Thermodynamic consistency in the structure-based integral equation coarse-grained method

An optimal coarse-grained arc consistency algorithm

The use of constraint propagation is the main feature of any constraint solver. It is thus of prime importance to manage the propagation in an efficient and effective fashion. There are two classes of propagation algorithms for general constraints: fine-grained algorithms where the removal of a value for a variable will be propagated to the corresponding values for other variables, and coarse-g...

Exploiting Multidirectionality in Coarse-Grained Arc Consistency Algorithms

Arc consistency plays a central role in solving Constraint Satisfaction Problems. This is the reason why many algorithms have been proposed to establish it. Recently, an algorithm called AC2001 and AC3.1 has been independently presented by their authors. This algorithm which is considered as a refinement of the basic algorithm AC3 has the advantage of being simple and competitive. However, it d...

The Boundary Integral Equation Method

State-dependent diffusion: Thermodynamic consistency and its path integral formulation.

The friction coefficient of a particle can depend on its position, as it does when the particle is near a wall. We formulate the dynamics of particles with such state-dependent friction coefficients in terms of a general Langevin equation with multiplicative noise, whose evaluation requires the introduction of specific rules. Two common conventions, the Ito and the Stratonovich, provide alterna...

High-Resolution Coarse-Grained Modeling Using Oriented Coarse-Grained Sites.

We introduce a method to bring nearly atomistic resolution to coarse-grained models, and we apply the method to proteins. Using a small number of coarse-grained sites (about one per eight atoms) but assigning an independent three-dimensional orientation to each site, we preferentially integrate out stiff degrees of freedom (bond lengths and angles, as well as dihedral angles in rings) that are ...