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Production of energy is a foundation of life. Metabolic rate of organisms (amount of energy produced per unit time) generally increases slower than organisms' mass, which has important implications for life organization. This phenomenon,…
As metabolomics datasets are becoming larger and more complex, there is an increasing need for model-based data integration and analysis to optimally leverage these data. Dynamical models of metabolism allow for the integration of…
Biological systems operate under simultaneous energetic and informational constraints, yet direct evidence that such constraints shape real metabolic networks is limited. The Network-Weighted Action Principle predicts that networks under…
This paper introduces a linear state-space model with time-varying dynamics. The time dependency is obtained by forming the state dynamics matrix as a time-varying linear combination of a set of matrices. The time dependency of the weights…
Metabolomics is becoming a mature part of analytical chemistry as evidenced by the growing number of publications and attendees of international conferences dedicated to this topic. Yet, a systematic treatment of the fundamental structure…
Atomistic modelling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an…
In a mathematical model of interacting biological organisms, where external interventions may alter behavior over time, traditional models that assume fixed parameters usually do not capture the evolving dynamics. In oncology, this is…
Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables(CVs) it can explore complex free energy surfaces…
We study feedback control of classical Hamiltonian systems with the controlling parameter varying slowly in time. The control aims to change system's energy. We show that the control problems can be solved with help of an adiabatic…
This paper investigates the role of size in biological organisms. More specifically, how the energy demand, expressed by the metabolic rate, changes according to the mass of an organism. Empirical evidence suggests a power-law relation…
Metabolism plays a central role in cell physiology because it provides the molecular machinery for growth. At the genome-scale, metabolism is made up of thousands of reactions interacting with one another. Untangling this complexity is key…
The galactose network is a complex system responsible for galactose metabolism. It has been extensively studied experimentally and mathematically at the unicellular level to broaden our understanding of its regulatory mechanisms at higher…
Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and…
Organisms have evolved a variety of mechanisms to cope with the unpredictability of environmental conditions, and yet mainstream models of metabolic regulation are typically based on strict optimality principles that do not account for…
Obesity is a global health concern associated with high morbidity and mortality. Therapeutic strategies include synthetic drugs and surgery, which may entail high costs and serious complications. Plant-based medicinal agents offer an…
Networks of biochemical reactions, like cellular metabolic networks, are kept in non-equilibrium steady states by the exchange fluxes connecting them to the environment. In most cases, feasible flux configurations can be derived from…
The adiabatic theorem in quantum mechanics implies that if a system is in a discrete eigenstate of a Hamiltonian and the Hamiltonian evolves in time arbitrarily slowly, the system will remain in the corresponding eigenstate of the evolved…
It has long been hypothesized that futile cycles in cellular metabolism are involved in the regulation of biochemical pathways. Following the work of Newsholme and Crabtree, we develop a quantitative theory for this idea based on…
To advance understanding of cellular metabolism and reduce batch-to-batch variability in cell culture processes, this study introduces a multi-scale hybrid modeling framework designed to simulate and predict the dynamic behavior of CHO cell…
Mobility edge transitions from localized to extended states have been observed in two and three dimensional systems, for which sound theoretical explanations have also been derived. One-dimensional lattice models have failed to predict…