Related papers: A "fast growth" method of computing free energy di…
Quantum--Mechanical methods that are both computationally fast and accurate are not yet available for electronic excitations having charge transfer character. In this work, we present a significant step forward towards this goal for those…
The chemical potential of a component in a solution is defined as the free energy change as the amount of the component changes. Computing this fundamental thermodynamic property from atomistic simulations is notoriously difficult, because…
Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables(CVs) it can explore complex free energy surfaces…
The computation time required by standard finite difference methods with fixed timesteps for solving fractional diffusion equations is usually very large because the number of operations required to find the solution scales as the square of…
A system of a solvated canonical B-DNA of 12 base pairs with the specified sequence is initially equilibrated in a state of zero external force $f$ acting on it. After equilibration, a switching experiment is performed over the system by…
Different computational techniques in combination with molecular dynamics computer simulation are used to to determine the wall-liquid and the wall-crystal interfacial free energies of a modified Lennard-Jones (LJ) system in contact with a…
Biomolecular machines transduce between different forms of energy. These machines make directed progress and increase their speed by consuming free energy, typically in the form of nonequilibrium chemical concentrations. Machine dynamics…
One of the difficulties in adiabatic quantum computation is the limit on the computation time. Here we propose two schemes to speed-up the adiabatic evolution. To apply this controlled adiabatic evolution to adiabatic quantum computation,…
We investigate slow non-equilibrium dynamical processes in two-dimensional $q$--state Potts model with both ferromagnetic and $\pm J$ couplings. Dynamical properties are characterized by means of the mean-flipping time distribution. This…
A new method for implementing the kinetic energy operator for real-space, grid-based electronic structure codes is developed. It is based on multi-order Adaptive Finite Differencing (AFD) and uses atomic pseudo orbitals produced by the…
We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coarse grained (CG) potential and test it for a biomolecular…
A one-dimensional model on a line of the length L is investigated, which involves particle diffusion as well as single particle annihilation. There are also creation and annihilation at the boundaries. The static and dynamical behaviors of…
We derive the bias function that minimizes the statistical error of free energy differences calculated in work-biased fast-switching simulations. The optimum bias function is compared to other bias functions using a particle pulled through…
This investigation is a part of a research program aiming to characterize the extreme behavior possible in hydrodynamic models by analyzing the maximum growth of certain fundamental quantities. We consider here the rate of growth of the…
In this study, a machine learning-based technique is developed to reduce the computational cost required to explore large design spaces of substitutional alloys. The first advancement is based on a neural network approach to predict the…
We introduce a quantum algorithm to efficiently prepare states with a small energy variance at the target energy. We achieve it by filtering a product state at the given energy with a Lorentzian filter of width $\delta$. Given a local…
We introduce and study the adiabatic dynamics of free-fermion models subject to a local Lindblad bath and in the presence of a time-dependent Hamiltonian. The merit of these models is that they can be solved exactly, and will help us to…
Multiple equilibrium states arise in many physical systems, including various types of liquid crystal structures. Having the ability to reliably compute such states enables more accurate physical analysis and understanding of experimental…
In this review we focus on the determination of phase diagrams by computer simulation with particular attention to the fluid-solid and solid-solid equilibria. The calculation of the free energy of solid phases using the Einstein crystal and…
We use analytic theory and computer simulation to study patterns formed during the growth of two-component assemblies in 2D and 3D. We show that these patterns undergo a nonequilibrium phase transition, at a particular growth rate, between…