Questions tagged [biomaterials]

Questions relating to biomaterials modeling.

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Simulating a circuit diagram for action potential [closed]

Cable theory is a good simulation for the resting potential. It imagines patches of cell membrane lipid bilayer as capacitors and transmembrane ion channels as resistors. But it seems this model is ...
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Is there a site to obtain or create membranes?

I am interested in creating an enterocyte intestinal basal membrane. So, I wonder if there is a database or site where the membrane could be downloaded or created.
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How do I model drug diffusion from polymeric matrix? [closed]

I have been redirected to this forum from Chemistry SE. My problem consists of a structure (say a cylinder) made from a homogenous distribution of a drug from a polymeric matrix. These compounds are ...
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2 votes
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Chemical Structure of Iron Manganese Silicate Nanoparticle (IMSN) Nanozyme? [closed]

Hope you're doing well. Actually I am working on a project related to DNA regulated Nanozyme and I have a nanozyme of mesoporous silica "Iron Manganese Silicate nanoparticle (IMSN) nanozyme"....
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9 votes
1 answer
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What is the purpose of DSSP when using martinize2?

I am studying an IDP with a lot of helical secondary structure, and trying to find a trajectory that I can use as an ensemble that fits my SAXS data. My starting models are the output from the Robetta ...
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Has there been any work done on fluid dynamic or acoustic modeling of the human oral (or nasal) cavity?

The purpose is for me to develop a deeper understanding of speech production and how distinct features that identify a phenome are produced. ab initio models based on classical & statistical ...
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12 votes
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How much of a difference in a protein's radius of gyration can be considered significant?

In molecular dynamics simulations of proteins, the radius of gyration is often used to assess the compactness of a protein. When comparing two protein radius of gyration, what difference can be ...
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Docking proteins with glycans

Do you know of a good software or web server tool that helps doing docking of proteins with rather large glycans? An example I'm interested in is tens of dimers of sugars (or similar), docked to ...
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How to do molecular dynamics calculations and analyse trajectories of small molecules? [closed]

I need to perform some MD calculations and then trajectories of some small molecules analyzed. What I have is protein cofactor (FAD) small molecule (either single O2 molecule or single Chlorine atom) ...
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12 votes
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Theoretical origins of stereochemistry

What are the current theories of computational chemistry for studying homochirality (for example the phenomenon discussed here, here and in many other places)? Electroweak chemistry has been developed ...
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15 votes
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How to characterize surface features in proteins?

When looking at the structure of protein domains I notice many of them show a cleft-like structure in the same location (when aligned to each other). What is a recommended way of characterizing these ...
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Protein cavities - methodological starting point for basic characterization

Characterizing surface properties is important for understanding how proteins execute their function by interacting with other molecules. This includes characterizing cavities. Perhaps the simplest ...
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How are quantum computers being used in drug design? [closed]

A biomaterials question this time. How are quantum computers being used in drug discovery and design?
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