相关论文: Hamiltonian replica-exchange in GROMACS: a flexibl…

In order to perform numerical studies of long-term stability in nonlinear Hamiltonian systems, one needs a numerical integration algorithm which is symplectic. Further, this algorithm should be fast and accurate. In this paper, we propose…

The ability to simulate one Hamiltonian with another is an important primitive in quantum information processing. In this paper, a simulation method for arbitrary $\sigma_z \otimes \sigma_z$ interaction based on Hadamard matrices…

The leapfrog integrator is routinely used within the Hamiltonian Monte Carlo method and its variants. We give strong numerical evidence that alternative, easy to implement algorithms yield fewer rejections with a given computational effort.…

The Hamiltonian for a system of relativistic bodies interacting by their gravitational field is found in the post-Minkowskian approximation, including all terms linear in the gravitational constant. It is given in a surprisingly simple…

A novel scheme to simulate the evolution of a restricted set of observables of a quantum system is proposed. The set comprises the spectrum-generating algebra of the Hamiltonian. The idea is to consider a certain open-system evolution,…

We prove the existence of a unitary transformation that enables two arbitrarily given Hamiltonians in the same Hilbert space to be transformed into one another. The result is straightforward yet, for example, it lays the foundation to…

Hamiltonian Flow Monte Carlo(HFMC) methods have been implemented in engineering, biology and chemistry. HFMC makes large gradient based steps to rapidly explore the state space. The application of the Hamiltonian dynamics allows to estimate…

We describe the special relativistic extension of the CRONOS code, which has been used for studies of gamma-ray binaries in recent years. The code was designed to be easily adaptable, allowing the user to easily change existing…

Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…

We introduce a recent symplectic integration scheme derived for solving physically motivated systems with non-separable Hamiltonians. We show its relevance to Riemannian manifold Hamiltonian Monte Carlo (RMHMC) and provide an alternative to…

We consider 1D lattices described by Hubbard or Bose-Hubbard models, in the presence of periodic high-frequency perturbations, such as uniform ac force or modulation of hopping coefficients. Effective Hamiltonians for interacting particles…

In this report, we explore the use of a quantum optimization algorithm for obtaining low energy conformations of protein models. We discuss mappings between protein models and optimization variables, which are in turn mapped to a system of…

Digital quantum simulation of many-body dynamics relies on Trotterization to decompose the target time evolution into elementary quantum gates operating at a fixed equidistant time discretization. Recent advances have outlined protocols…

It was recently demonstrated that a simple Monte Carlo (MC) algorithm involving the swap of particle pairs dramatically accelerates the equilibrium sampling of simulated supercooled liquids. We propose two numerical schemes integrating the…

Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities,…

Gradients in free energies are the driving forces of physical and biochemical systems. To predict free energy differences with high accuracy, Molecular Dynamics (MD) and other methods based on atomistic Hamiltonians conduct sampling…

Representing massless Dirac fermions on a spatial lattice poses a potential challenge known as the Fermion Doubling problem. Addition of a quadratic term to the Dirac Hamiltonian circumvents this problem. We show that the modified…

We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…

This paper presents a renormalization approach to many-particle systems. By starting from a bare Hamiltonian ${\cal H}= {\cal H}_0 +{\cal H}_1$ with an unperturbed part ${\cal H}_0$ and a perturbation ${\cal H}_1$,we define an effective…

A model subspace configuration interaction method is developed to obtain chemically accurate electron correlations by diagonalising a very compact effective Hamiltonian of realistic molecule. The construction of the effective Hamiltonian is…