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Strategies for articulated multibodybased adaptive coarse grain simulation of RNA
"... ABSTRACT Efficient modeling approaches are necessary to accurately predict largescale structural behavior of biomolecular systems like RNA (Ribonucleic Acid). Coarse grained approximations of such complex systems can significantly reduce the computational costs of the simulation while maintaining ..."
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ABSTRACT Efficient modeling approaches are necessary to accurately predict largescale structural behavior of biomolecular systems like RNA (Ribonucleic Acid). Coarse grained approximations of such complex systems can significantly reduce the computational costs of the simulation while maintaining sufficient fidelity to capture the biologically significant motions. However, given the coupling and nonlinearity of RNA systems (and effectively all biopolymers), it is expected that different parameters such as geometric and dynamic boundary conditions, states, and applied forces will affect the system's dynamic behavior. Consequently, static coarse grained models (i.e., models for which the coarse graining is time invariant) are not always able to adequately sample the conformational space of the molecule. We introduce here the concept of adaptive coarsegrained molecular dynamics of RNA, which automatically adapts the coarseness of the model dynamically, in an effort to more optimally increase simulation speed, while maintaining accuracy. Adaptivity requires two basic algorithmic developments; first, a set of integrators that seamlessly allow transitions between higher and lower fidelity models while preserving the laws of motion. Secondly, we propose and validate metrics for determining when and where more or less fidelity needs to be integrated into the model to allow sufficiently accurate dynamics simulation. Given the central role that multibody dynamics plays in the proposed framework, and the nominally large number of dynamic degrees of freedom being considered in these applications, a computationally efficient multibody method which lends itself well to adaptivity is essential to the success of this effort. A suite of DivideAndConquer Algorithm (DCA)based approaches are employed to this end, because these methods offer a good combination of computational efficiency and adaptive structure.
MULTIBODY MOLECULAR DYNAMICS II : APPLICATIONS AND RESULTS
"... ABSTRACT This is the second paper in a series of two papers on using multibody dynamics algorithms and methods for coarse grained molecular dynamics simulations. In the previous paper, the theoretical discussions on this topic have been presented. This paper presents results obtained from simulatin ..."
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ABSTRACT This is the second paper in a series of two papers on using multibody dynamics algorithms and methods for coarse grained molecular dynamics simulations. In the previous paper, the theoretical discussions on this topic have been presented. This paper presents results obtained from simulating several biomolecular and bulk materials using multibody dynamics algorithms. The systems studied include water boxes, alkane chains, alanine dipeptide and carboxyl terminal fragments of Calmodulin, Ribosomal, and Rhodopsin proteins. The atomistic representations of these systems include several thousand degrees of freedom and results of several nanosecond simulations of these systems are presented. The stability and validity of the simulations are studied through conservation of energy, thermodynamics properties and conformational analysis. In these simulations, a speed up of an order of magnitude is realized for conservative error bounds. A discussion is presented on the opensource software developed to facilitate future research using multibody dynamics with molecular dynamics.
A ROBUST FRAMEWORK FOR ADAPTIVE MULTISCALE MODELING OF BIOPOLYMERS USING HIGHLY PARALLELIZABLE METHODS Proceedings of the ASME 2013 2nd Global Congress on NanoEngineering for Medicine and Biology NEMB2013 NEMB201393099
"... EXTENDED ABSTRACT For many biopolymers (RNA, DNA, enzymes and proteins) the nature of the molecules interaction within the cell has been determined to be highly a function of its conformational structure. Understanding how to influence and control this structure thus is of critical importance if on ..."
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EXTENDED ABSTRACT For many biopolymers (RNA, DNA, enzymes and proteins) the nature of the molecules interaction within the cell has been determined to be highly a function of its conformational structure. Understanding how to influence and control this structure thus is of critical importance if one wishes to manipulate the intercellular processes of which these biopolymers play such a central role. In molecular dynamics (MD) simulations, a fully atomistic model represents the system at the finest scale and as such captures all the dynamics of the system. If the simulation is permitted to run sufficiently long important emergent behaviors can develop and show themselves. Such MD simulations represent a direct applications of Newton's Laws of Motion to the individual atoms in the system, and are conceptually the easiest to implement. An advantage of this procedure is that the simulation yields important information not only about the intermediate states and the mechanisms which produced them, but also provides the rates at which these processes occur. These intermediate conformational states have repeatedly been implicated in many known biological function [1],
Proceedings of ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology NEMB2010 NEMB201013123 DIVIDEANDCONQUER BASED ADAPTIVE COARSE GRAINED SIMULATION OF RNA
"... INTRODUCTION Molecular modeling has gained increasing importance in recent years for predicting important structural properties of large biomolecular systems such as RNA which play a critical role in various biological processes. Given the complexity of biopolymers and their interactions within liv ..."
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INTRODUCTION Molecular modeling has gained increasing importance in recent years for predicting important structural properties of large biomolecular systems such as RNA which play a critical role in various biological processes. Given the complexity of biopolymers and their interactions within living organisms, efficient and adaptive multiscale modeling approaches are necessary if one is to reasonably perform computational studies of interest. These studies nominally involve multiple important physical phenomena occurring at different spatial and temporal scales. These systems are typically characterized by large number of degrees of freedom O(10 3 ) − O(10 7 ). The temporal domains range from subfemto seconds (O(10 −16 )) associated with the small high frequency oscillations of individual tightly bonded atoms to milliseconds (O(10 −3 )) or greater for the larger scale conformational motion. The traditional approach for molecular modeling involved fully atomistic models which results in fully decoupled equations of motion. The problems with this approach are well documented in literature. One promising alternative approach for molecular modeling is to treat groups of atoms as rigid or flexible bodies connected via kinematic joints. This results in an articulated multibody representation of the biomolecular system. The coarse grain structure used to model a particular molecular system is usually knowledge based. For larger systems, often a finest coarse grain structure is used for simulation. For most systems of interest, these coarse grained models are still prohibitively slow. Conse
SubstructuredMolecular Dynamics usingMultibodyDynamics Algorithms
"... This paper presents results obtained from simulating several biomolecular and bulk materials using multibody dynamics algorithms. The systems studied include bulk water, alkane chains, alanine dipeptide and carboxyl terminal fragments of calmodulin, ribosomal protein, and rhodopsin. The atomistic re ..."
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This paper presents results obtained from simulating several biomolecular and bulk materials using multibody dynamics algorithms. The systems studied include bulk water, alkane chains, alanine dipeptide and carboxyl terminal fragments of calmodulin, ribosomal protein, and rhodopsin. The atomistic representations of these systems include several thousand degrees of freedom and the results of nanosecond long simulations of several of these systems are presented. The stability and validity of the simulations are studied through conservation of energy, thermodynamics properties and conformational analysis. In these simulations, a speed up of an order of magnitude is realized for conservative error bounds with a fixed time step integration scheme. A discussion is presented on the opensource software developed to facilitate future research using multibody dynamics with molecular dynamics.