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Due to quasicrystals having long-range orientational order but without translational symmetry, traditional numerical methods usually suffer when applied as is. In the past decade, the projection method has emerged as a prominent solver for…
The response of proteins to chemical reactions or impulsive excitation that occurs within the molecule has fascinated chemists for decades. In recent years ultrafast X-ray studies have provided ever more detailed information about the…
Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and…
A method to generate reactive trajectories, namely equilibrium trajectories leaving a metastable state and ending in another one is proposed. The algorithm is based on simulating in parallel many copies of the system, and selecting the…
In this paper we propose a contour mean calculation and interpolation method designed for averaging manual delineations of objects performed by experts and interpolate 3D layer stack images. The proposed method retains all visible…
Model reduction methods are relevant when the computation time of a full convection-diffusion-reaction simulation based on detailed chemical reaction mechanisms is too large. In this article, we review a model reduction approach based on…
In the last decade, advances in molecular dynamics (MD) and Markov State Model (MSM) methodologies have made possible accurate and efficient estimation of kinetic rates and reactive pathways for complex biomolecular dynamics occurring on…
Motivated by what is required for real-time path planning, the paper starts out by presenting sRMPD, a new recursive "local" planner founded on the key notion that, unless made necessary by an obstacle, there must be no deviation from the…
This paper is devoted to the development of a theoretical and computational framework to efficiently sample the statistically significant thermally activated reaction pathways, in multi-dimensional systems obeying Langevin dynamics. We show…
Mobile robots frequently navigate on roadmaps, i.e., graphs where edges represent safe motions, in applications such as healthcare, hospitality, and warehouse automation. Often the environment is quasi-static, i.e., it is sufficient to…
Gyroscopic interconnections enable redistribution of energy among degrees of freedom while preserving passivity and total energy, and they play a central role in controlled Lagrangian methods and IDA-PBC. Yet their quantitative effect on…
This Feature Article presents an overview of the current status of Ring Polymer Molecular Dynamics (RPMD) rate theory. We first analyze the RPMD approach and its connection to quantum transition-state theory. We then focus on its practical…
We present a method to sample reactive pathways via biased molecular dynamics simulations in trajectory space. We show that the use of enhanced sampling techniques enables unconstrained exploration of multiple reaction routes. Time…
Simulating transition dynamics between metastable states is a fundamental challenge in dynamical systems and stochastic processes with wide real-world applications in understanding protein folding, chemical reactions and neural activities.…
Experimental studies of protein-pattern formation have stimulated new interest in the dynamics of reaction-diffusion systems. However, a comprehensive theoretical understanding of the dynamics of such highly nonlinear, spatially extended…
Mapping the chemical reaction pathways and their corresponding activation barriers is a significant challenge in molecular simulation. Given the inherent complexities of 3D atomic geometries, even generating an initial guess of these paths…
Simulating chemical reactions is a central challenge in computational chemistry, characterized by an uneven difficulty profile: while equilibrium reactant and product geometries are often classically tractable, intermediate transition…
Many chemical reactions can be formulated in terms of particle diffusion in a complex energy landscape. Transition path theory (TPT) is a theoretical framework for describing the direct (reaction) pathways from reactant to product states…
We introduce mapping-variable ring polymer molecular dynamics (MV-RPMD), a model dynamics for the direct simulation of multi-electron processes. An extension of the RPMD idea, this method is based on an exact, imaginary time path-integral…
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…