Questions tagged [theoretical-biology]
Questions relating to biological theory or theoretical developments that deals with biological processes.
429
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Guide to learning about Population biology / ecology / dynamics for a non-Biologist
I'm an applied mathematician who works in the field of feedback control systems but has been becoming interested in looking at population biology (e.g. Lotka-Volterra, Mathusian growth,etc.) from a ...
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Why are considered to be exceptions to the cell theory? [closed]
If I am not mistaken, the cell theory states that:
All living organisms are made up of one or more cells
Cells are the smallest units of life
Cells arise from pre-existing cells
Aseptate fungal ...
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A state model of sodium channels
I am studying by myself Human Physiology.
I have encountered the following question:
In the following given model of sodium channel with 3 states open closed blocked (which I assume means inactivated)...
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0
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Effective population size of a metapopulation structured on a grid
Scenario
Consider a rectangular metapopulation consisting of $x \cdot y$ demes, where $x$ is the number of deme horizontally and $y$ is the number of demes vertically. The population size per deme is ...
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Is "A" inhibiting "B" and vice-versa, a positive feedback loop?
If product A inhibits the expression of product B, and product B inhibits the expression of product A, is this a positive feedback loop?
My thinking was to consider the scenario that A starts off ...
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Identity By Descent vs Identity By State
Background
The concepts of Identity By Descent (IBD) vs Identity By State (IBS) are central in population genetics, yet I fail to fully wrap my head around the definitions.
You can find examples ...
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1
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1
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Hardy-Weinberg equilibrium generalized to add inbreeding (non-random mating)
Background
Quoting from Gillespie's book
The level of inbreeding is measured by the inbreeding coefficient, $F_I$, which is the probability that two alleles in an individual are identity by ...
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Why is the probability of fixation of an allele equal to its frequency?
Introduction
In a panmictic population, the probability of fixation of an allele at a neutral locus is equal to its frequency at that time. I will refer to this probability of fixation as calculated ...
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4
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How can I obtain a computer readable model of Dr. Gerhard Michal's biological pathways map?
I want to run simulations of various metabolic pathways – the project could end up becoming quite large, and having a machine readable chart would make thing a lot easier. Does anyone know if there is ...
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Concentration gradients across membranes with different ions
I'm trying to gain an intuition for the dynamics of across neuronal membranes. The overarching idea here is they are controlled by ion concentration gradients across the membrane (which we can ...
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In theory how fast could nerve signals travel if the nerve fibre was perfectly insulated?
My question is purely theoretical and my main aim is to find out the maximum speed that a nerve signal can travel within a nervous system and and whether this speed represents the physical limit of ...
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A good software for agent based modelling?
Hello i'm gonna start my master degree in systems biology and i'm thinking of working with agent based modelling, but i really don´t know which platform can be the best to simulate interactions ...
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0
answers
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Need to solve a "pseudo-metabolic" network for rates
following problem:
I have data on a certain complex association network (from monomers 1 ... 8 to complexes of all combinations, such as, 12 ... 13 ... 18 and so on until 12345678, so that I know
...
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2
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Goodwin oscillator explained
Hello I have been reading papers about the Goodwin oscillator and I found that the equations are kind of tricky. Specially the part of the hill coefficient. In his paper "An entrainment model for ...
2
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answer
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Does the Michaelis-Menten equation take in account the non-enzyme formation of products?
I only recently learned about the Michaelis-Menten equation, since I am not studying biology or anything related. Let's write the equation as
$$\frac{d[P]}{dt} = V_{max} \cdot \frac{[S]}{K + [S]}$$
If ...
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1
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Is there a resource that has quantitative data about cell proteins?
I am a MSc student working in mathematical biology. In my thesis I am modelling diffusion of a protein that can bind to cell surface receptors. In order to simulate this I need some rough figures ...
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Population dynamics ODE with Allee Effects
From reading about Allee effects, it appears that there is a modification of the one-dimensional logistic equation to account for an allee effect given by:
$$\frac{dN(t)}{dt} = rN\left(1-\frac{N}{K} \...
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What is the probability of genetic reincarnation? [closed]
Parents pass on 23 chromosomes to their children, with a 50/50 chance for each chromosome. Considering that people of a families lived over millennia in the same region the abundance of some ...
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1
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Can heritability be deduced from a correlation coefficient?
I am trying to understand the concept of heritability and from what I can gather, the heritability of a factor (say birth weight) must be closely related to the correlation coefficient of that factor ...
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What are the basic skills required to pursue future studies in theoretical ecology? [closed]
I am a student and just about to choose a project for my Master's thesis in biology. I want to pursue studies in theoretical ecology in the future. Between field ecology and computational biology (as ...
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Where can one find completed and processed Hi-C datasets?
I and a statistics graduate student at UCR, and I am working on Optimal Binning schemes and peak detection in Hi-C data analysis (a dataset that conveys information about proximity of a DNA strand ...
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1
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Mechanisms and Assumptions of the Species-Area Realtionship
I would like to choose a model to use to describe a species area relationship based on plant species richness data that I have collected. Rather than choosing the power model a priori, I am ...
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Why is marginal reconstruction "more correct" than joint reconstruction in some cases?
When reconstructing the ancestral states on a phylogenetic tree given the states at the tips, there are a number of methods for performing the reconstruction. This question is about marginal and joint ...
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What are we missing about the real workings of the evolutionary process? [closed]
As a scientist (and a computer scientist at that) my view is that if we cannot simulate a process we have not understood it properly. I have been following the interesting field of Artificial Life for ...
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Why are fifth order Markov Models, the ones most often used for gene prediction?
As far as we know that smallest polypeptide chain length is 60 amino acids - so if we found an Open Reading Frame (ORF) of about 60 codons without the interruption of stop codon we can consider it to ...
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Diffusion approximation to genetic drift
I am reading from the classical textbook Principles of Population Genetics, Hartl and Clark (pdf here).
Introduction
Let $f(p,x,t)$ denote the distribution of allele frequency $x$ at time $t$ ...
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3
votes
1
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Proof of the equivalence between two ways of defining ESS
Background
Two common ways of defining what an Evolutionary Stable Strategy (ESS) are:
First definition:
Consider a population composed of populations playing two strategies, $\mathbf{p}$ and $\...
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1
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I know how to solve these equations, but I'm not sure what t' represents?
I am investigating the Wilson Cowan neuron population model, and I can follow most of it, but I'm not sure what is meant by t' in the equation for proportion of neurons in the refractory period. The ...
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0
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Values of Miu_max and Ks from parameter estimation?
Background
I have this simple biomass growth model:
$$
\mu = \mu_{max}\cdot \left(\frac{S}{K_S+S}\right) \cdot \left(\frac{1}{1+S/K_{iS}}\right) \cdot \left(\frac{K_{iP}}{K_{iP}+P}\right) \\
\frac{...
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Math backbone in biology/genetic
Are there any good books, that shows some advanced models in genetics particularly?
The problem is i don't see any good math model in genetics interactions exept combinatorics. I'd like to know what ...
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metabolic heat generation and exercise intensity
Is there a relationship between bio heat equation (found here) and exercise intensity as described here
That is I am trying to include the effect from exercises to the tempertaure variation in skin. I ...
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1
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relationship between cytokines
This is for a mathematical research. I am building a model to identify severe dengue patients through the interaction of cytokines S1P,IL1b,TNFa,PAF and IL10.
For this I would like to know if there ...
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Games with non-uniform interaction rates
Background:
Many models in evolutionary game theory assume uniform interaction rates. For instance, consider the $2\times 2$ game:
\begin{array}{l c c}
& A & B \\
A & a & b \\
...
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Do the claims in this paper have any degree of validity?
The paper The waiting time problem in a model hominin population talks about a problem of waiting time, etc. Is the methodology of this numerical simulation, and the conclusion right or is it wrong?
...
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Replicator equation for mixed strategies?
The the replicator equation is usually defined for pure strategies. More specifically, the replicator eqn for $n$ strategies is given by:
\begin{equation}
\dot x_{i} = x_{i} \left( \sum_{j=1}^{n} a_{...
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3
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Can/Have cancer cells be/been used in stem cell culture lines?
Since Cancer cells have unlimited growth potential, can they be induced towards totipotency and pluripotency?
If so, can cancer cells be used in stem cell culture because of similar properties of ...
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2
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Stochastic parameters in population growth equations
I'm more of a mathematician than a biologist, so I had a question about an application of the population growth equation to real-life models, and thus would like to ask biologists for their insights. ...
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1
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Can DNA base pairs go through each other? [closed]
Consider the simplified version of the motion one DNA base pair held together by a hydrogen bond:
Use u and v to denote the displacements of the bases from their equilibrium position along the ...
3
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1
answer
515
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Is the Basic Reproduction Number in epidemiology dependent on population size?
I am assuming that the basic reproduction number $R_0$ of a disease depends on the population size (or the number of susceptible individuals). When $R_0$ is reported it seems to be without such ...
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0
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Metabolic control theory: proof of the summation theorem?
I'm looking for a rigorous proof of the summation theorem of metabolic control theory. The only sources I find are the original papers by Kacser and Burns 1973 and Heinrich and Rapoport 1974, both of ...
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Are there any theories using thermodynamics/statistical mechanics or information theory principles to modelling in ecology?
So far, I've only known one: the MaxEnt theory. It uses the maximum information entropy developed by information theorist, which in turn inspired by the thermodynamics from physics, to predict the ...
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How does one calculate the amount of oxygen produced by trees?
I'm currently working on a project to measure the impact of tree planting.
Calculating the amount of oxygen seems harder than I imagined.
Of-course there's the type and size of the tree and the ...
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How to determine the relationship of competition or cooperation?
I am currently studying the interaction of Twitter memes (two or many), such as competition and cooperation. Is there any model or method in biology that can identify the types of the relationship, ...
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Discrete vs Continuous Replicator Dynamics
The replicator eqn in the case of discrete non-overlapping generations and asexual reproduction is given by the discrete replicator eqn:
$$x_i(t+1) = x_i (t)\frac{f_i(t)}{\bar f (t)}$$
where $x_i$ is ...
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2
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How quantitative is the theory of evolution right now? [closed]
We developed complex structures like eyes and brain, whose mechanisms rely on specific species of molecules and relevant chemical reactions. But we did not develop an enhanced night vision, the ...
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The replicator equation vs the Lotka-Volterra equation
Background
The replicator equation with $n$ strategies is given by the differential equation:
\begin{equation}
\dot x_{i} = x_{i} \left( \sum_{j=1}^{n} a_{ij}x_{j} - \phi \right)
\qquad i = 1, \...
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Variance in reproductive success and effective population size
Background
The effective population size $N_e$ is the size of the Wright-Fisher population that experience the same amount of drift than the population under consideration.
The higher the variance ...
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3
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Do biological phenomena follow Gaussian statistics?
I have recently entered the life sciences (from physics). I am concerned about the use of p values in the life sciences literature. For example, in this article, they test 9 - 12 rats in a control ...
1
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0
answers
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What is the distribution of the expected number of lineages in a birth-death tree after time T?
I've been looking at The reconstructed evolutionary process by Nee et al. 1994 and they provide a number of equations dealing with the birth-death process, specifically the "reconstructed" birth-death ...
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Variance in Fst in the infinite island model
The most famous result in the study of structured populations come from Sewall Wright. He showed that in an island model, where each subpopulation is of size $N$ and the migration rate is $m$, then ...
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