Related papers: Reaction Automata
Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
Chemical equilibrium is fully characterized by thermodynamics, while the rates of chemical reactions can be calculated for ideal solutions by using mass-action equations. The evaluation of the rates of reactions in a non-ideal system is…
A method to calculate reactions in quantum mechanics is outlined. It is advantageous, in particular, in problems with many open channels of various nature i.e. when energy is not low. In the method there is no need to specify reaction…
The aim of my Ph.D. thesis concerns Reasoning in Highly Reactive Environments. As reasoning in highly reactive environments, we identify the setting in which a knowledge-based agent, with given goals, is deployed in an environment subject…
Understanding realistic complex systems requires confronting significant conceptual, theoretical and experimental limitations rooted in the persistence of views that originated in the mechanics of simple moving bodies. We define the…
Reactive synthesis is a framework for modeling and automatically synthesizing strategies in robotics, typically through computing a \emph{winning} strategy in a 2-player game between the robot and the environment. Winning strategies,…
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…
The role of response operators is well established in quantum mechanics. We investigate their use for universal quantum machine learning models of response properties in molecules. After introducing a theoretical basis, we present and…
Complex robot behaviour typically requires the integration of multiple robotic and Artificial Intelligence (AI) techniques and components. Integrating such disparate components into a coherent system, while also ensuring global properties…
Question answering (QA) systems are among the most important and rapidly developing research topics in natural language processing (NLP). A reason, therefore, is that a QA system allows humans to interact more naturally with a machine,…
Complex biochemical pathways or regulatory enzyme kinetics can be reduced to chains of elementary reactions, which can be described in terms of chemical kinetics. This discipline provides a set of tools for quantifying and understanding the…
Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic…
This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…
Controlling a dynamical system is the ability of changing its configuration arbitrarily through a suitable choice of inputs. It is a very well studied concept in control theory, with wide ranging applications in medicine, biology, social…
Reaction-diffusion processes play an important role in a variety of physical, chemical, and biological systems. Conventionally, the kinetics of these processes are described by the law of mass action. However, there are various cases where…
Chemical reactions involving diffusion of reactants and subsequent chemical fixation steps are generally termed "diffusion-influenced" (DI). Virtually all biochemical processes in living media can be counted among them, together with those…
We propose an approach to test embodied AI agents for interaction awareness and believability, particularly in scenarios where humans push them to their limits. Turing introduced the Imitation Game as a way to explore the question: "Can…
Organic synthesis stands as a cornerstone of the chemical industry. The development of robust machine learning models to support tasks associated with organic reactions is of significant interest. However, current methods rely on…
Stochastic reaction networks are mathematical models with a wide range of applications in biochemistry, ecology, and epidemiology, and are often complex to analyze. Except for some special cases, it is generally difficult to predict how the…
Patterns are ubiquitous in nature, but how they form is often unclear. Turing developed a seminal theory to explain patterns based on reactions that counteract the equalizing tendency of diffusion. These reactions require continuous energy…