Related papers: Fast and accurate multidimensional free energy int…
In this paper, we propose an improvement of the adaptive biasing force (ABF) method, by projecting the estimated mean force onto a gradient. The associated stochastic process satisfies a non linear stochastic differential equation. Using…
The Position Based Fluids (PBF) method is a state-of-the-art approach for fluid simulations in the context of real-time applications like games. It uses an iterative solver concept that tries to maintain a constant fluid density…
Enhanced sampling techniques have become an essential tool in computational chemistry and physics, where they are applied to sample activated processes that occur on a time scale that is inaccessible to conventional simulations. Despite…
Under the most common experimental conditions, the adsorption of proteins to solid surfaces is an spontaneous process that leads to a rather compact layer of randomly oriented molecules. Due to the importance of this process for the…
We present a combination of the recently developed double incremental expansion of potential energy surfaces with the well-established adaptive density-guided approach to grid construction. This unique methodology is based on the use of an…
In this work, we propose a novel adaptive stochastic gradient-free (ASGF) approach for solving high-dimensional nonconvex optimization problems based on function evaluations. We employ a directional Gaussian smoothing of the target function…
Machine learning interatomic force fields are promising for combining high computational efficiency and accuracy in modeling quantum interactions and simulating atomistic dynamics. Active learning methods have been recently developed to…
Removing geometrical details from a complex domain is a classical operation in computer aided design. This procedure simplifies the meshing process, and it enables faster simulations with less memory requirements. However, depending on the…
We introduce a new numerical technique, namely triangular tessellation, to calculate the free energy associated with the adsorption of a colloidal particle at a flat interface. The theory and numerical scheme presented here are sufficiently…
Gaussian process (GP) emulator has been used as a surrogate model for predicting force field and molecular potential, to overcome the computational bottleneck of molecular dynamics simulation. Integrating both atomic force and energy in…
In the paper a new method to solve the tree-dimensional reference interaction site model (3DRISM) integral equations is proposed. The algorithm uses the multi-grid technique which allows to decrease the computational expanses. 3DRISM…
Since the advent of mesh-free methods as a tool for the numerical analysis of systems of Partial Differential Equations (PDEs), many variants of differential operator approximation have been proposed. In this work, we propose a local…
This study presents an advanced sharp-interface immersed boundary method (IBM) integrated with the blastFOAM library on the OpenFOAM platform for high-speed compressible flow simulations. The developed solver extends the existing IBM…
We present a detailed comparison of computational efficiency and precision for several free energy difference ($\Delta F$) methods. The analysis includes both equilibrium and non-equilibrium approaches, and distinguishes between…
We present a spectrally accurate, efficient FFT-based method for the three-dimensional free-space Poisson equation with smooth, compactly supported sources. The method adopts a super-potential formulation: we first compute the convolution…
We present a fast adaptive method for the evaluation of heat potentials, which plays a key role in the integral equation approach for the solution of the heat equation, especially in a non-stationary domain. The algorithm utilizes a…
Metadynamics (MTD) is a very powerful technique to sample high-dimensional free energy landscapes, and due to its self-guiding property, the method has been successful in studying complex reactions and conformational changes. MTD sampling…
This work further improves the pseudo-transient approach for the Poisson Boltzmann equation (PBE) in the electrostatic analysis of solvated biomolecules. The numerical solution of the nonlinear PBE is known to involve many difficulties,…
Calculating free energies is an important and notoriously difficult task for molecular simulations. The rapid increase in computational power has made it possible to probe increasingly complex systems, yet extracting accurate free energies…
Exploring the free-energy landscape along reaction coordinates or system parameters $\lambda$ is central to many studies of high-dimensional model systems in physics, e.g. large molecules or spin glasses. In simulations this usually…