# Tag Info

Accepted

### Gillespie Stochastic Simulation Algorithm

Yes you can. Below is a fairly general, Mathematica-compiled, fast and robust version. Examples 1. Michaelis-Menten kinetics Michaelis-Menten kinetics for enzyme-directed substrate conversion. The ...
• 47.2k
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### visualizing a normal mode vibration of a molecule in mathematica

Using a few undocumented functions that have been discussed here on the stack exchange before, ...
• 69.7k
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### Minimum energy path of a potential energy surface

Smooth Equations Let $\varphi \colon \mathbb{R}^d \to \mathbb{R}$ denote a potential function (e.g., from OP's data file). We attempt to solve the system  \left\{ \begin{aligned} \gamma(0) &...

### What's the principle behind the new MoleculeRecognize function?

Using ResourceFunction["PrintDefinitions"][MoleculeRecognize], one can determine that the source implementation is MolVec. The specific source code is: ...
• 13.2k

### Plot 3D model of DNA in Mathematica

Here is a function that can wrap a double helix around any (sufficiently smooth) parameterized curve. Among other things, the function below computes a Bishop frame along the curve; twisting it leads ...
Accepted

### Chemical data of Lactic acid

I've struggled with How Mathematica expects the end-user to interact with knowledge databases for quite some time. While this solution is likely not universal, it has been reasonably successful for ...
• 19.7k

### ChemistryData — where is specific gravity?

Specific gravity is not on the property list of curated chemical properties, so you can't get it directly. However, here is a function that will compute it. ...
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### Minimum energy path of a potential energy surface

Interesting problem. Decided to treat it as a graph problem, rather than fitting an InterpolatingFunction to it and getting descent directions from there. If I knew ...
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### Why does Molecule return a molecule for an incorrect SMILES string?

This is a bug, the most basic manifestation of which is ...
• 69.7k

### Computing the surface area and volume of molecules

I can offer a solution by discretization to ElementMesh with external meshing software Gmsh. Currently it produces better quality mesh on curved surfaces that built-...
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### What's the principle behind the new MoleculeRecognize function?

I am one of the authors of Molvec. It was designed in a classical approach using various image processing heuristics to guess the structure. While it's on my todo list, we still haven't published a ...
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### Mass Transport Model

OK. Let me extend my comments to an answer. First of all, I'd like to point out why OP's attempt doesn't work: "NDSolveValue should return a list with three ...
• 67.7k
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### Plot polygonal surface

(grabbing a lot of code from this answer) This is just to get you started, adding in colors to the final GraphicsComplex should be pretty easy. ...
• 69.7k

### How to apply different equations to different parts of a geometry in PDE?

Denote the disk by $\varOmega$ and its boundary by $\varGamma = \partial \varOmega$. I'd prefer to denote the function residing on the boundary by $u \colon \varGamma \to \mathbb{R}$; the function on ...

### Computing the surface area and volume of molecules

The paper Fast Calculation of van der Waals Volume as a Sum of Atomic and Bond Contributions and Its Application to Drug Compounds, pointed out by theorist gives an approximate formula for the ...
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### MoleculePlot3D - how to replace spheres?

How to replace the spheres in the plot with other 3d figures, say "N" with a Cylinder, "O" with a Cuboid, and "H" with a sphere. This answer takes points from the ...
• 37.9k
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### Connectivity in a molecule and permutations

Getting the graph from the XYZ file You have only a set of coordinates and atom types in an XYZ file. When you import it in Mathematica you can import 3 elements: the 3D plot, the coordinates, and ...
• 69.7k
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### Molecule fingerprint functions v13

edit: For direct access to the underlying fingerprint functions behind FeatureExtraction for molecules, see the Molecule Fingerprints paclet in the new paclet ...
• 69.7k
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### Proteins, ProteinData, WolframAlpha

Here's a workaround that directly queries the PDB search API and returns the first num search results as a Dataset[]. The ...
Accepted

### ChemicalData returns the correct result for "Sulfuric" but an empty list for "Sulfuric Acid". Why?

Consider using a dedicated search pattern making function. Here is an example. ...
• 37.9k

### DFT for Helium atom

Here's what I mentioned in the comments. Life is better with NDEigensystem and NDSolve: ...
• 47k
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### How to apply different equations to different parts of a geometry in PDE?

Since I have the code to solve the original problem described in the article GDI-Mediated Cell Polarization in Yeast Provides Precise Spatial and Temporal Control of Cdc42 Signaling, I will give here ...
• 47.8k

### When looking at a chemical's bond lengths, which bonds do they represent?

There must be a better way, but here is a first pass. This method is based on [Experimental] functions, two of which are new in MMA 12, BondList and ...
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### How to apply different equations to different parts of a geometry in PDE?

What about: Noting that equations 1 and 3 form a complete set, and solve them first, treating the remaining equation 2 for m afterwards. Noting that your imposed ...
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### Chemical formulas with Mathematica

ClearAll["Global`*"] Assuming that you are starting with a chemical formula ...
• 161k
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### MoleculePlot draws sucrose benzoate with overlapping bonds

Mathematica uses a number of libraries for generating 2D structure diagram coordinates. The automatic method produces a suboptimal result for this molecule. Probably the system should try to check ...
• 69.7k

### Plot polygonal surface

...
• 161k
The plot you were trying to reproduce is a plot of the reduced van der Waals equation; that is, it is using the reduced pressure $P_r=\frac{P}{P_c}$ and reduced temperature $T_r=\frac{T}{T_c}$ as the ...