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Due to structural and functional abnormalities or genetic variations and mutations, there may be dysfunctional molecules within an intracellular signaling network that do not allow the network to correctly regulate its output molecules,…
Molecular computation in chemical reaction networks (CRNs) now constitutes a foundational framework for designing programmable biological systems. However, prevailing design methodologies primarily treat parallelism of chemical reactions as…
Recent advances in large language models (LLMs) have enabled molecular reasoning for property prediction. However, toxicity arises from complex biological mechanisms beyond chemical structure, necessitating mechanistic reasoning for…
Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. CRNs are widely used to describe information processing occurring in natural cellular regulatory networks, and with upcoming advances in synthetic biology,…
We propose semantic communication over wireless channels for various modalities, e.g., text and images, in a task-oriented communications setup where the task is classification. We present two approaches based on memory and learning. Both…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
Recent advances in biochemical computing, i.e., information processing with cascades of primarily enzymatic reactions realizing computing gates, such as AND, OR, etc., as well as progress in networking these gates and coupling of the…
We study two specific measures of quality of chemical reaction networks, Precision and Sensitivity. The two measures arise in the study of sensory adaptation, in which the reaction network is viewed as an input-output system. Given a step…
Information processing relying on biochemical interactions in the cellular environment is essential for biological organisms. The implementation of molecular computational systems holds significant interest and potential in the fields of…
Sampled structure sequences obtained, for instance, from real-time reactivity explorations or first-principles molecular dynamics simulations contain valuable information about chemical reactivity. Eventually, such sequences allow for the…
We report the first study of a network of connected enzyme-catalyzed reactions, with added chemical and enzymatic processes that incorporate the recently developed biochemical filtering steps into the functioning of this biocatalytic…
Networks coming from protein-protein interactions, transcriptional regulation, signaling, or metabolism may appear to have "unusual" properties. To quantify this, it is appropriate to randomize the network and test the hypothesis that the…
We propose a novel measure valued process which models the behaviour of chemical reaction networks in spatially heterogeneous systems. It models reaction dynamics between different molecular species and continuous movement of molecules in…
Many chemical concepts can be well defined in the context of quantum chemical theories. Examples are the electronegativity scale of Mulliken and Jaffe and the hard and soft acids and bases concept of Pearson. The sound theoretical basis…
Molecular biology and biochemistry interpret microscopic processes in the living world in terms of molecular structures and their interactions, which are quantum mechanical by their very nature. Whereas the theoretical foundations of these…
Complex systems often have features that can be modeled by advanced mathematical tools [1]. Of special interests are the features of complex systems that have a network structure as such systems are important for modeling technological and…
Chemical Reaction Networks (CRNs) provide a useful abstraction of molecular interaction networks in which molecular structures as well as mass conservation principles are abstracted away to focus on the main dynamical properties of the…
We present a new method to analyse and reduce chemical networks and apply this technique to the chemistry in molecular clouds. Using the technique, we investigated the possibility of reducing the number of chemical reactions and species in…
This paper seeks to model human language by the mathematical framework of quantum physics. With the well-designed mathematical formulations in quantum physics, this framework unifies different linguistic units in a single complex-valued…
We define {\em semantic complexity} using a new concept of {\em meaning automata}. We measure the semantic complexity of understanding of prepositional phrases, of an "in depth understanding system", and of a natural language interface to…