相关论文: Automaton of molecular perceptions in biochemical …
Autonomous computations that rely on automated reaction network elucidation algorithms may pave the way to make computational catalysis on a par with experimental research in the field. Several advantages of this approach are key to…
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…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
The modern thermodynamics of discrete systems is based on graph theory, which provides both algebraic methods to define observables and a geometric intuition of their meaning and role. However, because chemical reactions are usually…
We simulate reaction-diffusion processes with discrete fields. We use a novel algorithm to simulate different autocatalytic processes with trace densities. Anderson localization with a diffusive potential is studied. A reaction-diffusion…
Current single-molecule imaging techniques are incapable of providing stochastic information of individual chemical reactions. We have developed an optical imaging method for stochastic analysis of individual electrochemical reactions. The…
Biological systems are notorious for complex behavior within short timescales (e.g. metabolic activity) and longer time scales (e.g. evolutionary selection), along with their complex spatial organization. Because of their complexity and…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
In many scientific fields, there is an interest in understanding the way in which complex chemical networks evolve. The chemical networks which researchers focus upon, have become increasingly complex and this has motivated the development…
The photonic environment can significantly influence emission properties and interactions among atomic systems. In such scenarios, frequently the electric dipole approximation is assumed that is justified as long as the spatial extent of…
The control of chemical reactions is a recurring theme in physics and chemistry. Traditionally, chemical reactions have been investigated by tuning thermodynamic parameters, such as temperature or pressure. More recently, physical methods…
Chemotaxis is the process by which cells behave in a way that follows the chemical gradient. Applications to bacteria growth, tissue inflammation, and vascular tumors provide a focus on optimization strategies. Experiments can characterize…
A central concern of molecular dynamics simulations are the potential energy surfaces that govern atomic interactions. These hypersurfaces define the potential energy of the system, and have generally been calculated using either predefined…
Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge…
The concept of the limiting step is extended to the asymptotology of multiscale reaction networks. Complete theory for linear networks with well separated reaction rate constants is developed. We present algorithms for explicit…
It is now well accepted that cellular responses to materials in a biological medium reflect greatly the adsorbed biomolecular layer, rather than the material itself. Here, we study by molecular dynamic simulations the competitive protein…
We study a family of networks of autocatalytic reactions, which we call hyperchains, that are a generalization of hypercycles. Hyperchains, and the associated dynamical system called replicator equations, are a possible mechanism for…
Safe human-robot interactions require robots to be able to learn how to behave appropriately in \sout{humans' world} \rev{spaces populated by people} and thus to cope with the challenges posed by our dynamic and unstructured environment,…
Time perception - how humans and animals perceive the passage of time - forms the basis for important cognitive skills such as decision-making, planning, and communication. In this work, we propose a framework for examining the mechanisms…
Agent-based modeling is a powerful simulation technique to understand the collective behavior and microscopic interaction in complex financial systems. Recently, the concept for determining the key parameters of the agent-based models from…