample the spectra of fluctuating forces acted on the clusters in the MD system, and find that the white noise used in the conventional DPD simulations should be replaced by colored noise. In order to reproduce the spectra, finite impulse response filters are employed in NMDPD simulations. Finally we evaluate the NMDPD models by comparing the simulation results with the MD counterparts. [Preview Abstract] |
Monday, March 18, 2013 10:12AM - 10:24AM |
A43.00006: Solvation free energies of aqueous mixtures in a ``truly" open boundary simulation Debashish Mukherji, Kurt Kremer (Bio)macromolecular solvation in water cosolvent mixtures are dictated by the preferential interaction of cosolvents with the proteins. The numerical studies in the field are limited to the closed boundary schemes, which, however, suffers from severe system size effects. More specifically, when the conformational transitions are intimately linked to the large concentration fluctuations, the excess of cosolvents near a protein lead to depletion elsewhere in a small-sized closed boundary setup. This disturbs solvent equilibrium within the bulk solution. Therefore, by combining the adaptive resolution scheme (AdResS) with a metropolis particle exchange criterion, we propose a ``truly'' open boundary method that heals the particle depletion in a closed boundary setup. In AdResS, an all-atom region, containing protein, is coupled to a coarse-grained (CG) reservoir. Particle exchange is performed in the CG region, which otherwise would be impossible in an all-atom setup of dense fluids. We calculate solvation free energies within the all-atom region using Kirkwood-Buff theory. Our method produces well converged solvation energies that are impossible in a brute force all-atom MD of small system sizes. We will discuss two cases of triglycine in aqueous urea and PNIPAm in aqueous methanol. [Preview Abstract] |
Monday, March 18, 2013 10:24AM - 10:36AM |
A43.00007: Coarse-Grained Modeling of Mixtures of Charged Macroions Jun Kyung Chung, Alan R. Denton In suspensions of charged macroions, such as charge-stabilized colloids and polyelectrolyte microgels, the electrostatic interactions between macroions are relatively easily controlled by changing the sizes and charges of the macroions, as well as the concentration of salt. This tunability of interactions can be exploited to stabilize various structures that self-assemble under appropriate conditions. In this talk, a statistical mechanical coarse-graining approach to modeling effective electrostatic interactions in mixtures of charged spherical macroions will be discussed. Taking effective interactions as input, we perform molecular dynamics simulations to calculate pair distribution functions of binary mixtures of charged colloids. For highly charged macroions, incorporating charge renormalization is found to be important. Using thermodynamic perturbation theory, we also analyze phase behavior and explore the possibility of a demixing instability as a function of size and charge asymmetry. [Preview Abstract] |
Monday, March 18, 2013 10:36AM - 10:48AM |
A43.00008: Coarse-Grained Modeling of Colloid-Nanoparticle Mixtures Alan R. Denton, Jun Kyung Chung Colloid-nanoparticle mixtures have attracted much recent attention for their rich phase behavior. The potential to independently vary size and charge ratios greatly expands the possibilities for tuning interparticle interactions and stabilizing unusual phases. Experiments have begun to explore the self-assembly and stability of colloid-nanoparticle mixtures, which are characterized by extreme size and charge asymmetries. In modeling such complex soft materials, coarse-grained methods often prove essential to surmount computational challenges posed by multiple length and time scales. We describe a hierarchical approach to modeling effective interactions in ultra-polydisperse mixtures. Using a sequential coarse-graining procedure, we show that a mixture of charged colloids and nanoparticles can be mapped onto a one-component model of pseudo-colloids interacting via a Yukawa effective pair potential and a one-body volume energy, which contributes to the free energy of the system. Nanoparticles are found to enhance electrostatic screening and to modify the volume energy. Taking the effective interactions as input to simulations and perturbation theory, we calculate structural properties and explore phase stability of highly asymmetric charged colloid-nanoparticle mixtures. [Preview Abstract] |
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