相关论文: Long-Time Mean Square Displacements in Proteins

The maximum mean discrepancy (MMD) is a recently proposed test statistic for two-sample test. Its quadratic time complexity, however, greatly hampers its availability to large-scale applications. To accelerate the MMD calculation, in this…

We develop an efficient parallel multiscale method that bridges the atomistic and mesoscale regimes, from nanometer to micron and beyond, via concurrent coupling of atomistic simulation and mesoscopic dynamics. In particular, we combine an…

The dynamic mode decomposition (DMD) is a broadly applicable dimensionality reduction algorithm that approximates a matrix containing time-series data by the outer product of a matrix of exponentials, representing Fourier-like time…

We review a molecular dynamics method for nucleon many-body systems called the quantum molecular dynamics (QMD) and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to the…

Kernel mean embeddings are a popular tool that consists in representing probability measures by their infinite-dimensional mean embeddings in a reproducing kernel Hilbert space. When the kernel is characteristic, mean embeddings can be used…

Diffusive molecular dynamics is a novel model for materials with atomistic resolution that can reach diffusive time scales. The main ideas of diffusive molecular dynamics are to first minimize an approximate variational Gaussian free energy…

Simulations of macromolecular diffusion and adsorption in confined environments can offer valuable mechanistic insights into numerous biophysical processes. In order to model solutes at atomic detail on relevant time scales, Brownian…

We propose a continuous-time formulation of persistent contrastive divergence (PCD) for maximum likelihood estimation (MLE) of unnormalised densities. Our approach expresses PCD as a coupled, multiscale system of stochastic differential…

Due to particle conservation, Canonical Molecular Dynamics (MD) simulations fail in the description of surface phase transitions involving coverage or lateral density changes. However, a step on the surface can act effectively as a source…

We present extensive molecular dynamics simulations of the motion of a single linear rigid molecule in a two-dimensional random array of fixed obstacles. The diffusion constant for the center of mass translation, $D_{\rm CM}$, and for…

Only a small fraction of the data generated in state-of-the-art all-atom multi-microsecond molecular dynamics (MD) simulations is typically analyzed. With femtosecond integration steps, microsecond simulations generate billions of time…

We consider the dynamics of a linear stochastic approximation algorithm driven by Markovian noise, and derive finite-time bounds on the moments of the error, i.e., deviation of the output of the algorithm from the equilibrium point of an…

The evolution of molecular dynamics (MD) simulations has been intimately linked to that of computing hardware. For decades following the creation of MD, simulations have improved with computing power along the three principal dimensions of…

Diffusion in a multidimensional energy surface with minima and barriers is a problem of importance in statistical mechanics and also has wide applications, such as protein folding. To understand it in such a system, we carry out theory and…

In recent years, machine learning interatomic potentials (MLIPs) have attracted significant attention as a method that enables large-scale, long-time atomistic simulations while maintaining accuracy comparable to electronic structure…

A dynamical atomistic chain to simulate mechanical properties of a one-dimensional material with zero temperature may be modelled by the molecular dynamics (MD) model. Because the number of particles (atoms) is huge for a MD model, in…

The (asymptotic) behaviour of the second moment of solutions to stochastic differential equations is treated in mean-square stability analysis. This property is discussed for approximations of infinite-dimensional stochastic differential…

We present a study of single-mode Rayleigh-Taylor instabilities (smRTI) with a modified Direct Simulation Monte Carlo (mDSMC) code in two dimensions. The mDSMC code is aimed to capture the dynamics of matter for a large range of Knudsen…

We consider the problem of detecting change-points in univariate time series by fitting a continuous piecewise linear signal using the residual sum of squares. Values of the inferred signal at slope breaks are restricted to a finite set of…

The use of molecular dynamics (MD) simulations has led to promising results to unravel the atomistic origins of adhesive wear, and in particular for the onset of wear at nanoscale surface asperities. However, MD simulations come with a high…