Related papers: Recent Developments in Methods for Identifying Rea…
Detecting rare events, those defined to give rise to high impact but have a low probability of occurring, is a challenge in a number of domains including meteorological, environmental, financial and economic. The use of machine learning to…
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that…
With the rise of service-oriented computing, applications are more and more based on coordination of autonomous services. Envisioned over largely distributed and highly dynamic platforms, expressing this coordination calls for alternative…
In a stochastic reaction network setting we consider the problem of tracking the fate of individual molecules. We show that using the classical large volume limit results, we may approximate the dynamics of a single tracked molecule in a…
Stochastic simulation is a widely used method for estimating quantities in models of chemical reaction networks where uncertainty plays a crucial role. However, reducing the statistical uncertainty of the corresponding estimators requires…
As an optimal one-dimensional reaction coordinate, the committor function not only describes the probability of a trajectory initiated at a phase space point first reaching the product state before reaching the reactant state, but also…
Contact processes describe the transmission of distinct properties of nodes via the links of a network. They provide a simple framework for many phenomena, such as epidemic spreading and opinion formation. Combining contact processes with…
To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve…
With the rise of data-centric process management paradigms, interdependent processes, such as artifacts or object lifecycles, form a business process through their interactions. Coordination processes may be used to coordinate these…
The definition of heat in quantum mechanics is ambiguous. Complications arise in particular when the coupling between a quantum system and a thermal environment is non-negligible, as the boundary between the two becomes blurred, making the…
The formation and dissociation of specific noncovalent interactions between a variety of macromolecules play a crucial role in the function of biological systems. During the last few years, three main lines of research led to a dramatic…
The dynamical systems found in Nature are rarely isolated. Instead they interact and influence each other. The coupling functions that connect them contain detailed information about the functional mechanisms underlying the interactions and…
As a complement to experimental and theoretical approaches, numerical modeling has become an important component to study asteroid collisions and impact processes. In the last decade, there have been significant advances in both…
In these notes we collect some results from several of the authors' works in order to make available a single source and show how the approximate geometric methods for regulation have been developed, and how the control design strategy has…
Recent applications of machine learning and statistical inference provide case studies demonstrating how such approaches can accelerate the discovery process in physical chemistry and related fields. Examples discussed in this review…
Estimating the probability of failures or accidents with aerospace systems is often necessary when new concepts or designs are introduced, as it is being done for Autonomous Aircraft. If the design is safe, as it is supposed to be, accident…
We propose an efficient novel path sampling-based framework designed to accelerate the investigation of rare events in complex molecular systems. A key innovation is the shift from sampling restricted path ensemble distributions, as in…
The method of integral transforms is reviewed. In the framework of this method reaction observables are obtained with the bound--state calculation techniques. New developments are reported.
Moment closure methods appear in myriad scientific disciplines in the modelling of complex systems. The goal is to achieve a closed form of a large, usually even infinite, set of coupled differential (or difference) equations. Each equation…
The analysis of complex reaction networks is of great importance in several chemical and biochemical fields (interstellar chemistry, prebiotic chemistry, reaction mechanism, etc). In this article, we propose to simultaneously refine and…