Related papers: Discretization errors in molecular dynamics simula…
We consider numerical schemes for computing the linear response of steady-state averages of stochastic dynamics with respect to a perturbation of the drift part of the stochastic differential equation. The schemes are based on Girsanov's…
Recent experiments on liquid water show collective dipole orientation fluctuations dramatically slower then expected (with relaxation time $>$ 50 ns) [D. P. Shelton, Phys. Rev. B {\bf 72}, 020201(R) (2005)]. Molecular dynamics simulations…
Variational algorithms may enable classically intractable simulations on near-future quantum computers. However, their potential is limited by hardware errors. It is therefore crucial to develop efficient ways to mitigate these errors.…
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…
We develop several statistical tests of the determinant of the diffusion coefficient of a stochastic differential equation, based on discrete observations on a time interval $[0,T]$ sampled with a time step $\Delta$. Our main contribution…
Relativistic generalization of hydrodynamic theory has attracted much attention from a theoretical point of view. However, it has many important practical applications in high energy as well as astrophysical contexts. Despite various…
In this paper, we propose a new approach for the time-discretization of the incompressible stochastic Stokes equations with multiplicative noise. Our new strategy is based on the classical Milstein method from stochastic differential…
We perform an error analysis for numerical approximation methods of continuous time Markov chain models commonly found in the chemistry and biochemistry literature. The motivation for the analysis is to be able to compare the accuracy of…
We investigate the potential of numerical algorithms to decipher the kinetic parameters involved in multi-step chemical reactions. To this end we study a dimerization kinetics of protein as a model system. We follow the dimerization…
In a recent publication, Trentin et al employed Molecular Dynamics (MD) simulations for the theoretical study of the wetting of the different polymorphs of cellulose by water, using the widely employed TIP3P model of water. Here we show…
We present results predicting experimentally measurable structural quantities from molecular dynamics studies of hydrogen. In doing this, we propose a paradigm shift for experimentalists -- that the predictions from such calculations should…
A microscopic model able to describe simultaneously the dynamic viscosity and the self-diffusion coefficient of fluids is presented. This model is shown to emerge from the introduction of fractional calculus in a usual model of condensed…
We report the results of a computer simulation study of the thermodynamic properties and the thermal conductivity of supercooled water as a function of pressure and temperature using the TIP4P-2005 water model. The thermodynamic properties…
This paper proposes a numerical upscaling procedure for elliptic boundary value problems with diffusion tensors that vary randomly on small scales. The resulting effective deterministic model is given through a quasilocal discrete integral…
We present a hybrid computational method for simulating the dynamics of macromolecules in solution which couples a mesoscale solver for the fluctuating hydrodynamics (FH) equations with molecular dynamics to describe the macromolecule. The…
All liquids are topologically disordered materials; however, the degree of disorder can vary as a result of internal fluctuations in structure and topology. These fluctuations depend on both the composition and temperature of the system.…
Numerous studies have identified large quantum mechanical effects in the dynamics of liquid water. In this paper, we suggest that these effects may have been overestimated due to the use of rigid water models and flexible models in which…
We examine five different popular rigid water models (SPC, SPCE, TIP3P, TIP4P and TIP5P) using MD simulations in order to investigate the hydrophobic hydration and interaction of apolar Lennard-Jones solutes as a function of temperature in…
State estimation incorporates the feedback in optimization based advanced process control systems and is very important for the performance of model predictive control. We describe the extended Kalman filter, the unscented Kalman filter,…
We consider the Euler equation of quasi-geostrophic fluids which is widely used in weather forecast. Our goal is to study explicit volume-preserving numerical methods for very long simulations on an energy and enstrophy preserving…