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It is often useful, if not necessary, to reason about the syntactic structure of an expression in an interpreted language (i.e., a language with a semantics). This paper introduces a mathematical structure called a syntax framework that is…
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…
Chemical reactions are the fundamental building blocks of drug design and organic chemistry research. In recent years, there has been a growing need for a large-scale deep-learning framework that can efficiently capture the basic rules of…
We describe modeling approaches to a "network" of connected enzyme-catalyzed reactions, with added (bio)chemical processes that introduce biochemical filtering steps into the functioning of such a biocatalytic cascade. Theoretical…
Interaction Grammar (IG) is a grammatical formalism based on the notion of polarity. Polarities express the resource sensitivity of natural languages by modelling the distinction between saturated and unsaturated syntactic structures.…
A unified mathematical language for medicine and science will be presented. Using this language, models for DNA replication, protein synthesis, chemical reactions, neurons and a cardiac cycle of a heart have been built. Models for Turing…
The chapter reviews the syntax to store machine-readable annotations and describes the mapping between rule-based modelling entities (e.g., agents and rules) and these annotations. In particular, we review an annotation framework and the…
Modeling molecules as undirected graphs and chemical reactions as graph rewriting operations is a natural and convenient approach tom odeling chemistry. Graph grammar rules are most naturally employed to model elementary reactions like…
We provide a category theoretical framework capturing two approaches to graph-based models of chemistry: formal reactions and disconnection rules. We model a translation from the latter to the former as a functor, which is faithful, and…
Recent work shows issues of consistency with explanations, with methods generating local explanations that seem reasonable instance-wise, but that are inconsistent across instances. This suggests not only that instance-wise explanations can…
We propose a technique to detect and generate patterns in a network of locally interacting dynamical systems. Central to our approach is a novel spatial superposition logic, whose semantics is defined over the quad-tree of a partitioned…
Traditional chemical kinetics may be inappropriate to describe chemical reactions in micro-domains involving only a small number of substrate and reactant molecules. Starting with the stochastic dynamics of the molecules, we derive a…
We introduce a mathematical framework for retrosynthetic analysis, an important research method in synthetic chemistry. Our approach represents molecules and their interaction using string diagrams in layered props - a recently introduced…
There has been considerable attention devoted to models that learn to jointly infer an expression's syntactic structure and its semantics. Yet, \citet{NangiaB18} has recently shown that the current best systems fail to learn the correct…
Both experimental and computational biology is becoming increasingly automated. Laboratory experiments are now performed automatically on high-throughput machinery, while computational models are synthesized or inferred automatically from…
Studying chemical reactions, particularly in the gas phase, relies heavily on computing scattering matrix elements. These elements are essential for characterizing molecular reactions and accurately determining reaction probabilities.…
Recent research in molecular discovery has primarily been devoted to small, drug-like molecules, leaving many similarly important applications in material design without adequate technology. These applications often rely on more complex…
A new kinetic approach is developed and a quasi-practical gas is defined to which the new approach can be applied. One of the advantages of this new approach over the standard one is direct calculability in terms of today's computational…
The primary goal of this paper is to characterize solutions to coupled reaction-diffusion systems. Indeed, we use operators theory to show that under suitable assumptions, then the solutions to the reaction-diffusion equations exist. As…
Recently we developed a formalism for the scattering from linear and acyclic branched structures build of mutually non-interacting sub-units.{[}C. Svaneborg and J. S. Pedersen, J. Chem. Phys. 136, 104105 (2012){]} We assumed each sub-unit…