Related papers: Transition State Theory for dissipative systems wi…
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…
Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables(CVs) it can explore complex free energy surfaces…
Given a discrete-state continuous-time reactive system, like a digital circuit, the classical approach is to first model it as a state transition system and then prove its properties. Our contribution advocates a different approach: to…
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…
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…
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…
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…
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…
The crossing of a transition state in a multidimensional reactive system is mediated by invariant geometric objects in phase space: An invariant hyper-sphere that represents the transition state itself and invariant hyper-cylinders that…
The transformation of a system from one state to another is often mediated by a bottleneck in the system's phase space. In chemistry these bottlenecks are known as \emph{transition states} through which the system has to pass in order to…
We investigate the critical behavior of a reaction-diffusion system exhibiting a continuous absorbing-state phase transition. The reaction-diffusion system strictly conserves the total density of particles, represented as a non-diffusive…
A new formulation of statistical mechanics is put forward according to which a random variable characterizing a macroscopic body is postulated to be infinitely divisible. It leads to a parametric representation of partition function of an…
A statistical-mechanical treatment of collision leads to a formal connection with transition-state theory, suggesting that collision theory and transition-state theory might be joined ultimately as a collision induced transition state…
We develop a mean-field theory for the totally asymmetric simple exclusion process (TASEP) with open boundaries, in order to investigate the so-called dynamical transition. The latter phenomenon appears as a singularity in the relaxation…
We present a means of studying rare reactive pathways in open quantum systems using Transition Path Theory and ensembles of quantum jump trajectories. This approach allows for elucidation of reactive paths for dissipative, nonadiabatic…
To mimic the complex transport-like collective phenomena in a man-made or natural system, we study an open network junction model of totally asymmetric simple exclusion process with bulk particle attachment and detachment. The stationary…
We overview the concept of dynamical phase transitions in isolated quantum systems quenched out of equilibrium. We focus on non-equilibrium transitions characterized by an order parameter, which features qualitatively distinct temporal…
The rate of escape of an ideal bead-spring polymer in a symmetric double-well potential is calculated using transition state theory (TST) and the results compared with direct dynamical simulations. The minimum energy path of the transitions…
A geometrical model which captures the main ingredients governing atom-diatom collinear chemical reactions is proposed. This model is neither near-integrable nor hyperbolic, yet it is amenable to analysis using a combination of the recently…
Autocatalytic reaction system with a small number of molecules is studied numerically by stochastic particle simulations. A novel state due to fluctuation and discreteness in molecular numbers is found, characterized as extinction of…