相关论文: Automaton of molecular perceptions in biochemical …
Recent research in molecular discovery has primarily been devoted to small, drug-like molecules, leaving many similarly important applications in material design without adequate technology. These applications often rely on more complex…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
One approach to studying the system-wide organization of biochemistry is to use statistical graph theory. Even in such a heavily simplified method, which disregards most of the dynamic aspects of biochemistry, one is faced with fundamental…
Autocatalytic systems are very often incorporated in the "origin of life" models, a connection that has been analyzed in the context of the classical hypercycles introduced by Manfred Eigen. We investigate the dynamics of certain networks…
In this paper we introduce a general estimation methodology for learning a model of human perception and control in a sensorimotor control task based upon a finite set of demonstrations. The model's structure consists of i the agent's…
In this paper, the early design of our self-organized agent-based simulation model for exploration of synaptic connections that faithfully generates what is observed in natural situation is given. While we take inspiration from…
Exploring large chemical reaction networks with automated exploration approaches and accurate quantum chemical methods can require prohibitively large computational resources. Here, we present an automated exploration approach that focuses…
Interactions play a key role in understanding objects and scenes, for both virtual and real world agents. We introduce a new general representation for proximal interactions among physical objects that is agnostic to the type of objects or…
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…
There are many processes in biology in which mechanical forces are generated. Force-bearing networks can transduce locally developed mechanical signals very extensively over different parts of the cell or tissues. In this article we conduct…
A recent article by Weidner et al. [2021] presents a method to extract graph properties that are predictive of the dynamical behavior of multivariate, discrete models of biochemical regulation. In other words, a method that uses only…
In this work, we present an application of Locally Interpretable Machine-Agnostic Explanations to 2-D chemical structures. Using this framework we are able to provide a structural interpretation for an existing black-box model for…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Droplets are essential for spatially controlling biomolecules in cells. To work properly, cells need to control the emergence and morphology of droplets. On the one hand, driven chemical reactions can affect droplets profoundly. For…
In this paper, we propose a new method to identify biochemical reaction networks (i.e. both reactions and kinetic parameters) from heterogeneous datasets. Such datasets can contain (a) data from several replicates of an experiment performed…
A small-world cellular automaton network has been formulated to simulate the long-range interactions of complex networks using unconventional computing methods in this paper. Conventional cellular automata use local updating rules. The new…
Particles that are catalytically-active and chemotactic can interact through the concentration fields upon which they act, which in turn may lead to wide-scale spatial self-organization. When these active particles interact through several…
Computer-based modelling and simulation have become useful tools to facilitate humans to understand systems in different domains, such as physics, astrophysics, chemistry, biology, economics, engineering and social science. A complex system…
In most natural sciences there is currently the insight that it is necessary to bridge gaps between different processes which can be observed on different scales. This is especially true in the field of chemical reactions where the…
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…