Self-assembly of Janus ellipsoids: a Brownian dynamics simulation with a quantitative nonspherical-particle model

Soft Matter ◽  
2015 ◽  
Vol 11 (37) ◽  
pp. 7433-7439 ◽  
Author(s):  
Jing Xu ◽  
Yali Wang ◽  
Xuehao He
Keyword(s):  
Self Assembly ◽  
Brownian Dynamics ◽  
Minimum Energy ◽  
Saddle Points ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Particle Model ◽  
Brownian Dynamics Simulation ◽  
Nonspherical Particle ◽  
Minimum Energy Paths

Three-dimensional isosurface plots of potential energy and energy curves along the minimum energy paths between saddle points of oblate Janus ellipsoids.

A mesoscopic numerical study of shear flow effects on asphaltene self-assembly behavior in organic solvents

2020 ◽  
Vol 22 (36) ◽  
pp. 20758-20770
Author(s):  
Mohammad Ahmadi ◽  
Hassan Hassanzadeh ◽  
Jalal Abedi
Keyword(s):  
Shear Flow ◽  
Organic Solvents ◽  
Self Assembly ◽  
Brownian Dynamics ◽  
Numerical Study ◽  
The Self ◽  
Dynamics Simulation ◽  
Brownian Dynamics Simulation ◽  
Assembly Behavior ◽  
Flow Effects

We employ the Brownian dynamics simulation to examine the shear flow effects on the self-assembly behavior of asphaltenes.

scholarly journals Variational implicit-solvent predictions of the dry–wet transition pathways for ligand–receptor binding and unbinding kinetics

2019 ◽  
Vol 116 (30) ◽  
pp. 14989-14994 ◽  
Author(s):  
Shenggao Zhou ◽  
R. Gregor Weiß ◽  
Li-Tien Cheng ◽  
Joachim Dzubiella ◽  
J. Andrew McCammon ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Brownian Dynamics ◽  
Minimum Energy ◽  
Planck Equation ◽  
Environmental Water ◽  
Dynamics Simulation ◽  
Implicit Solvent ◽  
Brownian Dynamics Simulation ◽  
Stochastic Motion ◽  
Solvent Model

Ligand–receptor binding and unbinding are fundamental biomolecular processes and particularly essential to drug efficacy. Environmental water fluctuations, however, impact the corresponding thermodynamics and kinetics and thereby challenge theoretical descriptions. Here, we devise a holistic, implicit-solvent, multimethod approach to predict the (un)binding kinetics for a generic ligand–pocket model. We use the variational implicit-solvent model (VISM) to calculate the solute–solvent interfacial structures and the corresponding free energies, and combine the VISM with the string method to obtain the minimum energy paths and transition states between the various metastable (“dry” and “wet”) hydration states. The resulting dry–wet transition rates are then used in a spatially dependent multistate continuous-time Markov chain Brownian dynamics simulation and the related Fokker–Planck equation calculations of the ligand stochastic motion, providing the mean first-passage times for binding and unbinding. We find the hydration transitions to significantly slow down the binding process, in semiquantitative agreement with existing explicit-water simulations, but significantly accelerate the unbinding process. Moreover, our methods allow the characterization of nonequilibrium hydration states of pocket and ligand during the ligand movement, for which we find substantial memory and hysteresis effects for binding vs. unbinding. Our study thus provides a significant step forward toward efficient, physics-based interpretation and predictions of the complex kinetics in realistic ligand–receptor systems.

Self-assembly of two-patch particles in solution: a Brownian dynamics simulation study

2013 ◽  
Vol 40 (6) ◽  
pp. 449-457 ◽  
Author(s):  
Yang Li ◽  
You-Liang Zhu ◽  
Yan-Chun Li ◽  
Hu-Jun Qian ◽  
Chia-Chung Sun
Keyword(s):  
Simulation Study ◽  
Self Assembly ◽  
Brownian Dynamics ◽  
Dynamics Simulation ◽  
Brownian Dynamics Simulation
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