Related papers: Multicanonical molecular dynamics by variable-temp…
We derived a number of numerical methods to treat biomolecular systems with multiple time scales. Based on the splitting of the operators associated with the slow-varying and fast-varying forces, new multiple time-stepping (MTS) methods are…
The mesoscopic properties of a plasma in a cylindrical magnetic field are investigated from the view point of test-particle dynamics. When the system has enough time and spatial symmetries, a Hamiltonian of a test particle is completely…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
Molecular dynamics is one of the most commonly used approaches for studying the dynamics and statistical distributions of many physical, chemical, and biological systems using atomistic or coarse-grained models. It is often the case,…
The first-order phase transitions and related thermodynamics properties are primary concerns of materials sciences and engineering. In traditional atomistic simulations, the phase transitions and the estimation of their thermodynamic…
A variational method is used to derive a self-consistent macro-particle model for relativistic electromagnetic kinetic plasma simulations. Extending earlier work [E. G. Evstatiev and B. A. Shadwick, J. Comput. Phys., vol. 245, pp. 376-398,…
Computer simulations generate trajectories at a single, well-defined thermodynamic state point. Statistical reweighting offers the means to reweight static and dynamical properties to different equilibrium state points by means of analytic…
Polynomial dynamical systems are widely used to model and study real phenomena. In biochemistry, they are the preferred choice for modelling the concentration of chemical species in reaction networks with mass-action kinetics. These systems…
Multiscale thermodynamics is a theory of relations among levels of investigation of complex systems. It includes the classical equilibrium thermodynamics as a special case but it is applicable to both static and time evolving processes in…
We review some recent coarse-graining and multi-scale methods, but also put forward some new ideas for addressing such issues. We find that, if one is guided by nonequilibrium statistical mechanics and thermodynamics, it is possible to…
We present a differentiable formalism for learning free energies that is capable of capturing arbitrarily complex model dependencies on coarse-grained coordinates and finite-temperature response to variation of general system parameters.…
The thermodynamics with medium effects expressed by the dispersion relation of the temperature and density dependent particle mass is studied. Many previous treatments have been reviewed. A new thermodynamical treatment based on the…
We consider nonlinear multibody systems and present a suitable set of coordinates for the internal dynamics which allow to decouple the internal dynamics without the need to compute the Byrnes-Isidori form. Furthermore, we derive sufficient…
A simple deterministic and time reversal invariant type of thermostat is proposed to be used for computer simulations of classical systems. It acts on collisions with the walls of the container exclusively. It maps the incoming and outgoing…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
We calculate the density of states of a binary Lennard-Jones glass using a recently proposed Monte Carlo algorithm. Unlike traditional molecular simulation approaches, the algorithm samples distinct configurations according to…
From the point of view of statistical mechanics, a full characterisation of a molecular system requires the experimental determination of its possible states, their populations and the respective interconversion rates. Well-established…
We present a novel Ensemble Monte Carlo Growth method to sample the equilibrium thermodynamic properties of random chains. The method is based on the multicanonical technique of computing the density of states in the energy space. Such a…
We present a numerical method for learning the dynamics of slow components of unknown multiscale stochastic dynamical systems. While the governing equations of the systems are unknown, bursts of observation data of the slow variables are…
Stochastic thermodynamics has largely succeeded in characterizing both equilibrium and far-from-equilibrium phenomena. Yet many opportunities remain for application to mesoscopic complex systems -- especially biological ones -- whose…