Related papers: Maximum Flux Transition Paths of Conformational Ch…
Molecular systems often remain trapped for long times around some local minimum of the potential energy function, before switching to another one -- a behavior known as metastability. Simulating transition paths linking one metastable state…
Our goal is to develop a flux limiter of the Flux-Corrected Transport method for a nonconservative convection-diffusion equation. For this, we consider a hybrid difference scheme that is a linear combination of a monotone scheme and a…
Production of chemicals from engineered organisms in a batch culture involves an inherent trade-off between productivity, yield, and titer. Existing strategies for strain design typically focus on designing mutations that achieve the…
We consider the problem of sampling transition paths between two given metastable states of a molecular system, e.g. a folded and unfolded protein or products and reactants of a chemical reaction. Due to the existence of high energy…
A central concern across the natural sciences is a quantitative understanding of the mechanism governing rare transitions between two metastable states. Recent research has uncovered a fundamental equality between the time-reversal…
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,…
The transmission switching problem aims to determine the optimal network topology that minimizes the operating costs of a power system. This problem is typically formulated as a mixed-integer optimization model, which involves big-M…
A wide variety of methods have been used to compute percolation thresholds. In lattice percolation, the most powerful of these methods consists of microcanonical simulations using the union-find algorithm to efficiently determine the…
The maximum likelihood state for a simplified stochastic thermohaline circulation model is investigated. It is shown that a jump occurs for the maximum likelihood state during transitions between two metastable states. The jump helps to…
The traffic assignment problem is essential for traffic flow analysis, traditionally solved using mathematical programs under the Equilibrium principle. These methods become computationally prohibitive for large-scale networks due to…
Adaptive multilevel splitting algorithms have been introduced rather recently for estimating tail distributions in a fast and efficient way. In particular, they can be used for computing the so-called reactive trajectories corresponding to…
Simulations with an adaptive time-dependent bias, such as metadynamics, enable an efficient exploration of the conformational space of a system. However, the dynamic information of the system is altered by the bias. With infrequent…
A path information is defined in connection with the different possible paths of chaotic system moving in its phase space between two cells. On the basis of the assumption that the paths are differentiated by their actions, we show that the…
The dynamics in a confined turbulent convection flow is dominated by multiple long-lived macroscopic circulation states, which are visited subsequently by the system in a Markov-type hopping process. In the present work, we analyze the…
We determine the most probable length of paths at finite temperatures, with a preassigned end-to-end distance and a unit of energy assigned to every step on a $D$-dimensional hypercubic lattice. The asymptotic form of the most probable…
The main goal of this paper is to understand the formation of hexagonal patterns from the dynamical transition theory point of view. We consider the transitions from a steady state of an abstract nonlinear dissipative system. To shed light…
In this paper we provide an algorithm which given any $m$-edge $n$-vertex directed graph with integer capacities at most $U$ computes a maximum $s$-$t$ flow for any vertices $s$ and $t$ in $m^{11/8+o(1)}U^{1/4}$ time with high probability.…
We present a novel method for the accurate numerical determination of the phase behavior of fluid mixtures having large particle size asymmetries. By incorporating the recently developed geometric cluster algorithm within a restricted Gibbs…
In this short paper, we propose a new multi-fractal flow model, aiming to provide a possible explanation for the crossover phenomena that appear in the estimation of Hurst exponent for network traffic. It is shown that crossover occurs if…
Flow cytometry is a powerful quantitative assay supporting high-throughput collection of single-cell data with a high dynamic range. For flow cytometry to yield reproducible data with a quantitative relationship to the underlying biology,…