Systematic Coarse Graining of Biomolecular and Soft-Matter Systems
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Graining of Biomolecular and Soft-Matter Systems Gary S. Ayton, Will G. Noid, and Gregory A. Voth
Abstract Coarse-grained modeling is a key component in the field of multiscale simulation. Many biomolecular and otherwise complex systems require the characterization of phenomena over multiple length and time scales in order to fully resolve and understand their behavior. These different scales range from atomic to near macroscopic dimensions, and they are generally not independent of one another, but instead coupled. That is, phenomena occurring at atomic length scales have an effect at macroscopic dimensions and vice versa. Systematic transfer of information between these different scales represents a core challenge in the field of multiscale simulation. Coarse-grained modeling works at an intermediate resolution that can bridge the very high resolution (atomic) scale to the very low resolution (macroscopic) scale. As such, a significant challenge is the development of a systematic methodology whereby coarse-grained models can be derived from their high-resolution atomistic-scale counterpart. Here, a systematic theoretical and computational methodology will be described for developing coarse-grained representations of biomolecular and other soft-matter systems. At the heart of the methodology is a variational statistical mechanical algorithm that uses forcematching of atomistic molecular dynamics data to a coarse-grained representation. A theoretical analysis of the coarse-graining methodology will be presented, along with illustrative applications to membranes, peptides, and carbohydrates.
Introduction The need for multiscale modeling has been motivated by the inherent design of many complex systems. In order to understand the multiscale nature of a particular complex system, it is necessary to first recast the problem in terms of its multiple spatial and temporal scales. The same system, for example, a protein or a phaseseparated fluid, is therefore reconstructed at different levels of spatial resolution. One scale models the system at an atomistic level of resolution, while another scale may model the system as a continuum viscoelastic object. In between, a coarse-grained (CG) resolution is often used, which is part-way between an atomistic and a continuum-level description of the system. The need for coarse-grained
representations arises because it is generally quite challenging in complex, inhomogeneous systems to directly bridge the atomistic and continuum-level scales. In between these two disparate regimes, a host of emergent mesoscopic phenomena can occur, and a new intermediate CG representation is required in order to connect the two “end point” scales. As such, coarse graining has become a key component in the full multiscale description of complex systems. From a computational standpoint, CG modeling allows for significantly larger spatial and temporal scales to be examined, as the CG representation of a system has fewer degrees of freedom than its atomistic counterpart, and the CG interac-
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