Related papers: Diffusive search and trajectories on spatial netwo…
The mitotic spindle is an important intermediate structure in eukaryotic cell division, in which each of a pair of duplicated chromosomes is attached through microtubules to centrosomal bodies located close to the two poles of the dividing…
The propagation of signalling molecules within cellular networks is affected by network topology, but also by the spatial arrangement of cells in the networks. Understanding the collective reaction--diffusion behaviour in space of signals…
In many biological systems, the movement of individual agents is commonly characterized as having multiple qualitatively distinct behaviors that arise from various biophysical states. This is true for vesicles in intracellular transport,…
To maximize the accuracy of background simulation and event reconstruction, high-energy neutrino telescopes require detailed knowledge of light propagation over a large volume of detection medium. If light scattering and absorption leng ths…
Long time-duration low-thrust nonlinear optimal spacecraft trajectory global search is a computationally and time expensive problem characterized by clustering patterns in locally optimal solutions. During preliminary mission design,…
Effective trajectory stitching for long-horizon planning is a significant challenge in robotic decision-making. While diffusion models have shown promise in planning, they are limited to solving tasks similar to those seen in their training…
Retrosynthesis, which aims to identify viable synthetic pathways for target molecules by decomposing them into simpler precursors, is often treated as a search problem. However, its complexity arises from multi-branched tree-structured…
We introduce propagation kernels, a general graph-kernel framework for efficiently measuring the similarity of structured data. Propagation kernels are based on monitoring how information spreads through a set of given graphs. They leverage…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
Intracellular transport is essential for maintaining proper cellular function in most eukaryotic cells, with perturbations in active transport resulting in several types of disease. Efficient delivery of critical cargos to specific…
Supernova remnants are expected to contain braided (or stochastic) magnetic fields, which are in some regions directed mainly perpendicular to the shock normal. For particle acceleration due to repeated shock crossings, the transport in the…
Biological neural networks are often modeled as systems of coupled, nonlinear, ordinary or partial differential equations. The number of differential equations used to model a network increases with the size of the network and the level of…
We briefly review the principles, mathematical bases, numerical shortcuts and applications of fast random walk (FRW) algorithms. This Monte Carlo technique allows one to simulate individual trajectories of diffusing particles in order to…
Active cellular transport is a fundamental mechanism for protein and vesicle delivery, cell cycle and molecular degradation. Viruses can hijack the transport system and use it to reach the nucleus. Most transport processes consist of…
Two crucial elements facilitate the understanding and control of communicable disease spread within a social setting. These components are, the underlying contact structure among individuals that determines the pattern of disease…
In molecular simulations, efficient methods for investigating equilibration and slow relaxation in dense systems are crucial yet challenging. This study focuses on the diffusional characteristics of monodisperse hard disk systems at…
Diffusion processes in networks are increasingly used to model the spread of information and social influence. In several applications in computational sustainability such as the spread of wildlife, infectious diseases and traffic mobility…
Diffusion models have transformed image synthesis through iterative denoising, by defining trajectories from noise to coherent data. While their capabilities are widely celebrated, a critical challenge remains unaddressed: ensuring…
The replica exchange method is a powerful tool for overcoming slow relaxation in molecular simulations, but its efficiency depends strongly on the choice of the number and interval of replicas and their exchange probabilities. Here, we…
Granular materials, whose features range from the particle scale to the force-chain scale to the bulk scale, are usually modeled as either particulate or continuum materials. In contrast with either of these approaches, network…