Related papers: Persistence of transition state structure in chemi…
Transition path theory provides a statistical description of the dynamics of a reaction in terms of local spatial quantities. In its original formulation, it is limited to reactions that consist of trajectories flowing from a reactant set A…
The physics of activated escape of objects out of a metastable state plays a key role in diverse scientific areas involving chemical kinetics, diffusion and dislocation motion in solids, nucleation, electrical transport, motion of flux…
Diffusion-mediated surface phenomena are crucial for human life and industry, with examples ranging from oxygen capture by lung alveolar surface to heterogeneous catalysis, gene regulation, membrane permeation and filtration processes.…
We review a theoretical perspective of the dynamics of glass forming liquids and the glass transition. It is a perspective we have developed with our collaborators during this decade. It is based upon the structure of trajectory space. This…
The rate of a chemical reaction can often be determined by the properties of a rank-1 saddle and the associated transition state separating reactants and products. We have found evidence that such rates can be controlled and even enhanced…
Phyllotactic states are regular lattice-like structures on cylinders and are a botanical classification scheme. In this communication, we report a sequence of transitions between phyllotactic states for particles with a repulsive…
Understanding anomalous transport and reaction kinetics due to microscopic physical and chemical disorder is a long-standing goal in many fields including geophysics, biology, and engineering. We consider reaction-diffusion characterized by…
A one-dimensional reaction-diffusion model consisting of two species of particles and vacancies on a ring is introduced. The number of particles in one species is conserved while in the other species it can fluctuate because of creation and…
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…
In this article, we review the analytical and numerical approaches for computing the phase space structures in two degrees-of-freedom Hamiltonian systems that arise in chemical reactions. In particular, these phase space structures are the…
Reaction networks are widely used models to describe biochemical processes. Stochastic fluctuations in the counts of biological macromolecules have amplified consequences due to their small population sizes. This makes it necessary to favor…
The atmospheric reaction of H$_2$S with Cl has been reinvestigated to check if, as previously suggested, only explicit dynamical computations can lead to an accurate evaluation of the reaction rate because of strong recrossing effects and…
In Part I [J. Chem. Phys. 138, 084108 (2013)] we derived a quantum transition-state theory by taking the t->0+ (short-time) limit of a new form of quantum flux-side time-correlation function containing a ring-polymer dividing surface. This…
The existence and search for thermodynamic phase transitions is of unfading interest. In this paper, we present numerical evidence of dynamical phase transitions occurring in boundary driven systems with a constrained integrated current. It…
The barriers between metastable states near the glass transition of a random heteropolymer are studied using replicas by describing inhomogeneous states. The instanton solution for a replica space free energy functional is found numerically…
Quantum vacuum fluctuations of the electromagnetic field in empty space seem not to produce observable effects over the motion of a charged test particle. However, when a change in the background vacuum state is implemented, as for instance…
Continuous time crystals, i.e., nonequilibrium phases with a spontaneously broken continuous time-translational symmetry, have been studied and recently observed in the long-time dynamics of open quantum systems. Here, we investigate a…
Droplets help organize cells by compartmentalizing biomolecules and by mediating mechanical interactions. When bridging two structures, such droplets generate capillary forces, which depend on surface properties and distance. While the…
A spatially extended classical system with metastable states subject to weak spatiotemporal noise can exhibit a transition in its activation behavior when one or more external parameters are varied. Depending on the potential, the…
Nonequilibrium steady state of isothermal biochemical cycle kinetics has been extensively studied, but much less investigated under non-isothermal conditions. However, once the heat exchange between subsystems is rather slow, the isothermal…