Questions tagged [theoretical-biology]

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

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1answer
27 views

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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How do I compute the reproduction number given a differential equation?

Problem 2.3 in Introduction to Mathematical Epidemiology asks us to "compute the reproduction number" for a disease modeled by the following equation: $$I'=\frac{\alpha\beta I}{\alpha I+r}(1-I)-\mu I$...
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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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36 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
70 views

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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16 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
97 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
47 views

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
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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
65 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
54 views

Why is there a mass limit on biological powered flight?

So, this is one thing I never fully understood. There are a lot of reasons for a flying creature to be limited in mass, from energy consumption to material strength. However there seems to be a reason ...
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Inheritance percentiles

I am aware that the average DNA contribution from each grandparent is 25%, while the possible range is 0%-50%. I found a source citing 18%-32% as the "normal" range but this was undefined. I assume ...
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1answer
59 views

Help on selecting 2 tests - unsure if they are paired or non-paired statistical test

I have data that measures the temperature of flowers and leaves on different plant species. These are the comparisons I am trying to make: Comparing the flower and leaf of the same plant at the same ...
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Length at which a branch 'branches'?

An image from this question (and originally from Karl Niklas' computer model) has prompted the following question: The branches in this tree divide with increasing frequency as we progress from the ...
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1answer
47 views

Growth rate oscillation in the a population of non-interacting bacteria

I have come across this theoretical paper claiming that if you start a batch culture from a single E. coli cell, the exponential growth rate of the population defined as $$k = \frac1N \frac{dN}{dt}$$ ...
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28 views

Understand SIR Model

I am quite unsure if I understand the concept of individual-based models(IBMS) in epidemiology. Is SIR model an example of IBMS?
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13 views

What are the methods to measure the surface density of animals in biology?

In biology there is a rule found by Damuth (https://www.nature.com/articles/290699a0): a relationship between the size of an animal species $l$ and its local abundance (surface density) $N/S$ $$N/S=...
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1answer
108 views

Where does this equation in the electrophysiology literature form come from?

In my studies I keep coming across the form of an equation that is used in many different mathematical models for voltage gated ion channels. The most general form I have found is in the 1977 paper ...
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0answers
40 views

Starting to learn biology [closed]

Well, I've not any biological background but I feel interested towards it. Can you biologists suggest me how to start? Like, from where I can start learning it, from the basic level. I'm from ...
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27 views

How are codocytes or target cells formed?

How are codocytes or target cells formed in conditions like Thalassemia? And why do they appear like a target(as in why is there a central red surrounded by pallor surrounded by red?)
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1answer
43 views

Classes of Graphs used in Biology

I am a student of Mathematics.Since I found no better place to ask my question I post it here. I was looking for some classes of graphs which are used in biology. I came across this particular class ...
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1answer
62 views

Is DNA from more parents (than two) better for the fitness of the offspring?

I'm designing a system (a computer system actually) and (a whole while ago) I spoke with a friend about it and he had this opinion: If you combine DNA of more parents (than 2) it's better for the ...
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1answer
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Formula for Oxygen Consumption for Atlantic Salmon (Mathematical) - insecurities regarding variable

The oxygen is calculated in mg per kg per something, so what does $h^{-1}$ stand for? hours maybe? The formula given below is an estimation of oxygen consumption for Atlantic salmon \begin{...
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1answer
96 views

A cure for radiation exposure?

Some of the greatest inventions of my lifetime have been from looking at nature and copying. I found out tadigrades in outer space have the ability to repair their own DNA when exposed to radiation ...
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3answers
961 views

Isn't sexy son hypothesis circular?

Sexy son hypothesis. It states that females are attracted to certain traits in males, because these traits will be attractive in her sons either. But isn't this circular? Like "I'm attracted to that ...
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1answer
55 views

Approximate Cell Doubling Time?

If I know it takes 12 min to occur in mitotic fibroblast cells and I count there are 32 dividing cells in the microscope slide out of a total population of 32034 cells, how do I calculate the ...
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1answer
94 views

Is there any independent non-DNA based information system in the cell

The information in protein is not neccessarily independent of the genome as the information of amino-acid sequence comes directly from the genome. The process of post-translational modification may ...
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45 views

What's a reasonable time constant for a mathematical model of a neuron?

Background I've been studying various mathematical models of neurons. So far I've covered the classic Hodgkin-Huxley model (to describe the potential difference of a single neuron) and the integrate ...
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1answer
33 views

Analysis of dynamic connectome data?

I have heard about existence of full brain connectome data of some worms or fishes. I have heard about GEVI - genetically engineered voltage indicators - that allow to see voltage data at subcellular ...
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0answers
67 views

What is the status of the “Free Energy Principle” as a theory of living organisms?

The free energy principle states that biological organisms maintain their order by minimizing a function called variational free energy (VFE). While it is the case that the minimum to VFE also ...
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46 views

How to derive the deactivation time constant in this model of Acetylcholine Receptor state kinetics?

I came across this simple analytical expression of time constant of deactivation in Elenes et al., 2006. How does one derive this expression $$\displaystyle\tau_\text{deactivation}\approx\frac{1}{D_+ ...
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1answer
52 views

The Hawk-Dove game: why is the average payoff half of the difference between reward and cost?

My question is about the well known Hawk-Dove model used in game theory. It concerns two strategies: the Hawk, which always fights the opponent, and the Dove, which does not fight and will either ...
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1answer
124 views

Calculating fraction of protein unfolded from spectroscopy data

This is a question from a homework pset of previous year. We are given the absorbance at 222nm of both a wild type and mutant protein at different temperatures. We are then asked to calculate various ...
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0answers
81 views

Are evolutionary algorithms calculated in polynomial time? [closed]

How complex are evolutionary algorithms? Also, what is the relationship between variational principles (Lagrangians, minima and maxima,) and evolutionary algorithms? Basically, how hard is it right ...
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1answer
62 views

How to determine the number of parameters in a phylogenetic model?

I want to calculate the AIC for a phylogeny that I inferred via maximum likelihood. To calculate the AIC I need to know the number of parameters in the model. But how do I determine this?
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1answer
1k views

Why are semi log graphs used in drug Dose response curves?

Why are Dose response curves, as well as most biological graphs shown in semi log graphs and not normal graphs? What is the advantage of semi log graphs over regular graphs? I still haven't gotten an ...
4
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1answer
76 views

What physiological processes give rise to a linear cell survival curve?

If we plot the number of surviving cells in a structure over time (assuming no replacement), the shape of that curve should imply something about the underlying process responsible for cell death. For ...
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2answers
208 views

What are the differences in the two possible methods to calculate the Hardy-Weinberg Equation?

I am more than flabbergasted by calculations of Hardy-Weinberg equilibria. The formula's theory assumes a binomal distribution of allele frequencies in a population, and hence allows the comparison of ...
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2answers
54 views

Interesting examples of models [closed]

I am studying the general use of models in biology in terms of methodology, applications, usefulness etc, and I would really appreciate any recommendations of some specific examples of models from any ...
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1answer
98 views

Learning tensors for evolutionary or developmental biology

I'm looking for book recommendations on tensor algebra for use in biology. Tensors are being used increasingly in evolutionary biology and developmental biology, it seems. For example, here is an ...
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1answer
123 views

How long does it take for a blocked dopamine receptor to be broken down by the body?

Do the blocked dopamine receptors get broken down by the body and if so how often ? In other words how long does it take for the dopamine receptors blocked by irreversible dopamine antagonists to ...
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0answers
72 views

Epidemic threshold on a directed network

I am trying to understand the equations used in a paper (https://www.nature.com/articles/srep00469.pdf) Mainly I'm trying to understand how the epidemic thershold was calculated using the ...
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3answers
275 views

(Reference request) Formal abstract theory of evolution? [closed]

EDIT: please feel free to suggest books that are the closest you can come up with to what I'm looking for, even if it doesn't exactly overlap! I am very well acquainted with the theory of evolution ...
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1answer
203 views

Easy derivation of Kimura's approximation for the probability of fixation of a mutation

Kimura's approximation for the probability of fixation of a mutation under selection finds recurrent use in population genetics models till date. I am trying to understand the mathematical basis of ...
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0answers
51 views

What is a good approximate functional form for an equation relating plant growth to sunlight?

Question is in the title. I've got daily measurements of daily mean shortwave radiation at the surface, and annual measurements of plant growth (some measure, be it height or biomass or something). ...
5
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1answer
142 views

Looking for the closest example of life forms similar to some mathematical patterns

Caveat: this is my first question here, it is quite interdisciplinary, but I hope to be in the correct place to ask. I am a user of Mathematics Stack Exchange since some years ago, and this question ...
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0answers
87 views

Is there any example, where cooperative behaviour of predators induce fear in prey population?

I am basically from math background and doing Ph.D in mathematical biology. So I am not so efficient in biology. But my problem based on cooperative behaviour of animals during hunting which is ...
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3answers
358 views

In the Selfish Gene, the chapter about ESS, how do the doves spread their genes?

In his explanation of the Evolutionary Stable Strategy, in the Selfish Gene, Richard Dawkins repeats a couple of times, that a population of hawk-type males would make the ground for a dove-type ...
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0answers
54 views

Measurement equation of Tree-Step pathway model

I am not specialist in biology but I want to test a parameters estimation method (based on Kalman filter) on the Tree-Step pathway model, but I cannot find a document that gives the measurement ...
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1answer
44 views

How plausible would it be for animals to normalize the birth of monozygotic twins in their reproductive cycles? [closed]

I'm currently trying to develop the world of a sci-fi story I'm working on, and a concept I've thought of adopting with the environment and characters is a common breeding system where identical twins ...

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