Related papers: Metabolic rate beyond the 3/4 law
The paper analyses stochastic systems describing reacting molecular systems with a combination of two types of state spaces, a finite-dimensional, and an infinite dimenional part. As a typical situation consider the interaction of larger…
Muscles consume metabolic energy (ATP) to produce force. A mathematical model for energy expenditure can be useful in estimating real-time costs of movements or to predict energy optimal movements. Metabolic cost models developed so far…
We have modeled the metabolic process running in aerobic cells as open nonlinear dissipative systems. The map of metabolic paths and the general scheme of a dissipative system participating in the transformation of steroids are constructed.…
Kinetic modeling of microbial growth is essential for the design, optimization, and scale-up of industrial bioprocesses. Classical empirical models often lack biologically interpretable parameters or fail to capture complex multiphasic…
In this paper we address some modelling issues related to biological growth. Our treatment is based on a recently-proposed, general formulation for growth within the context of Mixture Theory (Journal of the Mechanics and Physics of Solids,…
Morphoelasticity represents a foundational theory for tracing back growth, remodelling, and morphogenesis, yet crucial challenges persist. A unified growth law -- independent of a priori assumptions about constitutive relations or specified…
We propose a modelling framework to analyse the stochastic behaviour of heterogeneous, multi-scale cellular populations. We illustrate our methodology with a particular example in which we study a population with an oxygen-regulated…
Stem cell heterogeneity is essential for the homeostasis in tissue development. This paper established a general formulation for understanding the dynamics of stem cell regeneration with cell heterogeneity and random transitions of…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
Machine learning has been successfully used in critical domains, such as medicine. However, extracting meaningful insights from biomedical data is often constrained by the lack of their available disease labels. In this research, we…
Predicting cellular metabolic states is a central problem in biophysics. Conventional approaches, however, sensitively depend on the microscopic details of individual metabolic systems. In this Letter, we derived a universal linear…
This is the first report, to our knowledge, on a systematic method for constructing a large scale kinetic metabolic model with incomplete information on kinetic parametersr, and its initial application to the modeling of central metabolism…
In prokaryotic genomes the number of transcriptional regulators is known to quadratically scale with the total number of protein-coding genes. Toolbox model was recently proposed to explain this scaling for metabolic enzymes and their…
Resource Balance Analysis (RBA) is a framework for predicting steady-state cellular growth under resource constraints. However, classical RBA formulations are static and do not capture the dynamic regulation of biosynthetic resources or…
The metabolic network plays a crucial role in regulating bacterial metabolism and growth, but it is subject to inherent molecular stochasticity. Previous studies have utilized flux balance analysis and the maximum entropy method to predict…
This paper deals with a model of cellular growth called "Epigenetic Tracking", whose key features are: i) distinction bewteen "normal" and "driver" cells; ii) presence in driver cells of an epigenetic memory, that holds the position of the…
To maintain bone mass during bone remodelling, coupling is required between bone resorption and bone formation. This coordination is achieved by a network of autocrine and paracrine signalling molecules between cells of the osteoclast…
Cell growth in size is a complex process coordinated by intrinsic and environmental signals. In a recent work [Tzur et al., Science, 2009, 325:167-171], size distributions in an exponentially growing population of mammalian cells were used…
We introduce an in silico model for the initial spread of an aberrant phenotype with Warburg-like overflow metabolism within a healthy homeostatic tissue in contact with a nutrient reservoir (the blood), aimed at characterizing the role of…
Binding and unbinding of ligands to specific sites of a macromolecule are one of the most elementary molecular interactions inside the cell that embody the computational processes of biological regulations. The interaction between…