Langevin thermostat for rigid body dynamics

Davidchack, Ruslan L.; Handel, Richard; Tretyakov, Michael V.

doi:10.1063/1.3149788

Cited by 297 publications

(258 citation statements)

References 23 publications

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“…To sample equilibrium thermodynamics, we employ Virtual Move Monte Carlo (VMMC), 38,39 an efficient Monte Carlo algorithm which moves clusters of interacting particles. For kinetic results, we use the rigid-body Langevin Dynamics (LD) algorithm of Davidchack et al 40 Langevin algo-rithms both reproduce the diffusive motion of particles and sample from the equilibrium ensemble.…”

Section: Methodsmentioning

confidence: 99%

Optimizing DNA Nanotechnology through Coarse-Grained Modeling: A Two-Footed DNA Walker

et al. 2013

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DNA has enormous potential as a programmable material for creating artificial nanoscale structures and devices. For more complex systems, however, rational design and optimization can become difficult. We have recently proposed a coarse-grained model of DNA that captures the basic thermodynamic, structural and mechanical changes associated with the fundamental process in much of DNA nanotechnology, the formation of duplexes from single strands.In this article we demonstrate that the model can provide powerful insight into the operation of complex nanotechnological systems through a detailed investigation of a two-footed DNA

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Section: Methodsmentioning

confidence: 99%

Optimizing DNA Nanotechnology through Coarse-Grained Modeling: A Two-Footed DNA Walker

et al. 2013

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“…For oxDNA, thermodynamic averages are typically calculated using the Virtual Move Monte Carlo (VMMC) algorithm. 162,194 Dynamical studies reported in this work use a Langevin Dynamics (LD) algorithm for rigid bodies, 163 which samples from the Boltzmann distribution and generates diffusive particle motion.…”

Section: Discussionmentioning

confidence: 99%

“…These forces are chosen so that particles move diffusively and the system samples from the Boltzmann distribution. The kinetic results reported in this work were obtained using the quaternion-based algorithm for rigid bodies of Davidchack et al 163 Other work on oxDNA has been performed with an Andersen-like thermostat.…”

Section: Langevin Dynamicsmentioning

confidence: 99%

DNA nanotechnology: understanding and optimisation through simulation

Ouldridge

2014

Molecular Physics

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DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article I review the state-of-the art of DNA nanotechnology, highlighting the need for a more detailed understanding of the key processes, both in terms of theoretical modelling and experimental characterisation. I then consider coarse-grained models of DNA, mesoscale descriptions that have the potential to provide great insight into the operation of DNA nanotechnology if they are well designed. In particular, I discuss a number of nanotechnological systems that have been studied with oxDNA, a recently developed coarse-grained model, highlighting the subtle interplay of kinetic, thermodynamic and mechanical factors that can determine behaviour. Finally, new results highlighting the importance of mechanical tension in the operation of a two-footed walker are presented, demonstrating that recovery from an unintended 'overstepped' configuration can be accelerated by three to four orders of magnitude by application of a moderate tension to the walker's track. More generally, the walker illustrates the possibility of biasing strand-displacement processes to affect the overall rate.

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“…This model treats some parts of polymer as rigid bodies and phenomenologically introduces the effects of ignored degrees of freedom by the friction and fluctuation terms. Numerical efficiencies have been investigated for some rigid body Langevin simulations [3,4,10]. The mathematical formal structure of Eq.…”

Section: Analyses Of Coarse Grained Equation Of Motion For Systems Hamentioning

confidence: 99%

“…Recent interests are mainly focused on the simulation procedure which is efficient to reach equilibrium condition by introducing the effects of thermal bath. The Langevin-type equations of motion can be accepted as an efficient and stable method for finding thermal equilibrium in the atomistic molecular dynamics simulations [3,4]. Unfortunately most of all the previous numerical studies like ones mentioned above are based on the phenomenologically introduced equation of motions and then the bases of the theoretical backgrounds are not sufficient for constructing the multiscale-simulation procedures for inhomogeneous structured materials.…”

Section: Introductionmentioning

confidence: 98%

Coarse-grained equation of motion for many particle system containing internal degrees of freedom

Hyodo

2011

Japan J. Indust. Appl. Math.

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In order to numerically investigate dynamics in large and complicated systems, it is important to derive the explicit equation of motion of an extracted tagged degree of freedom under the statistical influence of the other parts. This corresponds to adopting the procedure usually called "coarse-graining". Up-to-now, many kinds of coarse grained (CG) simulation method have been proposed based on phenomenological equations of motion and investigated about their numerical efficiencies for practical applications. We can now investigate a dynamics of appropriate degrees of freedom, i.e., the center of mass, the orientation, the internal vibration modes, etc. of CG particles, for suitably chosen characteristics in a system. Although each of the phenomenological CG methods is well established for practical usages, it is still not sufficient to construct a multiscale simulation procedure for large and complicated systems. Some explicit relation between the coarser and finer descriptions should be grasped for deducing the CG expression based on atomistic pictures. Although Langevin equation, a typical CG equation of motion, has been derived from an atomistic equation of motion in previous literatures, most of these descriptions are limited within the equation of center-of-mass motions. In the present study, a microscopic description for arbitrarily extracted degree(s) of freedom was derived by restricting the system of CG particles constructed by tightly bounded finer particles, like polyatomic molecules. The derived equation of motion was shown to be applicable to dynamics simulation of reorientation and/or internal vibration motions of CG-particle systems by analyses of the equation for realistic conditions.

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Langevin thermostat for rigid body dynamics

Cited by 297 publications

References 23 publications

Optimizing DNA Nanotechnology through Coarse-Grained Modeling: A Two-Footed DNA Walker

Optimizing DNA Nanotechnology through Coarse-Grained Modeling: A Two-Footed DNA Walker

DNA nanotechnology: understanding and optimisation through simulation

Coarse-grained equation of motion for many particle system containing internal degrees of freedom

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