Related papers: A Novel Path Sampling Method for the Calculation o…
We address the problem of efficient phase diagram sampling by adopting active learning techniques from machine learning, and achieve an 80% reduction in the sample size (number of sampled statepoints) needed to establish the phase boundary…
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…
One key issue in the probability density function (PDF) approach for disperse two-phase turbulent flows is to close the diffusion term in the phase space. This study aimed to derive a kinetic equation for particle dispersion in turbulent…
The efficiency of traffic routing on complex networks can be reflected by two key measurements i.e. the system capacity and the average data packets travel time. In this paper, we propose a mixing routing strategy by integrating local…
Sampling from unnormalized target distributions is a fundamental yet challenging task in machine learning and statistics. Existing sampling algorithms typically require many iterative steps to produce high-quality samples, leading to high…
We present a fully-explicit, iteration-free, weakly-compressible method to simulate immiscible incompressible two-phase flows. To update pressure, we circumvent the computationally expensive Poisson equation and use the general pressure…
We explore the distribution of paths followed in fluctuation-induced switching between coexisting stable states. We introduce a quantitative characteristic of the path distribution in phase space that does not require a priori knowledge of…
We formulate two estimation problems for pipeline systems in which measurements of compressible gas flow through a network of pipes is affected by time-varying injections, withdrawals, and compression. We consider a state estimation problem…
Rare events such as nucleation processes are of ubiquitous importance in real systems. The most popular method for nonequilibrium systems, forward flux sampling (FFS), samples rare events by using interfaces to partition the whole…
We present an alternative "encapsulated" formulation of the Selective Frequency Damping method for finding unstable equilibria of dynamical systems, which is particularly useful when analysing the stability of fluid flows. The formulation…
Many applications of computational fluid dynamics require multiple simulations of a flow under different input conditions. In this paper, a numerical algorithm is developed to efficiently determine a set of such simulations in which the…
The nested sampling algorithm has been shown to be a general method for calculating the pressure-temperature-composition phase diagrams of materials. While the previous implementation used single-particle Monte Carlo moves, these are…
Signals comprised of a stream of short pulses appear in many applications including bio-imaging and radar. The recent finite rate of innovation framework, has paved the way to low rate sampling of such pulses by noticing that only a small…
We derived a number of numerical methods to treat biomolecular systems with multiple time scales. Based on the splitting of the operators associated with the slow-varying and fast-varying forces, new multiple time-stepping (MTS) methods are…
The efficiency of atomic simulations of materials and molecules can rapidly deteriorate when large free energy barriers exist between local minima. We propose smooth basin classification, a universal method to define reaction coordinates…
We introduce a novel framework for efficient sampling from complex, unnormalised target distributions by exploiting multiscale dynamics. Traditional score-based sampling methods either rely on learned approximations of the score function or…
The increasing application of cardiorespiratory simulations for diagnosis and surgical planning necessitates the development of computational methods significantly faster than the current technology. To achieve this objective, we leverage…
This paper investigates the use of stratified sampling as a variance reduction technique for approximating integrals over large dimensional spaces. The accuracy of this method critically depends on the choice of the space partition, the…
Computing stationary states is an important topic for phase field crystal (PFC) models. Great efforts have been made for energy dissipation of the numerical schemes when using gradient flows. However, it is always time-consuming due to the…
Umbrella sampling is an efficient method for the calculation of free energy changes of a system along well-defined reaction coordinates. However, when multiple parallel channels along the reaction coordinate or hidden barriers in directions…