Molecular dynamics models the motion of atoms within molecules using classical mechanics. Many resources exist online and in print on molecular mechanics. I wanted to learn more about molecular mechanics by implementing it in Python code. Yet, when I searched for resources to lead me in writing my code, I found them scattered online. Pulling them together into a cohesive whole was difficult. In this post, I make a simple molecular dynamics simulation using velocity Verlet integration in Python and compare its results to empirical and analytical values.

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Introduction Convolutional neural networks (CNNs) are a deep learning technology to use for classifying images. For this demonstration I used images from an introductory organic chemistry class. My problem was one of binary classification: could the CNN distinguish images with a structure called a benzene ring from images without a benzene ring? While I encountered challenges of working with a small dataset (with 205 images in each class), I did train the CNN to 73% accuracy of test data.

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Author's picture

Alicia Key

I am passionate about data and science.

PhD student

Aurora, Colorado, USA