Related papers: A molecular-dynamics algorithm for mixed hard-core…
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…
The Variational Quantum Eigensolver (VQE) is a key algorithm for near-term quantum computers, yet its performance is often limited by the classical optimization of circuit parameters. We propose using the velocity Verlet algorithm, inspired…
A new method is proposed to numerically integrate a dynamical system on a manifold such that the trajectory stably remains on the manifold and preserves first integrals of the system. The idea is that given an initial point in the manifold…
In the formalism of constrained mechanics, such as that which underlies the SHAKE and RATTLE methods of molecular dynamics, we present an algorithm to convert any one-step integration method to a variational integrator of the same order.…
A new algorithm is introduced to integrate the equations of rotational motion. The algorithm is derived within a leapfrog framework and the quantities involved into the integration are mid-step angular momenta and on-step orientational…
We develop a new algorithm for the Brownian dynamics of soft matter systems that evolves time by spatially correlated Monte Carlo moves. The algorithm uses vector wavelets as its basic moves and produces hydrodynamics in the low Reynolds…
Hamiltonian splitting methods are an established technique to derive stable and accurate integration schemes in molecular dynamics, in which additional accuracy can be gained using force gradients. For rigid bodies, a tradition exists in…
We present a revision to the well known Stormer-Verlet algorithm for simulating second order differential equations. The revision addresses the inclusion of linear friction with associated stochastic noise, and we analytically demonstrate…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
Polynomial dynamical systems describing interacting particles in the plane are studied. A method replacing integration of a polynomial multi--particle dynamical system by finding polynomial solutions of a partial differential equations is…
Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model…
We present a practical numerical method for evaluating the Lagrange multipliers necessary for maintaining a constrained linear geometry of particles in dynamical simulations. The method involves no iterations, and is limited in accuracy…
We describe and summarize a class of minimal numerical models emerged from recent development of simulation methods for dense particle suspensions in overdamped linear flows. The main ingredients include (i) a frame-invariant, short-range…
This paper presents a mixed-integer quadratic programming formulation of an existing data-driven approach to computational elasticity. This formulation is suitable for application of a standard mixed-integer programming solver, which finds…
The insertion of solvent particles in molecular dynamics simulations of complex fluids is required in many situations involving open systems, but this challenging task has been scarcely explored in the literature. We propose a simple and…
Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a…
We introduce a `virtual-move' Monte Carlo (VMMC) algorithm for systems of pairwise-interacting particles. This algorithm facilitates the simulation of particles possessing attractions of short range and arbitrary strength and geometry, an…
We developed a general theoretical approach and a user-ready computer code that permit to study the dynamics of collisional energy transfer and ro-vibrational energy exchange in complex molecule-molecule collisions. The method is a mixture…
Symplectic integration algorithms have become popular in recent years in long-term orbital integrations because these algorithms enforce certain conservation laws that are intrinsic to Hamiltonian systems. For problems with large variations…
Intramolecular symmetry-adapted perturbation theory (ISAPT) is a method to compute and decompose the noncovalent interaction energy between two molecular fragments A and B connected via a linker C. The existing ISAPT algorithm displays…