We introduce two new thermostats, one of Langevin type and one of gradient (Brownian) type, for rigid body dynamics. We formulate rotation using the quaternion representation of angular coordinates; both thermostats preserve the unit length of quaternions. The Langevin thermostat also ensures that the conjugate angular momenta stay within the tangent space of the quaternion coordinates, as requ...

A systematic computational approach to describe the conformational dynamics of biomolecules in reduced dimensionality is presented. The method is based on (i) the decomposition of a high-dimensional molecular dynamics trajectory into a few "system" and (many) "bath" degrees of freedom and (ii) a Langevin simulation of the resulting model. Employing principal component analysis, the dimension of...

Abstract: The generalized elastic model encompasses several linear stochastic models describing the dynamics of polymers, membranes, rough surfaces, and fluctuating interfaces. While usually defined in the overdamped case, in this paper we formally include the inertial term to account for the initial diffusive stages of the stochastic dynamics. We derive the generalized Langevin equation for a ...

We consider numerical methods for thermodynamic sampling, i.e., computing sequences of points distributed according to the Gibbs–Boltzmann distribution, using Langevin dynamics and overdamped Langevin dynamics (Brownian dynamics). A wide variety of numerical methods for Langevin dynamics may be constructed based on splitting the stochastic differential equations into various component parts, ea...

We study a Dirichlet boundary value problem for Langevin equation involving two fractional orders. Langevin equation has been widely used to describe the evolution of physical phenomena in fluctuating environments. However, ordinary Langevin equation does not provide the correct description of the dynamics for systems in complex media. In order to overcome this problem and describe dynamical pr...