Other Quantitative Biology
Homicide investigations often depend on the determination of a minimum post-mortem interval (PMI$_{min}$) by forensic entomologists. The age of the most developed insect larvae (mostly blow fly larvae) gives reasonably reliable information…
The subject of analysis is a non-linear three-compartment model, widely used in pharmacological absorption studies. It has been transformed into a general form, thus leading automatically to an appropriate approximation. This made the…
The genome is software because it a set of verbal instructions for a programmable computer, the ribosome. The theory of evolution now reads: evolution is the software developer responsible for the existence of the genome. We claim that this…
Plants at high population density compete for light, showing a series of physiological responses known as the shade avoidance syndrome. These responses are controlled by the synthesis of the hormone auxin, which is regulated by two signals,…
Constraint-based modeling has been widely used on metabolic networks analysis, such as biosynthetic prediction and flux optimization. The linear constraints, like mass conservation constraint, reversibility constraint, biological capacity…
Living organisms are the most complex, interesting and significant objects regarding all substructures of the universe. Life science is regarded as a science of the 21st century and one can expect great new discoveries in the near futures.…
The possible mechanisms of communications between distant bio-systems by means of optical and UV photons are studied. It is argued that their main production mechanism is owed to the biochemical reactions, occurring during the cell…
The Metropolis implementation of the Monte Carlo algorithm has been developed to study the equilibrium thermodynamics of many-body systems. Choosing small trial moves, the trajectories obtained applying this algorithm agree with those…
The effects of pure multiplicative noise on stochastic resonance in an anti-tumor system modulated by a seasonal external field are investigated by using theoretical analyses of the generalized potential and numerical simulations. For…
The genetic code structure into distinct multiplet-classes as well as the numeric degeneracies of the latter are revealed by a two-step process. First, an empirical inventory of the degeneracies (of the shuffled multiplets) in two specific…
A spatiotemporal noise is assumed to reflect the environmental fluctuation in a spatially extended tumor system. We introduce firstly the structure factor to reveal the invasive tumor growth quantitatively. The homogenous environment can…
The amount of mutual information contained in time series of two elements gives a measure of how well their activities are coordinated. In a large, complex network of interacting elements, such as a genetic regulatory network within a cell,…
Neural activity patterns related to behavior occur at many scales in time and space from the atomic and molecular to the whole brain. Here we explore the feasibility of interpreting neurophysiological data in the context of many-body…
As a first step in the search of an analytical study of mechanical denaturation of DNA in terms of the sequence, we study stable, stationary solutions in the discrete, finite and homogeneous Peyrard-Bishop DNA model. We find and classify…
A variety of physical, social and biological systems generate complex fluctuations with correlations across multiple time scales. In physiologic systems, these long-range correlations are altered with disease and aging. Such correlated…
Recently, several theoretical and experimental studies have been undertaken to probe the effect of stochasticity on gene expression (GE). In experiments, the GE response to an inducing signal in a cell, measured by the amount of…
We present the first systematic evidence for the origins of 1/f-type temporal scaling in human heart rate. The heart rate is regulated by the activity of two branches of the autonomic nervous system: the parasympathetic (PNS) and the…
The response of the immune system to different vaccination patterns is studied with a simple model. It is argued that the history and characteristics of the pattern defines very different secondary immune responses in the case of infection.…
Many emerging pathogens infect multiple host species, and multi-host pathogens may have very different dynamics in different host species. This research addresses how pathogen replication rates and Immune System (IS) response times are…
Two recent investigations are reviewed: quantum effects for DNA aggregates and scars formation on virus capsids. The possibility that scars could explain certain data recently obtained by Sundquist's group in electron cryotomography of…