Brownian dynamics

Author(s):  
Aykut Argun ◽  
Agnese Callegari ◽  
Giovanni Volpe
Keyword(s):  
1998 ◽  
Vol 94 (3) ◽  
pp. 447-454 ◽  
Author(s):  
D.M. HEYES ◽  
A.C. BRANKA

2018 ◽  
Author(s):  
Benjamin R. Jagger ◽  
Christoper T. Lee ◽  
Rommie Amaro

<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>


2019 ◽  
Vol 150 (16) ◽  
pp. 164116 ◽  
Author(s):  
Brennan Sprinkle ◽  
Aleksandar Donev ◽  
Amneet Pal Singh Bhalla ◽  
Neelesh Patankar

2012 ◽  
Vol 45 (19) ◽  
pp. 8109-8116 ◽  
Author(s):  
Brandon L. Peters ◽  
Abelardo Ramírez-Hernández ◽  
Darin Q. Pike ◽  
Marcus Müller ◽  
Juan J. de Pablo

Soft Matter ◽  
2021 ◽  
Author(s):  
Michael Bley ◽  
Joachim Dzubiella ◽  
Arturo Moncho Jorda

We employ reactive dynamical density functional theory (R-DDFT) and reactive Brownian dynamics (R-BD) simulations to study the non-equilibrium structure and phase behavior of an active dispersion of soft Gaussian colloids...


Author(s):  
Konstantinos Manikas ◽  
Markus Hütter ◽  
Patrick D. Anderson

AbstractThe effect of time-dependent external fields on the structures formed by particles with induced dipoles dispersed in a viscous fluid is investigated by means of Brownian Dynamics simulations. The physical effects accounted for are thermal fluctuations, dipole-dipole and excluded volume interactions. The emerging structures are characterised in terms of particle clusters (orientation, size, anisotropy and percolation) and network structure. The strength of the external field is increased in one direction and then kept constant for a certain amount of time, with the structure formation being influenced by the slope of the field-strength increase. This effect can be partially rationalized by inhomogeneous time re-scaling with respect to the field strength, however, the presence of thermal fluctuations makes the scaling at low field strength inappropriate. After the re-scaling, one can observe that the lower the slope of the field increase, the more network-like and the thicker the structure is. In the second part of the study the field is also rotated instantaneously by a certain angle, and the effect of this transition on the structure is studied. For small rotation angles ($$\theta \le 20^{{\circ }}$$ θ ≤ 20 ∘ ) the clusters rotate but stay largely intact, while for large rotation angles ($$\theta \ge 80^{{\circ }}$$ θ ≥ 80 ∘ ) the structure disintegrates and then reforms, due to the nature of the interactions (parallel dipoles with perpendicular inter-particle vector repel each other). For intermediate angles ($$20<\theta <80^{{\circ }}$$ 20 < θ < 80 ∘ ), it seems that, during rotation, the structure is altered towards a more network-like state, as a result of cluster fusion (larger clusters). The details provided in this paper concern an electric field, however, all results can be projected into the case of a magnetic field and paramagnetic particles.


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