scholarly journals Effect of chromatin flexibility on diffusive loop extrusion via molecular slip-links

2018 ◽  
Author(s):  
C. A. Brackley ◽  
J. Johnson ◽  
D. Michieletto ◽  
D. Marenduzzo
Keyword(s):  
Physical Properties ◽  
Brownian Dynamics ◽  
Dynamical Process ◽  
Base Pairs ◽  
Chromatin Fibre ◽  
Chromatin Loops ◽  
Eukaryotic Chromatin ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations

AbstractWe use Brownian dynamics simulations to study the formation of chromatin loops through diffusive sliding of molecular slip links, mimicking the behaviour of cohesin-like molecules. We recently proposed that diffusive sliding is sufficient to explain the extrusion of chromatin loops of hundreds of kilo-base-pairs (kbp), which may then be stabilised by interactions between cohesin and CTCF proteins. Here we show that the elasticity of the chromatin fibre strongly affects this dynamical process, and find that diffusive loop extrusion is more efficient on stiffer chromatin regions. Efficiency is also enhanced if cohesin loading sites are close to regions where CTCF is bound. In light of the heterogeneous physical properties of eukaryotic chromatin, we suggest that our results should be relevant to the looping and organisation of interphase chromosomes in vivo.

Understanding Topological Defects in Fluidized Dry Active Nematics

Soft Matter ◽  
2022 ◽  
Author(s):  
Bryce Palmer ◽  
Sheng Chen ◽  
Patrick Govan ◽  
Wen Yan ◽  
Tong Gao
Keyword(s):  
Physical Properties ◽  
Brownian Dynamics ◽  
Large Scale ◽  
Topological Defects ◽  
Collective Behaviors ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations

Dense assemblies of self-propelling rods (SPRs) may exhibit fascinating collective behaviors and anomalous physical properties that are far away from equilibrium. Using large-scale Brownian dynamics simulations, we investigate the dynamics...

scholarly journals Magnetic Polymer Models for Epigenetics-Driven Chromosome Folding

2019 ◽  
Author(s):  
Davide Coli ◽  
Davide Michieletto ◽  
Davide Marenduzzo ◽  
Enzo Orlandini
Keyword(s):  
Brownian Dynamics ◽  
Regulatory Networks ◽  
Mean Field ◽  
Thermal Fluctuations ◽  
First Order Phase Transition ◽  
Polymer Models ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations ◽  
First Order Phase

Epigenetics is a driving force of important and ubiquitous phenomena in nature such as cell differentiation or even metamorphosis. Oppositely to its widespread role, understanding the biophysical principles that allow epigenetics to control and rewire gene regulatory networks remains an open challenge. In this work we study the effects of epigenetic modifications on the spatial folding of chromosomes -- and hence on the expression of the underlying genes -- by mapping the problem to a class of models known as magnetic polymers. In this work we show that a first order phase transition underlies the simultaneous spreading of certain epigenetic marks and the conformational collapse of a chromosome. Further, we describe Brownian Dynamics simulations of the model in which the topology of the polymer and thermal fluctuations are fully taken into account and that confirm our mean field predictions. Extending our models to allow for non-equilibrium terms yields new stable phases which qualitatively agrees with observations in vivo. Our results show that statistical mechanics techniques applied to models of magnetic polymers can be successfully exploited to rationalize the outcomes of experiments designed to probe the interplay between a dynamic epigenetic landscape and chromatin organization.

Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach

2018 ◽  
Author(s):  
Benjamin R. Jagger ◽  
Christoper T. Lee ◽  
Rommie Amaro
Keyword(s):  
Molecular Dynamics ◽  
Drug Discovery ◽  
Small Molecule ◽  
Brownian Dynamics ◽  
Model Simulation ◽  
Computational Cost ◽  
Lead Selection ◽  
Delta G ◽  
Dynamics Simulations

<p>The ranking of small molecule binders by their kinetic (kon and koff) and thermodynamic (delta G) properties can be a valuable metric for lead selection and optimization in a drug discovery campaign, as these quantities are often indicators of in vivo efficacy. Efficient and accurate predictions of these quantities can aid the in drug discovery effort, acting as a screening step. We have previously described a hybrid molecular dynamics, Brownian dynamics, and milestoning model, Simulation Enabled Estimation of Kinetic Rates (SEEKR), that can predict kon’s, koff’s, and G’s. Here we demonstrate the effectiveness of this approach for ranking a series of seven small molecule compounds for the model system, -cyclodextrin, based on predicted kon’s and koff’s. We compare our results using SEEKR to experimentally determined rates as well as rates calculated using long-timescale molecular dynamics simulations and show that SEEKR can effectively rank the compounds by koff and G with reduced computational cost. We also provide a discussion of convergence properties and sensitivities of calculations with SEEKR to establish “best practices” for its future use.</p>

scholarly journals Structure evolution of suspensions under time-dependent electric or magnetic field

2021 ◽  
Author(s):  
Konstantinos Manikas ◽  
Markus Hütter ◽  
Patrick D. Anderson
Keyword(s):  
Magnetic Field ◽  
Field Strength ◽  
Brownian Dynamics ◽  
Thermal Fluctuations ◽  
Time Dependent ◽  
Structure Evolution ◽  
Strength Increase ◽  
Large Rotation ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations

AbstractThe effect of time-dependent external fields on the structures formed by particles with induced dipoles dispersed in a viscous fluid is investigated by means of Brownian Dynamics simulations. The physical effects accounted for are thermal fluctuations, dipole-dipole and excluded volume interactions. The emerging structures are characterised in terms of particle clusters (orientation, size, anisotropy and percolation) and network structure. The strength of the external field is increased in one direction and then kept constant for a certain amount of time, with the structure formation being influenced by the slope of the field-strength increase. This effect can be partially rationalized by inhomogeneous time re-scaling with respect to the field strength, however, the presence of thermal fluctuations makes the scaling at low field strength inappropriate. After the re-scaling, one can observe that the lower the slope of the field increase, the more network-like and the thicker the structure is. In the second part of the study the field is also rotated instantaneously by a certain angle, and the effect of this transition on the structure is studied. For small rotation angles ($$\theta \le 20^{{\circ }}$$ θ ≤ 20 ∘ ) the clusters rotate but stay largely intact, while for large rotation angles ($$\theta \ge 80^{{\circ }}$$ θ ≥ 80 ∘ ) the structure disintegrates and then reforms, due to the nature of the interactions (parallel dipoles with perpendicular inter-particle vector repel each other). For intermediate angles ($$20<\theta <80^{{\circ }}$$ 20 < θ < 80 ∘ ), it seems that, during rotation, the structure is altered towards a more network-like state, as a result of cluster fusion (larger clusters). The details provided in this paper concern an electric field, however, all results can be projected into the case of a magnetic field and paramagnetic particles.

scholarly journals Influence of size polydispersity on magnetic field tunable structures in magnetic nanofluids containing superparamagnetic nanoparticles.

2021 ◽  
Author(s):  
Dillip Kumar Mohapatra ◽  
Philip James Camp ◽  
John Philip
Keyword(s):  
Magnetic Field ◽  
Particle Size ◽  
Light Scattering ◽  
Optical Microscopy ◽  
Brownian Dynamics ◽  
Phase Contrast ◽  
Superparamagnetic Nanoparticles ◽  
Magnetic Nanofluids ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations

We probe the influence of particle size polydispersity on field-induced structures and structural transitions in magnetic fluids (ferrofluids) using phase contrast optical microscopy, light scattering and Brownian dynamics simulations. Three...

scholarly journals Hard discs under steady shear: comparison of Brownian dynamics simulations and mode coupling theory

2009 ◽  
Vol 367 (1909) ◽  
pp. 5033-5050 ◽  
Author(s):  
Oliver Henrich ◽  
Fabian Weysser ◽  
Michael E. Cates ◽  
Matthias Fuchs
Keyword(s):  
Brownian Dynamics ◽  
Mode Coupling ◽  
Transition Density ◽  
Two Dimensions ◽  
Coupling Theory ◽  
Mode Coupling Theory ◽  
Stationary Structure ◽  
Homogeneous Shear Flow ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations

Brownian dynamics simulations of bidisperse hard discs moving in two dimensions in a given steady and homogeneous shear flow are presented close to and above the glass transition density. The stationary structure functions and stresses of shear-melted glass are compared quantitatively to parameter-free numerical calculations of monodisperse hard discs using mode coupling theory within the integration through transients framework. Theory qualitatively explains the properties of the yielding glass but quantitatively overestimates the shear-driven stresses and structural anisotropies.

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