Related papers: On Metropolis Integrators for Molecular Dynamics
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
This paper deals with the numerical integration of Hamiltonian systems in which a stiff anharmonic potential causes highly oscillatory solution behavior with solution-dependent frequencies. The impulse method, which uses micro- and…
Simulations of the dynamics generated by partial differential equations (PDEs) provide approximate, numerical solutions to initial value problems. Such simulations are ubiquitous in scientific computing, but the correctness of the results…
We propose the powerful integration of the Hybrid Monte Carlo (hybridMC) algorithm and Well-Tempered Metadynamics. This new algorithm, hybridMC-MetaD, enhances the flexibility and applicability of metadynamics by allowing for the…
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…
Classical molecular dynamics (MD) simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail. However, the inherent scalability problem of particle-particle…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Molecular dynamics (MD) simulations are a central tool in science and engineering enabling the study of dynamical behavior and the link between microscopic structure and macroscopic function. Their high computational cost, however, has…
The multiple-try Metropolis (MTM) algorithm is an extension of the Metropolis-Hastings (MH) algorithm by selecting the proposed state among multiple trials according to some weight function. Although MTM has gained great popularity owing to…
We introduce a lattice gas implementation that is based on coarse-graining a Molecular Dynamics (MD) simulation. Such a lattice gas is similar to standard lattice gases, but its collision operator is informed by an underlying MD simulation.…
Molecular dynamics (MD) simulation is a widely used technique to simulate molecular systems, most commonly at the all-atom resolution where equations of motion are integrated with timesteps on the order of femtoseconds…
We show how the integrators used for the molecular dynamics step of the Hybrid Monte Carlo algorithm can be further improved. These integrators not only approximately conserve some Hamiltonian $H$ but conserve exactly a nearby shadow…
Magnetic quadrupoles are essential components of particle accelerators like the Large Hadron Collider. In order to study numerically the stability of the particle beam crossing a quadrupole, a large number of particle revolutions in the…
Simulation of contact and friction dynamics is an important basis for control- and learning-based algorithms. However, the numerical difficulties of contact interactions pose a challenge for robust and efficient simulators. A…
A fluid flow in a simple dense liquid, passing an obstacle in a two-dimensional thin film geometry, is simulated by Molecular Dynamics (MD) computer simulation and compared to results of Lattice Boltzmann (LB) simulations. By the…
The multiple-try Metropolis (MTM) algorithm is a generalization of the Metropolis-Hastings algorithm in which the transition kernel uses a compound proposal consisting of multiple candidate draws. Since its seminal paper there have been…
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…
Integer linear programming (ILP) remains computationally challenging due to its NP-complete nature despite its central role in scheduling, logistics, and design optimization. We introduce a fully quantum Metropolis-Hastings algorithm for…
Molecular Dynamics (MD) codes predict the fundamental properties of matter by following the trajectories of a collection of interacting model particles. To exploit diverse modern manycore hardware, efficient codes must use all available…
Molecular dynamics (MD) simulation with modified Brenner's reactive empirical bond order (REBO) potential is a powerful tool to investigate plasma wall interaction on divertor plates in a nuclear fusion device. However, MD simulation box's…