Rotational Brownian Dynamics simulations of clathrin cage formation

Abstract

(2013)] has shown intriguing abilities to accurately describe potential energy surfaces in various notoriously difficult cases. The question that still remained open is to what extend the accuracy and the stability of the method is due to the special choice of orbital-relaxation treatment. In this paper we introduce orbital relaxation in terms of Brueckner orbitals, orbital optimization, and projective singles into the distinguishable cluster approximation and investigate its importance in single-and multireference cases. All three resulting methods are able to cope with many multiple-bond breaking problems, but in some difficult cases where the Hartree-Fock orbitals seem to be entirely inadequate the orbital-optimized version turns out to be superior. © 2014 AIP Publishing LLC. [http://dx

Hydrodynamics and Brownian motions of a spheroid near a rigid wall

“…Although the principles behind Eqs. (13) and (14) are well known in the literature 31 and many authors have numerically tested the drift terms, 27,30,32,39 to the best of our knowledge, this is the first time that a Langevin equation for a confined uniaxial particle is explicitly in this discretized complete form, fully embodying roto-translational coupling.…”

“…22 Many examples of numerical simulations on Brownian non-spherical particles are reported in the recent literature. Brownian dynamics simulations of unbounded suspensions of rod-like particles [23][24][25][26][27] and arbitrarily shaped particles [28][29][30] have been carried out for different volume fractions, ranging from dilute to concentrated regimes, although interparticle hydrodynamic interactions are often neglected. The inclusion of hydrodynamic interactions gives rise to "corrective terms" in the Brownian dynamics.…”

Chameleon behaviour of a-synuclein : brownian dynamics simulations of protein aggregation

“…3.3(b). For completeness a 'random' body-fixed unit vector parallel that act as rigid units, thereby opening routes to study the dynamics of their self-assembly into ordered aggregates [86]. Bonds between the particles are readily included in the interaction potential, thereby creating patchy-particle 'molecules'.…”

“…These authors did include metric and drift corrections and found that the propagator differs from the intuitively expected ∆a = (∂a/∂φ b )∆φ b [55,56,57,58,131]. This technique was recently successfully used to simulate the self-assembly of anisotropic particles into well-ordered structures [86], but it is fairly involved and requires multiple Taylor expansions to solve weak singularities.…”

“…They make excellent model systems to study and analyse the aggregation processes of various systems, such as fibrils [38], virus capsids [203] and crystals [214]. Besides experiments [20,51,103,119,128,220], patchy particles are also being studied by computer simulations [18,86,124,125,145,147,209,217,226]. Most simulations of patchy particles use Monte Carlo (MC) techniques, which rely on random trial moves in combination with acceptance-rejection rules to sample the Boltzmann probability distribution.…”