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Information processing relying on biochemical interactions in the cellular environment is essential for biological organisms. The implementation of molecular computational systems holds significant interest and potential in the fields of…

Dynamical Systems · Mathematics 2023-12-01 Yuzhen Fan , Xiaoyu Zhang , Chuanhou Gao , Denis Dochain

Multienzyme cascaded reactions are widely utilized because they can generate value-added biomaterials and biodevices from simple raw materials. However, how to promote the catalytic efficiency and synergistic effect of the multienzyme…

Biological Physics · Physics 2021-01-27 Zhexu Xi

High-throughput molecular profiling technologies have produced high-dimensional multi-omics data, enabling systematic understanding of living systems at the genome scale. Studying molecular interactions across different data types helps…

Machine Learning · Computer Science 2020-10-23 Ehsan Hajiramezanali , Arman Hasanzadeh , Nick Duffield , Krishna R Narayanan , Xiaoning Qian

Artificial Intelligence (AI) and Machine Learning (ML) are weaving their way into the fabric of society, where they are playing a crucial role in numerous facets of our lives. As we witness the increased deployment of AI and ML in various…

Emerging Technologies · Computer Science 2022-12-23 Sasitharan Balasubramaniam , Samitha Somathilaka , Sehee Sun , Adrian Ratwatte , Massimiliano Pierobon

Cooperative interactions among the binding of multiple signaling molecules is a common mechanism for enhancing the sensitivity of biological signaling systems. It is widely assumed that this increase in sensitivity of the mean response…

Molecular Networks · Quantitative Biology 2007-05-23 William Bialek , Sima Setayeshgar

Self-sustaining nonlinear oscillators of practically any type can function as latches and registers if Boolean logic states are represented physically as the phase of oscillatory signals. Combinational operations on such phase-encoded logic…

Emerging Technologies · Computer Science 2017-03-09 Jaijeet Roychowdhury

So far proposed quantum computers use fragile and environmentally sensitive natural quantum systems. Here we explore the new notion that synthetic quantum systems suitable for quantum computation may be fabricated from smart nanostructures…

General Physics · Physics 2009-11-07 Reginald T. Cahill

Sensitivity analysis of biochemical reactions aims at quantifying the dependence of the reaction dynamics on the reaction rates. The computation of the parameter sensitivities, however, poses many computational challenges when taking…

Molecular Networks · Quantitative Biology 2018-11-07 Vo Hong Thanh , Roberto Zunino , Corrado Priami

Artificially engineered biosensors are highly inefficient in accurately measuring the concentration of biomarkers, particularly, during early diagnosis of diseases. On the other hand, single cellular systems such as chemotactic bacteria can…

Biological Physics · Physics 2019-07-12 Tuhin Chakrabortty , Manoj M Varma

In this paper we show that living cells can multiplex biochemical signals, i.e. transmit multiple signals through the same signaling pathway simultaneously, and yet respond to them very specifically. We demonstrate how two binary input…

Molecular Networks · Quantitative Biology 2012-06-01 Wiet de Ronde , Filipe Tostevin , Pieter Rein ten Wolde

Research in Cognitive Science suggests that humans understand and represent knowledge of the world through causal relationships. In addition to observations, they can rely on experimenting and counterfactual reasoning -- i.e. referring to…

Artificial Intelligence · Computer Science 2021-05-24 Kanvaly Fadiga , Etienne Houzé , Ada Diaconescu , Jean-Louis Dessalles

Innovation in synthetic biology often still depends on large-scale experimental trial-and-error, domain expertise, and ingenuity. The application of rational design engineering methods promise to make this more efficient, faster, cheaper…

Molecular Networks · Quantitative Biology 2021-08-18 Robyn P. Araujo , Sean T. Vittadello , Michael P. H. Stumpf

Conventional biomedical research is increasingly labor-intensive due to the exponential growth of scientific literature and datasets. Artificial intelligence (AI), particularly Large Language Models (LLMs), has the potential to…

Multiagent Systems · Computer Science 2025-07-08 Yi Luo , Linghang Shi , Yihao Li , Aobo Zhuang , Yeyun Gong , Ling Liu , Chen Lin

Despite tremendous potential of highly sensitive electronic detection of bio-molecules by nanoscale biosensors for genomics and proteomic applications, many aspects of experimentally observed sensor response (S) are unexplained within…

Soft Condensed Matter · Physics 2015-05-13 Pradeep R. Nair , Muhammad A. Alam

Autonomous edge computing in robotics, smart cities, and autonomous vehicles relies on the seamless integration of sensing, processing, and actuation for real-time decision-making in dynamic environments. At its core is the…

Machine learning (ML) is becoming increasingly crucial in many fields of engineering but has not yet played out its full potential in bioprocess engineering. While experimentation has been accelerated by increasing levels of lab automation,…

Application of Microelectronic to bioanalysis is an emerging field which holds great promise. From the standpoint of electronic and system design, biochips imply a radical change of perspective, since new, completely different constraints…

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…

Molecular Networks · Quantitative Biology 2012-10-25 Ozgur Akman , Steven Watterson , Andrew Parton , Nigel Binns , Andrew Millar , Peter Ghazal

Human decisional processes result from the employment of selected quantities of relevant information, generally synthesized from environmental incoming data and stored memories. Their main goal is the production of an appropriate and…

Artificial Intelligence · Computer Science 2016-09-08 Graziano Barnabei , Franco Bagnoli , Ciro Conversano , Elena Lensi

As the global population continues to age, there is an increasing demand for ways to accurately quantify the biological processes underlying aging. Biological age, unlike chronological age, reflects an individual's physiological state,…

Quantitative Methods · Quantitative Biology 2025-08-29 Jared A Kushner , Mohit Pandey , Sandeep , S Kohli
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