Related papers: Unwrapping NPT simulations to calculate diffusion …

Particle number fluctuations $N(t)$, measured in virtual observation boxes of an image or a simulation, offer a way to quantify particle dynamics when particle tracking is impractical, such as in high-density systems. While traditionally…

A key overall goal of biomolecular simulations is the characterization of "mechanism" -- the pathways through configuration space of processes such as conformational transitions and binding. Some amount of heterogeneity is intrinsic to the…

A significant challenge in molecular dynamics (MD) simulations is ensuring that sampled configurations converge to the equilibrium or nonequilibrium stationary distribution of interest. Lack of convergence constrains the estimation of free…

We develop a statistical theory for the dynamics of non-aligning, non-interacting self-propelled particles confined in a convex box in two dimensions. We find that when the size of the box is small compared to the persistence length of a…

The statistical analysis of covariance matrices occurs in many important applications, e.g. in diffusion tensor imaging and longitudinal data analysis. We consider the situation where it is of interest to estimate an average covariance…

Particle physics simulations are the cornerstone of nuclear engineering applications. Among them radiotherapy (RT) is crucial for society, with 50% of cancer patients receiving radiation treatments. For the most precise targeting of tumors,…

Hypothesis:Diffusion in confinement is an important fundamental problem with significant implications for applications of supported liquid phases. However, resolving the spatially dependent diffusion coefficient, parallel and perpendicular…

Machine learning models have emerged as a very effective strategy to sidestep time-consuming electronic-structure calculations, enabling accurate simulations of greater size, time scale and complexity. Given the interpolative nature of…

Matrix inversion problems are often encountered in experimental physics, and in particular in high-energy particle physics, under the name of unfolding. The true spectrum of a physical quantity is deformed by the presence of a detector,…

This paper series aims to establish a complete correspondence between fine-grained (FG) and coarse-grained (CG) dynamics by way of excess entropy scaling (introduced in Paper I). While Paper II successfully captured translational motions in…

We propose a new semiparametric approach for modelling nonlinear univariate diffusions, where the observed process is a nonparametric transformation of an underlying parametric diffusion (UPD). This modelling strategy yields a general class…

Transport and acceleration of charged particles in turbulent media is a topic of great interest in space physics and interstellar astrophysics. These processes are dominated by the scattering of particles off magnetic irregularities. The…

Monte Carlo methods are state-of-the-art when it comes to dosimetric computations in radiotherapy. However, the execution time of these methods suffers in high-collisional regimes. We address this problem by introducing a kinetic-diffusion…

We propose an approach to analysing single trajectories of a particle, which moves randomly on a landscape distinct parts of which result in sufficiently various diffusion coefficients. The method based on the mapping the cumulative sum of…

Particle diffusion in rotating drums is studied via computer simulations using a full 3-D model which does not involve any arbitrary input parameters. The diffusion coefficient for single-component systems agree qualitatively with previous…

We studied the self-diffusion of colloidal ellipsoids in a monolayer near a flat wall by video microscopy. The image processing algorithm can track the positions and orientations of ellipsoids with sub-pixel resolution. The translational…

We introduce a novel algorithm to perform event-driven simulations of hard rigid bodies of arbitrary shape, that relies on the evaluation of the geometric distance. In the case of a monodisperse system of uniaxial hard ellipsoids,we perform…

Depending on their mechanism of self-propulsion, active particles can exhibit a time-dependent, often periodic, propulsion velocity. The precise propulsion velocity profile determines their mean square displacement and their effective…

In molecular dynamics (MD) simulations, accessing transition probabilities between states is crucial for understanding kinetic information, such as reaction paths and rates. However, standard MD simulations are hindered by the capacity to…

Nominal payload ratings for articulated robots are typically derived from worst-case configurations, resulting in uniform payload constraints across the entire workspace. This conservative approach severely underutilizes the robot's…