Questions tagged [computational-model]

A computational model is a mathematical model in computational science that requires extensive computational resources to study the behavior of a complex system by computer simulation.

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Are there computational models verifying the feasibility that complex biological systems can emerge by random mutations plus natural selection?

I am interested in studying the theoretical feasibility that very complex systems such as the vascular system, the respiratory system, the nervous system, the digestive system, among others, could ...
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Scoring matrices (BLOSUM & PAM) in BLAST and other sequence-comparison programs

The Wikipedia page on BLAST states that: The scores are created by comparing the word in the list in step 2* with all the 3-letter words. By using the scoring matrix (substitution matrix) to score ...
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Dynamic of the number of cells over time as the embryo grows

I would like to investigate the dynamic of the number of cells over time as the embryo grows. I am interested in any multicellular animal species for which we can have some data. How does the number ...
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Which molecular dynamic simulation software is more applicable for protein and large-area surface interaction simulation? And how to run it?

I am trying to do the molecular dynamic simulation for protein-surface interaction, the surface (like cellulose or PET) is a film-like or crystalline material with large surface area, I had tried ...
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Outlining cell edges of an epithelium

Is there any free software (for Windows, preferably) to detect cell edges in pictures of an epithelium, for example? I know Packing Analyzer does this, any other suggestions? Ideally, I would like ...
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1answer
93 views

How to do research in bioinformatics without wet lab experiments?

I graduated in physics from Bangladesh and keen to work in the field of biology. Like, systems biology, computational biology, bioinformatics or systems medicine. I have not produced any research work ...
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1answer
288 views

How many atoms has the smallest known bacterium? [closed]

Background thoughts before this question: is it feasible to simulate a complete bacterium, atom by atom, in a computer simulation? On modern systems, either in an upcoming exascale computer? In ...
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56 views

Can enzymes be modeled using classical mechanics?

When enzymes interact with substrates (i.e. a small ADP molecule and the much larger ATP synthase), does quantum mechanics play a significant role? Or can the interactions be relatively accurately be ...
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1answer
53 views

How does collaboration on reconstructing metabolic networks work?

I am a researcher in psychology and I am trying to come up with a framework/platform in which psychological phenomena can be studied from a dynamical systems / computational perspective in ...
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18 views

Species Distribution Modeling: Mammal river species

When working with mammal river species, what parameters would you use to study them (I have max and min temperature, average rain, slope and obstacles in the river) Something like type of riparian ...
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1answer
47 views

Application of molecular dynamics simulation (or alternatives) for the full pathways of protein interactions?

If one would like to control the biological system (e.g. to treat disease or aging/senescence) then one should introduce the drugs in the system, that initiate complex protein interaction pathways ...
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Computational approaches for making hypotheses about the effects of genetic engineering? Experiment planning methods?

Let's assume that I am searching for gene editing candidates for curing human adiposis. Are there computational frameworks that can allow me to select the best candidate-genes for editing via some ...
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1answer
107 views

Is this model of understanding of what's natural selection and what's not, correct? [closed]

Here in this account I just want to make sure, that I've grasped the concept of natural selection as is usually spoken by evolutionary biologists, truly the wording here are non standard and in some ...
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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 ...
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1answer
79 views

How many residues can a reliable ab initio structural model contain?

A recent question on ab initio that I answered involved touching on the limitations of ab initio modelling. A review from 2009 put forward that typically only in the order of 100-110 residues could be ...
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How did Smith et al 2004 deal with missing HI [Hemagglutination Inhibition assay] values and HI values <10?

In the scientific paper "Mapping the Antigenic and Genetic Evolution of Influenza Virus's" Supporting Material, Smith et al write about determining antigenic distance Dij. However, I don't understand ...
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Projects in DNA Computing [closed]

I am physicist and have recently heard about DNA computing. I want to work in this area. I want your ideas on a "feasible but new project" (maximum time I can put on the project: 6 Months ), I can ...
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55 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
66 views

Homology modelling of protein with two identical subunits in its quaternary structure

I am using homology modelling to assign the 3D structure of Torpedo acetylcholine receptor (Unwin 2004, 2bg9 in RCSB) to human muscle nAChR. The problem is, both Torpedo receptor, and human receptor ...
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Can cognitive functioning of the human brain change the physical state of the brain? [closed]

Can cognitive functioning of the human brain change the physical state of the brain? E.g. does self-awareness, self-reflection change the number of neurons or synapses among neurons? I.e. I am trying ...
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1answer
101 views

Effect and functional role of voltage-gated channels on dendrites [closed]

I'd like to understand better the effect and functional role of voltage-gated channels on dendrites. What I believe to have understood: It is important that a more distal post-synaptical potential (...
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1answer
64 views

Calcium concentration in activated dendritic spines?

What are the typical calcium levels reached in single postsynaptic spines following activation of NMDA receptors by an EPSP or backpropagating spike? Everyone seems to refer to that one Neuron paper (...
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2answers
88 views

Using evolutionary algorithms in molecular biology? [closed]

I am currently an MSc student studying molecular biology (on paper I'm a chemist) and soon I have to talk to my supervisor about my future, PhD research topic. Besides molecular biology I'm also ...
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1answer
99 views

white blood cells and cancer cells transport through lymphatic vessels

It is a well-known fact that both of these cells can reach the lymphatic vessels from interstitial space. How does it do so physically? Are there any mathematical models describing this process? It ...
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226 views

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 ...
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77 views

Why Differential equation is not a good way to model chemical reaction networks [closed]

I'm a computer scientist and mostly code and have worked with Boolean models of cell level molecule transfer. Now i'm reading about the Biological pathways and modelling chemical reaction networks / ...
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3D Object Modelling in the Brain

Could somebody point out the neuroscience literature dedicated to the modelling of 3D objects in the human mind? I'm interested in the brain regions, and particularly the details of the circuitry, ...
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2answers
100 views

Can two arms-racing species be stabilized?

I am trying to build an evolution simulator in which there is group A and group B, each group has 9 members each generation. Each generation, each member of group A will enter a competition (in the ...
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1answer
115 views

Do free computer programs exist that can simulate drug permeability in bacterial membranes?

I am currently trying to make derivatives of a molecule in hopes of making it more permeable to bacterial membranes. I wanted to know whether there are any bacterial membrane simulating programs where ...
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2answers
85 views

How do you derive steady-state conditions from the open-state differential equation of ion channels?

My books describes this differential equation for the open state of an ion channel: Where $k$ are the rate constants, $k_1$ denotes a forward reaction $k_{-1}$ denotes a reverse reaction in the ...
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1answer
107 views

Spatiotemporal patterns in neural networks

It turns out that my work in nonlinear dynamics directly maps to a close variant of the Integrate and Fire model. My model produces spatiotemporal patterns that resemble foam. I have to stress that ...
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1answer
108 views

Success of computer simulations in biology, new discoveries [closed]

In an interview with Tim Hunt, Hunt makes the following comment: There are some people nowadays who think you can sort of model everything on a computer. But I'm not one of those. I don't think ...
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1answer
101 views

What is neuronal computation? [closed]

Can someone give me a good explanation of what is neuronal computation and some examples of its use in neuroscience investigation?
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1answer
269 views

Are neurons roughly a magnetic dipole?

I would like to make a simulation (concerning genetic evolution) and I want to use a very simplistic model of neurons. I don't really care there are different kinds of neurons, I don't care much ...
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1answer
68 views

Number of Bacteria

I am creating a mathematical model for the growth of Synechocystis. sp PCC 6803 and Methanosarcina barkeri Fusaro in photobioreactors and anaerobic membrane bioreactors respectively. I have a couple ...
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420 views

How can computer predictions of protein folding be verified computationally?

Currently, there is a lot of research focused on solving the folding patterns of proteins using computers (Folding@Home, https://fold.it/portal/, etc.). The question that I have is: How do you know ...
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1answer
70 views

Olympic's epidemiological impact on Zika?

I've seen a lot of fear mongering, misinformation and overall general panic concerning the zika virus surrounding the Rio Olympics. However, little has been said about the actual epidemiological ...
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1answer
181 views

Neural coupling between Pinsky-Rinzel (reduced Traub) neuron with a Wang-Buzsaki neuron?

I have read two papers related to modeling neurons. The first one is the paper by Pinsky and Rinzel and the second one by Wang and Buzsaki. The first mentioned neuron model is a excitatory neuron ...
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1answer
16k views

What is the difference between a mechanistic and a statistical predictive model?

The simplest description of the difference between these two approaches that I have found are on this site who summarise the difference as: Mechanistic model: a hypothesized relationship between the ...
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1answer
274 views

What are some useful (starter) metrics to use on phylogenetic trees?

I'm doing a computational biology project in which I simulate evolution under different inheritance rulesets and I am generating phylogenetic trees (beautifully visualised in Python with ete3). My ...
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1answer
172 views

Phylogenetic algorithms: How to interpret multiple ML trees from the same dataset?

There's still something that confuses me about how many of these algorithms work, and how results are presented in the literature. Let's consider a Maximum Likelihood based algorithm like MrBayes or ...
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5answers
619 views

What was the first piece of work in computational biology?

What was the first piece of work in computational biology? I'm ideally looking for a paper. I am not interested in works that involve data management or data analysis but work that model biological ...
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107 views

How can I perform a 1:1 sequence-structure alignment for a pdb template dimer and homologous dimer sequence?

I have: 1. A PDB dimer protein structure template of a real solved protein. 2. An unsolved, but highly homologous dimer protein (>90% sequence identity.) How can I use MODELLER to make a theoretical ...
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1answer
561 views

Examples of biological turing machines [closed]

Are there any examples of biological Turing machines? And what can they do?
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1answer
128 views

Can exhaustive algorithms produce MSAs that are suitable for 3D structure modelling?

While predicting 3D structure of a protein through homology modelling, the most important step is Multiple Sequence Alignment of template sequences with the target protein whose 3D model is to be ...
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104 views

Where to go next with clustered C elegans neuronal time series

I'm doing some independent research with the C Elegans nervous system (with the OpenWorm project) and was looking for some guidance as to where I should go next. Right now, I'm dealing with calcium ...
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1answer
218 views

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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41 views

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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2answers
576 views

Is it possible to create a restriction map using python? [closed]

I have some fragments of DNA from single and double digests using three different restriction enzymes. I'm trying to construct a restriction map of a linear fragment of DNA. The map needs indicate the ...
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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 ...