Related papers: Dynamic metabolic resource allocation based on the…
Production of energy (metabolism) and its distribution is vital for living organisms, both at individual level - between different functions of an organism, as well as between species of communities at different organizational levels,…
Flux balance analysis has proven an effective tool for analyzing metabolic networks. In flux balance analysis, reaction rates and optimal pathways are ascertained by solving a linear program, in which the growth rate is maximized subject to…
Quite generally, constraint-based metabolic flux analysis describes the space of viable flux configurations for a metabolic network as a high-dimensional polytope defined by the linear constraints that enforce the balancing of production…
Dynamic flux balance analysis uses a quasi-steady state assumption to calculate an organism's metabolic activity at each time-step of a dynamic simulation, using the well-known technique of flux balance analysis. For microbial communities,…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
Cell cultures exhibit rich and complex behaviors driven by dynamic metabolic interactions among cells. In this work, we present a model that captures these interactions through a framework inspired by statistical mechanics. Using Monte…
We revisit the modeling of the diauxic growth of a pure microorganism on two distinct sugars which was first described by Monod. Most available models are deterministic and make the assumption that all cells of the microbial ecosystem…
Dynamic processes on networks are fundamental to understanding modern-day phenomena such as information diffusion and opinion polarization on the internet or epidemics spreading through society. However, such processes are notoriously…
Intercellular exchange networks are essential for the adaptive capabilities of populations of cells. While diffusional exchanges have traditionally been difficult to map, recent advances in nanotechnology enable precise probing of exchange…
We consider dynamical systems evolving near an equilibrium statistical state where the interest is in modelling long term behavior that is consistent with thermodynamic constraints. We adjust the distribution using an entropy-optimizing…
Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…
Maximum entropy principle (MEP) offers an effective and unbiased approach to inferring unknown probability distributions when faced with incomplete information, while neural networks provide the flexibility to learn complex distributions…
Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalyzed biochemical reactions, is the most investigated complex intercellular web of molecular interactions. While the topological…
Cells adapt their metabolic fluxes in response to changes in the environment. We present a framework for the systematic construction of flux-based graphs derived from organism-wide metabolic networks. Our graphs encode the directionality of…
Living systems maintain or increase local order by working against the Second Law of Thermodynamics. Thermodynamic consistency is restored as they dissipate heat, thereby increasing the net entropy of their environment. Recently introduced…
Stochastic and soft optimal policies resulting from entropy-regularized Markov decision processes (ER-MDP) are desirable for exploration and imitation learning applications. Motivated by the fact that such policies are sensitive with…
The interplay between energy efficiency and evolutionary mechanisms is addressed. One important question is how evolutionary mechanisms can select for the optimised usage of energy in situations where it does not lead to immediate…
Existing strategies for determining the optimal treatment or monitoring strategy typically assume unlimited access to resources. However, when a health system has resource constraints, such as limited funds, access to medication, or…
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…
In this paper, we present a novel maximum entropy formulation of the Differential Dynamic Programming algorithm and derive two variants using unimodal and multimodal value functions parameterizations. By combining the maximum entropy…