Related papers: Unwrapping NPT simulations to calculate diffusion …
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
Diffusive transport is a universal phenomenon, throughout both biological and physical sciences, and models of diffusion are routinely used to interrogate diffusion-driven processes. However, most models neglect to take into account the…
A new approach to the modeling of nonfree particle diffusion is presented. The approach uses a general setup based on geometric graphs (networks of curves), which means that particle diffusion in anything from arrays of barriers and pore…
Predictive simulations of mixed plasma discharges, like deuterium-tritium plasmas, rely on self-consistent models for particle transport. These models have to be validated with interpretive analysis of existing experiments. Accounting for…
Propagating uncertainties introduced by chemical reaction rate parameters to high-fidelity numerical simulations of complex combustion devices is necessary to ascertain impact on computational predictions. However, the high cost of detailed…
Transport and dispersion of active particles in structured environments such as corrugated channels and porous media are important for the understanding of both natural and engineered active systems. Owing to their continuous…
A wide range of physical problems can be described by randomly-oriented linear trajectories, including any system of objects, organisms, particles, or rays that follow a linear path. Dependent upon the particular random variables that…
Understanding transition pathways between two meta-stable states of a molecular system is crucial to advance drug discovery and material design. However, unbiased molecular dynamics (MD) simulations are computationally infeasible because of…
The diffusion of active microscopic organisms in complex environments plays an important role in a wide range of biological phenomena from cell colony growth to single organism transport. Here, we investigate theoretically and…
One-dimensional non-equilibrium models of particles subjected to a coagulation-diffusion process are important in understanding non-equilibrium dynamics, and fluctuation-dissipation relation. We consider in this paper transport properties…
Phase unwrapping is a fundamental problem in InSAR data processing, supporting geophysical applications such as deformation monitoring and hazard assessment. Its reliability is limited by noise and decorrelation in radar acquisitions, which…
Rectification and diffusion of non-interacting self-propelled particles is numerically investigated in a two-dimensional corrugated channel. From numerical simulations, we obtain the average velocity and the effective diffusion coefficient.…
The implicit theory that a simulation represents is precisely not in the individual choices but rather in the 'envelope' of possible trajectories - what is important is the shape of the whole envelope. Typically a huge amount of computation…
Correcting for detector effects in experimental data, particularly through unfolding, is critical for enabling precision measurements in high-energy physics. However, traditional unfolding methods face challenges in scalability,…
Based on multiple simulation trajectories, which started from dispersively selected initial conformations, the weighted ensemble dynamics method is designed to robustly and systematically explore the hierarchical structure of complex…
The diffusion of gas through porous material is important to understand the physical processes underlying cometary activity. We study the diffusion of a rarefied gas (Knudsen regime) through a packed bed of monodisperse spheres via…
The continuous-time random walk (CTRW) model is useful for alleviating the computational burden of simulating diffusion in actual media. In principle, isotropic CTRW only requires knowledge of the step-size, $P_l$, and waiting-time, $P_t$,…
The computer simulation of many molecular processes is complicated by long time scales caused by rare transitions between long-lived states. Here, we propose a new approach to simulate such rare events, which combines transition path…
The study of moving particles (e.g. molecules, virus, vesicles, organelles, or whole cells) is crucial to decipher a plethora of cellular mechanisms within physiological and pathological conditions. Powerful live-imaging approaches enable…
We consider diffusion-controlled release of particles from $d$-dimensional radially-symmetric geometries. A quantity commonly used to characterise such diffusive processes is the proportion of particles remaining within the geometry over…