Stochastic Dynamics of Bionanosystems: Multiscale Analysis and Specialized Ensembles

An approach for simulating bionanosystems, such as viruses and ribosomes, is presented. This calibration-free approach is based on an all-atom description for bionanosystems, a universal interatomic force field, and a multiscale perspective. The supramillion-atom nature of these bionanosystems prohibits the use of a direct molecular dynamics approach for phenomena like viral structural transitions or self-assembly that develop over milliseconds or longer. A key element of these multiscale systems is the cross-talk between, and consequent strong coupling of, processes over many scales in space and time. We elucidate the role of interscale cross-talk and overcome bionanosystem simulation difficulties with automated construction of order parameters (OPs) describing supra-nanometer scale structural features, construction of OP dependent ensembles describing the statistical properties of atomistic variables that ultimately contribute to the entropies driving the dynamics of the OPs, and the derivation of a rigorous equation for the stochastic dynamics of the OPs. Since the atomic scale features of the system are treated statistically, several ensembles are constructed that reflect various experimental conditions. The theory provides a basis for a practical, quantitative bionanosystem modeling approach that preserves the cross-talk between the atomic and nanoscale features. A method for integrating information from nanotechnical experimental data in the derivation of equations of stochastic OP dynamics is also introduced.Comment: 24 page

Quasicontinuum representations of atomic-scale mechanics: From proteins to dislocations

Computation is one of the centerpieces of both the physical and biological sciences. A key thrust in computational science is the explicit mechanistic simulation of the spatiotemporal evolution of materials ranging from macromolecules to intermetallic alloys. However, our ability to simulate such systems is in the end always limited in both the spatial extent of the systems that are considered, as well as the duration of the time that can be simulated. As a result, a variety of efforts have been put forth that aim to finesse these challenges in both space and time through new techniques in which constraint is exploited to reduce the overall computational burden. The aim of this review is to describe in general terms some of the key ideas that have been set forth in both the materials and biological setting and to speculate on future developments along these lines. We begin by developing general ideas on the exploitation of constraint as a systematic tool for degree of freedom thinning. These ideas are then applied to case studies ranging from the plastic deformation of solids to the interactions of proteins and DNA

Computational techniques to illuminate secrets of the monoamine transporters

The solute carrier family regulates the flow of various substances such as drugs, amino acids, sugars and inorganic ions across the cell membrane. In particular, the monoamine transporters (MATs) are responsible for the regulation of synaptic neurotransmitter levels. Their structures and conformational rearrangements associated with transport remain unsolved. We employed novel computational techniques to identify the binding pocket of cocaine in the dopamine transporter (DAT) and two intracellular pathways for substrate egress in LeuT and DAT. We review possible coarse grained molecular dynamics techniques to extend the temporal scale accessible in simulations of the MATs. Finally, we present the first computational study of DAT in the presence of an explicit electrochemical gradient. In these simulations, we identify a water wire in DAT that may suggest that DAT does not follow an alternating access mechanism

Roadmap on multiscale materials modeling

Modeling and simulation is transforming modern materials science, becoming an important tool for the discovery of new materials and material phenomena, for gaining insight into the processes that govern materials behavior, and, increasingly, for quantitative predictions that can be used as part of a design tool in full partnership with experimental synthesis and characterization. Modeling and simulation is the essential bridge from good science to good engineering, spanning from fundamental understanding of materials behavior to deliberate design of new materials technologies leveraging new properties and processes. This Roadmap presents a broad overview of the extensive impact computational modeling has had in materials science in the past few decades, and offers focused perspectives on where the path forward lies as this rapidly expanding field evolves to meet the challenges of the next few decades. The Roadmap offers perspectives on advances within disciplines as diverse as phase field methods to model mesoscale behavior and molecular dynamics methods to deduce the fundamental atomic-scale dynamical processes governing materials response, to the challenges involved in the interdisciplinary research that tackles complex materials problems where the governing phenomena span different scales of materials behavior requiring multiscale approaches. The shift from understanding fundamental materials behavior to development of quantitative approaches to explain and predict experimental observations requires advances in the methods and practice in simulations for reproducibility and reliability, and interacting with a computational ecosystem that integrates new theory development, innovative applications, and an increasingly integrated software and computational infrastructure that takes advantage of the increasingly powerful computational methods and computing hardware

Multiscale modelling of mesoscopic behaviour in soft matter systems

Soft matter modelling has a wide range of applications, such as polymer additive manufacturing, organics electronics, and biomolecular engineering. Many physical properties and phenomena of soft matter are determined by interactions and processes at a wide range of length and time scales. Therefore, it is challenging for theoretical models to simulate processes involving features from multiple scales. To reach the mesoscopic scales for soft matter behaviour, coarse-grained models have been developed to accelerate the atomistic models by projecting out the relevant degrees of freedom, allowing coverage of a wider range of scales. However, due to the lack of a formalism to capture the dynamics and anisotropy of the system, conventional coarse-grained model shows significant errors in dynamical properties and inconsistent soft matter behaviour. In this thesis, a generalised systematic formalism for coarse-graining is presented. The Mori-Zwanzig formalism provides a dynamically-guided projection to construct a mesoscopic system directly from the underlying microscopic system. Moreover, the Gay-Berne functional is introduced to describe the anisotropic effect of the pairwise interactions at mesoscopic level. The performance of the model is demonstrated by comparing it to other coarse-grained models using benzene as an example, which shows significant improvement in both static and dynamical properties. For application, crystallization of pentacene is studied by treating pentacene molecule as ellipsoidal particle. Furthermore, a modified atomistic model and a modified continuum model are employed to simulate mesosopic behaviour of polymers in electrospinning and electro-optical poling, demonstrating mesoscopic modelling from the atomistic and continuum limits

State of the Art Assessment of Simulation in Advanced Materials Development

Advances in both the underlying theory and in the practical implementation of molecular modeling techniques have increased their value in the advanced materials development process. The objective is to accelerate the maturation of emerging materials by tightly integrating modeling with the other critical processes: synthesis, processing, and characterization. The aims of this report are to summarize the state of the art of existing modeling tools and to highlight a number of areas in which additional development is required. In an effort to maintain focus and limit length, this survey is restricted to classical simulation techniques including molecular dynamics and Monte Carlo simulations

Ballistic-diffusive phonon heat transport across grain boundaries

The propagation of a heat pulse in a single crystal and across grain boundaries (GBs) is simulated using a concurrent atomistic-continuum method furnished with a coherent phonon pulse model. With a heat pulse constructed based on a Bose-Einstein distribution of phonons, this work has reproduced the phenomenon of phonon focusing in single and polycrystalline materials. Simulation results provide visual evidence that the propagation of a heat pulse in crystalline solids with or without GBs is partially ballistic and partially diffusive, i.e., there is a co-existence of ballistic and diffusive thermal transport, with the long-wavelength phonons traveling ballistically while the short-wavelength phonons scatter with each other and travel diffusively. To gain a quantitative understanding of GB thermal resistance, the kinetic energy transmitted across GBs is monitored on the fly and the time-dependent energy transmission for each specimen is measured; the contributions of coherent and incoherent phonon transport to the energy transmission are estimated. Simulation results reveal that the presence of GBs modifies the nature of thermal transport, with the coherent long-wavelength phonons dominating the heat conduction in materials with GBs. In addition, it is found that phonon-GB interactions can result in reconstruction of GBs