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We present a new method, Non-Stationary Forward Flux Sampling, that allows efficient simulation of rare events in both stationary and non-stationary stochastic systems. The method uses stochastic branching and pruning to achieve uniform…

Molecular Networks · Quantitative Biology 2015-06-03 Nils B. Becker , Rosalind J. Allen , Pieter Rein ten Wolde

Destination prediction is an essential task in a variety of mobile applications. In this paper, we optimize the matrix operation and adapt a semi-lazy framework to improve the prediction accuracy and efficiency of a state-of-the-art…

Databases · Computer Science 2018-07-11 Zhou Yang , Heli Sun , Jianbin Huang , Xiaolin Jia , Ziyu Guan , Zhongmeng Zhao

Many processes in nature such as conformal changes in biomolecules and clusters of interacting particles, genetic switches, mechanical or electromechanical oscillators with added noise, and many others are modeled using stochastic…

Optimization and Control · Mathematics 2023-10-13 Jiaxin Yuan , Amar Shah , Channing Bentz , Maria Cameron

Rare events in molecular dynamics are often related to noise-induced transitions between different macroscopic states (e.g., in protein folding). A common feature of these rare transitions is that they happen on timescales that are on…

Probability · Mathematics 2026-01-06 Carsten Hartmann , Annika Jöster , Christof Schütte , Alexander Sikorski , Marcus Weber

Dynamical fluctuations or rare events associated with atypical trajectories in chaotic maps due to specific initial conditions can crucially determine their fate, as the may lead to stability islands or regions in phase space otherwise…

Statistical Mechanics · Physics 2024-01-31 Ricardo Gutiérrez , Adrián Canella-Ortiz , Carlos Pérez-Espigares

We present three algorithms for calculating rate constants and sampling transition paths for rare events in simulations with stochastic dynamics. The methods do not require a priori knowledge of the phase space density and are suitable for…

Soft Condensed Matter · Physics 2009-11-11 Rosalind J. Allen , Daan Frenkel , Pieter Rein ten Wolde

Simulating rare events, such as the transformation of a reactant into a product in a chemical reaction typically requires enhanced sampling techniques that rely on heuristically chosen collective variables (CVs). We propose using…

We propose a new Monte Carlo method for efficiently sampling trajectories with fixed initial and final conditions in a system with discrete degrees of freedom. The method can be applied to any stochastic process with local interactions,…

Statistical Mechanics · Physics 2012-03-30 Thierry Mora , Aleksandra M. Walczak , Francesco Zamponi

Importance sampling of trajectories has proved a uniquely successful strategy for exploring rare dynamical behaviors of complex systems in an unbiased way. Carrying out this sampling, however, requires an ability to propose changes to…

Statistical Mechanics · Physics 2015-07-01 Todd R. Gingrich , Phillip L. Geissler

We have shown recently that a Markov process conditioned on rare events involving time-integrated random variables can be described in the long-time limit by an effective Markov process, called the driven process, which is given…

Statistical Mechanics · Physics 2015-12-17 Raphael Chetrite , Hugo Touchette

In stochastic resonance, a periodically forced Brownian particle in a double-well potential jumps between minima at rare increments, the prediction of which poses a major theoretical challenge. Here, we use a path-integral method to find a…

Data Analysis, Statistics and Probability · Physics 2020-04-02 L. T. Giorgini , S. H. Lim , W. Moon , J. S. Wettlaufer

The Doob transform technique enables the study of a killed random walk (KRW) via a random walk (RW) with transition probabilities tilted by a discrete massive harmonic function. The main contribution of this paper is to transfer this…

Probability · Mathematics 2024-12-17 Lucas Rey

Learning-based motion planning can quickly generate near-optimal trajectories. However, it often requires either large training datasets or costly collection of human demonstrations. This work proposes an alternative approach that quickly…

Robotics · Computer Science 2025-10-13 Dominik Urbaniak , Alejandro Agostini , Pol Ramon , Jan Rosell , Raúl Suárez , Michael Suppa

This paper proposes a simple yet highly accurate prediction-correction algorithm, SHARP, for unconstrained time-varying optimization problems. Its prediction is based on an extrapolation derived from the Lagrange interpolation of past…

Optimization and Control · Mathematics 2025-04-09 Tomoya Kamijima , Naoki Marumo , Akiko Takeda

The primary goal of this paper is to provide an efficient solution algorithm based on the augmented Lagrangian framework for optimization problems with a stochastic objective function and deterministic constraints. Our main contribution is…

Optimization and Control · Mathematics 2023-12-29 Raghu Bollapragada , Cem Karamanli , Brendan Keith , Boyan Lazarov , Socratis Petrides , Jingyi Wang

The dynamical formulation of the optimal transport can be extended through various choices of the underlying geometry (kinetic energy), and the regularization of density paths (potential energy). These combinations yield different…

Machine Learning · Computer Science 2024-07-04 Kirill Neklyudov , Rob Brekelmans , Alexander Tong , Lazar Atanackovic , Qiang Liu , Alireza Makhzani

Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…

Chemical Physics · Physics 2023-07-31 Gianmarco Lazzeri , Hendrik Jung , Peter G. Bolhuis , Roberto Covino

A strategy for finding transition paths connecting two stable basins is presented. The starting point is the Hamilton principle of stationary action; we show how it can be transformed into a minimum principle through the addition of…

Materials Science · Physics 2009-11-07 Daniele Passerone , Matteo Ceccarelli , Michele Parrinello

To explain day-to-day (DTD) route-choice behaviors and traffic dynamics observed in a series of lab experiments, Part I of this research proposed a discrete choice-based analytical dynamic model (Qi et al., 2023). Although the deterministic…

Physics and Society · Physics 2023-03-08 Hang Qi , Ning Jia , Xiaobo Qu , Zhengbing He

We study the trajectory optimization problem under chance constraints for continuous-time stochastic systems. To address chance constraints imposed on the entire stochastic trajectory, we propose a framework based on the set erosion…

Optimization and Control · Mathematics 2025-04-08 Zishun Liu , Liqian Ma , Yongxin Chen