Multi-resolution dimer models in heat baths with short-range and long-range interactions

Gunaratne, Ravinda; Wilson, Daniel B.; Flegg, Mark B.; Erban, Radek

doi:10.1098/rsfs.2018.0070

Cited by 4 publications

(3 citation statements)

References 82 publications

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“…The advantage of the presented approach is that we can directly replace the linear model by equations (2)-(5) in multiscale methods which use all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain. Coupling MD and BD models is a possible approach to incorporate atomic-level information into models of intracellular processses which include transport of molecules between different parts of the cell (Erban, 2014(Erban, , 2016Gunaratne et al, 2019). The nonlinear SCG model (2)-(5) is studied in Section 4 for N = 1.…”

Section: Discussionmentioning

confidence: 99%

Coarse-graining molecular dynamics: stochastic models with non-Gaussian force distributions

Erban

2019

J. Math. Biol.

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Dedicated to Professor Hans Othmer on the occasion of his 75th birthday.Abstract Incorporating atomistic and molecular information into models of cellular behaviour is challenging because of a vast separation of spatial and temporal scales between processes happening at the atomic and cellular levels. Multiscale or multi-resolution methodologies address this difficulty by using molecular dynamics (MD) and coarse-grained models in different parts of the cell. Their applicability depends on the accuracy and properties of the coarsegrained model which approximates the detailed MD description. A family of stochastic coarse-grained (SCG) models, written as relatively low-dimensional systems of nonlinear stochastic differential equations, is presented. The nonlinear SCG model incorporates the non-Gaussian force distribution which is observed in MD simulations and which cannot be described by linear models. It is shown that the nonlinearities can be chosen in such a way that they do not complicate parametrization of the SCG description by detailed MD simulations. The solution of the SCG model is found in terms of gamma functions.

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Section: Discussionmentioning

confidence: 99%

Coarse-graining molecular dynamics: stochastic models with non-Gaussian force distributions

Erban

2019

J. Math. Biol.

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“…24,25 Multi-resolution modelling has also been used in the literature to coarsegrain the description of the solvent in the parts of computational domain, which is relatively far from the biological structure of interest, [26][27][28] and for replacing the explicit solvent representation in parts of the domain by a stochastic coarse-grained model, which describes the solvent implicitly. [29][30][31] To obtain multi-resolution methods with mutually consistent microscopic and macroscopic models, the parameters of such stochastic coarse-grained models can be inferred from all-atom MD simulations, 31,32 by estimating effective force distributions on coarse-grained sites. [33][34][35] In this way, both microscopic and macroscopic models consistently provide quantitatively the same information at the macroscopic level, while the monomer-based model provides an additional level of detail in the parts of the simulated system which is of interest to a modeller.…”

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On Stretching, Bending, Shearing and Twisting of Actin Filaments II: Multi-Resolution Modelling

Gunaratne¹,

Floyd²,

Ni³

et al. 2022

Preprint

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We present a multi-resolution methodology for modelling F-actin filaments. It provides detailed microscopic information at the level of individual monomers at a lower computational cost by replacing the monomer-based model in parts of the simulated filament by a rod-based macroscopic model. In the monomer-based description, G-actin is represented by ellipsoids bound at the surface in a double helical configuration to form F-actin. The rod-based model is coarser, in which Factin is described using a Cosserat model, as seen in the preceding paper. 1 The multi-resolution methodology is illustrated using three case studies, designed to test the properties of F-actin under stretching, bending, shearing and twisting. The methodology is especially suited for situations where filaments are subject to bending deformations. We investigate the limitations of using the standard Cosserat model to capture the complete torsional behaviour of F-actin, presenting its extensions which account for curvature dependent rigidities and a twist-stretch coupling to improve accuracy of the overall multi-resolution scheme.

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“…Zavadlav et al [3] consider methods for coupling atomistic and supramolecular water models with applications to solvated proteins. Gunaratne et al [4] analyse this approach using two theoretical heat baths, for which one can prove the convergence of the detailed molecular dynamics model to a coarser stochastic modelling approach. They model a biomolecule at a much coarser bead-spring approach.…”

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confidence: 99%

Multi-resolution simulations of intracellular processes

2019

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Multi-resolution dimer models in heat baths with short-range and long-range interactions

Cited by 4 publications

References 82 publications

Coarse-graining molecular dynamics: stochastic models with non-Gaussian force distributions

Coarse-graining molecular dynamics: stochastic models with non-Gaussian force distributions

On Stretching, Bending, Shearing and Twisting of Actin Filaments II: Multi-Resolution Modelling

Multi-resolution simulations of intracellular processes

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