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This article describes a very high-level language for clear description of distributed algorithms and optimizations necessary for generating efficient implementations. The language supports high-level control flows where complex…
We present a systematic formulation of scattering theory for nonlinear interactions in one dimension and develop a nonlinear generalization of the transfer matrix that has a composition property similar to its linear analog's. We offer…
Accurately modeling chemical reactions in molecular dynamics simulations requires detailed pre- and post-reaction templates, often created through labor-intensive manual workflows. This work introduces a Python-based algorithm that…
While numerous attempts have been made to jointly parse syntax and semantics, high performance in one domain typically comes at the price of performance in the other. This trade-off contradicts the large body of research focusing on the…
Microscopic optical model potential results for reaction cross sections of proton elastic scattering are presented. The applications cover the 10-1000 MeV energy range and consider both stable and unstable nuclei. The study is based on…
Interpretability provides a means for humans to verify aspects of machine learning (ML) models and empower human+ML teaming in situations where the task cannot be fully automated. Different contexts require explanations with different…
Building software-driven systems that are easily understood becomes a challenge, with their ever-increasing complexity and autonomy. Accordingly, recent research efforts strive to aid in designing explainable systems. Nevertheless, a common…
Embedding efficient command operation into biochemical system has always been a research focus in synthetic biology. One of the key problems is how to sequence the chemical reactions that act as units of computation. The answer is to design…
Synthetic biology is a rapidly emerging research area, with expected wide-ranging impact in biology, nanofabrication, and medicine. A key technical challenge lies in embedding computation in molecular contexts where electronic…
Stochastic reaction networks, which are usually modeled as continuous-time Markov chains on $\mathbb Z^d_{\ge 0}$, and simulated via a version of the "Gillespie algorithm," have proven to be a useful tool for the understanding of processes,…
Discrete chemical reaction networks formalize the interactions of molecular species in a well-mixed solution as stochastic events. Given their basic mathematical and physical role, the computational power of chemical reaction networks has…
This paper discusses SYNTAGMA, a rule based NLP system addressing the tricky issues of syntactic ambiguity reduction and word sense disambiguation as well as providing innovative and original solutions for constituent generation and…
We present a comprehensive language theoretic causality analysis framework for explaining safety property violations in the setting of concurrent reactive systems. Our framework allows us to uniformly express a number of causality notions…
Automated synthesis of reactive systems from specifications has been a topic of research for decades. Recently, a variety of approaches have been proposed to extend synthesis of reactive systems from proposi- tional specifications towards…
Reaction networks are widely used models to describe biochemical processes. Stochastic fluctuations in the counts of biological macromolecules have amplified consequences due to their small population sizes. This makes it necessary to favor…
Response theory provides a pathway for understanding the sensitivity of a system and for predicting how its statistical properties change when a perturbation is applied. In the case of complex and multiscale systems, to achieve enhanced…
We introduce the term Super-Reactive Systems to refer to reactive systems whose construction and behavior are complex, constantly changing and evolving, and heavily interwoven with other systems and the physical world. Finding hidden faults…
E-RES is a system that implements the Language E, a logic for reasoning about narratives of action occurrences and observations. E's semantics is model-theoretic, but this implementation is based on a sound and complete reformulation of E…
In open-shell atoms and ions, processes such as photoionization, combination (Raman) scattering, electron scattering and recombination, are often mediated by many-electron compound resonances. We show that their interference (neglected in…
A computational procedure is developed for determining the conversion probability for reaction-diffusion systems in which a first-order catalytic reaction is performed over active particles. We apply this general method to systems on metric…