相关论文: Enzyme-Based Logic Systems for Information Process…

The applications of large language models (LLMs) in various biological domains have been explored recently, but their reasoning ability in complex biological systems, such as pathways, remains underexplored, which is crucial for predicting…

Boolean functions and networks are commonly used in the modeling and analysis of complex biological systems, and this paradigm is highly relevant in other important areas in data science and decision making, such as in the medical field and…

We quantify the influence of the topology of a transcriptional regulatory network on its ability to process environmental signals. By posing the problem in terms of information theory, we may do this without specifying the function…

The first realization of a designed, rather than natural, biochemical filter process is reported and analyzed as a promising network component for increasing the complexity of biomolecular logic systems. Key challenge in biochemical logic…

Enzymes are essential to maintain organisms alive. Some of the reactions they catalyze are associated with a change in reagents chirality, hence their activity can be tracked by using optical means. However, illumination affects enzyme…

We realize autonomous Boolean networks by using logic gates in their autonomous mode-of-operation on a field-programmable gate array. This allows us to implement time-continuous systems with complex dynamical behaviors that can be…

The gene networks that comprise the circadian clock modulate biological function across a range of scales, from gene expression to performance and adaptive behaviour. The clock functions by generating endogenous rhythms that can be…

We study quantum information processing using superpositions of Fock states in superconducting resonators, as quantum $d$-level systems (qudits). A universal set of single and coupled logic gates is theoretically proposed for resonators…

We offer a theoretical design of new systems that show promise for digital biochemical computing, including realizations of error correction by utilizing redundancy, as well as signal rectification. The approach includes information…

Motivated by the pressing challenges in the digital twin development for biomanufacturing systems, we introduce an adjoint sensitivity analysis (SA) approach to expedite the learning of mechanistic model parameters. In this paper, we…

Interacting biological systems at all organizational levels display emergent behavior. Modeling these systems is made challenging by the number and variety of biological components and interactions (from molecules in gene regulatory…

Information transmission in biological signaling circuits has often been described using the metaphor of a noise filter. Cellular systems need accurate, real-time data about their environmental conditions, but the biochemical reaction…

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…

A ubiquitous building block of signaling pathways is a cycle of covalent modification (e.g., phosphorylation and dephosphorylation in MAPK cascades). Our paper explores the kind of information processing and filtering that can be…

Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…

Electronic logic gates are the basic building blocks of every computing and micro controlling system. Logic gates are made of switches, such as diodes and transistors. Ion-selective, ionic switches may emulate electronic switches [1-8]. If…

Living systems contain intricate biochemical networks whose structure is closely related to their function and allows them to exhibit robust behavior in the presence of external stimuli. Such networks typically involve catalytic enzymes,…

This paper presents EINCASM, a prototype system employing a novel framework for studying emergent intelligence in organisms resembling slime molds. EINCASM evolves neural cellular automata with NEAT to maximize cell growth constrained by…

Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living…

To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…