Related papers: Tunneling-splittings from path-integral molecular …
The Lindblad equation determines the time evolution of the density operator of open quantum systems. While valid for any system size, its use is, in practice, restricted to prototype/surrogate models with the aim of tackling specific…
The formation of biomolecular condensates inside cells often involve intrinsically disordered proteins (IDPs), and several of these IDPs are also capable of forming droplet-like dense assemblies on their own, through liquid-liquid phase…
Ion channels are important proteins for physiological information transfer and functional control. To predict the microscopic origins of their voltage-conductance characteristics, we here applied dissipation-corrected targeted Molecular…
We present a new method for isothermal rigid body simulations using the quaternion representation and Langevin dynamics. It can be combined with the traditional Langevin or gradient (Brownian) dynamics for the translational degrees of…
Strong electric fields can be used to align molecules. However, a non-polar molecule such as H$_2$ has no preference for its orientation. There are thus two equivalent configurations with equal energy separated by a potential-energy…
Following on our previous work [S. Delong and B. E. Griffith and E. Vanden-Eijnden and A. Donev, Phys. Rev. E, 87(3):033302, 2013], we develop temporal integrators for solving Langevin stochastic differential equations that arise in…
Efficient and accurate integration of stochastic (partial) differential equations with multiplicative noise can be obtained through a split-step scheme, which separates the integration of the deterministic part from that of the stochastic…
We follow up the work, where in light of the Picard-Lefschetz thimble approach, we split up the real-time path integral into two parts: the initial density matrix part which can be represented via an ensemble of initial conditions, and the…
Via computer simulations of the standard binary Lennard-Jones glass former we have obtained in a systematic way a large set of close-by pairs of minima on the potential energy landscape, i.e. double-well potentials (DWP). We analyze this…
In light of the recently published complete set of statistically correct Gronbech-Jensen (GJ) methods for discrete-time thermodynamics, we revise a differential operator splitting method for the Langevin equation in order to comply with the…
Traditionally, neural networks are parameterized using optimization procedures such as stochastic gradient descent, RMSProp and ADAM. These procedures tend to drive the parameters of the network toward a local minimum. In this article, we…
Within path sampling framework, we show that probability distribution divergences, such as the Chernoff information, can be estimated via thermodynamic integration. The Boltzmann-Gibbs distribution pertaining to different Hamiltonians is…
The quantum mechanical tunneling through multiple quantum barriers is a long-standing and well-known problem. Three methods proposed earlier to calculate the tunneling probabilities and energy splitting: (1). Instanton Method (2) WKb…
In this work we compare and characterize the behavior of Langevin and Dissipative Particle Dynamics (DPD) thermostats in a broad range of non-equilibrium simulations of polymeric systems. Polymer brushes in relative sliding motion,…
The study of tunneling splitting is fundamental to get insight into the dynamics of a multitude of molecular systems. In this paper, a novel approach to the analysis of the ground-state tunneling splitting is presented and explicitly…
We introduce a powerful iterative algorithm to compute protein folding pathways, with realistic all-atom force fields. Using the path integral formalism, we explicitly derive a modified Langevin equation which samples directly the ensemble…
Accurate temperature estimation of pouch cells with indirect liquid cooling is essential for optimizing battery thermal management systems for transportation electrification. However, it is challenging due to the computational expense of…
Given a particle system obeying overdamped Langevin dynamics, we demonstrate that it is always possible to construct a thermodynamically consistent macroscopic model which obeys a gradient flow with respect to its non-equilibrium free…
Including the effect of thermal fluctuations in traditional computational fluid dynamics requires developing numerical techniques for solving the stochastic partial differential equations of fluctuating hydrodynamics. These Langevin…
In this article we derive the effective pairwise interactions in a Langevin type united atoms model of water. The interactions are determined from the trajectories of a detailed molecular dynamics simulation of simple point charge water. A…