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 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 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

Monte Carlo as Brownian dynamics

1998 ◽  
Vol 94 (3) ◽  
pp. 447-454 ◽  
Author(s):  
D.M. HEYES ◽  
A.C. BRANKA
Keyword(s):  
Monte Carlo ◽  
Brownian Dynamics

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 Dynamics of confined suspensions of swimming particles

2009 ◽  
Vol 21 (20) ◽  
pp. 204107 ◽  
Author(s):  
Juan P Hernandez-Ortiz ◽  
Patrick T Underhill ◽  
Michael D Graham
Keyword(s):  
Confined Suspensions

scholarly journals Untangling superposed double layer and structural forces across confined nanoparticle suspensions

2021 ◽  
Author(s):  
Michael Ludwig ◽  
Regine von Klitzing
Keyword(s):  
Double Layer ◽  
Interaction Force ◽  
Charged Surfaces ◽  
Structural Forces ◽  
Nanoparticle Suspensions ◽  
Confined Suspensions ◽  
Force Profiles

Complete interaction force profiles of charged surfaces across confined suspensions were successfully described using a superposition of double layer and structural forces.

Nonequilibrium Simulations of Lamellae Forming Block Copolymers under Steady Shear: A Comparison of Dissipative Particle Dynamics and Brownian Dynamics

2012 ◽  
Vol 45 (19) ◽  
pp. 8109-8116 ◽  
Author(s):  
Brandon L. Peters ◽  
Abelardo Ramírez-Hernández ◽  
Darin Q. Pike ◽  
Marcus Müller ◽  
Juan J. de Pablo
Keyword(s):  
Block Copolymers ◽  
Brownian Dynamics ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
Steady Shear
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