Related papers: Minima Hopping Guided Path Search: An Efficient Me…
The multi-gradient descent algorithm (MGDA) finds a common descent direction that can improve all objectives by identifying the minimum-norm point in the convex hull of the objective gradients. This method has become a foundational tool in…
Experiments, in particular on biological systems, typically probe lower-dimensional observables which are projections of high-dimensional dynamics. In order to infer consistent models capturing the relevant dynamics of the system, it is…
The computational efficiency of stochastic simulation algorithms is notoriously limited by the kinetic trapping of the simulated trajectories within low energy basins. Here we present a new method that overcomes kinetic trapping while still…
Efficient and reliable identification and optimization of transition state structures is a longstanding challenge in computational chemistry. Popular chain-of-states methods require hundreds if not thousands of ab initio calculations to…
Molecular search phenomena are observed in a variety of chemical and biological systems. During the search the participating particles frequently move in complex inhomogeneous environments with random transitions between different dynamic…
Several different methods exist for efficient approximation of paths in multiscale stochastic chemical systems. Another approach is to use bursts of stochastic simulation to estimate the parameters of a stochastic differential equation…
Interest in equilibrium-based sampling methods has grown with recent advances in computational hardware and Markov state modeling (MSM) methods, yet outstanding questions remain that hinder widespread adoption. Namely, how do sampling…
This paper introduces a new paradigm of optimal path planning, i.e., passage-traversing optimal path planning (PTOPP), that optimizes paths' traversed passages for specified optimization objectives. In particular, PTOPP is utilized to find…
Mobile robots frequently navigate on roadmaps, i.e., graphs where edges represent safe motions, in applications such as healthcare, hospitality, and warehouse automation. Often the environment is quasi-static, i.e., it is sufficient to…
When examining dynamics occurring at non-zero temperatures, both energy and entropy must be taken into account while describing activated barrier crossing events. Furthermore, good reaction coordinates need to be constructed to describe…
Shortcut to isothermality is a driving strategy to steer the system to its equilibrium states within finite time, and enables evaluating the impact of a control promptly. Finding optimal scheme to minimize the energy cost is of critical…
This paper presents an event-driven way finding algorithm for pedestrians in an evacuation scenario, which operates on a graph-based structure. The motivation of each pedestrian is to leave the facility. The events used to redirect…
We consider the problem of sampling transition paths between two given metastable states of a molecular system, e.g. a folded and unfolded protein or products and reactants of a chemical reaction. Due to the existence of high energy…
A global optimization method called Greedy Neighborhood Search (GNS) and a novel conformational sampling method using a spherical distribution is proposed to find the minimum energy conformation of a protein-like heteropolymer model called…
Random walks can be used to search a complex networks for a desired resource. To reduce the number of hops necessary to find the resource, we propose a search mechanism based on building random walks connecting together partial walks that…
Recent advances in reaction prediction have achieved near-saturated accuracy on standard benchmarks (e.g., USPTO), yet most state-of-the-art models formulate the task as a one-shot mapping from reactants to products, offering limited…
Ad hoc networks are wireless mobile networks that can operate without infrastructure and without centralized network management. Traditional techniques of routing are not well adapted. Indeed, their lack of reactivity with respect to the…
Molecular dynamics (MD)-based path sampling algorithms are a very important class of methods used to study the energetics and kinetics of rare (bio)molecular events. They sample the highly informative but highly unlikely reactive…
Optimal power flow (OPF) is a critical optimization problem for power systems to operate at points where cost or other operational objectives are optimized. Due to the non-convexity of the set of feasible OPF operating points, it is…
Hopping transport in a one-dimensional system is studied numerically. A fast algorithm is devised to find the lowest-resistance path at arbitrary electric field. Probability distribution functions of individual resistances on the path and…