Related papers: Minima Hopping Guided Path Search: An Efficient Me…
Finding optimal reaction coordinates and predicting accurate kinetic rates for activated processes are two of the foremost challenges of molecular simulations. We introduce an algorithm that tackles the two problems at once: starting from a…
Mapping reaction pathways and transition states (TS) is fundamental to chemistry but computationally expensive at scale. The minimum energy pathway (MEP) dictates reaction rates and mechanisms, yet recovering it via electronic-structure…
Flow matching trains a neural velocity field by regression against a target velocity associated with a prescribed probability path connecting a simple initial distribution to the data distribution. A central design choice is the path…
In this work, we present a transition-state optimization protocol based on the Mode-Tracking algorithm [J. Chem. Phys. 118 (2003) 1634]. By calculating only the eigenvector of interest instead of diagonalizing the full Hessian matrix and…
We present a simple protocol which allows fully automated discovery of elementary chemical reaction steps using in cooperation single- and double-ended transition-state optimization algorithms - the freezing string and Berny optimization…
Finding synthesis routes for molecules of interest is an essential step in the discovery of new drugs and materials. To find such routes, computer-assisted synthesis planning (CASP) methods are employed which rely on a model of chemical…
In order to efficiently explore the chemical space of all possible small molecules, a common approach is to compress the dimension of the system to facilitate downstream machine learning tasks. Towards this end, we present a data driven…
We study the energy-optimal shortest path problem for electric vehicles (EVs) in large-scale road networks, where recuperated energy along downhill segments introduces negative energy costs. While traditional point-to-point pathfinding…
Autonomous agents face the challenge of coordinating multiple tasks (perception, motion planning, controller) which are computationally expensive on a single onboard computer. To utilize the onboard processing capacity optimally, it is…
Rare transition events in meta-stable systems under noisy fluctuations are crucial for many non-equilibrium physical and chemical processes. In these processes, the primary contributions to reactive flux are predominantly near the…
We apply the conformational space annealing (CSA) method to the Lennard-Jones clusters and find all known lowest energy configurations up to 201 atoms, without using extra information of the problem such as the structures of the known…
When studying unconstrained behaviour and allowing mice to leave their cage to navigate a complex labyrinth, the mice exhibit foraging behaviour in the labyrinth searching for rewards, returning to their home cage now and then, e.g. to…
Optimizing paths on networks is crucial for many applications, from subway traffic to Internet communication. As global path optimization that takes account of all path-choices simultaneously is computationally hard, most existing routing…
The minimum action method (MAM) is to calculate the most probable transition path in randomly perturbed stochastic dynamics, based on the idea of action minimization in the path space. The accuracy of the numerical path between different…
We apply energy landscape methods to digital alchemy, defining a system in which the parameters of the potential are treated as degrees of freedom. Using geometrical optimisation, we locate minima and transition states on the landscape for…
In molecular mechanics, current generation potential energy functions provide a reasonably good compromise between accuracy and effectiveness. This paper firstly reviewed several most commonly used classical potential energy functions and…
In this paper a search algorithm is proposed to find a sub optimal path for a non-holonomic system. For this purpose the algorithm starts sampling the front part of the vehicle and moves towards the destination with a cost function. The…
We numerically investigate the performance of the short path optimization algorithm on a toy problem, with the potential chosen to depend only on the total Hamming weight to allow simulation of larger systems. We consider classes of…
We discuss the ``soft-ratcheting'' algorithm which generates targeted stochastic trajectories in molecular systems with scores corresponding to their probabilities. The procedure, which requires no initial pathway guess, is capable of…
Understanding the transition events between metastable states in complex systems is an important subject in the fields of computational physics, chemistry and biology. The transition pathway plays an important role in characterizing the…