相关论文: Automaton of molecular perceptions in biochemical …

Efforts toward a comprehensive description of behavior have indeed facilitated the development of representation-based approaches that utilize deep learning to capture behavioral information. As behavior complexity increases, the expressive…

Living systems are capable of locomotion, reconfiguration, and replication. To perform these tasks, cells spatiotemporally coordinate the interactions of force-generating, "active" molecules that create and manipulate non-equilibrium…

We present a benchmark study of autonomous, chemical agents exhibiting associative learning of an environmental feature. Associative learning has been widely studied in cognitive science and artificial intelligence, but are most commonly…

Atomistic simulations using accurate energy functions can provide molecular-level insight into functional motions of molecules in the gas- and in the condensed phase. Together with recently developed and currently pursued efforts in…

We review existing approaches to mathematical modeling and analysis of multi-agent systems in which complex collective behavior arises out of local interactions between many simple agents. Though the behavior of an individual agent can be…

Compartmentalised biochemical reactions are a ubiquitous building block of biological systems. The interplay between chemical and compartmental dynamics can drive rich and complex dynamical behaviors that are difficult to analyse…

In this exploratory paper we introduce the problem of cognitive agents that learn how to modify their environment according to local sensing to reach a global goal. We concentrate on discrete dynamics (cellular automata) on a…

Motor enzymes catalyze chemical reactions, like the hydrolysis of ATP, and in the process they also perform work. Recent studies indicate that motor enzymes perform work with specific intermediate steps in their catalyzed reactions,…

Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…

Graphs are central to the chemical sciences, providing a natural language to describe molecules, proteins, reactions, and industrial processes. They capture interactions and structures that underpin materials, biology, and medicine. This…

We describe a mechanism for pronounced biochemical oscillations, relevant to microscopic systems, such as the intracellular environment. This mechanism operates for reaction schemes which, when modeled using deterministic rate equations,…

The addition of individual quanta of rotational excitation to a molecule has been shown to markedly change its reactivity by significantly modifying the intermolecular interactions. So far, it has only been possible to observe these…

Machine learning (ML) has emerged as a pervasive tool in science, engineering, and beyond. Its success has also led to several synergies with molecular dynamics (MD) simulations, which we use to identify and characterize the major…

The properties of supercritical fluids are dictated by intermolecular interactions that involve two or more molecules. Such intermolecular interactions were described via intermolecular potentials in historical supercritical combustion…

Autocatalytic Sets are reaction networks theorised as networks at the basis of life. Their main feature is the ability of spontaneously emerging and self-reproducing. The Reflexively and Food-generated theory provides a formal definition of…

Within the field of automated driving, a clear trend in environment perception tends towards more sensors, higher redundancy, and overall increase in computational power. This is mainly driven by the paradigm to perceive the entire…

The ability of a cell to communicate with its environment is essential for key cellular functions like replication, metabolism, or cell fate decisions. The involved molecular mechanisms are highly dynamic and difficult to capture…

The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…

Biological systems and processes are networks of complex nonlinear regulatory interactions between nucleic acids, proteins, and metabolites. A natural way in which to represent these interaction networks is through the use of a graph. In…

The simulation of intrinsic contributions to molecular properties holds the potential to allow for chemistry to be directly inferred from changes to electronic structures at the atomic level. In the present study, we demonstrate how such…