Related papers: Constraint methods for determining pathways and fr…
Many theories are formulated as constrained systems. We provide a mechanism that explains the origin of physical states of a constrained system by a process of selection of noiseless subsystems when the system is coupled to an external…
Simulation-based design space exploration (DSE) aims to efficiently optimize high-dimensional structured designs under complex constraints and expensive evaluation costs. Existing approaches, including heuristic and multi-step reinforcement…
A semiclassical method of complex trajectories for the calculation of the tunneling exponent in systems with many degrees of freedom is further developed. It is supplemented with an easily implementable technique, which enables one to…
Sequences of experimental ground-state energies are mapped onto concave patterns cured from convexities due to pairing and/or shell effects. The same patterns, completed by a list of excitation energies, can be used to give numerical…
Chemical reactions involve the movement of charges, and this work presents a mathematical model for describing chemical reactions in electrolytes. The model is developed using an energy variational method that aligns with classical…
While sophisticated numerical methods for studying equilibrium states have well advanced, quantitative predictions of kinetic behaviour remain challenging. We introduce a reactant-to-barrier (R2B) machine learning model that rapidly and…
A comprehensive description of molecular electron transfer reactions is essential for our understanding of fundamental phenomena in bio-energetics and molecular electronics. Experimental studies of molecular systems in condensed-phase…
Traditional stochastic modeling of reactive systems limits the domain of applicability of the associated path thermodynamics to systems involving a single elementary reaction at the origin of each observed change in composition. An…
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…
Boundary constraints in physical, environmental and engineering models restrict smooth states such as temperature to follow known physical laws at the edges of their spatio-temporal domain. Examples include fixed-state or fixed-derivative…
We report several important observations that underscore the distinctions between the constrained-path Monte Carlo method and the continuum and lattice versions of the fixed-node method. The main distinctions stem from the differences in…
We use analytical calculations and event-driven molecular dynamics simulations to study a small number of hard sphere particles in a spherical cavity. The cavity is taken also as the thermal bath so that the system thermalizes by collisions…
Reaction coordinates (RCs) are the few essential coordinates of a protein that control its functional processes, such as allostery, enzymatic reaction, and conformational change. They are critical for understanding protein function and…
Protein folding processes are generally described statistically with the help of multidimensional free energy landscape, typically reduced to a 1-D free energy profile along good reaction co-ordinate. There are many physical parameters…
Chemical reaction rates must increasingly be determined in systems that evolve under the control of external stimuli. In these systems, when a reactant population is induced to cross an energy barrier through forcing from a temporally…
In this paper, we consider Markov Decision Processes (MDPs) with error states. Error states are those states entering which is undesirable or dangerous. We define the risk with respect to a policy as the probability of entering such a state…
Molecule- and particle-based simulations provide the tools to test, in microscopic detail, the validity of classical nucleation theory. In this endeavour, determining nucleation mechanisms and rates for phase separation requires an…
We analyse a dynamic control problem for scalar reaction-diffusion equations, focusing on the emulation of pattern formation through the selection of appropriate active controls. While boundary controls alone prove inadequate for…
The analysis of non-equilibrium steady states of biochemical reaction networks relies on finding the configurations of fluxes and chemical potentials satisfying stoichiometric (mass balance) and thermodynamic (energy balance) constraints.…
The ability to predict accurate thermodynamic and kinetic properties in biomolecular systems is of both scientific and practical utility. While both remain very difficult, predictions of kinetics are particularly difficult because rates, in…