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In the first paper of this series, we included the effects of population genetics in the agent-based Monte Carlo code HERITAGE under the hypothesis of neutral phenotypic effects. It implied that mutations (genetic changes) had only neutral…
Cellular decision making allows cells to assume functionally different phenotypes in response to microenvironmental cues, without genetic change. It is an open question, how individual cell decisions influence the dynamics at the tissue…
We present the derivation of a new model to describe neutron spin echo spectroscopy and quasi-elastic neutron scattering data on liposomes. We compare the new model with existing approaches and benchmark it with experimental data. The…
Genetic diversity is central to the process of evolution. Both natural selection and random genetic drift are influenced by the level of genetic diversity of a population; selection acts on diversity while drift samples from it. At a given…
Dengue, a mosquito-borne viral disease common in tropical areas, is spread by Aedes aegypti and Aedes albopictus. Temperature changes driven by climate affect vector ecology and expand regions of species coexistence. The combined effect of…
This study aimed to investigate the effects of genetic polymorphisms on tacrolimus blood levels and intra-individual variability in recipients of heart transplants during the early post-transplantation period. Demographic information,…
We introduce LNODE, a mechanism-based phenomenological model for amyloid beta (A$\beta$) dynamics, calibrated using positron emission tomography (PET) imaging. A$\beta$ is a key biomarker of Alzheimer's disease. LNODE is designed to support…
We build a model for the hepatic fatty acid metabolism and its metabolic and genetic regulations. The model has two functioning modes: synthesis and oxidation of fatty acids. We provide a sufficient condition (the strong lipolytic…
The L\'evy walk process with rests is discussed. The jumping time is governed by an $\alpha$-stable distribution with $\alpha>1$ while a waiting time distribution is Poissonian and involves a position-dependent rate which reflects a…
Atherosclerotic plaques form in artery walls due to a chronic inflammatory response driven by lipid accumulation. A key component of the inflammatory response is the interaction between monocyte-derived macrophages and extracellular lipid.…
Motivated by recent understandings in the stochastic natures of gene expression, biochemical signaling, and spontaneous reversible epigenetic switchings, we study a simple deterministic cell population dynamics in which subpopulations grow…
Breathing is one of the most important body functions because it provides it with oxygen, which is vital for energy production. In addition, the removal of carbon dioxide actively regulates the acid-base level, which is essential for the…
The thermodynamic (TD) properties of biological membranes play a central role for living systems. It has been suggested, for instance, that nonlinear pulses such as action potentials (APs) can only exist if the membrane state is in vicinity…
The biological world, especially its majority microbial component, is strongly interacting and may be dominated by collective effects. In this review, we provide a brief introduction for statistical physicists of the way in which living…
The level of supercoiling in the chromosome can affect gene expression. To clarify the basis of supercoiling sensitivity, we analyzed the structural features of nucleotide sequences in the vicinity of promoters for the genes with expression…
We present an SI epidemic model whereby a continuous variable captures variability in proliferative potential and resistance to infection among susceptibles. The occurrence of heritable, spontaneous changes in these phenotype and the…
The component Allee effect (AE) is the positive correlation between an organism's fitness component and population density. Depending on the population spatial structure, which determines the interactions between organisms, a component AE…
Entropy plays a key role in statistical physics of complex systems, which in general exhibit diverse aspects of emergence on different scales. However, it still remains not fully resolved how entropy varies with the coarse-graining level…
The supramolecular assembly of lipids into bilayer membranes is essential for cellular structure and function. However, the impact of lipid structural variations such as acyl chain length, degree of unsaturation, and headgroup type on…
Understanding and manipulating the interactions between foreign bodies and cell membranes during endo- and phagocytosis is of paramount importance, not only for the fate of living cells but also for numerous biomedical applications. This…