Related papers: Efficient path sampling on multiple reaction chann…

Identifying minimum-energy paths (MEPs) is crucial for understanding chemical reaction mechanisms but remains computationally demanding. We introduce MEPIN, a scalable machine-learning method for efficiently predicting MEPs from reactant…

Scientists often search for phenomena of interest while exploring new environments. Autonomous vehicles are deployed to explore such areas where human-operated vehicles would be costly or dangerous. Online control of autonomous vehicles for…

For sampling multiple pathways in a rugged energy landscape, we propose a novel action-based path sampling method using the Onsager-Machlup action functional. Inspired by the Fourier-path integral simulation of a quantum mechanical system,…

Searching for reaction pathways describing rare events in large systems presents a long-standing challenge in chemistry and physics. Incorrectly computed reaction pathways result in the degeneracy of microscopic configurations and inability…

Ergodic coverage effectively generates exploratory behaviors for embodied agents by aligning the spatial distribution of the agent's trajectory with a target distribution, where the difference between these two distributions is measured by…

This work introduces progressive spatio-temporal filtering, an efficient method to build all-frequency approximations to the light transport distribution into a scene by filtering individual samples produced by an underlying path sampler,…

Mapping the chemical reaction pathways and their corresponding activation barriers is a significant challenge in molecular simulation. Given the inherent complexities of 3D atomic geometries, even generating an initial guess of these paths…

Network sampling is a crucial technique for analyzing large or partially observable networks. However, the effectiveness of different sampling methods can vary significantly depending on the context. In this study, we empirically compare…

In reaction path optimization, such as the calculation of a minimum energy path (MEP) between given reactant and product configurations of atoms, it is advantageous to start with an initial guess where close proximity of atoms is avoided…

Molecular transitions -- such as protein folding, allostery, and membrane transport -- are central to biology yet remain notoriously difficult to simulate. Their intrinsic rarity pushes them beyond reach of standard molecular dynamics,…

Conventional rendering techniques are primarily designed and optimized for single-frame rendering. In practical applications, such as scene editing and animation rendering, users frequently encounter scenes where only a small portion is…

We consider the problem of sampling $n$ numbers from the range $\{1,\ldots,N\}$ without replacement on modern architectures. The main result is a simple divide-and-conquer scheme that makes sequential algorithms more cache efficient and…

Reaction networks in the bulk and on surfaces are widespread in physical, chemical and biological systems. In macroscopic systems, which include large populations of reactive species, stochastic fluctuations are negligible and the reaction…

Reaction-diffusion models are widely used to study spatially-extended chemical reaction systems. In order to understand how the dynamics of a reaction-diffusion model are affected by changes in its input parameters, efficient methods for…

In this work, we consider the problem of estimating summary statistics to characterise biochemical reaction networks of interest. Such networks are often described using the framework of the Chemical Master Equation (CME). For…

Experiments on particles' motion in living cells show that it is often subdiffusive. This subdiffusion may be due to trapping, percolation-like structures, or viscoelatic behavior of the medium. While the models based on trapping (leading…

A number of coupling strategies are presented for stochastically modeled biochemical processes with time-dependent parameters. In particular, the stacked coupling is introduced and is shown via a number of examples to provide an…

Ergodic exploration has spawned a lot of interest in mobile robotics due to its ability to design time trajectories that match desired spatial coverage statistics. However, current ergodic approaches are for continuous spaces, which require…

Effective communication is crucial for deploying robots in mission-specific tasks, but inadequate or unreliable communication can greatly reduce mission efficacy, for example in search and rescue missions where communication-denied…

The prediction of reaction pathways for solid-solid transformations remains a key challenge. Here, we develop a pathway sampling method via swarm intelligence and graph theory, and demonstrate that our PALLAS method is an effective tool to…