Questions tagged [theoretical-biology]

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

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Strong activation of MAPK signaling pathway

I am reading a paper named "Mathematical models of protein kinase signal transduction". In that paper, I encountered a condition called "strongly activated pathways". In that ...
이영규's user avatar
2 votes
1 answer
38 views

No. of genes and organismal complexity?

Why do humans contain trillions of cells arranged in many complex organs, and worms contain many less cells and less organs, but we and the worm have a similar number of genes? See for example Table 1 ...
li tchi.'s user avatar
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Universal mathematical statements in biology similar to Price Equation

I just read about Price Equation and I thoroughly enjoyed the concept, as well as the elegance of the mathematical formulation. I especially enjoyed the fact that (to quote Wikipedia) it is "a ...
blehblehblecksheep's user avatar
3 votes
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Is there a functional model of the human retina for simulation of conversion of illuminance pattern to nerve signals?

I'm looking for a model that would take a pattern of spectral irradiance over the retina as a function of time and space and convert this into the signals propagating through the fibers of the optic ...
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In search of motivation (Examples from nature) for reaction-diffusion systems with a conservation law

I'm an applied mathematician with a huge interest in mathematical biology. While looking at this paper, I came across with the following: Examples of reaction-diffusion systems (1)-(2), falling into ...
kaithkolesidou's user avatar
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Mathematical periodic turns in DNA

Today our college professor gave us a mathematical biological challenge in DNA. He challenged us to find the pattern in which DNA follows the following equation in its periodic turn. How can we crack ...
Y-nobu's user avatar
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5 votes
2 answers
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Why would decreased temperature be associated with increased cell size, in deep-sea crustaceans (or in general?)

I was reading Wikipedia regarding deep-sea gigantism -- the fact that deep-sea species are often much larger than their shallow-dwelling counterparts. The article said, Decreasing temperature is ...
Ryan's user avatar
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Modeling and Predicting Squirrel Populations

I was recommended to come here from the MathSE site. Here is the question: I am interested in modeling the growth of the Eastern Fox squirrel population in Los Angeles, not only in terms of numbers ...
JoanGi's user avatar
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8 votes
5 answers
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Examples of Differential equations in Biology

I am a mathematician currently teaching some math classes at a university. Next semester, I'll have bachelor's degree biochemistry students. I want to know where certain math tools might be needed in ...
Duarte Costa's user avatar
1 vote
1 answer
46 views

Mapping Ion Channel mRNA Copy Number to Channel Conductance

At least in invertebrates, it appears that within identified cell types, there are robust correlations between ion channel mRNA copy number (as identified by single-cell qRT-PCR) and the maximal whole-...
nguzman's user avatar
  • 113
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1 answer
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Overly stabilised population dynamics model

My project aims to model population dynamics of a 3 trophic levels system: primary producers, herbivores and predator. I try to predict how changes in the vegetation abundance might affect higher ...
Rachel's user avatar
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1 vote
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How is the Allee effect modeled in the presence of a highly variable carrying capacity?

Consider a rather standard model of population dynamics in the presence of a strong Allee effect: $$ \frac{du}{dt}=u\left(1-\frac{u}{K}\right)\left(\frac{u}{A}-1\right),$$ where $u(t)$ is population, $...
Plutoro's user avatar
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Why do V_Na and V_K stay unchanged in Hodgkin-Huxley model?

In the Hodgkin-Huxley model, ionic current $i_\mathrm{Na}$ and $i_\mathrm{K}$ are given by $$ i_\mathrm{Na}=g_\mathrm{Na}(V_\mathrm{m}-V_\mathrm{Na})\\ i_\mathrm{K}=g_\mathrm{K}(V_\mathrm{m}-V_\mathrm{...
Jasmine's user avatar
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Linking models of spreading of infection to type of network describing the relationships of animals of a habitat

I am studying networks describing the relationships between animals in a habitat.There are many types of networks studied which are useful and we can approximate a real network to one of the studied ...
Cerise's user avatar
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1 answer
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Why is there a negative sign before voltage in the gate variable functions of the Hodgkin-Huxley model?

In Hodgkin and Huxley's articles (1952, J. Physiol.; 1990, Bulletin of Mathematical Biology), the gate variables are formulated as In particular, as $V$ increases, $\alpha_n$ decreases and $\beta_n$ ...
Jasmine's user avatar
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Reproduction number in SAIQR model

$$ \dot S (t)=\Lambda-\beta_1 S(t)A(t)-\beta_2S(t)I(t)-\mu S(t)$$ $$ \dot A (t)= \beta_1 S(t)A(t)+\beta_2S(t)I(t)-(\mu+\alpha) A(t)$$ $$ \dot I (t)=\alpha A(t)-(\mu+\theta)I(t)$$ $$ \dot Q (t)=\theta ...
Mahmood Dadkhah's user avatar
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1 answer
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Understanding infection rate of a complex network

Suppose we have a complex network of people and the spread of a disease is modelled as a branching process (Diekmann et al. 1998) The rate of infection of the complex network is: $r = \tau(n-2)-g$ ...
Cerise's user avatar
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0 votes
1 answer
34 views

Calculation for underlying genetic value of a phenotype given parents genetic values

What is the most accurate way to calculate a child's genetic predisposition to a phenotype, given both parents' genotypic predispositions? Assume trait X is 50% heritable and controlled by an ...
BigMistake's user avatar
2 votes
0 answers
38 views

Can the concept of fisherian runaway be explained using simple models?

I want to understand the concept of fisherian runaway. Dawkins' book tells about this, but it's not clear enough. It can be seen that the essence of Fisher's idea is that when a male peacock with a ...
Linkey's user avatar
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How can combusted methane from landfill samples be quantified? [closed]

Background: For my studies I'm wanting and attempting to make a landfill greenhouse gas emissions (GHG) model that predicts the amount of greenhouse gas equivalent emissions ($GHG_{eq}$ [tonnes/year]) ...
Hendrix13's user avatar
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2 votes
1 answer
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Mathematical aspects of the study of dinosaur locomotion

I'm interested in getting a better understanding of dinosaur locomotion. Therefore, I am looking for a book that will cover various mathematical aspects and discuss various mathematical tools for ...
dtn's user avatar
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1 vote
1 answer
39 views

Questions about ChIP-seq reads and MACS

I had a few questions raised by the below diagram in relation to how ChIP-seq reads look like (source). I would be very grateful for your insight on them! From the below diagram, it seems that, in a ...
algebroo's user avatar
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1 answer
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Cross correlation metric in ChIP-seq experiments

I found this explanation of cross-correlation metric in ChIP-seq. Now, the definition of Pearson's correlation coefficient between two random variables $X$ and $Y$ is $$\rho_x = \frac{Cov(X,Y)}{\...
algebroo's user avatar
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10 votes
4 answers
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How do you calculate the time until the steady-state of a drug?

I encountered a mathematically intriguing conundrum, in that it's related to medicine but is centered around mathematics. Suppose drug A has a half-life in the body of 30 hours. The patient takes 40mg ...
askquestions4's user avatar
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31 views

PCR: From transgene/microgram to cell concentration

I am doing research on CAR T-cell kinetics. The measurement of CAR T-cell concentrations across time is normally carried out with qPCR (see here, Fig. 1). These concentrations are generally reported ...
amr95's user avatar
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1 answer
133 views

What is the latest estimated probability for the self assembly of a primitive cell? [closed]

Peusner (Concepts in Bioenergetics, 1974) estimated the probability of the self-assembly of a primitive cell as $10^{-254}$. Given how much more we now know about cell biology, what is the latest ...
Jack's user avatar
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1 answer
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Resources for understanding the basics of cell signaling, gene expression and cell fate determination, for a physics student?

I'm a physics student who will join a theoretical biology/applied mathematics research group this September. I'll link some papers at the end for further context. The main problem I have is that my ...
agaminon's user avatar
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7 votes
1 answer
73 views

Finding population dynamics models for multi-generational species evolution with delays

I am working on a problem from economics, to understand how populations evolve within business organizations. I have found that some of the population dynamics literature is very relevant to my own ...
krishnab's user avatar
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1 answer
268 views

Examples of bifurcations in real-life systems

Does period-doubling bifurcation and Neimark-Sacker bifurcation happen in real-life systems? Are there some examples? I'm particularly interested in biological host-parasitoid and predator-prey models....
User154's user avatar
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1 vote
1 answer
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What could be a refuge in host-parasitoid models

I was reading about refuge effect in host-parasitoid models and I found somewhere that refuge does not have to be only a place in habitat where hosts can hide, but also some "situation" ...
user121's user avatar
  • 125
2 votes
0 answers
39 views

Ecosystem Control Theory

I've used EcoNet online tool to analyze an ecosystem. You can run the default model by pressing "run model" in order to follow my question. Among the extended results there are 2 'Control ...
Mirko's user avatar
  • 221
27 votes
2 answers
4k views

Why don't viruses reach broad concentration outdoors in a city like allergens?

Why don't airborne viruses reach concentrations that infect most people vulnerable outdoors in a city the way an allergen can cause inflammation to everyone sensitive to it. Both are (often) ...
davolfman's user avatar
  • 387
4 votes
2 answers
159 views

How does genetic feedback shape the evolution of whole ecosystems?

While looking into the organization of ecosystems and how evolution shapes it, I've been reading "Ecology" (1975) by Eugene Odum. In chapter 6, p. 167, Odum speaks about the mutualistic ...
Martin P.'s user avatar
0 votes
0 answers
62 views

Price Equation in Evolution

I am trying to solve for $\text{cov}(w_i,z_i)+E(w_i\Delta z_i)$ as it apears in Price Equations in terms of the mean $\overline{w}$ and variance $\sigma_{w}^2$ of the fitness of a population where I ...
Alexander's user avatar
2 votes
0 answers
221 views

Difference between IC50 and Michaelis-Menten constant

I am new to biology, and getting to know the term IC50, I found that there is a connection between IC50 and Michaelis-Menten constant by the Cheng-Prusoff equation $K_{i}=\frac{\mathrm{IC}_{50}}{1+\...
LOVEMATH's user avatar
2 votes
0 answers
92 views

What did Masatoshi Nei 1972 mean by "However, evolution does not occur so as to assure this property at least at the nucleotide level."?

In Nei 1972 he describes what is now called Nei's standard genetic distance. This math.SE post provides an exerpt to the definition of Nei's standard genetic distance. In this paper he states In the ...
Galen's user avatar
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1 vote
0 answers
42 views

Calculation of drug efficacy- mathematical biology approach

I am participating in a mathematical biology project. I would like to discuss the following problem: Let A be a drug such that $x_{o}$ chemical units of it kills 12% of $y$ cells per 1 day, I would ...
LOVEMATH's user avatar
0 votes
2 answers
312 views

How many cells does a single blood cell generally visit in its lifespan?

Taking the point of view of a single RBC travelling through blood vessels, approximately how many cells will it affect throughout its lifetime? As blood tends to provide O2 as a whole, I am taking &...
Imran Q's user avatar
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1 vote
1 answer
114 views

Method of determining base values of traits in isolated populations

Prelude: I came across a discussion about the correct formula for calculating the average IQ of offspring, which goes something like the following $$ 100 + \frac35 \left( \left(\text{father's IQ} + \...
Maximilian's user avatar
4 votes
2 answers
283 views

Which approach is the common one in the literature for determining the bacterial growth rate?

I have the following data, which is OD600 (the second component) vs. time (the first component): ...
user68022's user avatar
2 votes
0 answers
63 views

Genetic evolution without crossover

Can someone please point me to the origin of the system of coupled differential equations (1) in Section 2 of Shahshahani's book$^\star$? $$ \dot{x}_i = x_i \sum_{j=1}^n m_{ij} \frac{x_j}{|x|} $$ ...
DavideL's user avatar
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0 answers
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Can deterministic and stochastic models be used to models different parts of the same phenomenon?

A biological phenomenon including two different causally dependent phenomenon occurs in the cell. (Phenomenon2 initiates as a result of phenomenon1). Phenomenon1 and phenomenon2 are linked with ...
confused's user avatar
2 votes
2 answers
394 views

Is there such a science in which the knowledge of biological processes (e.g., evolution) would be mathematically axiomatized and inferred (deduced)? [duplicate]

There is the following Mathematical Challenge Twenty-three Mathematical Challenge Twenty-three: What are the Fundamental Laws of Biology? * This question will remain front and center for the next 100 ...
Nam Nguyen's user avatar
2 votes
0 answers
67 views

Difference between heritability on the scale of liability versus the scale of observation

I was reading a paper on disease heritability ("Estimating Missing Heritability for Disease from Genome-wide Association Studies") and it struck me that I don't have a great understanding of ...
xavayey244's user avatar
6 votes
2 answers
511 views

Understanding expected mean number of breeding seasons

I've recently come across an equation for the expected mean number of breeding seasons after the first breeding season, as a function of the annual survival rate (S) and the probability of breeding, $$...
user13317's user avatar
  • 183
6 votes
3 answers
367 views

What does it mean to quantitatively describe a cell?

To begin this question, I will quote Molecular Biology of the Cell (page 38): ... Biological systems are, ..., full of feedback loops, and the behavior of even the simplest of systems with feedback ...
seamos's user avatar
  • 177
4 votes
1 answer
56 views

Interpreting replicator dynamic for simplest population model

Suppose the simplest population model where we track the size $y$ of a population: $$\frac{dy}{dt} = ry$$ for a positive constant $r$ and some $y$ such that $y(0) > 0$. For this population model ...
John_Krampf's user avatar
-2 votes
4 answers
321 views

Remarkable attempts of studying biological systems axiomatically

I am reading Anti-Tech Revolution by Theodore Kaczynski, in the second chapter the author talks about how technology will cause problems in society and before he begins the discussion, he introduces ...
user avatar
0 votes
0 answers
68 views

Understanding the paper "Why war is a man's game"

I have read this article https://royalsocietypublishing.org/doi/10.1098/rspb.2018.0975 but I don't understand the mathematics which tries to explain why war is male-exclusive. In which branch of ...
kryomaxim's user avatar
  • 245
1 vote
0 answers
37 views

Is there any reliable data about the correlation between the size of a species and number of individuals that belong to it?

I'm curious to know if such a collection of data exists, so I could visualize it with a graph, and see how humans compare to other spieces of similar size.
Enlico's user avatar
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