Related papers: Metabolic rate beyond the 3/4 law
We study viscoelastic subdiffusion in bistable and periodic potentials within the Generalized Langevin Equation approach. Our results justify the (ultra)slow fluctuating rate view of the corresponding bistable non-Markovian dynamics which…
Local perturbations of individual metabolic reactions may result in different levels of lethality, depending on their roles in metabolism and the size of subsequent cascades induced by their failure. Moreover, essentiality of individual…
We study a two parameter ($u,p$) extension of the conformally invariant raise and peel model. The model also represents a nonlocal and biased-asymmetric exclusion process with local and nonlocal jumps of excluded volume particles in the…
In this work we upscale a prototypical kinetic transport equation which models a cell population moving in a fibrous environment with a chemo- or haptotactic signal influencing both the direction and the magnitude of the cell velocity. The…
We cast the metabolism of interacting cells within a statistical mechanics framework considering both, the actual phenotypic capacities of each cell and its interaction with its neighbors. Reaction fluxes will be the components of…
We study the statistical underpinnings of life. We question some common assumptions about the thermodynamics of life and illustrate how, contrary to widespread belief, even in a closed system entropy growth can accompany an increase in…
The identification of cellular objectives is one of the central topics in the research of microbial metabolic networks. In particular, the information about a cellular objective is needed in flux balance analysis which is a commonly used…
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…
We devise a new 1D atomistic scale model of vicinal growth based on Cellular Automaton. In it the step motion is realized by executing the automaton rule prescribing how adatoms incorporate into the vicinal crystal. Time increases after…
Understanding the organization of reaction fluxes in cellular metabolism from the stoichiometry and the topology of the underlying biochemical network is a central issue in systems biology. In this task, it is important to devise reasonable…
A model of mutation rate evolution for multiple loci under arbitrary selection is analyzed. Results are obtained using techniques from Karlin (1982) that overcome the weak selection constraints needed for tractability in prior studies of…
During embryonic development tissue morphogenesis and signaling are tightly coupled. It is therefore important to simulate both tissue morphogenesis and signaling simultaneously in in silico models of developmental processes. The resolution…
The heterogeneity of reaction fluxes present in a metabolic network within a single flux state can be exploited to construct the so-called backbone as a reduced version of metabolism. The backbone maintains all significant fluxes producing…
Scaling laws illuminate Nature's fundamental biological principles and guide bioinspired materials and structural designs. In simple cases they are based on the fundamental principle that all laws of nature remain unchanged (i.e.,…
We propose a multiscale mechanobiological model of bone remodelling to investigate the site-specific evolution of bone volume fraction across the midshaft of a femur. The model includes hormonal regulation and biochemical coupling of bone…
We consider the problem of inferring the probability distribution of flux configurations in metabolic network models from empirical flux data. For the simple case in which experimental averages are to be retrieved, data are described by a…
The goal of this work is to analyze a model for the rate-independent evolution of sets with finite perimeter. The evolution of the admissible sets is driven by that of a given time-dependent set, which has to include the admissible sets and…
Systematic variation is a common issue in metabolomics data analysis. Therefore, different scaling and normalization techniques are used to preprocess the data for metabolomics data analysis. Although several scaling methods are available…
Understanding the cross-species behavior of cancer is important for uncovering fundamental mechanisms of carcinogenesis, and for translating results of model systems between species. One of the most famous interspecific considerations of…
Efforts to catalogue the structure of metabolic networks have generated highly detailed, genome-scale atlases of biochemical reactions in the cell. Unfortunately, these atlases fall short of capturing the kinetic details of metabolic…