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Discrete-state, continuous-time Markov models are becoming commonplace in the modelling of biochemical processes. The mathematical formulations that such models lead to are opaque, and, due to their complexity, are often considered…
Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…
This paper deals with temporal enzyme distribution in the activation of biochemical pathways. Pathway activation arises when production of a certain biomolecule is required due to changing environmental conditions. Under the premise that…
It has recently been proposed that proteins embedded in lipidic bio-membranes can spontaneously self-organize into stable small clusters, or membrane nano-domains, due to the competition between short-range attractive and longer-range…
Mendelian randomization implemented through instrumental variable analysis is frequently discussed in causality and recently the number of applications on real data is increasing. However, there are very few discussions to address modern…
The stochastic description of chemical reaction networks with the kinetic chemical master equation (CME) is important for studying biological cells, but it suffers from the curse of dimensionality: The amount of data to be stored grows…
The bigraph embedding problem is crucial for many results and tools about bigraphs and bigraphical reactive systems (BRS). Current algorithms for computing bigraphical embeddings are centralized, i.e. designed to run locally with a complete…
Natural Immune system plays a vital role in the survival of the all living being. It provides a mechanism to defend itself from external predates making it consistent systems, capable of adapting itself for survival incase of changes. The…
We present a novel multi-scale embedding scheme that links conventional QM/MM embedding and bootstrap embedding (BE) to allow simulations of large chemical systems on limited quantum devices. We also propose a mixed-basis BE scheme that…
Complex systems are ubiquitous in the real world and tend to have complicated and poorly understood dynamics. For their control issues, the challenge is to guarantee accuracy, robustness, and generalization in such bloated and troubled…
We report a realization of an associative memory signal/information processing system based on simple enzyme-catalyzed biochemical reactions. Optically detected chemical output is always obtained in response to the triggering input, but the…
Stochastic reaction networks with mass-action kinetics provide a useful framework for understanding processes -- biochemical and otherwise -- in homogeneous environments. However, cellular reactions are often compartmentalized, either at…
Polymerization and formation of crosslinked polymer networks are important processes in manufacturing, materials fabrication, and in the case of hydrated polymer networks, synthesis of biomedical materials, drug delivery, and tissue…
Surfaces serve as highly efficient catalysts for a vast variety of chemical reactions. Typically, such surface reactions involve billions of molecules which diffuse and react over macroscopic areas. Therefore, stochastic fluctuations are…
Biomolecules composed of a limited set of chemical building blocks can co-localize into distinct, spatially segregated compartments known as biomolecular condensates. While many condensates are known to form spontaneously via phase…
Phase separation is the thermodynamic process that explains how droplets form in multicomponent fluids. These droplets can provide controlled compartments to localize chemical reactions, and reactions can also affect the droplets' dynamics.…
Recent advances in biochemical computing, i.e., information processing with cascades of primarily enzymatic reactions realizing computing gates, such as AND, OR, etc., as well as progress in networking these gates and coupling of the…
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…
We examine the stochastic dynamics of two enzymes that are mechanically coupled to each other, e.g., through an elastic substrate or a fluid medium. The enzymes undergo conformational changes during their catalytic cycle, which itself is…
Enzyme design plays a crucial role in both industrial production and biology. However, this field faces challenges due to the lack of comprehensive benchmarks and the complexity of enzyme design tasks, leading to a dearth of systematic…