Related papers: A multiple replica approach to simulate reactive t…
Humans routinely retrace paths in a novel environment both forwards and backwards despite uncertainty in their motion. This paper presents an approach for doing so. Given a demonstration of a path, a first network generates a path…
Many enhanced sampling techniques rely on the identification of a number of collective variables that describe all the slow modes of the system. By constructing a bias potential in this reduced space one is then able to sample efficiently…
It is well known that numerical simulations of high-speed reacting flows, in the framework of state-to-state formulations, are the most detailed but also often prohibitively computationally expensive. In this work, we start to investigate…
Large continuous-time Markov chains with exponentially small transition rates arise in modeling complex systems in physics, chemistry and biology. We propose a constructive graph-algorithmic approach to determine the sequence of critical…
Dynamical system models of complex biochemical reaction networks are usually high-dimensional, nonlinear, and contain many unknown parameters. In some cases the reaction network structure dictates that positive equilibria must be unique for…
We present a new method for constructing equilibrium phase models for stellar systems, which we call the iterative method. It relies on constrained, or guided evolution, so that the equilibrium solution has a number of desired parameters…
Molecular dynamics simulations are a cornerstone in science, allowing to investigate from the system's thermodynamics to analyse intricate molecular interactions. In general, to create extended molecular trajectories can be a…
Trajectories of a signal that fluctuates between two states which originate from single molecule activities have become ubiquitous. Common examples are trajectories of ionic flux through individual membrane-channels, and of photon counts…
We used for the first time the method of periodic orbit dividing surfaces in a non-integrable Hamiltonian system with three degrees of freedom. We have studied the structure of these four dimensional objects in the five dimensional phase…
Machine learning approaches have recently been leveraged as a substitute or an aid for physical/mathematical modeling approaches to dynamical systems. To develop an efficient machine learning method dedicated to modeling and prediction of…
Relying on the recently proposed multicanonical algorithm, we present a numerical simulation of the first order phase transition in the 2d 10-state Potts model on lattices up to sizes $100\times100$. It is demonstrated that the new…
A computational procedure is developed for determining the conversion probability for reaction-diffusion systems in which a first-order catalytic reaction is performed over active particles. We apply this general method to systems on metric…
Algorithms to determine transition probabilities in Monte Carlo simulations are tested using a system of classical particles with effective interactions which reproduce Bose-Einstein statistics. The system is appropriate for testing…
Optimal state-feedback controllers, capable of changing between different objective functions, are advantageous to systems in which unexpected situations may arise. However, synthesising such controllers, even for a single objective, is a…
Rare transitions between long-lived metastable states underlie a great variety of physical, chemical and biological processes. Our quantitative understanding of reactive mechanisms has been driven forward by the insights of transition state…
The neural dynamics of the nematode C. elegans are experimentally low-dimensional and correspond to discrete behavioral states, where previous modeling work has found neural proxies for some of these states. Experimental results further…
An iterative method is derived for image reconstruction. Among other attributes, this method allows constraints unrelated to the radiation measurements to be incorporated into the reconstructed image. A comparison is made with the widely…
We discuss multi-dimensional generalizations of multicanonical algorithm, simulated tempering, and replica-exchange method. We generalize the original potential energy function $E_0$ by adding any physical quantity $V$ of interest as a new…
A time trajectory of an observable that fluctuates between two values (say, on and off), stemming from some unknown multi-substate kinetic scheme, is the output of many single molecule experiments. Here we show that when all successive…
Determining the kinetic bottlenecks that make transitions between metastable states difficult is key to understanding important physical problems like crystallization, chemical reactions, or protein folding. In all these phenomena, the…