Related papers: Red herrings and rotten fish
The gut microbiome plays a crucial role in human health, yet the mechanisms underlying host-microbiome interactions remain unclear, limiting its translational potential. Recent microbiome multiomics studies, particularly paired…
A model of optimal control of ventilation has recently been developed for humans. This model highlights the importance of the localization of the transition between a convective and a diffusive transport of respiratory gas. This…
We consider a general growth mechanism, which acts at cellular level and above (organs, systems and whole organisms). Using its mathematical representation, the growth equation, we study the growth and division mechanisms of amoeba and…
Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
The composition of cellular metabolism is different across species. Empirical data reveal that bacterial species contain similar numbers of metabolic reactions but that the cross-species popularity of reactions is so heterogenous that some…
Many-body localization (MBL) has been widely investigated for both fermions and bosons, it is, however, much less explored for anyons. Here we numerically calculate several physical characteristics related to MBL of a one-dimensional…
Murray's cubic branching law ($\alpha=3$) predicts a universal diameter scaling exponent for all hierarchical transport networks, yet arterial trees yield $\alpha \sim 2.7-2.9$. We show that this discrepancy has a structural origin:…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
Background. Emerging technologies now allow for mass spectrometry based profiling of up to thousands of small molecule metabolites (metabolomics) in an increasing number of biosamples. While offering great promise for revealing insight into…
It is shown that the dual to the linear programming problem that arises in constraint-based models of metabolism can be given a thermodynamic interpretation in which the shadow prices are chemical potential analogues, and the objective is…
Understanding design principles of complex cellular organization is one of the major challenges in biology. Recent analysis of the large-scale cellular organization has revealed the scale-free nature and robustness of metabolic and protein…
In population dynamics, mathematical models often contain too many parameters to be easily testable. A way to reliably estimate parameters for a broad range of systems would help us obtain clearer predictions from theory. In this paper, 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…
Social interaction between microbes can be described at many levels of details, ranging from the biochemistry of cell-cell interactions to the ecological dynamics of populations. Choosing the best level to model microbial communities…
Fat tailed statistics and power-laws are ubiquitous in many complex systems. Usually the appearance of of a few anomalously successful individuals (bio-species, investors, websites) is interpreted as reflecting some inherent "quality"…
Author's early work on aging is developed to yield a relationship between life spans and the velocity of aging. The mathematical analysis shows that the mean extent of the advancement of aging throughout one's life is conserved, or…
We undertake a detailed numerical study of the {\it Active Model B} proposed by Wittkowski et al. [Nature Comm. {\bf 5}, 4351 (2014)]. We find that the introduction of activity has a drastic effect on the ordering kinetics. First, the…
Understanding the system level adaptive changes taking place in an organism in response to variations in the environment is a key issue of contemporary biology. Current modeling approaches such as the constraint-based flux balance analyses…
Lately, experimental research on microbial symbioses based on nutrient exchange and interdependence has yielded a number of interesting findings, however an in-depth mathematical description of the exact underlying dynamics of such…
In the present work, via computational simulation we study the statistical distribution of people versus number of steps acquired by them in a learning process, considering Darwin classical theory of evolution, i.e. competition, learning…