Acta Biotheoretica

The COVID-19 pandemic has resulted in more than 524 million cases and 6 million deaths worldwide. Various drug interventions targeting multiple stages of COVID-19 pathogenesis can significantly reduce infection-related mortality. The current within-host mathematical modeling study addresses the optimal drug regimen and efficacy of combination therapies in the treatment of COVID-19. The drugs/interventions considered include Arbidol, Remdesivir, Interferon (INF) and Lopinavir/Ritonavir. It is concluded that these drugs, when administered singly or in combination, reduce the number of infected cells and viral load...

Reconstructing the genetic traits of the Last Common Ancestor (LCA) and the Tree of Life (TOL) are two examples of the reaches of contemporary molecular phylogenetics. Nevertheless, the whole enterprise has led to paradoxical results. The presence of Lateral Gene Transfer poses epistemic and empirical challenges to meet these goals; the discussion around this subject has been enriched by arguments from philosophers and historians of science. At the same time, a few but influential research groups have aimed to reconstruct the LCA with rich-in-detail hypotheses and high-resolution gene catalogs and metabolic traits...

This is a digest of how various researchers in biology and astrobiology have explored questions of what defines living organisms-definitions based on functions or structures observed in organisms, or on systems terms, or on mathematical conceptions like closure, chirality, quantum mechanics and thermodynamics, or on biosemiotics, or on Darwinian evolution-to clarify the field and make it easier for endeavors in artificial intelligence to make progress. Current ideas are described to promote work between astrobiologists and computer scientists, each concerned with living organisms...

A tight control of intracellular [Ca[Formula: see text]] is essential for the survival and normal function of cells. In this study we investigate key mechanistic steps by which calcium is regulated and calcium oscillations could occur using in silico modeling of membrane transporters. To do so we give a deterministic description of intracellular Ca[Formula: see text] dynamics using nonlinear dynamics in order to understand Ca[Formula: see text] signaling. We first present the ordinary differential equations (ODEs) system for cell calcium kinetics and make a preliminary work on Sobol indices...

Nonlocal reaction-diffusion equations describe various biological and biomedical applications. Their mathematical properties are essentially different in comparison with the local equations, and this difference can lead to important biological implications. This review will present the state of the art in the investigation of nonlocal reaction-diffusion models in biomedical applications. We will consider various models arising in mathematical immunology, neuroscience, cancer modelling, and we will discuss their mathematical properties, nonlinear dynamics, resulting spatiotemporal patterns and biological significance...

Predation and escaping from predation through hiding are two fundamental phenomena in ecology. The most common approach to reducing the chance of predation is to use a refuge. Here, we consider a three species fishery model system with prey refuge induced by a Holling type-II functional response. These three species of fish populations are named prey, middle predator, and top predator. Harvesting is employed in most fishery models to achieve both ecological and commercial benefits. Research proves that non-linear harvesting (Michaelis-Menten type) returns more realistic outcomes...

The susceptible-transmissible-removed (STR) model is a deterministic compartment model, based on the susceptible-infected-removed (SIR) prototype. The STR replaces 2 SIR assumptions. SIR assumes that the emigration rate (due to death or recovery) is directly proportional to the infected compartment's size. The STR replaces this assumption with the biologically appropriate assumption that the emigration rate is the same as the immigration rate one infected period ago. This results in a unique delay differential equation epidemic model with the delay equal to the infected period...

Schistosomiasis, a vector-borne chronically debilitating infectious disease, is a serious public health concern for humans and animals in the affected tropical and sub-tropical regions. We formulate and theoretically analyze a deterministic mathematical model with snail and bovine hosts. The basic reproduction number [Formula: see text] is computed and used to investigate the local stability of the model's steady states. Global stability of the endemic equilibrium is carried out by constructing a suitable Lyapunov function...

The challenges with modeling the spread of Covid-19 are its power-type growth during the middle stages of the waves with the exponents depending on time, and that the saturation of the waves is mainly due to the protective measures and other restriction mechanisms working in the same direction. The two-phase solution we propose for modeling the total number of detected cases of Covid-19 describes the actual curves for many its waves and in many countries almost with the accuracy of physics laws. Bessel functions play the key role in our approach...

The origin of the genetic code has been attributed in part to an accidental assignment of codons to amino acids. Although several lines of evidence indicate the subsequent expansion and improvement of the genetic code, the hypothesis of Francis Crick concerning a frozen accident occurring at the early stage of genetic code evolution is still widely accepted. Considering Crick's hypothesis, mathematical descriptions of hypothetical scenarios involving a huge number of possible coexisting random genetic codes could be very important to explain the origin and evolution of a selected genetic code...

A theorem on the partitioning of a randomly selected large population into stationary and non-stationary components by using a property of the stationary population identity is stated and proved. The methods of partitioning demonstrated are original and these are helpful in real-world situations where age-wise data is available. Applications of this theorem for practical purposes are summarized at the end.

Theoretical and experimental studies on prey-predator systems where predator is supplied with alternate sources of food have received significant attention over the years due to their relevance in achieving biological conservation and biological control. Some of the outcomes of these studies suggest that with appropriate quality and quantity of additional food, the system can be steered towards any desired state eventually with time. One of the limitations of previous studies is that the desired state is reached asymptotically, which makes the outcomes not easily applicable in practical scenarios...

Viruses are the simplest of pathogens, but possess sophisticated molecular mechanisms to manipulate host behavior, frequently utilizing molecular mimicry. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been shown to bind to the host receptor neuropilin-1 in order to gain entry into the cell. To do this, the virus utilizes its spike protein polybasic cleavage site (PCS), which mimics the CendR motif of neuropilin-1's endogenous ligands. In addition to facilitating cell entry, binding to neuropilin-1 has analgesic effects...

While evenness is understood to be maximal if all types (species, genotypes, alleles, etc.) are represented equally (via abundance, biomass, area, etc.), its opposite, maximal unevenness, either remains conceptually in the dark or is conceived as the type distribution that minimizes the applied evenness index. The latter approach, however, frequently leads to conceptual inconsistency due to the fact that the minimizing distribution is not specifiable or is monomorphic. The state of monomorphism, however, is indeterminate in terms of its evenness/unevenness characteristics...

In photoreceptors of a dark adapted eye, the inward flux of sodium and calcium ions in the outer segment is balanced by the outward flux of potassium ions. But in the presence of light the creation of cyclic guanosine monophosphate in the outer segment decreases. Due to low concentration of cG (cyclic GMP) the channels in the outer segment open relatively less and thus the influx of calcium ion decreases, leading finally to hyperpolarization of the photoreceptors. We have analyzed theoretically the effect of oxidizing iron ions on the photoreceptors...

It is often assumed that the transition between chemical evolution and biological evolution undergoes a smooth process; that once life has arisen, it will automatically 'flood' a solar system body. However, there is no a priori reason to assume that a link between them is a given. The fact that both chemical evolution and biological evolution meet in a single point can be critical. Thus, one may ask: can a world's environment be favourable for chemical evolution but not for biological evolution, or vice versa? This is an important question worth exploration because certain worlds in the solar system in the past seemed to possess the possibility of chemical evolution, while several worlds in the present seem to exhibit such a possibility...

Some contemporary theorists such as Mazzocchi, Theise and Kafatos are convinced that the reformed complementarity may redefine how we might exploit the complexity theory in 21st-century life sciences research. However, the motives behind the profound re-invention of "biological complementarity" need to be substantiated with concrete shreds of evidence about this principle's applicability in real-life science experimentation, which we found missing in the literature. This paper discusses such pieces of evidence by confronting Bohr's complementarity and ion channel modeling practice...

Lithopanspermia is a theory proposing a natural exchange of organisms between solar system bodies as a result of asteroidal or cometary impactors. Research has examined not only the physics of the stages themselves but also the survival probabilities for life in each stage. However, although life is the primary factor of interest in lithopanspermia, this life is mainly treated as a passive cargo. Life, however, does not merely passively receive an onslaught of stress from surroundings; instead, it reacts. Thus, planetary ejection, interplanetary transport, and planetary entry are only the first three factors in the equation...

Does natural selection favor veridical percepts-those that accurately (if not exhaustively) depict objective reality? Perceptual and cognitive scientists standardly claim that it does. Here we formalize this claim using the tools of evolutionary game theory and Bayesian decision theory. We state and prove the "Fitness-Beats-Truth (FBT) Theorem" which shows that the claim is false: If one starts with the assumption that perception involves inference to states of the objective world, then the FBT Theorem shows that a strategy that simply seeks to maximize expected-fitness payoff, with no attempt to estimate the "true" world state, does consistently better...

Complex, multigenic biological traits are shaped by the emergent interaction of proteins being the main functional units at the molecular scale. Based on a phenomenological approach, algorithms for quantifying two different aspects of emergence were introduced (Wegner and Hao in Progr Biophys Mol Biol 161:54-61, 2021) describing: (i) pairwise reciprocal interactions of proteins mutually modifying their contribution to a complex trait (denoted as weak emergence), and (ii) formation of a new, complex trait by a set of n 'constitutive' proteins at concentrations exceeding individual threshold values (strong emergence)...