相关论文: Minimum Energy Paths and Transition States by Curv…

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…

Chemical kinetics plays an important role in governing the thermal evolution in reactive flows problems. The possible interactions between chemical species increase drastically with the number of species considered in the system. Various…

Industrial robotics demands significant energy to operate, making energy-reduction methodologies increasingly important. Strategies for planning minimum-energy trajectories typically involve solving nonlinear optimal control problems…

Although machine-learning potentials have recently had substantial impact on molecular simulations, the construction of a robust training set can still become a limiting factor, especially due to the requirement of a reference ab initio…

When two distinct ordered phases contact, the interface may exhibit rich and fascinating structures. Focusing on the Cylinder-Gyroid interface system, transition pathways connecting various interface morphologies are studied armed with the…

We have developed a novel method to evaluate the potential profile of a molecular motor at each chemical state from only the probe's trajectory and applied it to a rotary molecular motor F$_1$-ATPase. By using this method, we could also…

We apply the minimum energy paths (MEPs) approach to study the helix unwinding transition in chiral nematic liquid crystals. A mechanism of the transition is determined by a MEP passing through a first order saddle point on the free energy…

The probability of trajectories of weakly diffusive processes to remain in the tubular neighbourhood of a smooth path is given by the Freidlin-Wentzell-Graham theory of large deviations. The most probable path between two states (the…

Parameter fitting of data to a proposed equation almost always consider these parameters as independent variables. Here, the method proposed optimizes an arbitrary number of variables by the minimization of a function of a single variable.…

Transition path sampling (TPS) is a powerful technique for investigating rare transitions, especially when the mechanism is unknown and one does not have access to the reaction coordinate. Straightforward application of TPS does not…

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…

We present a new method that enables the identification and analysis of both transition and metastable conformational states from atomistic or coarse-grained molecular dynamics (MD) trajectories. Our algorithm is presented and studied by…

Motivation: Many biochemical pathways are known, but the numerous parameters required to correctly explore the dynamics of the pathways are not known. For this reason, algorithms that can make inferences by looking at the topology of a…

Techniques for producing cold and ultracold molecules are enabling the study of chemical reactions and scattering at the quantum scattering limit, with only a few partial waves contributing to the incident channel, leading to the…

In this paper we present a procedure to integrate, up to quadratures, the matching conditions of the energy shaping method. We do that in the context of underactuated Hamiltonian systems defined by simple Hamiltonian functions. For such…

Transitions in the qualitative behavior of chemical reaction dynamics with a decrease in molecule number have attracted much attention. Here, a method based on a Markov process with a tridiagonal transition matrix is applied to the analysis…

A new method is developed for accurately approximating the solution to state-variable inequality path constrained optimal control problems using a multiple-domain adaptive Legendre-Gauss-Radau collocation method. The method consists of the…

First-order nonequilibrium phase transitions observed in active matter, fluid dynamics, biology, climate science, and other systems with irreversible dynamics are challenging to analyze because they cannot be inferred from a simple free…

This paper develops some basic principles to study autocatalytic networks and exploit their structural properties in order to characterize their inherent fundamental limits and tradeoffs. In a dynamical system with autocatalytic structure,…

Using the Dominant Reaction Pathways method, we perform an ab-initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of…