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Many monostable reaction-diffusion equations admit one-dimensional travelling waves if and only if the wave speed is sufficiently high. The values of these minimum wave speeds are not known exactly, except in a few simple cases. We present…
We present an effective field theory study of radiation and radiation reaction effects for scalar and electromagnetic fields in general spacetime dimensions. Our method unifies the treatment of outgoing radiation and its reaction force…
On the basis of the proposed algorithm for calculation of the hadron reaction rates, the space-time structure of the relativistic nucleus-nucleus collisions is studied. The reaction zones and the reaction frequencies for various types of…
The practical description of disordered chemical reactions, where reactions involve multiple species at multiple sites, is presently challenge using correlated electronic structure methods. Here we describe the gradient theory of…
We evaluate critically the use of pulsed gradient spin-echo nuclear magnetic resonance (PGSE NMR) to measure molecular mobility during chemical reactions. With raw NMR spectra available in a public depository, we confirm boosted mobility…
Reaction-nonlinear diffusion (RND) partial differential equations are a fruitful playground to model the formation of sharp travelling fronts, a fundamental pattern in nature. In this work, we demonstrate the utility and scope of…
We develop a computational method based on Dissipative Particle Dynamics (DPD) that introduces solvent hydrodynamic interactions to coarse-grained models of solutes, such as ions, molecules, or polymers. DPD-solvent (DPDS) is a fully…
Conventional molecular dynamics (MD) simulation approaches, such as $\textit{ab initio}$ MD (AIMD) and empirical force field MD (EFFMD), face significant trade-offs between physical accuracy and computational efficiency. This work presents…
The self-consistent random phase approximation (RPA), based on the framework of relativistic energy density functionals, is employed in the study of isovector and isoscalar dipole response in $^{68}$Ni, $^{132}$Sn, and $^{208}$Pb. The…
We recently proposed a new variational theory of "tensor-optimized antisymmetrized molecular dynamics" (TOAMD), which treats the strong interaction explicitly for finite nuclei [T. Myo et al., Prog. Theor. Exp. Phys. 2015, 073D02 (2015)].…
We present a new parton model approach for nuclear collisions at RHIC energies (and beyond). It is a selfconsistent treatment, using the same formalism for calculating cross sections like the total and the inelastic one and, on the other…
Molecular Dynamics - Green's Functions Reaction Dynamics (MD-GFRD) is a multiscale simulation method for particle dynamics or particle-based reaction-diffusion dynamics that is suited for systems involving low particle densities. Particles…
We study the rate of activated motion over multiple barriers, in particular the correlated double-jump of an adatom diffusing on a missing-row reconstructed Platinum (110) surface. We develop a Transition Path Theory, showing that the…
Rather than using the geometric method employed in the original Extended Quantum Molecular Dynamics (EQMD) model, this article employs a stochastic approach to analyze the collision term and examine the width of the isovector giant dipole…
This study develops an algorithm to reproduce reaction route maps (RRMs) in shape space from the outputs of potential search algorithms. To demonstrate this, GRRM is utilized as a potential search algorithm but the proposed algorithm should…
The parallel momentum distribution (PMD) of the residual nuclei of the 14O(p,pn)13O and 14O(p,2p)13N reactions at 100 and 200 MeV/nucleon in inverse kinematics is investigated with the framework of the distorted wave impulse approximation.…
We show how accurate kinetic information, such as the rates of protein folding and unfolding, can be extracted from replica-exchange molecular dynamics (REMD) simulations. From the brief and continuous trajectory segments between replica…
We review different models used for reactions involved in nuclear astrophysics. The reaction rate is defined for resonant as well as for non-resonant processes. For low-density nuclei, we describe the DWBA method, the potential model, the…
The random phase approximation (RPA) has emerged as a prominent first-principles method in material science, particularly to study the adsorption and chemisorption of small molecules on surfaces. However, its widespread application is…
An accurate treatment of the structures and dynamics that lead to enhanced chemical reactivity in enzymes requires explicit treatment of both electronic and nuclear quantum effects. The former can be captured in ab initio molecular dynamics…