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Electrocyclic reactions are characterized by the concerted formation and cleavage of both {\sigma} and {\pi} bonds through a cyclic structure. This structure is known as a pericyclic transition state for thermal reactions and a pericyclic…
Recently a non-empirical stochastic walker algorithm has been developed to search for the minimum-energy escape paths (MEP) from the minima of the potential surface [J. Phys. Soc. Jpn. 87, 063801 (2018); Physica A, 528, 121481 (2019)]. This…
Deriving emergent patterns from models of biological processes is a core concern of mathematical biology. In the context of partial differential equations (PDEs), these emergent patterns sometimes appear as local minimisers of a…
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…
Understanding kinetics including reaction pathways and associated transition rates is an important yet difficult problem in numerous chemical and biological systems especially in situations with multiple competing pathways. When these…
Electromagnetic transient (EMT) simulation is a crucial tool for power system dynamic analysis because of its detailed component modeling and high simulation accuracy. However, it suffers from computational burdens for large power grids…
In this letter, we develop a framework to study the mechanical response of athermal amorphous solids via a coupling of mesoscale and microscopic models. Using measurements of coarse grained quantities from simulations of dense disordered…
Understanding the applicability and limitations of electronic-structure methods needs careful and efficient comparison with accurate reference data. Knowledge of the quality and errors of electronic-structure calculations is crucial to…
Interconnection and Damping Assignment Passivity-Based Control (IDA-PBC) is a well-established stabilization technique for affine nonlinear systems. However, its application is generally hindered by the requirement of solving a set of…
RNA function is tied to secondary structure, operating through dynamic and heterogeneous structural ensembles. While current analysis tools typically output single static structures or averaged contact maps, chemical probing methods like…
The nuclear fission process is a dramatic example of the large-amplitude collective motion in which the nucleus undergoes a series of shape changes before splitting into distinct fragments. This motion can be represented by a pathway in the…
The prediction of energetically stable crystal structures formed by a given chemical composition is a central problem in solid-state physics. In principle, the crystalline state of assembled atoms can be determined by optimizing the energy…
The Empirical Valence Bond (EVB) method offers a suitable framework to obtain reactive potentials through the coupling of non-reactive force fields. However, most of the implemented functional forms for the coupling terms depend on complex…
We have developed an efficient crystal structure prediction (CSP) method for desired chemical compositions, specifically suited for compounds featuring recurring molecules or rigid bodies. We applied this method to two metal chalcogenides:…
An energy gap develops near quantum critical point of quantum phase transition in a finite many-body (MB) system, facilitating the ground state transformation by adiabatic parameter change. In real application scenarios, however, the…
Many physical properties of small organic molecules are dependent on the current crystal packing, or polymorph, of the material, including bioavailability of pharmaceuticals, optical properties of dyes, and charge transport properties of…
The asymmetric simple exclusion process (ASEP) with periodic boundary conditions is investigated for shuffled dynamics. In this type of update, in each discrete timestep the particles are updated in a random sequence. Such an update is…
The magnetic relaxation processes in disordered two-dimensional ensembles of dipole-coupled magnetic nanoparticles are theoretically investigated by performing numerical simulations. The energy landscape of the system is explored by…
For over 30 years, mode-coupling theory (MCT) has been the de facto theoretic description of dense fluids and the liquid-glass transition. MCT, however, is limited by its ad hoc construction and lacks a mechanism to institute corrections.…
Activated transitions have rates that are often exponentially small in system size. Extracting the associated activation barriers is challenging in practice, especially in the deeply metastable regimes and in the presence of disorder. Here,…