Related papers: Constrained Allocation Flux Balance Analysis
We study the convergence of a sequence of evolution equations for measures supported on the nodes of a graph. The evolution equations themselves can be interpreted as the forward Kolmogorov equations of Markov jump processes, or…
In this paper, the authors study the distributed optimal control of a system of three evolutionary equations involving fractional powers of three selfadjoint, monotone, unbounded linear operators having compact resolvents. The system is a…
In this paper, we derive an effective macroscale description suitable to describe the growth of biological tissue within a porous tissue-engineering scaffold. As in our recent work (Holden \textit{et al.} "A multiphase multiscale model for…
In many high-throughput experimental design settings, such as those common in biochemical engineering, batched queries are more cost effective than one-by-one sequential queries. Furthermore, it is often not possible to directly choose…
We study the costs and benefits of different quantum approaches to finding approximate solutions of constrained combinatorial optimization problems with a focus on Maximum Independent Set. In the Lagrange multiplier approach we analyze the…
In recent years dynamical modelling has been provided with a range of breakthrough methods to perform exact Bayesian inference. However it is often computationally unfeasible to apply exact statistical methodologies in the context of large…
Quantum annealing (QA) is a method for solving combinatorial optimization problems. We can estimate the computational time for QA using the adiabatic condition. The adiabatic condition consists of two parts: an energy gap and a transition…
Many biological processes discriminate between correct and incorrect substrates through the kinetic proofreading mechanism which enables lower error at the cost of higher energy dissipation. Elucidating physicochemical constraints for…
The metabolic wiring of patient cells is altered drastically in many diseases, including cancer. Understanding the nature of such changes may pave the way for new therapeutic opportunities, as well as the development of personalized…
Cell colonies of bacteria, tumour cells and fungi, under nutrient limited growth conditions, exhibit complex branched growth patterns. In order to investigate this phenomenon we present a simple hybrid cellular automaton model of cell…
Biological machines like molecular motors and enzymes operate in dynamic cycles representable as stochastic flows on networks. Current stochastic dynamics describes such flows on fixed networks. Here, we develop a scalable approach to…
Density dependence is important in the ecology and evolution of microbial and cancer cells. Typically, we can only measure net growth rates, but the underlying density-dependent mechanisms that give rise to the observed dynamics can…
The purpose of this paper is to show that it is possible to replace Monod's type model of a chemostat by a constraint based model of bacteria at the genome scale. This new model is an extension of the RBA model of bacteria developed in a…
In the landscape of generative artificial intelligence, diffusion-based models have emerged as a promising method for generating synthetic images. However, the application of diffusion models poses numerous challenges, particularly…
Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organisms environment, and evolution in changing environments is still poorly…
Growth (and resorption) of biological tissue is formulated in the continuum setting. The treatment is macroscopic, rather than cellular or sub-cellular. Certain assumptions that are central to classical continuum mechanics are revisited,…
We introduce a new method for performing clustering with the aim of fitting clusters with different scatters and weights. It is designed by allowing to handle a proportion $\alpha$ of contaminating data to guarantee the robustness of the…
Any process in which competing solutions replicate with errors and numbers of their copies depend on their respective fitnesses is the evolutionary optimization process. As during carcinogenesis mutated genomes replicate according to their…
We propose a model for the dynamics of a probe embedded in a living cell, where both thermal fluctuations and nonequilibrium activity coexist. The model is based on a confining harmonic potential describing the elastic cytoskeletal matrix,…
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…