相关论文: Automaton of molecular perceptions in biochemical …
Synthetic biology aims at designing modular genetic circuits that can be assembled according to the desired function. When embedded in a cell, a circuit module becomes a small subnetwork within a larger environmental network, and its…
Biomolecular condensates play a crucial role in the spatial organization of living matter. These membrane-less organelles, resulting from liquid-liquid phase separation, operate far from thermodynamic equilibrium, with their size and…
Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…
We propose that the behaviour of non-linear media can be controlled automatically through coevolutionary systems. By extension, forms of unconventional computing, i.e., massively parallel non-linear computers, can be realised by such an…
In living cells, chemical reactions form a complex network. Complicated dynamics arising from such networks are the origins of biological functions. We propose a novel mathematical method to analyze bifurcation behaviors of a reaction…
In this paper we present a computational modeling account of an active self in artificial agents. In particular we focus on how an agent can be equipped with a sense of control and how it arises in autonomous situated action and, in turn,…
Chemical reactions involve the movement of charges, and this work presents a mathematical model for describing chemical reactions in electrolytes. The model is developed using an energy variational method that aligns with classical…
Binding and unbinding of ligands to specific sites of a macromolecule are one of the most elementary molecular interactions inside the cell that embody the computational processes of biological regulations. The interaction between…
Organic reactions are usually assigned to classes containing reactions with similar reagents and mechanisms. Reaction classes facilitate the communication of complex concepts and efficient navigation through chemical reaction space.…
Biomolecular force fields have been traditionally derived based on a mixture of reference quantum chemistry data and experimental information obtained on small fragments. However, the possibility to run extensive molecular dynamics…
Biochemical reactions involving three or more reactants, called higher-molecular reactions, play an important role in theoretical systems and synthetic biology. In particular, such reactions underpin a variety of important bio-dynamical…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Quantum chemical studies of reactivity involve calculations on a large number of molecular structures and comparison of their energies. Already the set-up of these calculations limits the scope of the results that one will obtain, because…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…
To survive in ever-changing environments, living organisms need to continuously combine the ongoing external inputs they receive, representing present conditions, with their dynamical internal state, which includes influences of past…
Reactions forming a pathway can be rewritten by making explicit the different molecular components involved in them. A molecular component represents a biological entity (e.g. a protein) in all its states (free, bound, degraded, etc.). In…
Reaction coordinates are widely used throughout chemical physics to model and understand complex chemical transformations. We introduce a definition of the natural reaction coordinate, suitable for condensed phase and biomolecular systems,…
Reactive lattice gas automata provide a microscopic approachto the dynamics of spatially-distributed reacting systems. After introducing the subject within the wider framework of lattice gas automata (LGA) as a microscopic approach to the…
We advance the state of the art in biomolecular interaction extraction with three contributions: (i) We show that deep, Abstract Meaning Representations (AMR) significantly improve the accuracy of a biomolecular interaction extraction…
Can a micron sized sack of interacting molecules autonomously learn an internal model of a complex and fluctuating environment? We draw insights from control theory, machine learning theory, chemical reaction network theory, and statistical…