Related papers: Hamiltonian adaptive resolution simulation for mol…
Hyperbolic systems under nonconservative form arise in numerous applications modeling physical processes, for example from the relaxation of more general equations (e.g. with dissipative terms). This paper reviews an existing class of…
Hamiltonian systems with multiple timescales arise in molecular dynamics, classical mechanics, and theoretical physics. Long-time numerical integration of such systems requires resolving fast dynamics with very small time steps, which…
We present a multiscale hybrid particle-field scheme for the simulation of relaxation and diffusion behavior of soft condensed matter systems. It combines particle-based Brownian dynamics and field-based local dynamics in an adaptive sense…
It is shown that the equilibrium Generalized Mean Spherical Model of fluid structure may be extended to nonequilibrium states with equation of state information used in equilibrium replaced by an exact condition on the two-body distribution…
Integral equation theory of molecular liquids based on statistical mechanics is quite promising as an essential part of multiscale methodology for chemical and biomolecular nanosystems in solution. Beginning with a molecular interaction…
Stellar streams retain a memory of their gravitational interactions with small-scale perturbations. While perturbative models for streams have been formulated in action-angle coordinates, a direct transformation to these coordinates is only…
The histogram reweighting technique, widely used to analyze Monte Carlo data, is shown to be applicable to dynamic properties obtained from Molecular Dynamics simulations. The theory presented here is based on the fact that the correlation…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
Increasing spatial and temporal resolution of numerical models continues to propel progress in hydrological sciences, but, at the same time, it has strained the ability of modern automatic calibration methods to produce realistic model…
The Hamiltonian action of a Lie group on a symplectic manifold induces a momentum map generalizing Noether's conserved quantity occurring in the case of a symmetry group. Then, when a Hamiltonian function can be written in terms of this…
Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the…
Efficient sampling from ensembles of Hamiltonian cycles is critical for predicting the thermodynamic properties of compact polymers, with applications including modeling protein and RNA folding and designing soft materials. Although…
Classical atomistic simulations based on interatomic potentials resolve lattice instabilities, defect nucleation, and microstructure evolution with high fidelity, but their accessible system sizes remain far below those required for…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
This paper is centered on using chemical reaction as a computational metaphor for simultaneously solving problems. An artificial chemical reactor that can simultaneously solve instances of three unrelated problems was created. The reactor…
Conventional methods of quantum simulation involve trade-offs that limit their applicability to specific contexts where their use is optimal. In particular, the interaction picture simulation has been found to provide substantial asymptotic…
All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular…
For nonrelativistic Hamiltonians which are shape invariant, analytic expressions for the eigenvalues and eigenvectors can be derived using the well known method of supersymmetric quantum mechanics. Most of these Hamiltonians also possess…
Two-dimensional systems such as quantum spin liquids or fractional quantum Hall systems exhibit anyonic excitations that possess more general statistics than bosons or fermions. This exotic statistics makes it challenging to solve even a…
This study addresses the challenge of simulating realistic particle systems by proposing a novel particle decomposition scheme that improves the parallel performance of surface resolved particle simulations. Realistic particle systems often…