Questions tagged [theoretical-biology]
Questions relating to biological theory or theoretical developments that deals with biological processes.
425
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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 ...
2
votes
0
answers
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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 ...
1
vote
1
answer
138
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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 ...
2
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1
answer
81
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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
...
3
votes
1
answer
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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{...
2
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1
answer
112
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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 ...
2
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3
answers
1k
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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 ...
1
vote
1
answer
70
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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 ...
3
votes
1
answer
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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 ...
5
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0
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81
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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 ...
2
votes
1
answer
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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 ...
1
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0
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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 ...
0
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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_+ ...
0
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1
answer
228
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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 ...
0
votes
1
answer
1k
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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 ...
2
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0
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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 ...
1
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1
answer
210
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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?
1
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1
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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 ...
5
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1
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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 ...
3
votes
2
answers
334
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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 ...
3
votes
2
answers
72
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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 ...
4
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1
answer
216
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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 ...
2
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1
answer
281
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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 ...
1
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0
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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 ...
6
votes
3
answers
302
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(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 ...
7
votes
1
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442
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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 ...
4
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0
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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).
...
4
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1
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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 ...
3
votes
0
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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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3
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677
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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 ...
2
votes
0
answers
54
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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 ...
1
vote
1
answer
49
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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 ...
0
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2
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136
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Activity driven model threshold
So I am trying to figure out a threshold for an activity driven model. That is described in this paper: https://www.nature.com/articles/srep00469
That is I don't see how the researchers got ...
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votes
1
answer
191
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Can 2 people give rise to billions? Adam and Eve 2.0 [closed]
With with the advancement of GMOs the idea of giving rise to humans from 2 people is possible making questions like this invalid?
How many people are required to maintain genetic diversity?
With ...
0
votes
2
answers
118
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Are resonances the reason receptors work?
From Visual phototransduction - Wikipedia:
When struck by a photon, 11-cis retinal undergoes photoisomerization to all-trans retinal which changes the conformation of the opsin GPCR leading to ...
1
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1
answer
103
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Do axonal conduction delays have a function?
I'm reading about mathematical models of biological neural networks, which can be grouped into two categories:
The model accounts for the fact that a signal takes time to travel from the excitatory ...
1
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0
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39
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What are some good examples of open-source articles in which the synergy of two medicines is demonstrated?
I am doing research on Stochastic Cooperative Game Theory (a subfield in mathematics), which I will henceforth call SCGT for convenience. In this theory, entities can work together to receive a bigger ...
3
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1
answer
290
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How to give a biological interpretation to this phase portrait?
Consider the following system and analyze its behavior.
$$\begin{array}{rl} \frac{dA}{dt} &= A \left( 2-\frac{A}{5000}-\frac{L}{100} \right)\\ \frac{dL}{dt} &= L \left(-\frac{1}{2}+\frac{A}{...
0
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1
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99
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Are there laws in ecology? [closed]
Are there clearly defined ecological laws, as in the science of physics? If not, why is this the case?
2
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1
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211
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Mathematical model about the relationship between two animal species
I'd like to relate a mathematical model with two animal species. This is the model:
$$
\begin{split}
\frac{dN}{dt} & =rN-\frac{rN(N+M)}{k} \\
\frac{dM}{dt} & =r'M-\frac{r'M(N+M)}{k'}
\end{...
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0
answers
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What is known and what can be measured of biofilms?
Context for the question
I am a mathematics researcher working on the mathematics of imaging and parameter estimation (inverse problems). I found an interesting diffusion equation that models the ...
2
votes
1
answer
150
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Evolution of leukemia pluripotent short-term cells
I have a problem in understanding the introduction of this paper entitled "Stability and bifurcation in a model for the dynamics of stem-like cells in leukemia under treatment". As I have no ...
3
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0
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Kinetic mathematical model of glycolysis?
I am looking for papers containing kinetic mathematical models of glycolysis, hopefully in mammalian cells (or as close as possible, say yeast). The papers I have found do qualitative analysis (...
1
vote
1
answer
51
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Are pheromones capable of activating changes to the Phenotype of a complex organism?
I know that pheromones are means of communication between the same species, but are they capable of changing the phenotype of an organism, may be influencing the expression of the genes of a said ...
1
vote
0
answers
252
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Does the Histogen Theory apply to plant roots as well as stems?
My school textbook briefly mentions a certain "Histogen Theory" (von Hanstein) of plant growth/development. However, I can't find any authoritative source on this matter online.
According to my book, ...
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vote
1
answer
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Mathematical model for malaria
The simplest malaria model is as follows:
$$\frac{dI}{dt} = \frac{\alpha \beta I}{\alpha I + r} (1-I) - \mu I$$
where $r$ is the natural death rate of mosquitoes, $\mu$ is the death rate of humans, $\...
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0
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Units of parameters in epidemiological model
The simplest malaria model is given by $$\frac{dI}{dt} = \frac{\alpha \beta I}{\alpha I + r} (1-I) - \mu I$$
where $\mu$ is the death rate of humans, $\alpha$ is the transmission rate from humans to ...
0
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1
answer
39
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Are genes known or at least conjectured to evolve cyclically ?
I observed recently that some people born the same year in not too distant areas (say, in the same country whose size is not too big, like France) share similar phenotypical features, for example they ...
1
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0
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235
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How to correlate survival probability to gene expression profile?
I am reading up survival analysis of cancer patients and correlating them to gene expression. I came across this tutorial. Its mostly code. So what I still have not been able to understand is how ...
0
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1
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Query regarding calculation of survival analysis
According to this tutorial, for table to find the survival estimates, the square root of the 6th column is multiplied with the 4th column, which is Survival probability. The value that should come for ...