On standardised moments of force distribution in simple liquids

Utterson, Jonathan; Erban, Radek

doi:10.1039/d1cp04056a

Cited by 4 publications

(1 citation statement)

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“…[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. In addition to this 'bottom-up' approach, macroscopic models of actin filaments can also be developed by parametrising them against the available experimental data.…”

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

Gunaratne¹,

Floyd²,

Ni³

et al. 2022

Preprint

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Bulk viscosity of dilute monatomic gases revisited

Sharma

Pareek²,

Kumar

2023

European Journal of Mechanics - B/Fluids

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Langevin dynamics for a heavy particle immersed within a flow of light particles

Erban,

Van Gorder

2024

Proc. R. Soc. A.

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A micro-hydrodynamics model based on elastic collisions of light point solvent particles with a heavy solute particle is investigated in the setting where the light particles have velocity distribution corresponding to a background flow. Considering a range of stationary background flows and distributions for the solvent particle velocities, the macroscopic Langevin-type description of the behaviour of the heavy particle is derived in the form of a generalized Ornstein–Uhlenbeck process. At leading order, the drift term in this process depends upon both the geometric structure of the background flow and the size of the heavy particle, while both drift and diffusion terms scale with moments of the light particle velocity distribution. Computational methods for simulating the micro-hydrodynamics model are then designed to confirm the theoretical results. To enable long-time calculations, simulations are performed in a frame co-moving with the heavy particle. Efficient methods for sampling the position and velocity distributions of incoming solvent particles at the boundaries of the co-moving frame are derived for a range of distributions of solvent particles. The simulations show good agreement with the theoretical results.

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On standardised moments of force distribution in simple liquids

Abstract: The force distribution of a tagged atom in a Lennard-Jones fluid in the canonical ensemble is studied with a focus on its dependence on inherent physical parameters: number density (n)...

Cited by 4 publications

References 41 publications

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

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

Bulk viscosity of dilute monatomic gases revisited

Langevin dynamics for a heavy particle immersed within a flow of light particles

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