Related papers: Persistence of transition state structure in chemi…
The time evolution of many physical, chemical, and biological systems can be modelled by stochastic transitions between the minima of the potential energy surface describing the system of interest. We show that in cases where there are two…
Phase separation is the thermodynamic process that explains how droplets form in multicomponent fluids. These droplets can provide controlled compartments to localize chemical reactions, and reactions can also affect the droplets' dynamics.…
A transition state for a Hamiltonian system is a closed, invariant, oriented, codimension-2 submanifold of an energy-level that can be spanned by two compact codimension-1 surfaces of unidirectional flux whose union, called a dividing…
A known limitation of time-dependent mean-field approaches is a lack of quantum tunneling for collective motions such as in sub-barrier fusion reactions. As a first step toward a solution, a time-dependent model is considered using a…
When an interacting many-body system, such as a magnet, is driven in time by an external perturbation, such as a magnetic field,the system cannot respond instantaneously due to relaxational delay. The response of such a system under a…
Non-equilibrium critical phenomena generally exist in many dynamic systems, like chemical reactions and some driven-dissipative {reactive} particle systems. Here, by using computer simulation and theoretical analysis, we demonstrate the…
Many processes in chemistry, physics, and biology involve rare events in which the system escapes from a metastable state by surmounting an activation barrier. Examples range from chemical reactions, protein folding, and nucleation events…
Synthetic nanoscale complexes capable of mechanical movement are often studied theoretically using discrete-state models that involve instantaneous transitions between metastable states. A number of general results have been derived within…
Spontaneous breaking of continuous time translation symmetry into a discrete one is related to time crystal formation. While the phenomenon is not possible in the ground state of a time-independent many-body system, it can occur in an…
Mechanically induced crystallographic phase transformation that reflects dynamic stress responses of intrinsically stochastic nature is a pertinent yet much less well-understood phenomenon. We focus on understanding the physical…
We provide a dynamical interpretation of the recently identified `roaming' mechanism for molecular dissociation reactions in terms of geometrical structures in phase space. These are NHIMs (Normally Hyperbolic Invariant Manifolds) and their…
We study the effect of changes in the parameters of a two-dimensional potential energy surface on the phase space structures relevant for chemical reaction dynamics. The changes in the potential energy are representative of chemical…
Stochastic dynamics of chemical reactions in a mutually repressing two-gene circuit is numerically simulated. The circuit has a rich variety of different states when the kinetic change of DNA status is slow. The stochastic switching…
A model Hamiltonian for the reaction CH$_4^+ \rightarrow$ CH$_3^+$ + H, parametrized to exhibit either early or late inner transition states, is employed to investigate the dynamical characteristics of the roaming mechanism. Tight/loose…
The transient behaviour of highly concentrated colloidal liquids and dynamically arrested states (glasses) under time-dependent shear is reviewed. This includes both theoretical and experimental studies and comprises the macroscopic…
Major efforts in recent years have been directed towards understanding molecular transport in polymeric membranes, in particular reverse osmosis and nanofiltration membranes. Transition-state theory is an increasingly common approach to…
The transition states and dividing surfaces used to find rate constants for bimolecular reactions are shown to undergo qualitative changes, known as Morse bifurcations, and to exist for a large range of energies, not just immediately above…
We consider the existence of invariant manifolds in phase space governing reaction dynamics in situations where there are no saddle points on the potential energy surface in the relevant regions of configuration space. We point out that…
The use of fully or partially absorbing boundary conditions for diffusion-based problems has become paradigmatic in physical chemistry and biochemistry to describe reactions occurring in solutions or in living media. However, as chemical…
A multi-phase-field model for the description of the discontinuous precipitation reaction is formulated which takes into account surface diffusion along grain boundaries and interfaces as well as volume diffusion. Simulations reveal that…