brownian dynamics
Recently Published Documents


TOTAL DOCUMENTS

1497
(FIVE YEARS 188)

H-INDEX

73
(FIVE YEARS 6)

Soft Matter ◽  
2022 ◽  
Author(s):  
Chen Shen ◽  
chaoran qin ◽  
Tian-liang Xu ◽  
Kang Chen ◽  
Wen-De Tian

Structure and dynamics of a driven polymer on a smooth cylindrical surface are studied by Brownian dynamics simulations. The effect of driven force on the polymer adsorption behavior and the...


Soft Matter ◽  
2022 ◽  
Author(s):  
Kevin S. Silmore ◽  
Michael Strano ◽  
James W. Swan

We perform Brownian dynamics simulations of semiflexible colloidal sheets with hydrodynamic interactions and thermal fluctuations in shear flow. As a function of the ratio of bending rigidity to shear energy...


Soft Matter ◽  
2022 ◽  
Author(s):  
Bryce Palmer ◽  
Sheng Chen ◽  
Patrick Govan ◽  
Wen Yan ◽  
Tong Gao

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...


2021 ◽  
Author(s):  
Debabrata Dey ◽  
Ariane Nunes-Alves ◽  
Rebecca C. Wade ◽  
Gideon Schreiber

Crowded environments affect the pharmacokinetics of drug molecules. Here, we investigate how three macromolecular protein crowders, bovine serum albumin, hen egg-white lysozyme and myoglobin, influence the translational diffusion rates and interactions of four low molecular-weight drugs, fluorescein, doxorubicin, glycogen synthase kinase-3 inhibitor SB216763 and quinacrine. Using Fluorescence Recovery After Photo-bleaching in Line mode (Line FRAP), Brownian dynamics simulations and molecular docking, we find that the diffusive behavior of the small molecules is highly affected by self-aggregation, interactions with the proteins, and surface adhesion. Fluorescein diffusion is decreased by protein crowders due to their interactions. On the other hand, for doxorubicin, the presence of protein crowders increases diffusion by reducing surface interactions. SB216763 shows a third scenario, where BSA, but not myoglobin or lysozyme, reduces self-aggregation, resulting in faster diffusion. Quinacrine was the only small molecule whose diffusion was not affected by the presence of protein crowders. The mechanistic insights gained here into the effects of interactions of small molecules with proteins and surfaces on the translational diffusion of small molecules can assist in optimizing the design of compounds for higher mobility and lower occlusion in complex macromolecular environments.


Author(s):  
Angbo Fang

Abstract The recently proposed dynamical effective field model (DEFM) is quantitatively accurate for ferrofluid dynamics. It is derived in paper I within the framework of dynamical density functional theory (DDFT) along with a phenomenological description of nonadiabatic effects. However, it remains to clarify how the characteristic rotational relaxation time of a dressed particle, denoted by τr, is quantitatively related to that of a bare particle, denoted by τr0. By building macro-micro connections via two different routes, I reveal that under some gentle assumptions τr can be identified with the mean time characterizing long-time rotational self-diffusion. I further introduce two simple but useful integrated correlation factors, describing the effects of quasi-static (adiabatic) and dynamic (nonadiabatic) inter-particle correlations, respectively. In terms of both the dynamic magnetic susceptibility is expressed in an illuminating and elegant form. Remarkably, it shows that the macro-micro connection is established via two successive steps: a dynamical coarse-graining with nonadiabatic effects accounted for by the dynamic factor, followed by equilibrium ensemble averaging captured by the static factor. By analyzing data from Brownian dynamics simulations on monodisperse interacting ferrofluids, I find τr/τr0 is, somehow unexpectedly, insensitive to changes of particle volume fraction. A physical picture is proposed to explain it. Furthermore, an empirical formula is proposed to characterize the dependence of τr/τr0 on dipole-dipole interaction strength. The DEFM supplemented with this formula leads to parameter-free predictions in good agreement with results from Brownian dynamics simulations. The theoretical developments presented in this paper may have important consequences to studies of ferrofluid dynamics in particular and other systems modelled by DDFTs in general.


2021 ◽  
Author(s):  
Aykut Argun ◽  
Agnese Callegari ◽  
Giovanni Volpe
Keyword(s):  

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Christina Kurzthaler ◽  
Suvendu Mandal ◽  
Tapomoy Bhattacharjee ◽  
Hartmut Löwen ◽  
Sujit S. Datta ◽  
...  

AbstractEfficient navigation through disordered, porous environments poses a major challenge for swimming microorganisms and future synthetic cargo-carriers. We perform Brownian dynamics simulations of active stiff polymers undergoing run-reverse dynamics, and so mimic bacterial swimming, in porous media. In accord with experiments of Escherichia coli, the polymer dynamics are characterized by trapping phases interrupted by directed hopping motion through the pores. Our findings show that the spreading of active agents in porous media can be optimized by tuning their run lengths, which we rationalize using a coarse-grained model. More significantly, we discover a geometric criterion for the optimal spreading, which emerges when their run lengths are comparable to the longest straight path available in the porous medium. Our criterion unifies results for porous media with disparate pore sizes and shapes and for run-and-tumble polymers. It thus provides a fundamental principle for optimal transport of active agents in densely-packed biological and environmental settings.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mahmoud Sebtosheikh ◽  
Ali Naji

AbstractUsing Brownian Dynamics simulations, we study effective interactions mediated between two identical and impermeable disks (inclusions) immersed in a bath of identical, active (self-propelled), Brownian rods in two spatial dimensions, by assuming that the self-propulsion axis of the rods may generally deviate from their longitudinal axis. When the self-propulsion is transverse (perpendicular to the rod axis), the accumulation of active rods around the inclusions is significantly enhanced, causing a more expansive steric layering (ring formation) of the rods around the inclusions, as compared with the reference case of longitudinally self-propelling rods. As a result, the transversally self-propelling rods also mediate a significantly longer ranged effective interaction between the inclusions. The bath-mediated interaction arises due to the overlaps between the active-rod rings formed around the inclusions, as they are brought into small separations. When the self-propulsion axis is tilted relative to the rod axis, we find an asymmetric imbalance of active-rod accumulation around the inclusion dimer. This leads to a noncentral interaction, featuring an anti-parallel pair of transverse force components and, hence, a bath-mediated torque on the dimer.


Sign in / Sign up

Export Citation Format

Share Document