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Analysis of large continuous-time stochastic systems is a computationally intensive task. In this work we focus on population models arising from chemical reaction networks (CRNs), which play a fundamental role in analysis and design of…
Cells must continuously sense and respond to time-varying environmental stimuli. These signals are transmitted and processed by biochemical signalling networks. However, the biochemical reactions making up these networks are intrinsically…
Living cells communicate information about physiological conditions by producing signaling molecules in a specific timed manner. Different conditions can result in the same total amount of a signaling molecule, differing only in the pattern…
We use ideas from kinetic proofreading, an error-correcting mechanism in biology, to identify new kinetic regimes in non-equilibrium systems. These regimes are defined by the sensitivity of the occupancy of a state of the system to a change…
The Bond Graph approach and the Chemical Reaction Network approach to modelling biomolecular systems developed independently. This paper brings together the two approaches by providing a bond graph interpretation of the chemical reaction…
Hebbian theory seeks to explain how the neurons in the brain adapt to stimuli, to enable learning. An interesting feature of Hebbian learning is that it is an unsupervised method and as such, does not require feedback, making it suitable in…
Understanding and prediction of the chemical reactions are fundamental demanding in the study of many complex chemical systems. Reactive molecular dynamics (MD) simulation has been widely used for this purpose as it can offer atomic details…
Cellular ingredient concentrations can be stabilized by adjusting generation and consumption rates through multiple pathways. To explore the portion of cellular metabolism equipped with multiple pathways, we categorize individual metabolic…
With the widespread application of multimodal large language models in scientific intelligence, there is an urgent need for more challenging evaluation benchmarks to assess their ability to understand complex scientific data. Scientific…
One of the most important aims of the fields of robotics, artificial intelligence and artificial life is the design and construction of systems and machines as versatile and as reliable as living organisms at performing high level…
Quantum communication channels and quantum memories are the fundamental building blocks of large-scale quantum communication networks. Estimating their capacity to transmit and store quantum information is crucial in order to assess the…
We show how a quantum computer can be employed to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment…
The design and analysis of communication systems typically rely on the development of mathematical models that describe the underlying communication channel, which dictates the relationship between the transmitted and the received signals.…
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…
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…
Chemical reaction practicality is the core task among all symbol intelligence based chemical information processing, for example, it provides indispensable clue for further automatic synthesis route inference. Considering that chemical…
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…
This paper studies a system of Ordinary Differential Equations modeling a chemical reaction network and derives from it a simulation tool mimicking Loss of Function and Gain of Function mutations found in cancer cells. More specifically,…
Reversibility, weak reversibility and deficiency, detailed and complex balancing are generally not "encoded" in the kinetic differential equations but they are realization properties that may imply local or even global asymptotic stability…
Mathematical reasoning---a core ability within human intelligence---presents some unique challenges as a domain: we do not come to understand and solve mathematical problems primarily on the back of experience and evidence, but on the basis…