Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions

SE Farr, EJ Woods, JA Joseph, A Garaizar… - Nature …, 2021 - nature.com
Liquid–liquid phase separation (LLPS) is an important mechanism that helps explain the
membraneless compartmentalization of the nucleus. Because chromatin compaction and …

Molecular simulation of liquid crystals

MP Allen - Molecular Physics, 2019 - Taylor & Francis
This article reviews recent progress in the computer simulation of liquid crystals at the
molecular level. It covers the use of simple rigid-body models of the constituent molecules …

How to simulate patchy particles

L Rovigatti, J Russo, F Romano - The European Physical Journal E, 2018 - Springer
Patchy particles is the name given to a large class of systems of mesoscopic particles
characterized by a repulsive core and a discrete number of short-range and highly …

Diffusion and spatial correlations in suspensions of swimming particles

PT Underhill, JP Hernandez-Ortiz, MD Graham - Physical review letters, 2008 - APS
Populations of swimming micro-organisms produce fluid motions that lead to dramatically
enhanced diffusion of tracer particles. Using simulations of suspensions of swimming …

Dynamics of confined suspensions of swimming particles

JP Hernandez-Ortiz, PT Underhill… - Journal of Physics …, 2009 - iopscience.iop.org
Low Reynolds number direct simulations of large populations of hydrodynamically
interacting swimming particles confined between planar walls are performed. The results of …

Coarse-grained simulation of DNA using LAMMPS: An implementation of the oxDNA model and its applications

O Henrich, YA Gutiérrez Fosado, T Curk… - The European Physical …, 2018 - Springer
During the last decade coarse-grained nucleotide models have emerged that allow us to
study DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a …

Mechanisms of chromosome biorientation and bipolar spindle assembly analyzed by computational modeling

C Edelmaier, AR Lamson, ZR Gergely, S Ansari… - Elife, 2020 - elifesciences.org
The essential functions required for mitotic spindle assembly and chromosome biorientation
and segregation are not fully understood, despite extensive study. To illuminate the …

Field response and switching times in biaxial nematics

R Berardi, L Muccioli, C Zannoni - The Journal of chemical physics, 2008 - pubs.aip.org
We study by means of virtual molecular dynamics computer experiments the response of a
bulk biaxial nematic to an applied external field and, in particular, the relative speed of …

Systematic bottom-up molecular coarse-graining via force and torque matching using anisotropic particles

HTL Nguyen, DM Huang - The Journal of Chemical Physics, 2022 - pubs.aip.org
We derive a systematic and general method for parameterizing coarse-grained molecular
models consisting of anisotropic particles from fine-grained (eg, all-atom) models for …

Liquid crystal nanodroplets in solution

WM Brown, MK Petersen, SJ Plimpton… - The Journal of chemical …, 2009 - pubs.aip.org
The aggregation of liquid crystal nanodroplets from a homogeneous solution is studied by
molecular dynamics simulations. The liquid crystal particles are modeled as elongated …