Related papers: Multi-scale time-stepping in molecular dynamics
Periodic driving enables the engineering of complex quantum matter, yet in interacting systems it generically leads to energy absorption, which limits the lifetime of the engineered states. To address this challenge, dynamical freezing has…
The recent experimental progresses in handling microscopic systems have allowed to probe them at levels where fluctuations are prominent, calling for stochastic modeling in a large number of physical, chemical and biological phenomena. This…
The paper deals with the developing of the methodological backgrounds for the modeling and simulation of complex dynamical objects. Such backgrounds allow us to perform coordinate transformation and formulate the algorithm of its usage for…
Open quantum systems are studied from the thermodynamical point of view unifying the principle of maximum informational entropy and the hypothesis of relaxation times hierarchy. The result of the unification is a non-Markovian and local in…
Identifying and classifying quantum phases from measurable time series in many-body dynamics have significant values, yet face formidable challenges, requiring profound knowledge of physicists. Here, to achieve a pure data-driven machine…
Simulating physical problems involving multi-time scale coupling is challenging due to the need of solving these multi-time scale processes simultaneously. In response to this challenge, this paper proposed an explicit multi-time step…
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…
In molecular dynamics (MD), systems are molecules made up of atoms, and the aim is to determine their evolution over time. MD is based on a numerical resolution algorithm, whose role is to apply the forces generated by the various…
We propose a novel computational strategy to study the glass transition of molecular fluids. Our approach combines the construction of simple yet realistic models with the development of Monte Carlo algorithms to accelerate equilibration…
This thesis is focused on the implementation and the application of a novel kind of algorithm which is expected to overcome the limitations of older schemes. This new algorithm is named Multiboson Method. It allows to simulate an arbitrary…
We experimentally demonstrate the phenomenon of dynamical many-body freezing in a periodically driven Ising chain. Theoretically [Phys. Rev. B 82, 172402 (2010)], for certain values of the drive parameters all fundamental degrees of freedom…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
When addressing spatial biological questions using mathematical models, symmetries within the system are often exploited to simplify the problem by reducing its physical dimension. In a reduced-dimension model molecular movement is…
With the ever increasing computational power available and the development of high-performances computing, investigating the properties of realistic very large-scale nonlinear dynamical systems has been become reachable. It must be noted…
An adpative integration technique for time advancement of particle motion in the context of coupled computational fluid dynamics (CFD) - discrete element method (DEM) simulations is presented in this work. CFD-DEM models provide an accurate…
An important process for antimatter experiments is the cooling of particles in a Penning-Malmberg trap to experimentally useful temperatures. A non-neutral plasma of one species (e.g. antiprotons) can be collisionally cooled on another…
We present a new molecular-dynamics algorithm for integrating the equations of motion for a system of particles interacting with mixed continuous/impulsive forces. This method, which we call Impulsive Verlet, is constructed using operator…
The extension of thermodynamic principles to active matter remains a challenge due to the non-equilibrium nature inherent to active systems. In this study, we introduce a framework to assess entropy in our minimal macroscopic experiment…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…