Related papers: Topological methods for searching barriers and rea…
Discriminating between correct and incorrect substrates is a core process in biology but how is energy apportioned between the conflicting demands of accuracy ($\mu$), speed ($\sigma$) and total entropy production rate ($P$)? Previous…
This study introduces a pore morphology algorithm that emphasizes the central role of topology in multiphase flow through porous media. Analysis of drainage in lattice-based pore networks identifies two key quantities, the percolation…
Ring-polymer instanton theory has been developed to simulate the quantum dynamics of molecular systems at low temperatures. Chemical reaction rates can be obtained by locating the dominant tunneling pathway and analyzing fluctuations around…
Probing the reaction mechanisms of supramolecular processes in soft- and biological matter, such as protein aggregation, is inherently challenging. These processes emerge from the simultaneous action of multiple molecular mechanisms, each…
Algorithms based on the particle flow approach are becoming increasingly utilized in collider experiments due to their superior jet energy and missing energy resolution compared to the traditional calorimeter-based measurements. Such…
Present knowledge of the function of materials is largely based on studies (experimental and theoretical) that are performed at low temperatures and ultra-low pressures. However, the majority of everyday applications, like e.g. catalysis,…
The analysis of temporal networks heavily depends on the analysis of time-respecting paths. However, before being able to model and analyze the time-respecting paths, we have to infer the timescales at which the temporal edges influence…
The chaotical dynamics is studied in different Friedmann-Robertson- Walker cosmological models with scalar (inflaton) field and hydrodynamical matter. The topological entropy is calculated for some particular cases. Suggested scheme can be…
Surfaces serve as highly efficient catalysts for a vast variety of chemical reactions. Typically, such surface reactions involve billions of molecules which diffuse and react over macroscopic areas. Therefore, stochastic fluctuations are…
Models invoking the chemical master equation are used in many areas of science, and, hence, their simulation is of interest to many researchers. The complexity of the problems at hand often requires considerable computational power, so a…
Simulating transition dynamics between metastable states is a fundamental challenge in dynamical systems and stochastic processes with wide real-world applications in understanding protein folding, chemical reactions and neural activities.…
We develop a path-based approach to continuous-time random walks on networks with arbitrarily weighted edges. We describe an efficient numerical algorithm for calculating statistical properties of the stochastic path ensemble. After…
We present an algorithm to compute path homology for simple digraphs, and use it to topologically analyze various small digraphs en route to an analysis of complex temporal networks which exhibit such digraphs as underlying motifs. The…
Over the billions of years since the Big Bang, the lives, deaths and afterlives of stars have enriched the Universe in the heavy elements that make up so much of ourselves and our world. This review summarizes the methods used to evolve…
Recurrence is a fundamental characteristic of dynamical systems with complicated behavior. Understanding the inner structure of recurrence is challenging, especially if the system has many degrees of freedom and is subject to noise. We…
For many materials, a precise knowledge of their dispersion spectra is insufficient to predict their ordered phases and physical responses. Instead, these materials are classified by the geometrical and topological properties of their…
We use topological data analysis and machine learning to study a seminal model of collective motion in biology [D'Orsogna et al., Phys. Rev. Lett. 96 (2006)]. This model describes agents interacting nonlinearly via attractive-repulsive…
Recent discoveries have demonstrated that matter can be distinguished on the basis of topological considerations, giving rise to the concept of topological phase. Introduced originally in condensed matter physics, the physics of topological…
A method for integrating the chemical equations associated with nuclear combustion at high temperature is presented and extensively checked. Following the idea of E. M\"uller, the feedback between nuclear rates and temperature was taken…
We develop a broadly-applicable computational method for the automatic exploration of the bimolecular multi-reaction mechanism. The current methodology mainly involves the high-energy Born-Oppenheimer molecular dynamics (BOMD) simulation…