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 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

Investigating Applicability of the Meshfree Method to the Structural Analysis of Tires

2012 ◽  
Vol 40 (2) ◽  
pp. 60-82
Author(s):  
Ken Ishihara ◽  
Takehiro Noda ◽  
Hiroyuki Sakurai
Keyword(s):  
Meshfree Method ◽  
Alternative Methods ◽  
The Finite Element Method ◽  
Tire Industry ◽  
Academic Communities ◽  
The Past ◽  
New Methodologies ◽  
Tire Modeling ◽  
Point Data ◽  
Conducting Research

ABSTRACT In contrast to the finite element method (FEM), which is widely used in the tire industry nowadays, some alternative methods have been proposed by academic communities over the past decade or so. The meshfree method is one of those new methodologies. Originally intended to remove the burden of creating the mesh that is inherent in FEM, the meshfree method relies on the point data rather than the mesh, which makes it much easier to discretize the geometry. In addition to those modeling issues, it has been found that the meshfree method has several advantages over FEM in handling geometrical nonlinearities, continuities, and so forth. In accordance with those emerging possibilities, the authors have been conducting research on the matter. This article describes the results of the authors' preliminary research on the applicability of the meshfree method to tire analyses, which include the theoretical outline, the strategy of tire modeling, numerical results, comparisons with results of FEM, and conclusions.

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>

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