Related papers: Minima Hopping Guided Path Search: An Efficient Me…

During a crossover via a switching mechanism from one 2-body potential to another as might be applied in modeling (chemical) reactions in the vicinity of bond formation, energy violations would occur due to finite step size which determines…

Chemical kinetic mechanisms can be represented by sets of elementary reactions that are easily translated into mathematical terms using physicochemical relationships. The schematic representation of reactions captures the interactions…

We present a one-way shooting algorithm for transition path sampling that accepts every proposed trajectory, yet samples the correct transition path ensemble for systems with overdamped stochastic dynamics. The method is based on two key…

Transition state theory is a standard framework for predicting the rate of a chemical reaction. Although the transition state theory has been successfully applied to numerous chemical reaction analyses, many experimental and theoretical…

The rise of globalisation has led to a sharp increase in international trade, with high volumes of containers, goods and items moving across the world. Unfortunately, these trade pathways also facilitate the movement of unwanted pests,…

We present a novel multiscale simulation approach for modeling stochasticity in chemical reaction networks. The approach seamlessly integrates exact-stochastic and "leaping" methodologies into a single "partitioned leaping" algorithmic…

A method for locating first order saddle points on the energy surface of a magnetic system is described and several applications presented where the mechanism of various magnetic transitions is identified. The starting point for the…

Stable states in complex systems correspond to local minima on the associated potential energy surface. Transitions between these local minima govern the dynamics of such systems. Precisely determining the transition pathways in complex and…

The free energy profile of a reaction can be estimated in a molecular-dynamics approach by imposing a mechanical constraint along a reaction coordinate (RC). Many recent studies have shown that the temperature can greatly influence the path…

Transition-state searches are central to understanding reaction mechanisms, but the high computational cost of density-functional theory (DFT) limits their application in high-throughput catalyst and materials discovery. Machine-learned…

How systems transit between different stable states under external perturbation is an important practical issue. We discuss here how a recently-developed energy optimization method for identifying the minimal disturbance necessary to reach…

The paper presents a dynamic solution method for dynamic minimum parametric networks flow. The solution method solves the problem for a special parametric dynamic network with linear lower bound functions of a single parameter. Instead…

Finding the shortest paths in road network is an important query in our life nowadays, and various index structures are constructed to speed up the query answering. However, these indexes can hardly work in real-life scenario because the…

The identification of low-energy conformers for a given molecule is a fundamental problem in computational chemistry and cheminformatics. We assess here a conformer search that employs a genetic algorithm for sampling the low-energy segment…

Cell state determination is the outcome of intrinsically stochastic biochemical reactions. Tran- sitions between such states are studied as noise-driven escape problems in the chemical species space. Escape can occur via multiple possible…

Global optimization of crystal compositions is a significant yet computationally intensive method to identify stable structures within chemical space. The specific physical properties linked to a three-dimensional atomic arrangement make…

There is a rich recent literature on how to assist secure communication between a single transmitter and receiver at the physical layer of wireless networks through techniques such as cooperative jamming. In this paper, we consider how…

This paper deals with temporal enzyme distribution in the activation of biochemical pathways. Pathway activation arises when production of a certain biomolecule is required due to changing environmental conditions. Under the premise that…

Motion planning is a critical component of intelligent unmanned systems, enabling their complex autonomous operations. However, current planning algorithms still face limitations in planning efficiency due to inflexible strategies and weak…

We created a computational workflow to analyze the potential energy surface (PES) of materials using machine-learned interatomic potentials in conjunction with the minima hopping algorithm. We demonstrate this method by producing a…