Related papers: Topological methods for searching barriers and rea…
The consecutive microscopic solution is presented of the problem of tunneling of a particle through a potential barrier. The method is applied to the alpha and proton decay of compound systems formed in fusion reaction. Appearance of the…
Many models in natural and social sciences are comprised of sets of inter-acting entities whose intensity of interaction decreases with distance. This often leads to structures of interest in these models composed of dense packs of…
Chemical reactions subjected to time-varying external forces cannot generally be described through a fixed bottleneck near the transition state barrier or dividing surface. A naive dividing surface attached to the instantaneous, but moving,…
Discrete-state, continuous-time Markov models are widely used in the modeling of biochemical reaction networks. Their complexity often precludes analytic solution, and we rely on stochastic simulation algorithms to estimate system…
Estimating free energy differences, an important problem in computational drug discovery and in a wide range of other application areas, commonly involves a computationally intensive process of sampling a family of high-dimensional…
Langevin/Fokker-Planck processes can be immersed in a larger frame by adding fictitious fermion variables. The (super)symmetry of this larger structure has been used to derive Morse theory in an elegant way. The original physical diffusive…
Graph transformation systems have the potential to be realistic models of chemistry, provided a comprehensive collection of reaction rules can be extracted from the body of chemical knowledge. A first key step for rule learning is the…
Phase diagrams serve as a highly informative tool for materials design, encapsulating information about the phases that a material can manifest under specific conditions. In this work, we develop a method in which Bayesian inference is…
A non-linear conjugate gradient optimization scheme is used to obtain excitation energies within the Random Phase Approximation (RPA). The solutions to the RPA eigenvalue equation are located through a variational characterization using a…
We propose an analytical study of relativistic tunneling through opaque barriers. We obtain a closed formula for the phase time. This formula is in excellent agreement with the numerical simulations and corrects the standard formula…
Motion path planning is an intrinsically geometric problem which is central for design of robot systems. Since the early years of AI, robotics together with computer vision have been the areas of computer science that drove its development.…
The usual identification of reactive trajectories for the calculation of reaction rates requires very time-consuming simulations, particularly if the environment presents memory effects. In this paper, we develop a new method that permits…
Thermodynamic constraints on reactions directions are inherent in the structure of a given biochemical network. However, concrete procedures for determining feasible reaction directions for large-scale metabolic networks are not well…
Using a recently developed procedure - multiple wave packet decomposition - here we study the phase time formulation for tunneling/reflecting particles colliding with a potential barrier. To partially overcome the analytical difficulties…
Community detection is one of the most active fields in complex networks analysis, due to its potential value in practical applications. Many works inspired by different paradigms are devoted to the development of algorithmic solutions…
Time-variant systems have recently garnered considerable attention due to their unique potentials in manipulating electromagnetic waves. Here, a novel class of topological spacetime crystals is introduced, with a traveling-wave modulation…
Scaling analysis exploiting timescale separation has been one of the most important techniques in the quantitative analysis of nonlinear dynamical systems in mathematical and theoretical biology. In the case of enzyme catalyzed reactions,…
Coordinating multiple local power sources can restore critical loads after the major outages caused by extreme events. A radial topology is needed for distribution system restoration, while determining a good topology in real-time for…
Biomolecular folding, at least in simple systems, can be described as a two state transition in a free energy landscape with two deep wells separated by a high barrier. Transition paths are the short part of the trajectories that cross the…
Free energy landscapes decisively determine the progress of enzymatically catalyzed reactions[1]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [2-4] because both can be…