相关论文: Simulation of weak polyelectrolytes: A comparison …
We compare dynamical nonequilibrium molecular dynamics and continuum simulations of the dynamics of relaxation of a fluid system characterized by a non uniform density profile. Results match quite well as long as the lengthscale of density…
The osmotic coefficient of solutions of rod-like polyelectrolytes is considered by comparing current theoretical treatments and simulations to recent experimental data. The discussion is restricted to the case of monovalent counterions and…
Efficient computational methods that are capable of supporting experimental measures obtained at constant values of pH and redox potential are important tools as they serve to, among other things, provide additional atomic level information…
Extracting the kinetic properties of a system whose dynamics depend on the pH of the environment with which it exchanges energy and atoms requires sampling the Grand Canonical Ensemble. As an alternative, we present a novel strategy that…
The efficiency of water electrolysis in a photoelectrochemical cell is largely limited by the oxygen evolution reaction (OER) at its semiconductor photoanode. Reaction rate constants are key to investigating the slow kinetics of the…
Simulation of chemical reactions on quantum computing platforms using quantum classical hybrid algorithms such as the Variational Quantum Eigensolver (VQE) is challenged by the need for a reaction consistent treatment of electron…
Complex biochemical pathways or regulatory enzyme kinetics can be reduced to chains of elementary reactions, which can be described in terms of chemical kinetics. This discipline provides a set of tools for quantifying and understanding the…
We introduce a simple method for characterizing reactive pathways in quantum systems. Flux auto- correlation and cross-correlation functions are employed to develop a quantitative measure of dynamical coupling in quantum transition events,…
Understanding the evolution of electrified solid-liquid interfaces during electrochemical reactions is crucial. However, capturing the dynamic behavior of the interfaces with high temporal resolution and accuracy over long timescales…
In this thesis, we use classical, semi-classical and quantum-mechanical methods to simulate chemical reaction dynamics inside of an optical cavity. Within such a cavity, by selectively coupling vibrational modes of the reactants to the…
Based on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensemble dynamics (RED) method to more efficiently sample complex (biopolymer) systems, and to explore their hierarchical metastable…
The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations of biological molecules. These molecules suffer from a rough energy landscape. The resulting slowing down in numerical simulations is overcome by…
Aiming to approach the thermodynamical properties of hard-core systems by standard molecular dynamics simulation, we propose setting a repulsive constant-force for overlapping particles. That is, the discontinuity of the pair potential is…
We study the collective optical response of an atomic ensemble confined within a single-mode optical cavity by stochastic electrodynamics simulations that include the effects of atomic position correlations, internal level structure, and…
Many body trial wave functions are the key ingredient for accurate Quantum Monte Carlo estimates of total electronic energies in many electron systems. In the Coupled Electron-Ion Monte Carlo method, the accuracy of the trial function must…
Spatial reaction-diffusion models have been employed to describe many emergent phenomena in biological systems. The modelling technique most commonly adopted in the literature implements systems of partial differential equations (PDEs),…
The response of the uniform electron gas (UEG) to an external perturbation is of paramount importance for many applications. Recently, highly accurate results for the static density response function and the corresponding local field…
The elastic constants of hcp $^{4}$He are computed using the path-integral Monte Carlo (PIMC) method. The stiffness coefficients are obtained by imposing different distortions to a periodic cell containing 180 atoms, followed by measurement…
A method is formulated, based on combining self-consistent field theory with dynamically corrected transition state theory, for estimating the rates of adsorption and desorption of end-constrained chains (e.g. by crosslinks or…
It is often difficult to quantitatively determine if a new molecular simulation algorithm or software properly implements sampling of the desired thermodynamic ensemble. We present some simple statistical analysis procedures to allow…