相关论文: Minimum Energy Paths and Transition States by Curv…

In this paper we consider the problem of characterizing the minimum energy configurations of a finite system of particles interacting between them due to attracting or repulsive forces given by a certain inter molecular potential. We limit…

Solving chemistry is an integral part of reacting flow simulations, usually dominating the computational cost. Among the different strategies to accelerate the solution of chemistry and to achieve realizable simulations, the use of Dynamic…

Inverse problem or parameter estimation of ordinary differential equations (ODEs), the iterative process of minimizing the mismatch between model-predicted and experimental states by tuning the parameter values within an optimization…

Transition State Theory is a central cornerstone in reaction dynamics. Its key step is the identification of a dividing surface that is crossed only once by all reactive trajectories. This assumption is often badly violated, especially when…

The computer simulation of many molecular processes is complicated by long time scales caused by rare transitions between long-lived states. Here, we propose a new approach to simulate such rare events, which combines transition path…

Understanding mechanisms of rare but important events in complex molecular systems, such as protein folding or ligand (un)binding, requires accurately mapping transition paths from an initial to a final state. The committor is the ideal…

Optimization methods have been broadly applied to two classes of objects viz. (i) modeling and description of data and (ii) the determination of the stationary points of functions. Here, a theoretical basis is developed that optimizes an…

The accurate determination of the lowest electron attachment ($EA$) and ionization ($IP$) energies for molecules embedded in molecular junctions is important for correctly estimating, \emph{e.g.}, the magnitude of the currents ($I$) or the…

Shortcut schemes can accelerate quasi-static processes in passive systems by adding auxiliary controls to realize swift transitions between equilibrium states. In active systems, however, inherently directed motion driven by free energy…

In a wide range of applications it is desirable to optimally control a dynamical system with respect to concurrent, potentially competing goals. This gives rise to a multiobjective optimal control problem where, instead of computing a…

There are several applications in computational biophysics which require the optimization of discrete interacting states; e.g., amino acid titration states, ligand oxidation states, or discrete rotamer angles. Such optimization can be very…

A system containing a pre-steady state standard (non-autocatalytic) reaction, with multiple paths, evolves toward a kinetic state with the minimum attainable activation free energy. Displacement of the path frequency distribution in this…

Finding collective variables to describe some important coarse-grained information on physical systems, in particular metastable states, remains a key issue in molecular dynamics. Recently, machine learning techniques have been intensively…

We examine most-likely paths between initial and final states for diffusive quantum trajectories in continuously monitored pure-state qubits, obtained as extrema of a stochastic path integral. We demonstrate the possibility of "multipaths"…

One of the main challenges in diffusion-based molecular communication is dealing with the non-linearity of reaction-diffusion chemical equations. While numerical methods can be used to solve these equations, a change in the input signals or…

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…

The modern theory of rare events is grounded in near equilibrium ideas, however many systems of modern interest are sufficiently far from equilibrium that traditional approaches do not apply. Using the recently developed variational path…

Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…

We describe modeling approaches to a "network" of connected enzyme-catalyzed reactions, with added (bio)chemical processes that introduce biochemical filtering steps into the functioning of such a biocatalytic cascade. Theoretical…

Irradiation of cell monolayers by monoenergetic ions has made it possible to establish survival curves at individual values of linear energy transfer. The two-step model of radiobiological mechanism proposed recently by Judas and Lokajicek…