Related papers: Molecular hyperdynamics coupled with the nonorthog…
Parallelism of tight-binding molecular dynamics simulations is presented by means of the order-N electronic structure theory with the Wannier states, recently developed (J. Phys. Soc. Jpn. 69,3773 (2000)). An application is tested for…
Despite its widespread use in materials science, conventional molecular dynamics (MD) simulations are severely constrained by timescale limitations. To address this shortcoming, we propose an empirical formulation of accelerated MD method,…
The paper is devoted to a systematic account of the theory of conformational dynamics of protein molecules. As an example of application of this theory, we provide a complete analytical description of experiments on the kinetics of CO…
In this paper, a hybrid quasi-static atomistic simulation method at finite temperature is developed, which combines the advantages of MD for thermal equilibrium and atomic-scale finite element method (AFEM) for efficient equilibration. Some…
We report the capability to simulate in a quantum mechanical tight-binding (TB) atomistic fashion NW devices featuring several hundred to millions of atoms and diameter up to 18 nm. Such simulations go far beyond what is typically…
The theoretical investigation of non-adiabatic processes is hampered by the complexity of the coupled electron-nuclear dynamics beyond the Born-Oppenheimer approximation. Classically, the simulation of such reactions is limited by the…
Nonintegrability plays a crucial role in thermalization and transport processes in many-body Hamiltonian systems, yet its quantitative effects remain unclear. To reveal the connection between the macroscopic relaxation properties and the…
We consider the problem of finding the energy minimum of a complex quantum Hamiltonian by employing a non-Markovian bath prepared in a low energy state. The energy minimization problem is thus turned into a thermodynamic cooling protocol in…
-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…
We propose a variational formulation for the nonequilibrium thermodynamics of discrete open systems, i.e., discrete systems which can exchange mass and heat with the exterior. Our approach is based on a general variational formulation for…
Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular…
Non-adiabatic dynamics at molecule-metal interfaces govern diverse and technologically important phenomena, from heterogeneous catalysis to dye-sensitized solar energy conversion and charge transport across molecular junctions. Realistic…
We consider the aeroelastic simulation of flexible mechanical structures submerged in subsonic fluid flows at low Mach numbers. The nonlinear kinematics of flexible bodies are described in the total Lagrangian formulation and discretized by…
Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
The presented paper is an attempt to investigate the dynamical states of an hydrodynamical isothermal turbulent self-gravitating system using some powerful tools of the classical thermodynamics. Our main assumption, inspired by the work of…
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…
Ultrafast, time-resolved spectroscopies enable the direct observation of non-equilibrium processes in condensed-phase systems and have revealed key insights into energy transport, hydrogen-bond dynamics, and vibrational coupling. While ab…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Building on recent advances in quantum algorithms which measure and reuse qubits and in efficient classical simulation leveraging projective measurements, we extend these frameworks to real-time dynamics of quantum many-body systems…