相关论文: Molecular Codes in Biological and Non-Biological R…
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
To what extent do the characteristic features of a chemical reaction network reflect its purpose and function? In general, one argues that correlations between specific features and specific functions are key to understanding a complex…
Many biological decision-making processes can be viewed as performing a classification task over a set of inputs, using various chemical and physical processes as "biological hardware." In this context, it is important to understand the…
Life relies on a sophisticated metabolic molecular machinery that turns over high-energy molecules to evolve complex macromolecules and assemblies. At the molecular origin of life, such machinery was absent, implying the need for simple yet…
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 a molecular communication network, transmitters may encode information in concentration or frequency of signalling molecules. When the signalling molecules reach the receivers, they react, via a set of chemical reactions or a molecular…
Modern computational chemistry has reached a stage at which massive exploration into chemical reaction space with unprecedented resolution with respect to the number of potentially relevant molecular structures has become possible. Various…
Can a micron sized sack of interacting molecules understand, and adapt to a constantly-fluctuating environment? Cellular life provides an existence proof in the affirmative, but the principles that allow for life's existence are far from…
Chemical reaction networks describe interactions between biochemical species. Once an underlying reaction network is given for a biochemical system, the system dynamics can be modelled with various mathematical frameworks such as continuous…
Biological regulatory networks depend upon chemical interactions to process information. Engineering such molecular computing systems is a major challenge for synthetic biology and related fields. The chemical reaction network (CRN) model…
We mathematically prove that chemical reaction networks without hidden layers can solve tasks for which spiking neural networks require hidden layers. Our proof uses the deterministic mass-action kinetics formulation of chemical reaction…
Accurately capturing individual differences in semantic networks is fundamental to advancing our mechanistic understanding of semantic memory. Past empirical attempts to construct individual-level semantic networks from behavioral paradigms…
The automated inference of physically interpretable (bio)chemical reaction network models from measured experimental data is a challenging problem whose solution has significant commercial and academic ramifications. It is demonstrated,…
Here we focus on the challenge of verifying the correctness of molecular implementations of abstract chemical reaction networks, where operation in a well-mixed "soup" of molecules is stochastic, asynchronous, concurrent, and often involves…
We introduce and study semantic capacity of terms. For example, the semantic capacity of artificial intelligence is higher than that of linear regression since artificial intelligence possesses a broader meaning scope. Understanding…
In this paper, it is presented a methodology for implementing arbitrarily constructed time-homogenous Markov chains with biochemical systems. Not only discrete but also continuous-time Markov chains are allowed to be computed. By employing…
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,…
In living cells, biochemical reactions are catalyzed by specific enzymes and connect to one another by sharing substrates and products, forming complex networks. In our previous studies, we established a framework determining the responses…
A detailed understanding of biochemical networks at the molecular level is essential for studying complex cellular processes. In this paper, we provide a comprehensive description of biochemical networks by considering individual atoms and…