Questions tagged [chemistry]

For questions related to chemical concepts such as solving equations related to reaction kinetics, graphically visualizing molecules, and using the chemistry-related curated data sets.

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Is there something like DensityPlot3D to visualize atomic orbitals?

I'm visualizing some hydrogen like atomic orbitals. For looking at plane slices of the probability density, the DensityPlot function works well, and with something ...
4k views

How to get rid of the perspective effect in a 3D graphics

I have plotted a figure of MoS2 crytal structure. But the actual output looks like the spheres are not in the correct position due to the perspective effect. I obtained the correct position figure ...
951 views

How to transform and combine multiple Graphics3D into one?

ProteinData["A2M", "MoleculePlot"] gives you a Graphics3D object below. I'd like to display multiple of these proteins in a ...
1k views

Problems with NDSolve and stiffness

I am trying to solve an ODE in chemical kinetics: \begin{align*} \frac{\mathrm d[x]}{\mathrm dt} &= -k_1 [x][y]\\ \frac{\mathrm d[y]}{\mathrm dt} &= k_1 [x][y] - k_3[y] \end{align*} My ...
2k views

Gillespie Stochastic Simulation Algorithm

The Gillespie SSA is a Monte Carlo stochastic simulation algorithm to find the trajectory of a dynamic system described by a reaction (or interaction) network, e.g. chemical reactions or ecological ...
740 views

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

I want to solve two coupled partial differential equations on two dimension. There are two variables v and m. The geometry is a ...
2k views

Accessing list elements by name

First, a bit of a long introduction to my problem: I only have a few weeks of Mathematica experience. I am creating a mathematica application that calculates some material properties of steel based ...
639 views

How to save ChemicalData queries so that they are available immediately on notebook load?

If I put some viscosity (or density, ...) lookups in my notebook, such as: ...
2k views

Plot 3D model of DNA in Mathematica

My friend asked me if we can plot a 3D model of DNA (deoxyribonucleic acid) in Mathematica. However, I am not really familiar with this and I don't know if Mathematica can do this. Could you answer ...
4k views

How to change element color in Periodic Table?

The command ColorData["Atoms", "Panel"] generates a periodic table. As I don't want to reinvent the wheel, I asked myself how to change the color of each cell ...
563 views

Automatic formatting of isotope symbols in a text cell

InputAutoReplacements is an obvious choice for formatting isotope names in text cells. I'd like to be able to type "1H", for ...
1k views

How can I access the internal function that plots a molecule from a formatted XYZ file?

Mathematica has the ability to plot a molecule using the data contained in an XYZ file. This is a simple text file, of which this is an example. The molecule is plotted using the ...
2k views

Constructing primitive cell using information from ChemicalData

I would like to construct a primitive cell (figure shown) and possibly the two-dimensional layout (figure from here) using the following input. Any clues as to how this can be done? ...
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Using ChemicalData to make molecule graphics

$\require{mhchem}$I would like to take the acetone $\cf{((CH3)2CO)}$ and chloroform $\cf{(HCCl_3)}$ molecules that Mathematica's chemical data provides, and plot them together. I want to show how ...
3k views

Creating a Mathieu stability diagram

I am attempting to re-create a Mathieu stability diagram like the one shown here: I expected that I could use MathieuC to generate this graph by assuming that ...
776 views

Changing the atom color for plotting xyz-files

Mathematica takes the standard color code for atoms when plotting an *.xyz file, but I want to customize the color for the specific atoms. I really become desperate as I did not get it so far. ...
970 views

How to fit parameters in a system of coupled differential equations

Problem description: I'm studying a chemical reaction that can be modeled by a system of coupled differential equations, and I want to use measured data to determine the parameters that appear in the ...