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We construct path integrals for stochastic hybrid reaction-diffusion (RD) processes, in which the reaction terms depend on the discrete state of a randomly switching environment. We proceed by spatially discretizing a given RD system and…
A common approach to quantify excess dissipation in slowly driven thermodynamic processes is through the use of a Riemannian metric on the space of control parameters, where optimal driving protocols follow geodesics. Near phase…
Path following controllers make the output of a control system approach and traverse a pre-specified path with no apriori time parametrization. In this paper we present a method for path following control design applicable to framed curves…
We present an efficient method to compute transition rates between states for a two-state system. The method utilizes the equivalence between steady-state flux and mean first passage rate for such systems. More specifically, the procedure…
We analyze the efficiency of different methods for the calculation of reaction rates in the case of two simple analytical benchmark systems. Two classes of methods are considered: the first are based on the free energy calculation along a…
Modular verification is a technique used to face the state explosion problem often encountered in the verification of properties of complex systems such as concurrent interactive systems. The modular approach is based on the observation…
We present two approaches for describing chemical reactions taking place in fluid phase. The first method mirrors the usual derivation of the hydrodynamic equations of motion by relating conserved---or to account for chemical reactions,…
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…
We apply energy landscape methods to digital alchemy, defining a system in which the parameters of the potential are treated as degrees of freedom. Using geometrical optimisation, we locate minima and transition states on the landscape for…
Simulating transition dynamics between metastable states is a fundamental challenge in dynamical systems and stochastic processes with wide real-world applications in understanding protein folding, chemical reactions and neural activities.…
We demonstrate a method for controlling the outcome of an ultracold chemical few-body reaction by redirecting a tunable fraction of reaction flux from one selected product channel to another one. In the reaction, three ultracold atoms…
Given two metastable states A and B of a biomolecular system, the problem is to calculate the likely paths of the transition from A to B. Such a calculation is more informative and more manageable if done for a reduced set of collective…
Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables(CVs) it can explore complex free energy surfaces…
Analyzing synthesis pathways for target molecules in a chemical reaction network annotated with information on the kinetics of individual reactions is an area of active study. This work presents a computational methodology for searching for…
Motivation: Modeling biological signaling networks using ordinary differential equations (ODEs) has proven to be a powerful technique for generating insight into cellular dynamics, but it typically requires estimating rate parameters based…
We propose nearly-optimal control strategies for changing states of a quantum system. We argue that quantum control optimization can be studied analytically within some protocol families that depend on a small set of parameters for…
Pathways that describe the optimal evolution of energy systems across multiple decades are important in energy system research and policy literature, with net-zero and similar climate policies being common drivers behind them. While there…
We experimentally and theoretically study the thermodynamically optimal control of interacting multiple-particle systems, focusing on collections of colloidal particles individually confined in optical traps. We investigate protocols that…
The definition of metastable states is an ubiquitous task in the design and analysis of molecular simulations, and is a crucial input in a variety of acceleration methods for the sampling of long configurational trajectories. Although…
Free energy landscapes encode the kinetics, intermediates, and transition states that govern molecular processes and are thus a key target of single biomolecule research. Typical approaches to deriving optimal, error-minimizing,…