Theoretical models that explain a system using mathematical equations.

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22 views

Looking for detailed nutrient/energy flow at the bottom of the freshwater food chain

I am trying to model the production and consumption of nutrients and waste at the bottom of the food chain in freshwater ecosystems. I can only find broad information on the Internet and don't know ...
2
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3answers
653 views

Michaelis-Menten Kinetics: Does measuring apparent Km and Vmax take into account competing reactions?

I am learning about why it is important to measure Km and Vmax for each experimental setup because measuring the "apparent" Km and Vmax includes enzyme inhibitions of which one might not be aware. ...
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1answer
115 views

Lineage selection in plasmid evolution

I've been reading through Paulsson (2002) and I am not sure what he means by "lineage selection" in the second to last section. The paper deals with plasmid replication, and mostly concentrates on the ...
9
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1answer
283 views

Structure of fitness landscapes in the NK model

The NK model of rugged fitness landscapes consists of $N$ sites where fitness contribution of each site depends on its state $\{0,1\}$ and is epistatically affected by $K$ other sites. When defining ...
2
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2answers
365 views

What would it take to recognize a deer by its photo?

I am trying to recognize a deer by its antlers or any other means. Elaborating: I was hoping to use their antlers to recognize them but I have heard that most deers shed their antlers every year so ...
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0answers
22 views

Do the antlers re-grow in the same pattern every year? [duplicate]

I am a software engineer and I am trying to develop a system to identify a deer by its photograph. Most deers lose their antlers every year. I would like to know if they re-grow in the same pattern ...
3
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1answer
186 views

Are there natural selection experiments that quantitatively agree with theoretical modeling?

Has anyone ever conducted an evolution experiment and quantitatively compared it to theory? For example, has anyone ever put bacteria in a million petri dishes filled with antibiotics and calculated ...
6
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2answers
212 views

Is local equilibrium a reasonable assumption for evolutionary processes?

Whenever I look at discussions of fitness landscapes (in particular, Kauffman's NK model) the questions tend to resemble: The population is at a local equilibrium, but another equilibrium of ...
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1answer
117 views

How to classify equilibrium points [closed]

I have the two differential equations: $$\frac{dN_1}{dt} = N_1(2 - N_1 - 2N_2)$$ $$\frac{dN_2}{dt} = N_2(3 - N_2 - 3N_1).$$ I worked out the equilibrium points to be at $N_1 = 0, \frac{4}{5}$ and ...
0
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2answers
204 views

Deterministic model of lambda-phage lysis/lysogeny [MATLAB] [closed]

Project 1 Base: Can someone please help me understand what I need from Project 1 Base code to do questions 1 and 2 from the first image? I'm new to MATLAB so a thorough explanation would be ...
9
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1answer
297 views

When does weak selection produce qualitatively different results from strong selection?

In evolutionary game theory, it is typical to model organisms as having a base fitness that is modified slightly by the game interaction. The ratio of the game effect versus the base fitness ...
6
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1answer
184 views

What is the minimum population size that Hardy-Weinberg calculations can be applied to?

I'm trying to find out if a particular allele is in Hardy-Weinberg disequilibrium, but the data is poor. What's the minimum population number that you can use to get any sort of respectable ...
2
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1answer
40 views

Range of feasible coefficients in an unlimited growth model

If you are given an unlimited growth model in the form: $\frac {dP(t)}{dt} = k P(t)$ Obviously the population growth would never be unlimited, but let's presume for the moment that we are ...
3
votes
2answers
213 views

What software is there available for Quantitative structure–activity relationship (QSAR) pharmacological studies?

QSAR modelling in pharmacology basically hangs on using mathematical modelling to approximate the effects different molecules will have on various pharmacological targets. I would like to know what ...
6
votes
2answers
105 views

How are Genetic Circuits Modelled?

I've read a recent Nature Methods paper by Moon T.S. et al, in which a synthetic genetic circuit consisting of layered logic gates was created. For example, the paper, a circuit is modelled in Figure ...
8
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2answers
778 views

Scoring sequence against position weight matrix

I have a weight matrix of length 20 x 15 (amino acids x sequence positions). Each element of my weight matrix is a relative probability If I have a sequence say "AAPGTGASMHSGLLW" how would I score it ...
3
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0answers
71 views

Experimental techniques to measure protein-protein and protein-ligand structure and dynamics

We would like to compare our simulation results with experimentation. When one wants to follow experimentally the dynamics (and possibly structure) of protein-protein or protein-ligand docking ...
6
votes
1answer
242 views

Models of quorum sensing for multi-agent systems

Quorum sensing is a system of stimulus and responses correlated to population density that is used by bacteria to coordinate gene-expression. I am looking for a simple computational/mathematical model ...
6
votes
3answers
685 views

How exactly are game theoretical evolutionary models described during implementation for computer simulations?

When a biologist or a layman tries to reason the evolutionary explanation for something, they would simply use English with some math thrown in (for a random example, pick any explanation out of "The ...
6
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1answer
115 views

Macromolecule levels in daughter cells after fission

When a prokaryote undergoes binary fission, how are the non-DNA macromolecules distributed between the two daughter cells? This is motivated by comments on a previous question and a G+ discussion. I ...
6
votes
1answer
285 views

Computational/mathematical models for predicting phenotype from genotype

Karr, Sanghvi, et al. (2012) propose a whole-cell computational model for predicting phenotype from genotype in Mycoplasma genitalium. Their model simulates myriad cell processes such as DNA ...
3
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2answers
226 views

Short-term Lamarckism in asexual single cell organisms

I was reading through the Karr et al. (2012) whole-cell computational model. One of the things they did was to induce single-gene disruptions in their model. They observed several to be fatal, but: ...
6
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1answer
144 views

Alternatives to fittest-win and Moran processes as simple mathematical models of selection

When modeling selective sweeps as a micro-building block in models of macroevolution (not to be confused with misuses of this in creationist arguments), I use the fittest-win model of selection as a ...
16
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2answers
975 views

Why is 'Grudger' an evolutionary stable strategy?

I am currently reading 'The Selfish Gene' by Richard Dawkins, which I am sure many here have read. The topic are evolutionary stable strategies (ESS) regarding cooperation. I apologise for the long ...
10
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1answer
174 views

(How) does coppicing fundamentally alter tree growth?

I am interested in adding the ability to model coppice tree production to a model of perennial crops (Miguez et al 2008).. Implementing the biomass pools and allocation parameters required for tree ...
26
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2answers
584 views

What are the trajectories of flying insects?

Many flying insects tend to have very jagged trajectories. For moves of a fruit fly looks like a random walk. Is there any research on the properties of trajectories (e.g. their fractal dimension or ...