Physics & Chemistry – Alicia’s Side Projects

PyTorch: Deep Learning Organic Chemistry

Convolutional neural networks (CNNs) are a deep learning technology to use for classifying images. For this demonstration I used images from an introductory organic…

Julia: Michaelis-Menten Kinetics

Basic Michaelis-Menten enzyme kinetics.

Julia: Connected Reversible Linear Reaction Network Solver

This system is taken from 4.4. Connected Reversible Linear Reactions in [1]. I have rewritten the chemical equation to simplify the notation of the fluxes over the reactions.

Julia: Molecular Dynamics of HCl

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

Python: Lennard-Jones Potential

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

Python: Hydrogen Atom

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

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

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

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

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

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

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…