Related papers: A Novel Path Sampling Method for the Calculation o…

We describe a generalized algorithm for evaluating the steady-state solution of the density matrix equation of motion, for the pump-probe scheme, when two fields oscillating at different frequencies couple the same set of atomic transitions…

This article describes two independent developments aimed at improving the Particle Tracking Method for measurements of flow or particle velocities. First, a stereoscopic multicamera calibration method that does not require any optical…

We present an algorithm to sample stochastic differential equations conditioned on rather general constraints, including integral constraints, endpoint constraints, and stochastic integral constraints. The algorithm is a pathspace…

In this paper, we suggest a novel sampling method for Monte Carlo molecular simulations. In order to perform efficient sampling of molecular systems, it is advantageous to avoid extremely high energy configurations while also retaining the…

Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…

To simulate the dynamics of fluid with polydisperse particles on macroscale level, one has to solve hydrodynamic equations with several relaxation terms, representing momentum transfer from fluid to particles and vice versa. For small…

Density ratio estimation in high dimensions can be reframed as integrating a certain quantity, the time score, over probability paths which interpolate between the two densities. In practice, the time score has to be estimated based on…

We introduce a temporal scheme for data sampling, based on a variable delay between two successive data acquisitions. The scheme is designed so as to reduce the average data flow rate, while still retaining the information on the data…

This work inspects the thermally activated transfer of solute particles across the interface between two interstitial solid solution phases that equilibrate internally by fast diffusion on conserved arrays of sites. When each phase is…

Understanding transition pathways between two meta-stable states of a molecular system is crucial to advance drug discovery and material design. However, unbiased molecular dynamics (MD) simulations are computationally infeasible because of…

The shift in chemical equilibria due to isotope substitution is often exploited to gain insight into a wide variety of chemical and physical processes. It is a purely quantum mechanical effect, which can be computed exactly using…

We introduce dynamic nested sampling: a generalisation of the nested sampling algorithm in which the number of "live points" varies to allocate samples more efficiently. In empirical tests the new method significantly improves calculation…

We present a method to study rare nonadiabatic dynamics in open quantum systems using transition path sampling and quantum jump trajectories. As with applications of transition path sampling to classical dynamics, the method does not rely…

We present a one-way shooting algorithm for transition path sampling that accepts every proposed trajectory, yet samples the correct transition path ensemble for systems with overdamped stochastic dynamics. The method is based on two key…

In this paper, a purely measurement-based method is proposed to estimate the dynamic system state matrix by applying the regression theorem of the multivariate Ornstein-Uhlenbeck process. The proposed method employs a recursive algorithm to…

Due to the time scale problem, rare events are not accessible by straight forward molecular dynamics. The presence of multiple reaction channels complicates the problem even further. The feasibility of the standard free energy based methods…

We present a family of algorithms for the fast determination of reaction paths and barriers in phase space and the computation of the corresponding rates. The method requires the reaction times be large compared to the microscopic time,…

We present a method to sample reactive pathways via biased molecular dynamics simulations in trajectory space. We show that the use of enhanced sampling techniques enables unconstrained exploration of multiple reaction routes. Time…

From the point of view of statistical mechanics, a full characterisation of a molecular system requires the experimental determination of its possible states, their populations and the respective interconversion rates. Well-established…

We present an energy-stable scheme for numerically approximating the governing equations for incompressible two-phase flows with different densities and dynamic viscosities for the two fluids. The proposed scheme employs a scalar-valued…