Brownian dynamics simulations of biological molecules

GA Huber, JA McCammon - Trends in chemistry, 2019 - cell.com
Brownian dynamics (BD) is a technique for carrying out computer simulations of physical
systems that are driven by thermal fluctuations. Biological systems at the macromolecular …

[HTML][HTML] The physics of active polymers and filaments

RG Winkler, G Gompper - The journal of chemical physics, 2020 - pubs.aip.org
Active matter agents consume internal energy or extract energy from the environment for
locomotion and force generation. Already, rather generic models, such as ensembles of …

Tangentially driven active polar linear polymers—An analytical study

CA Philipps, G Gompper, RG Winkler - The Journal of Chemical …, 2022 - pubs.aip.org
The conformational and dynamical properties of isolated flexible active polar linear polymers
(APLPs) are studied analytically. The APLPs are modeled as Gaussian bead-spring linear …

Collective dynamics of self-propelled semiflexible filaments

Ö Duman, RE Isele-Holder, J Elgeti, G Gompper - Soft matter, 2018 - pubs.rsc.org
The collective behavior of active semiflexible filaments is studied with a model of tangentially
driven self-propelled worm-like chains. The combination of excluded-volume interactions …

Dynamics of active polar ring polymers

CA Philipps, G Gompper, RG Winkler - Physical Review E, 2022 - APS
The conformational and dynamical properties of isolated semiflexible active polar ring
polymers are investigated analytically. A ring is modeled as a continuous Gaussian polymer …

Constrained motion of self-propelling eccentric disks linked by a spring

T Xu, C Qin, B Tang, J Gao, J Zhou, K Chen… - The Journal of …, 2024 - pubs.aip.org
It has been supposed that the interplay of elasticity and activity plays a key role in triggering
the non-equilibrium behaviors in biological systems. However, the experimental model …

Density and inertia effects on two-dimensional active semiflexible filament suspensions

G Janzen, DA Matoz-Fernandez - Soft Matter, 2024 - pubs.rsc.org
We examine the influence of density on the transition between chain and spiral structures in
planar assemblies of active semiflexible filaments, utilizing detailed numerical simulations …

Active Brownian ring polymers

SM Mousavi, G Gompper, RG Winkler - The Journal of chemical …, 2019 - pubs.aip.org
The conformational and dynamical properties of semiflexible active Brownian ring polymers
are investigated analytically. A ring is described by the Gaussian semiflexible polymer …

Non-equilibrium effects of molecular motors on polymers

M Foglino, E Locatelli, CA Brackley, D Michieletto… - Soft matter, 2019 - pubs.rsc.org
We present a generic coarse-grained model to describe molecular motors acting on polymer
substrates, mimicking, for example, RNA polymerase on DNA or kinesin on microtubules …

Local polar and long-range isotropic activity assisted swelling and collapse dynamics of an active ring polymer

S Kumar, S Thakur - Macromolecules, 2023 - ACS Publications
The circular and ring structures in many synthetic or natural systems simultaneously
experience local and long-range forces. In this work, we use numerical simulations to …