Derek Jones

Global Security Computing Applications Division

Lawrence Livermore National Laboratory

Computer Science and Engineering Dept.

University of California, San Diego

Hi, I’m Derek Jones.

I am a second-year Computer Science PhD student at University of California - San Diego in the Systems Energy Efficiency (SEE) Lab. My PhD work is focused on finding ways in which we can enable the acceleration of molecular simulations by augmenting traditional physics-based modeling with ideas from machine learning and hardware acceleration.

I work on scalable machine learning/deep learning research for drug discovery at Lawrence Livermore National Laboratory and the ATOM Constortium.

I graduated from the University of Kentucky in May of 2018 where I earned an M.Sc. in Computer Science with a research focus in Machine Learning/Deep Learning and its applications to Computational Biology and Drug Discovery. I was advised by Dr. Nathan Jacobs (Computer Science) and Dr. Sally R. Ellingson (Biomedical Informatics).

selected publications

Accelerators for Classical Molecular Dynamics Simulations of Biomolecules

Jones, Derek, Jonathan, Allen E, Yang, Yue, Bennett, W F D, Gokhale, Maya, Moshiri, Niema, and Rosing, Tajana

J. Chem. Theory Comput. 2022

Bib
@article{Jones_2022-uq, title = {Accelerators for Classical Molecular Dynamics Simulations of Biomolecules}, author = {Jones, Derek and Jonathan, Allen E and Yang, Yue and Bennett, W F D and Gokhale, Maya and Moshiri, Niema and Rosing, Tajana}, journal = {J. Chem. Theory Comput.}, volume = {}, number = {}, pages = {}, month = {}, year = {2022}, language = {en}, selected = {true}, bibtex_show = true }
Improved Protein-Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference

Jones, Derek, Kim, Hyojin, Zhang, Xiaohua, Zemla, Adam, Stevenson, Garrett, Bennett, W F Drew, Kirshner, Daniel, Wong, Sergio E, Lightstone, Felice C, and Allen, Jonathan E

J. Chem. Inf. Model. 2021

Bib
@article{Jones2021-al, title = {Improved {Protein-Ligand} Binding Affinity Prediction with {Structure-Based} Deep Fusion Inference}, author = {Jones, Derek and Kim, Hyojin and Zhang, Xiaohua and Zemla, Adam and Stevenson, Garrett and Bennett, W F Drew and Kirshner, Daniel and Wong, Sergio E and Lightstone, Felice C and Allen, Jonathan E}, journal = {J. Chem. Inf. Model.}, volume = {61}, number = {4}, pages = {1583--1592}, month = apr, year = {2021}, language = {en}, selected = {true}, bibtex_show = true }