相关论文: Simulation of weak polyelectrolytes: A comparison …
We present a general approach to isolate chemical reaction mechanism as an independently controllable variable across chemically distinct systems. Modern approaches to reduce the computational expense of molecular dynamics simulations often…
We examine the interactions between polyelectrolytes (PEs) and uncharged substrates at conditions corresponding to a dielectric discontinuity between the aqueous solution and the substrate. To this end, we vary the relevant system…
A simple comparison between the exact and approximate correlation components U of the electron-electron repulsion energy of several states of few-electron harmonium atoms with varying confinement strengths provides a superior validation…
Molecular dynamics simulations at a constant electric potential are an essential tool to study electrochemical processes, providing microscopic information on the structural, thermodynamic, and dynamical properties. Despite the numerous…
RNA molecules exhibit various biological functions intrinsically dependent on their diverse ecosystem of highly flexible structures. This flexibility arises from complex hydrogen-bonding networks defined by canonical and non-canonical base…
The probability distribution describing the state of a Stochastic Reaction Network evolves according to the Chemical Master Equation (CME). It is common to estimated its solution using Monte Carlo methods such as the Stochastic Simulation…
We present density response estimators for Monte Carlo simulations that are based on a reweighting procedure, where the samples of an unperturbed system are used to estimate the properties of a system perturbed by an external harmonic…
Osmotic coefficients, individual and mean activity coefficients of primitive model electrolyte solutions are computed at different molar concentrations using the symmetric Poisson-Boltzmann and modified Poisson-Boltzmann theories. The…
Weak values are traditionally obtained using a weak interaction between the measured system and a pointer state. It has, however, been pointed out that weak coupling can be replaced by a carefully tailored strong interaction. This paper…
We present the explicit bonding Reaction ensemble Monte Carlo (eb-RxMC) method, designed to sample reversible bonding reactions in macromolecular systems in thermodynamic equilibrium. Our eb-RxMC method is based on the Reaction ensemble…
The use of machine learning algorithms is an attractive way to produce very fast detector simulations for scattering reactions that can otherwise be computationally expensive. Here we develop a factorised approach where we deal with each…
Critical infrastructure systems must be both robust and resilient in order to ensure the functioning of society. To improve the performance of such systems, we often use risk and vulnerability analysis to find and address system weaknesses.…
In many applications, such as plasma edge simulation of a nuclear fusion reactor, a coupled PDE/kinetic description is required, which is usually solved with a coupled finite-volume/Monte-Carlo method. Different procedures have been…
We introduce a general Monte Carlo scheme for achieving atomistic simulations with monoelectronic Hamiltonians including the thermalization of both nuclear and electronic degrees of freedom. The kinetic Monte Carlo algorithm is used to…
State-of-the-art simulations of high-energy nuclear collisions rely on hybrid setups, involving in particular a pre-equilibrium stage to let the system evolve from a far-from-equilibrium initial condition towards a near-equilibrated state…
Deep Learning methods are known to suffer from calibration issues: they typically produce over-confident estimates. These problems are exacerbated in the low data regime. Although the calibration of probabilistic models is well studied,…
The system-level dynamics of multivalent biomolecular interactions can be simulated using a rule-based kinetic Monte Carlo method in which a rejection sampling strategy is used to generate reaction events. This method becomes inefficient…
Explicit-electron force fields introduce electrons or electron pairs as semi-classical particles in force fields or empirical potentials, which are suitable for molecular dynamics simulations. Even though semi-classical electrons are a…
Polyelectrolyte (PE) hydrogels can dynamically respond to external stimuli, such as changes in pH and temperature, which benefits their use for smart materials and nanodevices with tunable properties. We investigate equilibrium…
Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation and electrostatic energies and modulated by protein…