Hot answers tagged mathematical-models
18
Dickinson (2005) has a good review of insect flight, including behavior, biomechanics, electrophysiology, and neural control with links to more of the primary literature. What follows is a general summary thereof.
The jagged trajectories you mention are called saccades in the insect flight literature. In Drosophila, saccades are ~90° turns accomplished in ...
9
Unfortunately it is not necessary to invoke group selection to answer this question. This is one of the reasons that Dawkins likes this discussion so much - he does not believe in group selection and so the discussion in SG does not invoke group selection. ESSs are described in the book as the product of direct competition or interaction between genes.
...
7
The probabilities are correct. You must take the product (in log space this is equivalent to sum). The reason the probability looks small is just that you are perhaps thinking the score should be close to 1. However, this is not the case. To get a score of 1, you need the PWM to have 1/0/0/0 at all positions and get a perfect match.
So what should you ...
7
According to Deckmyn et al (2004), the primary effect of coppice management is that the fraction of total biomass in roots is relatively higher after coppicing, and that a substantial fraction of carbon in roots (~20% of root mass) is reallocated aboveground to support shoot growth in the spring following coppicing.
Because of this large re-allocation, ...
6
The particular language a bioligist uses depends on the trade-offs between speed and ease of programming. Many models are written in C or Fortran if speed is paramount. On the other hand people will write models in higher level languages if speed is less important. These would be Python, R, MatLab, etc... In my models, which are written mostly in Python, ...
6
Quick search - Some articles that may interest you:
1) Random walk model of insect movements
Kareiva P. M., Shigesada N. (1983). Analyzing insect movement as a correlated random walk. Oecologia 56(2-3) 234-238
2) Artificial life model of flying insects and its comparison to real insects navigation strategies.
Dale K., Collett T. C. (2001). Using ...
5
In an infinite, well mixed population with single pairwise encounters, Grudger is indeed not an ESS. In fact, as you correctly note, in such a model the Grudger and Sucker strategies are indistiguishable, as the probability of anyone encountering the same individual twice is zero.
To make it possible for the Grudger strategy to survive against invasion by ...
4
The Karr et al. paper attempts to capture most of the details in their model by combining features from the genome, transcriptome, proteome, and metabolome. This work heavily builds off of the coarse-grained models that you ask of especially on the work from Bernhard Palsson from which Markus Covert did his training. The answer to your question rests ...
4
The field most closely associated with game theoretic models in biology is evolutionary game theory. If modeling is required, then the typical paradigm is agent-based modeling, and a good introductory book is:
Yoav Shoham and Kevin Leyton-Brown
[2009], "Multiagent systems:
algorithmic, game-theoretic, and
logical foundations", Cambridge
...
4
You can use power analysis to work out answers depending on the specifics of your data. The things you need to consider are:
The power of the test. This is the probability that the test will
fail to reject the null hypothesis even if in truth it is false
(Type II error). If the population is not in equilibrium, what is
the probability that the test will ...
4
Classification of equilibrium points is done on the basis of the eigenvalues.
If the two eigenvalues have no real parts, it is a hyperbolic fixed point and represents undamped oscillation.
If both have a negative real part, it is a stable fixed point. If any of the eigenvalues has an imaginary part then it represents damped oscillations (in that case the ...
3
The following papers are a good starting point:
René Thomas, Boolean formalization of genetic control circuits, Journal of Theoretical Biology, Volume 42, Issue 3, December 1973, Pages 563-585 <= A classic paper in the field.
Thieffry D. Dynamical roles of biological regulatory circuits. Brief
Bioinform. 2007 Jul;8(4):220-5.
Remy E, Ruet P. From ...
3
Have you heard of something known as "Occam's Razor" ?
It says when you have multiple possible explanations/hypotheses then select the one which is simplest (i.e least number of assumptions)
Same with mathematical models. Chemical kinetics models usually assume first order unless there is some evidence against it. Similarly, for enzyme kinetics, as long ...
3
There is a lot of variation in how and when deer shed their antlers. In most arctic and temperate-zone species, antler growth and shedding is annual, and is controlled by the length of daylight. In tropical species, antlers may be shed at any time of year, and in some species such as the sambar, antlers last several years. Some equatorial deer never shed ...
3
On the G6G Directory of OMICS and Intelligent software, I searched for "QSAR Analysis, and received two product abstracts:
1) SYBYL®-X Suite which contained:
3D QSAR: use the power of industry leading CoMFA in a new way to
generate novel ideas for R-groups - predict the level of biological
activity or potency based on structure-activity data, Not just ...
2
Many years ago I worked in the field of bacterial chemotaxis, and your question brought this paper to mind:
JL Spudich & DE Koshland Jr. (1976) Non-genetic individuality: chance in the single cell. Nature 262:467-471.
The authors report an analysis of the chemotactic behaviour of individual bacterial cells from a single homogeneous culture. They ...
2
I found this paper[1], which might be relevant; it uses is a more chemically inspired approach. Another paper[2] also might be interesting, it takes a more dynamical systems approach.
My personal instinct would be to use ordinary differential equations: generate a population of cells in random positions, assign each cell levels of any relevant molecular ...
2
For homework questions, the policy is to see some work from the poster. Since you don't know programming, I've outlined what the code is doing, beyond the simple operations (+, -, /, *, ^), to get you started. I think you should be able to implement the models with this information, and I'd be happy to confirm your own answers.
So the best way to ...
2
He defines lineage selection as selection for traits which increase the fitness of a group of plasmids, rather than an individual plasmid with in a cell or a particular cell containing plasmids. He says that the unit of selection are "plasmid-host clades" : in other words the unit of selection is the group of closely related plasmids in separate cells. It is ...
2
As Arthur Kornberg said: "Don't waste clean thinking on dirty enzymes."
Discovering an assay for a biological event in a cell-free extract opens the way to its molecular resolution and reconstitution (Commandment I). Trying to devise a mechanism with a crude extract, even with ingenious experiments, is generally a waste of effort. An extract is too ...
1
The answer is no really, but some variants might allow you to study inhibition.
Michaelis Menten kinetics are experiments which try to characterize the catalysis characteristics of a reaction but to do so the numbers are obtained at concentrations of substrate that you dont find in a cell.
Vmax is defined as the maximum rate at which the reaction is run ...
1
The Open Source Computer Vision library OpenCV is pretty popular. I'm a Python guy, but it also has C, C++, and Java interfaces. The O'Reilly book Programming Computer Vision with Python was pretty good, and their C-oriented Learning OpenCV from 2008 is coming out with a new C++ edition in July, supposedly. There are also the OpenCV online docs, linking to ...
1
A solid limit: k must be greater than zero. Unless you're talking about some cannibalistic species or something that isn't suited to the model at all.
As long as the species is productive in the new environment: k is greater than 1. The population is probably growing or again you probably won't be using an exponential growth model.
As mentioned before you ...
1
I would also suggest Uri Alon's An Introduction to Systems Biology.
Personally, I learned using JJ Tyson's body of work and I would particullary recommend Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell
1
According to this page, you should take the sum and not the product:
Once a Profile has been derived from a set of functionally related
sites, the Profile can be used to scan a query sequence for the
presence of potential sites. Usually you run a window the length of
the matrix along the sequence, and sum the coefficients from the
matrix ...
1
This phenomenon is well known and can be observed in several species. In fact, if you look at the time it takes for E. coli to change its transcription program in order to react to the environment (signal->transcription->translation), you will find it can be longer than its ~20 minute doubling time. You can indeed think of it as a form of Lamarckism. ...
1
I may suggest to give a look to game theory based model and their generalization from homogenous spatial diatribution to network like model. An easy review can be found in Martin A. Nowak's Evolutionary Dynamics (Harvard press 2006).
In particular you can see the classical Moran process as an evolutionary graph game going on a complete graph with identical ...
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