scholarly journals Large scale Brownian dynamics of confined suspensions of rigid particles

2017 ◽  
Vol 147 (24) ◽  
pp. 244103 ◽  
Author(s):  
Brennan Sprinkle ◽  
Florencio Balboa Usabiaga ◽  
Neelesh A. Patankar ◽  
Aleksandar Donev
Keyword(s):  
Brownian Dynamics ◽  
Large Scale ◽  
Rigid Particles ◽  
Confined Suspensions

scholarly journals Brownian dynamics of fully confined suspensions of rigid particles without Green’s functions

2019 ◽  
Vol 150 (16) ◽  
pp. 164116 ◽  
Author(s):  
Brennan Sprinkle ◽  
Aleksandar Donev ◽  
Amneet Pal Singh Bhalla ◽  
Neelesh Patankar
Keyword(s):  
Brownian Dynamics ◽  
Green's Functions ◽  
Green’S Functions ◽  
Rigid Particles ◽  
Confined Suspensions

scholarly journals Brownian dynamics of rigid particles in an incompressible fluctuating fluid by a meshfree method

2016 ◽  
Vol 127 ◽  
pp. 174-181 ◽  
Author(s):  
Anamika Pandey ◽  
Steffen Hardt ◽  
Axel Klar ◽  
Sudarshan Tiwari
Keyword(s):  
Brownian Dynamics ◽  
Meshfree Method ◽  
Rigid Particles

scholarly journals Ephemeral protein binding to DNA shapes stable nuclear bodies and chromatin domains

2016 ◽  
Author(s):  
C. A. Brackley ◽  
B. Liebchen ◽  
D. Michieletto ◽  
F. Mouvet ◽  
P. R. Cook ◽  
...  
Keyword(s):  
Dna Binding ◽  
Self Assembly ◽  
Brownian Dynamics ◽  
Large Scale ◽  
Nuclear Bodies ◽  
Underlying Structure ◽  
Post Translational Modification ◽  
Equilibrium Process ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations

AbstractFluorescence microscopy reveals that the contents of many (membrane-free) nuclear “bodies” exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To shed light on this, we perform large-scale Brownian dynamics simulations of a chromatin fiber interacting with an ensemble of (multivalent) DNA-binding proteins; these proteins switch between two states – active (binding) and inactive (non-binding). This system provides a model for any DNA-binding protein that can be modified post-translationally to change its affinity for DNA (e.g., like the phosphorylation of a transcription factor). Due to this out-of-equilibrium process, proteins spontaneously assemble into clusters of self-limiting size, as individual proteins in a cluster exchange with the soluble pool with kinetics like those seen in photo-bleaching experiments. This behavior contrasts sharply with that exhibited by “equilibrium”, or non-switching, proteins that exist only in the binding state; when these bind to DNA non-specifically, they form clusters that grow indefinitely in size. Our results point to post-translational modification of chromatin-bridging proteins as a generic mechanism driving the self-assembly of highly dynamic, non-equilibrium, protein clusters with the properties of nuclear bodies. Such active modification also reshapes intra-chromatin contacts to give networks resembling those seen in topologically-associating domains, as switching markedly favors local (short-range) contacts over distant ones.

A Theoretical Evaluation of the Backfill Effect in Fracture of Gas Pressurized Pipelines

1984 ◽  
Vol 106 (1) ◽  
pp. 47-53 ◽  
Author(s):  
G. Alpa ◽  
E. Bozzo ◽  
L. Gambarotta
Keyword(s):  
Experimental Data ◽  
Large Scale ◽  
Absorption Rate ◽  
Fracture Propagation ◽  
Simplified Model ◽  
Geometrical Parameters ◽  
Theoretical Evaluation ◽  
Rigid Particles ◽  
Pressurized Pipelines ◽  
Axial Fracture

The constraining action exerted by the soil surrounding pipelines, when an axial fracture propagates, has been analyzed through a simplified model. In order to avoid large-scale numerical computations, two main hypotheses have been assumed: (a) the deformed configuration of the fractured pipe has been considered as defined by two geometrical parameters; (b) the soil has been schematized as a cohesionless medium composed of rigid particles with friction. The energy absorption rate by soil during fracture propagation and the constraining forces on the pipe walls has been obtained as a function of the fracture speed and acceleration, of kinematic and geometric parameters and of the soil properties. Available experimental data give factors supporting the engineering evaluation of the backfill effect developed in the paper.

scholarly journals Quenching an active swarm: Effects of light exposure on collective motility in swarmingSerratia marcescenscolonies

2018 ◽  
Author(s):  
Alison E Patteson ◽  
Junyi Yang ◽  
Paulo E Arratia ◽  
Arvind Gopinath
Keyword(s):  
Brownian Dynamics ◽  
Large Scale ◽  
Light Exposure ◽  
Ultra Violet ◽  
Dynamics Model ◽  
Planktonic Bacteria ◽  
Radial Extent ◽  
Active Bacteria ◽  
Macroscopic Domain ◽  
Independent Parameters

Swarming colonies of the light responsive bacteriaSerratia marcescensgrown on agar exhibit robust fluctuating large-scale collective flows that include arrayed vortices, jets, and sinuous streamers. We study the immobilization and quenching of these large-scale flows when the moving swarm is exposed to light with a substantial ultra-violet component. We map the response to light in terms of two independent parameters - the light intensity and duration of exposure and identify the conditions under which mobility is affected significantly. For small exposure times and/or low intensities, we find collective mobility to be negligibly affected. Increasing exposure times and/or intensity to higher values temporarily suppresses collective mobility. Terminating exposure allows bacteria regain motility and eventually reestablish large scale flows. For long exposure times or at high intensities, exposed bacteria become paralyzed, with macroscopic speeds eventually reducing to zero. In this process, they form highly aligned, jammed domains. Individual domains eventually coalesce into a large macroscopic domain with mean radial extent growing as the square root of exposure time. Post exposure, active bacteria dislodge exposed bacteria from these jammed configurations; initial dissolution rates are found to be strongly dependent on duration of exposure suggesting that caging effects are substantial at higher exposure times. Based on our experimental observations, we propose a minimal Brownian dynamics model to examine the escape of exposed bacteria from the region of exposure. Our results complement studies on planktonic bacteria and inform models for pattern formation in gradated illumination.

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 Brownian dynamics of confined suspensions of active microrollers

2017 ◽  
Vol 146 (13) ◽  
pp. 134104 ◽  
Author(s):  
Florencio Balboa Usabiaga ◽  
Blaise Delmotte ◽  
Aleksandar Donev
Keyword(s):  
Brownian Dynamics ◽  
Confined Suspensions

scholarly journals Quenching active swarms: effects of light exposure on collective motility in swarming Serratia marcescens

2019 ◽  
Vol 16 (156) ◽  
pp. 20180960 ◽  
Author(s):  
Junyi Yang ◽  
Paulo E. Arratia ◽  
Alison E. Patteson ◽  
Arvind Gopinath
Keyword(s):  
Serratia Marcescens ◽  
Brownian Dynamics ◽  
Large Scale ◽  
Light Exposure ◽  
Wide Spectrum ◽  
Dynamics Model ◽  
Planktonic Bacteria ◽  
Starting Point ◽  
Active Bacteria ◽  
Two Parameters

Swarming colonies of the light-responsive bacteria Serratia marcescens grown on agar exhibit robust fluctuating large-scale flows that include arrayed vortices, jets and sinuous streamers. We study the immobilization and quenching of these collective flows when the moving swarm is exposed to intense wide-spectrum light with a substantial ultraviolet component. We map the emergent response of the swarm to light in terms of two parameters—light intensity and duration of exposure—and identify the conditions under which collective motility is impacted. For small exposure times and/or low intensities, we find collective motility to be negligibly affected. Increasing exposure times and/or intensity to higher values suppresses collective motility but only temporarily. Terminating exposure allows bacteria to recover and eventually reestablish collective flows similar to that seen in unexposed swarms. For long exposure times or at high intensities, exposed bacteria become paralysed and form aligned, jammed regions where macroscopic speeds reduce to zero. The effective size of the quenched region increases with time and saturates to approximately the extent of the illuminated region. Post-exposure, active bacteria dislodge immotile bacteria; initial dissolution rates are strongly dependent on duration of exposure. Based on our experimental observations, we propose a minimal Brownian dynamics model to examine the escape of exposed bacteria from the region of exposure. Our results complement studies on planktonic bacteria, inform models of patterning in gradated illumination and provide a starting point for the study of specific wavelengths on swarming bacteria.

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