相关论文: Hamiltonian replica-exchange in GROMACS: a flexibl…
Long ranged electrostatic interactions are time consuming to calculate in molecular dynamics and Monte-Carlo simulations. We introduce an algorithmic framework for simulating charged particles which modifies the dynamics so as to allow…
We review the approach to glasses based on the replica formalism. The replica approach presented here is a first principle's approach which aims at deriving the main glass properties from the microscopic Hamiltonian. In contrast to the old…
Simulating the long-time evolution of Hamiltonian systems is limited by the small timesteps required for stable numerical integration. To overcome this constraint, we introduce a framework to learn Hamiltonian Flow Maps by predicting the…
In computer simulations, quantum delocalization of atomic nuclei can be modeled making use of the Path Integral (PI) formulation of quantum statistical mechanics. This approach, however, comes with a large computational cost. By restricting…
A new method is proposed for integrating the equations of motion of an elastic filament. In the standard finite-difference and finite-element formulations the continuum equations of motion are discretized in space and time, but it is then…
In order to solve quantum field theory in a non-perturbative way, Lagrangian lattice simulations have been very successful. Here we discuss a recently proposed alternative Hamiltonian lattice formulation - the Monte Carlo Hamiltonian. In…
Hamiltonian Monte Carlo (HMC) has become routinely used for sampling from posterior distributions. Its extension Riemann manifold HMC (RMHMC) modifies the proposal kernel through distortion of local distances by a Riemannian metric. The…
The recently proposed Hamiltonian Adaptive Resolution Scheme (H-AdResS) allows to perform molecular simulations in an open boundary framework. It allows to change on the fly the resolution of specific subset of molecules (usually the…
We propose an improved prediction method of the tertiary structures of $\alpha$-helical membrane proteins based on the replica-exchange method by taking into account helix deformations. Our method allows wide applications because…
Sampling complex potential energies is one of the most pressing challenges of contemporary computational science. Inspired by recent efforts that use quantum effects and discretized Feynman's path integrals to overcome large barriers we…
We present an approach to construct appropriate and efficient emulators for Hamiltonian flow maps. Intended future applications are long-term tracing of fast charged particles in accelerators and magnetic plasma confinement configurations.…
We provide a general method for efficiently simulating time-dependent Hamiltonian dynamics on a circuit-model based quantum computer. Our approach is based on approximating the truncated Dyson series of the evolution operator, extending the…
We use the replica method in order to obtain an expression for the variational free energy of an Ising ferromagnet on a Viana-Bray lattice in the presence of random external fields. Introducing a global order parameter, in the…
We develop a general method for constructing the many-body Hamiltonian of pairwise interactions describing homonuclear mixtures of atoms occupying states with different total angular momenta or other quantum numbers. The advantage of the…
We suggest a numerical integration procedure for solving the equations of motion of certain classical spin systems which preserves the underlying symplectic structure of the phase space. Such symplectic integrators have been successfully…
All elementary Hamiltonians in nature are expected to be invariant under rotation. Despite this restriction, we usually assume that any arbitrary measurement or unitary time evolution can be implemented on a physical system, an assumption…
Hamiltonian Monte Carlo (HMC) is a popular Markov Chain Monte Carlo (MCMC) algorithm to sample from an unnormalized probability distribution. A leapfrog integrator is commonly used to implement HMC in practice, but its performance can be…
The emergence of scanning probe and electron beam imaging techniques have allowed quantitative studies of atomic structure and minute details of electronic and vibrational structure on the level of individual atomic units. These microscopic…
We present \texttt{ESpinS} (Esfahan Spin Simulation) package to evaluate the thermodynamic properties of spin systems described by a spin model Hamiltonian. In addition to the Heisenberg exchange term, the spin Hamiltonian can contain…
We explore the construction of new symplectic numerical integration schemes to be used in Hamiltonian Monte Carlo and study their efficiency. Two integration schemes from Blanes et al. (2014), and a new scheme based on optimal acceptance…