Questions tagged [theoretical-biology]

Questions relating to biological theory or theoretical developments that deals with biological processes.

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63 views

Are there *illustrative* (images) examples of the fact that nature follows gaussian behaviour?

We see examples of mathematics in nature. For example, the Fibonacci sequence could be seen directly in nature. Some illustrations (images) : https://www.sciencefriday.com/educational-resources/...
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Conservation Law in Gene Regulatory Network modelling

I was going through the GRN modelling from Chemical and enzyme kinetics by D. Gonze & M. Kaufman (PDF). The gene has 2 sites for activator/repressor. It say the DNA $D_0$ combines with activator/...
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Mathematical/statistical models for forecasting population distributions of age, sex, weight, and height [closed]

I come from a mathematical background but I have no experience with the topic of mathematical biology. Are there well established mathematical/statistical models for forecasting the evolution of ...
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Do neurons have self-loops? [duplicate]

Consider a directed graph to be a model of neuronal structure where the vertices are the neurons and the arcs represent synapses between axon and dendritic terminals. Another question already asked ...
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Does parental conflict lead to genes combining important functions with functions only advantageous for one of the parents?

In a sitation of a mother-father conflict of interests, the mother might use epigenetics to turn off some genes only advantageous for the father's genes and not her own. I thought a logical father's ...
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110 views

How does the Endoplasmic Reticulum scale with Cell Volume in Epithelial Cells?

I am working on a mathematical model of a biological tissue (drosophila pupal notum; an epithelial tissue) where the tissue is built up from cells all described by the same cellular-model. The tissue ...
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93 views

Examples for oscillatory behaviour in the human body

I'm looking for examples in the human body which show periodicity, more precisely, I'm looking for examples of oscillating reactions that occur in the human body which can be modelled using the ...
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1answer
30 views

Can the fungal form of Malassezia morph into the fungal form of Candidia when feeling threatened? Resistance Mechanisms

Malassezia feeds on oils in the carbon chain 11-24 and Candida feeds on sugars. I recall learning that when these types of fungus feel they are under attack, they can morph. Does this mean they can ...
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56 views

Exact average molecular weight of a dsDNA basepair

I am trying to calculate the exact weight of a given dsDNA. On the Internet and the literature, different values for the av. molecular weight of one basepair are given : 660 g/mol (probably wrong), ...
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Is my understanding of the Bergmann's rule correct? (mass is secondary)

According to Wikipedia, Bergmann's rule applies because animals living in colder areas have greater surface-area-to-volume ratio. If I understand that correctly, the advantage of the bulkier bodies ...
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Estimate sex-specific survival from mark-recapture data using multi-site, sex-specific cormack-jolly-seber model?

I am interested in identifying sex-specific survival rates. I have a long-term dataset of individually marked birds from one breeding colony. Of these, I am able to genetically sex a subset. ...
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Is it possible to determine the initial population given the final one?

It is possible to determine the initial population of, say, bacteria given a measure at a later time? Let's say I use the logistic growth model $$\dot N (t) = rN(t)\left(1 - \frac{N(t)}{K}\right)$$ ...
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Quantitative Physiology Textbooks Recommendations?

I am currently completing a 2nd year (UK) Mamamilian Physiology Module and a Neuroscience Module. However, my degree is also 40% Maths and Statistics. So in order to learn the content better, I am ...
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How does gas equilibration occur in the alveolus, numerically?

I am attempting to model gas exchange across the alveolar membrane. My main question is there a direct exchange of O2 molecules for CO2 molecules? If so, then my model predicts (assuming alveolar ...
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2answers
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Does the magnitude of gene-expression changes decrease the more downstream a gene is from the origin of change?

If I have a decrease or increase in expression in one gene, will the decrease/increase in expression in the downstream genes always be of a magnitude lower than the previous ones, or can they be ...
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What are the interaction energies/chemical potential values for the cytoplasm - protein interactions within the cytoplasm?

I'm trying to simulate phase separation in a biological based system using a Cahn Hilliard model. I have 3 components, they are 2 theoretical enzymes and the cytoplasm. I have found plenty of sources ...
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1answer
44 views

Examples of real biological applications of the Keller-Segel system

I am working on a model of aggregation behavior modeled with the Keller-Segel PDE system. I recently gave a talk on this and was asked what other examples there were of the Keller-Segel system. Since ...
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1answer
100 views

Does ATP production increase with oxygen availability?

I'm not a biologist so pardon any ignorance on my part. I'm working on a speculative evolution project and I'm looking to understand how the partial pressure of oxygen effects the maximum aerobic ...
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Why is the null hypothesis of trait evolution Brownian motion?

Many models of continuous trait evolution assume that traits evolve according to Brownian motion. What is the biological or physical basis for this choice? I realize there are models that do not ...
2
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1answer
58 views

Expected number of SNPs in a sample of size `k`

Consider a Wright-Fisher population of constant size N. We sample k haplotypes in this population. What is the expected number ...
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36 views

When cancer is detectable, how many sub-clones are there at that stage?

I have read somewhere that cancer is detectable when the number of cells reaches $10^7 - 10^9$, which probably varies according to the specific tumor. At this early stage, what is the expected number ...
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Any kind of online “molecular modeling playground”?

I'm wondering if anyone has ever made a tool to try out new molecular modeling/simulation algorithms, where the tool itself handles the "boring" tasks of loading PDB files, building chains ...
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How are latence period and duration of infectiosity defined?

I assume that infectiosity of an individual is not a binary property but a quantity that grows and decays gradually, very much like the number of infected or infectious individuals in a population. ...
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1answer
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Can there be traits which aren't possible objects of selection, e.g. beneath a “threshold of genetic noise”?

Is it possible that there are traits that might not be possible objects of the selection because of highly sensitive dependence on genotypes? The context of my thought came when I was having a ...
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35 views

How does the human eye generate spikes?

Disclaimer: I have an academic background in computer vision but not biological vision. Background: Classical computer vision is concerned with images from cameras that have a fixed exposure time for ...
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What allows diverse ecology to thrive despite forces reducing species diversity?

Ecology and business are a useful model for understanding one another. One species fills a niche until it is outcompeted by another just as one business fills a niche until it is outcompeted by ...
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1answer
62 views

On stochastic Lotka-Volterra predator-prey model

I am currently working (as a mathematician) on some estimations involving an stochastic predator-prey type model in which some of the coefficients have been perturbed by a Brownian Motion yielding to ...
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Can human pathogens present on plants become plant pathogens?

Since human pathogens sometimes live on the surface of plant leaves(read here and and here), and there are plant-pathogen microbes also living on leaf surfaces, is it possible for plant virulence ...
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Is there a way to determine corresponding differential equations from fitted Hill equation parameters

I am currently doing some work with GCaMP, a genetically encoded calcium indicator. According to the literature the Hill equation parameters for GCaMP6m is $K_d=167\pm3\, \text{nM}$ and $n=2.96\pm0.04$...
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Are the social-distancing measures implemented against SARS-CoV-2 also suppressing the spread of other viruses?

With social-distancing measures being implemented in many countries I would expect other viruses, like the ones that cause seasonal flus, to have also a hard time propagating in these circumstances. ...
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Is there any evidence that discards the possibility of an organism-aided evolution?

The theory of evolution of Darwin is mostly accepted nowadays, while Lamark theory has been abandoned. There are many experiments that show that experiences do not alter the genes or are passed to ...
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1answer
41 views

Should I consider [H+] as substrate in MCT transport equation?

I'm trying to model the transport of lactate in cells (in both direction via Monocarboxylate transporters): [Lactate]intra + [H+] <----> [Lactate]extra + [H+] I found some data on kinetics of ...
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Range for which the Verhulst-Pearl model is a good approximate

The Verhulst-Pearl model describes the growth of a population using the differential equation, $$\frac{dN}{dt}=rN \left(\frac{K-N}{K} \right)$$ where N is the population (no. of organisms), r, the ...
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111 views

A question about entropy and Thermodynamics

According to the Second Law of Thermodynamics (also known as the laws of conversation of energy and mass), anything is an isolated system cannot increase in complexity. For example, a wearing suit ...
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2answers
61 views

Interpreting the reciprocal of $R_0$

$R_0$ is the average number of secondary cases arising from a single infectious individual in a fully susceptible population. In many of the compartmental models for epidemiology, the parameter $\...
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2answers
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The role of duration of infectiousness in SIR models

I refer to J.H. Jones' Notes on R0. The basic SIR model - as described in Jones' Notes - considers three factors that make up the reproduction number: $\tau$ = the transmissibility (i.e., ...
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Is there a bacterium that became a virus?

Is it possible for a virus to be a descendant of a bacterium that was not through horizontal gene transfer? How I think this could happen: Suppose a species of bacteria lives in an environment where ...
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2answers
39 views

Why do E.coli form parallel clusters?

Discalimer: I am not a biologist. I am modelling E.Coli growth and in the Wikipedia gif one can see observe some groups where the bacteria are one next to each other, oriented at approximately the ...
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Modeling the production of mRNA

I have the following example of how an equation for the production of mRNA in a particular organism could look like: Consider the following equation for the production of mRNA for a gene Y. Gene Y ...
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1answer
63 views

How do we formulate the mutational load for “junk DNA”?

Question(s) Based on Joe Felsenstein's textbook, I was trying to formulate the mutational load for the majority of eukaryotic genomes that are junk DNA ($L_{most\_of\_genome}$). (See background ...
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1answer
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What is the formula to calculate $R_0$ (basic reproduction number)?

What is the mathematical formula for $R_0$ and what does each variable represent? I have tried searching this to no avail.
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27 views

Tools for modelling and visualizing growth of cells

I am looking for a program/GUI app/package that would help me do simulations for cell growth. I have a microscopic mathematical model, and the scenario is basically the following: I start with a rod-...
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39 views

Is there a conformal transformation that maps the skull of Panthera tigris to the one of Panthera leo?

While visiting the Museum of Natural History in Rouen a few months ago, I was stunned by the similarity between the skulls of Panthera tigris and Panthera Leo: the overall shapes were very similar and ...
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1answer
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How to derive Hill equation (one specific part)

There is just one specific step in the derivation of the Hill equation for haemoglobin which I can't understand. Step from: $Y = \frac{(p\ce{O2})^n}{K_d + (p\ce{O2})^n}$ To: $Y = \frac{(p\ce{O2})^n}{(...
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18 views

Appropriate model to test if environmental variable is significant between two species?

I want to know if a given environmental variable has an effect on the range of two species/two groups of species. Specifically, I am interested in testing if one species has a "preference" for higher/...
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2answers
200 views

Lotka-Voltera predator prey model isocline?

In lotka voltera predator prey model, why do we get a straight isocline with variable prey/predator population for single value of corresponding predator/prey? I understand that we get the prey ...
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2answers
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How to model species interactions on population size dynamic?

Here are two classical discrete time models of population size dynamic. The exponential growth model $$N_{t+1} = r\cdot N_t \qquad\qquad(1)$$ and the logistic growth model $$N_{t+1} = r\cdot N_t \...
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1answer
85 views

Confusion about Lotka_Volterra model for two competing species

Lotka-Volterra model for two competing species in Boyce's Elementary Differential Equations and Boundary Value problems' is given by: \begin{align*} \frac{dx_{1}(t)}{dt}&=r_{1}x_{1}-a_{11}x_{1}...
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1answer
83 views

Original Lotka–Volterra model

I am looking for the articles in which Lotka and Volterra published their original predator prey model. I couldn’t find the model presented in many textbooks in Lotka’s book Elements of Physical ...
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1answer
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Why is there a mass limit on biological powered flight?

So, this is a thing I never fully understood. There are a lot of reasons for a flying creature to be limited in mass (though I'm unsure if I'm familiar with all of them), from energy consumption to ...

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