akey7

Julia: Molecular Dynamics of HCl

julia

physics

chemistry

Molecular dynamics models the motion of atoms within molecules using classical mechanics calculations. Molecular dynamics envisions atoms as balls on springs and calculates…

Julia: Positive and Negative Definite Matrices

julia

math

These functions implement the expression, which can calculate scalar quantities when given x1 and x2 components of a 2-element vector.

Python: Simple Gradient Descent

python

math

This is a simple polynomial gradient descent. It is a naive implmentation that is not optimized or vectorized. It is meant to be a simple demo on how gradient descent can be…

R: FFT with fftpipe

r

math

fftpipe is a package of functions that wrap around the base R fft() function. The fftpipe package enables workflows around the fft() function that use the pipe (%>%)…

Python: Lennard-Jones Potential

python

physics

chemistry

\[ V(r) = 4 \epsilon \biggl[ \biggl (\frac{\sigma}{r}\biggr)^{12} - \biggl (\frac{\sigma}{r}\biggr)^6 \biggr] \]

Python: Hydrogen Atom

python

physics

chemistry

In this post, I define a class to model the behavior of a hydrogen atom. In the process, I get to solve integrals like the following numerically to test my code:

Python: Rydberg Equation and Hydrogen Spectra

python

physics

chemistry

The Rydberg formula is used to predict emission spectrum lines from hydrogen. The significance of the Rydberg formula is that it was one of the first studies of quantum…

Python: Quantum harmonic oscillator

python

physics

chemistry

In this post, I will define Python code that models the quantum harmonic oscillator. This page follows page 290 to 297 in Physical Chemistry, 8th Ed. by Peter Atkins and…

Python: Quantum mechanics: two non-interacting particles

python

physics

chemistry

This code and these plots explore Molecular Modelling for Beginners, 2nd Ed. by Alan Hinchliffe Section 12.6, pages 181 to 184. In this Section, the author explores the…

Python: Quantum mechanics: particle in a box

Python

This post explores the simplest quatnum mechanical system: the particle in a one-dimensioanl infinite potential well, also known as the one-dimensional particle in a box.

R: Solubility Clustering

chemistry

r

solubility

In my prior aqueous solubility regression study, I did an exploratory data visualization and found intriguing plots of solubility versus other variables in the study. I…

R: Solubility Regression with Linear and Random Forest Models

chemistry

r

solubility

Aqueous solubility (ability to dissolve in water) is an essential property of a chemical compound important in the laboratory. Can the solubility of a compound be predicted…