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Reaction Systems (RSs) are a successful computational framework inspired by biological systems. A RS pairs a set of entities with a set of reactions over them. Entities can be used to enable or inhibit each reaction, and are produced by…
This article is motivated by the fact that there is a distinction between the descriptions of logical explosion from syntactic and semantic points of view. The discussion is illustrated using the concept of abstract model structures and the…
Spectra is a new specification language for reactive systems, specifically tailored for the context of reactive synthesis. The meaning of Spectra is defined by a translation to a kernel language. Spectra comes with the Spectra Tools, a set…
A scattering model is developed for ultracold molecular collisions, which allows inelastic processes, chemical reactions, and complex formation to be treated in a unified way. All these scattering processes and various combinations of them…
We consider forkable regular expressions, which enrich regular expressions with a fork operator, to establish a formal basis for static and dynamic analysis of the communication behavior of concurrent programs. We define a novel…
Reaction systems are a formal model that has been introduced to investigate the interactive behaviors of biochemical reactions. Based on the formal framework of reaction systems, we propose new computing models called reaction automata that…
The advent of ultrafast pulsed X-ray free-electron lasers with very high brightness has enabled the determination of transient molecular structures of small and medium-sized organic molecules in excited states and undergoing chemical…
Automation is becoming ubiquitous in all laboratory activities, leading towards precisely defined and codified laboratory protocols. However, the integration between laboratory protocols and mathematical models is still lacking. Models…
For two molecules to react they first have to meet. Yet, reaction times are rarely on par with the first-passage times that govern such molecular encounters. A prime reason for this discrepancy is stochastic transitions between reactive and…
We define a class of probabilistic models in terms of an operator algebra of stochastic processes, and a representation for this class in terms of stochastic parameterized grammars. A syntactic specification of a grammar is mapped to…
An understandable concrete syntax and a comprehensible abstract syntax are two central aspects of defining a modeling language. Both representations of a language significantly overlap in their structure and also information, but may also…
Event-driven automation of reactive functionalities for complex event processing is an urgent need in today's distributed service-oriented architectures and Web-based event-driven environments. An important problem to be addressed is how to…
We present a novel scattering emulator utilizing the complex scaling method to enhance nuclear reaction analysis. This approach leverages a single set of reduced bases, allowing for efficient and simultaneous emulation across multiple…
Reaction systems are discrete dynamical systems inspired by bio-chemical processes, whose dynamical behaviour is expressed by set-theoretic operations on finite sets. Reaction systems thus provide a description of bio-chemical phenomena…
Reaction RuleML is a general, practical, compact and user-friendly XML-serialized language for the family of reaction rules. In this white paper we give a review of the history of event / action /state processing and reaction rule…
We regard explanations as a blending of the input sample and the model's output and offer a few definitions that capture various desired properties of the function that generates these explanations. We study the links between these…
Reactive synthesis transforms a specification of a reactive system, given in a temporal logic, into an implementation. The main advantage of synthesis is that it is automatic. The main disadvantage is that the implementation is usually very…
Specifying and implementing flexible human-computer dialogs, such as those used in kiosks and smart phone apps, is challenging because of the numerous and varied directions in which each user might steer a dialog. The objective of this…
Recently, a simple but powerful language for expressing and learning general policies and problem decompositions (sketches) has been introduced in terms of rules defined over a set of Boolean and numerical features. In this work, we…
Based on the generalized non-Markovian equations obtained earlier for a nonequilibrium one-particle distribution function and potential part of the averaged enthalpy density [Markiv B.B., Omelyan I.P, Tokarchuk M.V., Condens. Matter Phys.,…