Ruijie (Ray) Zhu

2026

Sept 17 - Our preprint, "The ModelSEED Biochemistry Database, 2026 update: grading multi-source thermodynamics," was posted on bioRxiv. Preprint

July 20-24 - I attended the 2026 Deep Learning for Science (DL4SCI) Summer School hosted by Computing Sciences at Berkeley Lab. Website

Mar 23 - I started working as a teaching assistant for the course MENG 24400 Chemical Kinetics and Reaction Engineering.

Mar 22-23 - I presented a poster at the NRT annual meeting at the Colorado School of Mines.

Jan 23 - Our project, PALM (Physics-Aware Leakage Minimizer), received AIMEMS NRT team funding.

Jan 14 - Our paper, "Discovery of Stacking Heterogeneity, Layer Buckling, and Residual Water in COF-999-NH2 and Implications on CO2 Capture," was published in the Journal of the American Chemical Society. Paper

January - I completed my research mentorship with three middle school students at Francis W. Parker School for the Presidential AI Challenge.

2025

November - I started as a visiting student subcontractor at Argonne National Laboratory, working with Arvind Ramanathan on enzyme discovery and design.

September - I began developing autonomous AI agents for enzyme design with Arvind Ramanathan.

July 7-9 - I attended the CECAM-US-CENTRAL 2025 Conference Machine Learning Advances for Molecular and Materials Property Prediction at the University of Notre Dame.

July 7 - I started serving as a reviewer for the journal Machine Learning: Science and Technology.

June 25-27 - I attended the AI4Chemistry Summit at NYU.

June 23 - Our collaborative paper "Bayesian Optimization Hackathon for Chemistry and Materials" was posted on ChemRxiv. Link

June 21 - Our team PolymerSphere started working on the Open Polymer Challenge.

June 14 - I started working as a research assistant in Dr. Arvind Ramanathan's lab at Argonne.

May 18 - I finished Life Time Chicago Spring Half in 98th place with a finish time of 1:29:57.

May 9 - Our team, Catalyze Q, was featured on the Polsky Center website. Link

Apr 28 - Our paper "Cartesian Equivariant Representations for Learning and Understanding Molecular Orbitals" was posted on ChemRxiv. Link

Apr 15-29 - I participated in the AI + Science Hackathon hosted by the Data Science Institute at UChicago.

Mar 26 - I started serving as professional development chair of the Society of Asian Scientists and Engineers (SASE) UChicago chapter.

Jan 6 - Our paper "A generative artificial intelligence framework based on a molecular diffusion model for the design of metal-organic frameworks for carbon capture" was included in Communications Chemistry’s 2024 Editors' Highlights Collection. Link

Jan 6 - I started working as a research assistant in the PME department at UChicago.

Jan 3 - Our paper "Wide-ranging predictions of new stable compounds powered by recommendation engines" was published in Science Advances. Link

2024

Dec 3-6 - I visited UC Berkeley to discuss my ongoing research project.

Nov 26 - Our collaborative paper "Reflections from the 2024 Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry" was posted on arXiv. Link

Nov 25-27 - I attended Chem AI satellite events. Link

Nov 24 - I finished my first marathon in 3:34:53 during the Philadelphia Marathon weekend. Certificate Link

Oct 30 - The Climate Frontiers: Energy and Climate event was hosted at UChicago. Link

Oct 29-31 - I attended the 2024 ALCF Hands-on HPC Workshop at Argonne. Link

Oct 18 - The first session of the I-Corps program at the Polsky Center started.

Oct 11 - I became a mentor in the Global Mentor Network program at UChicago I-House. Link

Oct 10–11 - I attended the AI for Multidisciplinary Exploration and Discovery (AIMED) Workshop on Heterogeneous Catalysis. Link

Oct 1 - Nov 12 - I attended the ALCF Intro to AI-driven Science on Supercomputers workshop. Link

Sept 29 - I finished my first half marathon in 1:43:25 during the 2024 HOKA Life Time Chicago Half Marathon. Link

Sept 27 - I presented a poster on behalf of the Gagliardi group during PME orientation week.

Sept 24-25 - I presented a poster at the CD4DC All Hands Meeting. Link

Sept 19 - Our team, CatalyzeQ, was selected to participate in the Polsky I-Corps program. Link

Sept 13 - I attended the 1st Midwest MOF conference. Link

Sept 7 - I finished in 28th place (39:29) in the Run Mag Mile Chicago 10k run. Link Certificate

Sept 2 - I started as an NSF-NRT AIMEMS trainee. Link

Aug 6-7 - I attended the NCHC end-to-end LLM bootcamp hosted by the National Center for High-performance Computing. Link

July 31 - I was accepted as an NSF-NRT AIMEMS trainee. Link

July 23-24 - I attended "AI For Science and Nobel Turing Challenge Initiative Conference". Link

July 17-18 - I attended the Artificial Intelligence for Materials Science (AIMS) workshop at NIST. Link

July 15-17 - I attended the "Frontiers on Computational Reaction Prediction" workshop hosted by CECAM. Link

July 9-13 - I attended "Summer Virtual Workshop on Machine Learning Performance and Scalability" hosted by NCA Delta Project Office.

July 8-26 - I attended the SciFM Summer School organized by the University of Michigan and Argonne. Link

July 3 - Our team (Agent 47 Materials) won first place in the AI4Science Hackathon. Link Slides

June 28 - I attended "Crash Course in Supercomputing" hosted by LBNL. Link

June 26 - Our team advanced to the final round of the AI4Science Hackathon. Code Website

June 26 - I attended "Expanding AI and next generation simulation tools to accelerate scientific discovery" hosted by C&EN and Microsoft. Link

June 25-26 - I attended "Future of Materials Discovery Workshop" hosted by University College London. Link

June 14 - I completed my first paper review for the journal Transactions on Knowledge Discovery from Data.

June 13 - I participated in the AI4S Cup - OpenLAM Challenge - LAM Crystal Philately. Link

June 11 - I joined the Catalyst Design for Decarbonization Center (CD4DC), funded by the DOE. Link

June 10 - Our work appeared in the June 2024 DOE NETL Carbon Capture Newsletter. Link

June 10-14 - I remotely attended the AI≡Science: Strengthening the Bond Between the Sciences and Artificial Intelligence Workshop hosted by the Simons Institute. Link

May 30 - I scored 98 in TOPIK II 2024. Certificate

May 27 - I wrote a blog post titled "Hackathon 101". Blog

May 24 - I wrote a blog post titled "How we won reincarnate prize for LLM hackathon for applications in materials and chemistry 2024". Blog

May 13-17 - I attended the "Data Sciences for Mesoscale and Macroscale Materials Models" workshop organized by the Institute for Mathematical and Statistical Innovation (IMSI) at the University of Chicago. Link

May 10 - Our team won the "reincarnate prize" at the LLM Hackathon. Medium Code

May 9 - We successfully completed the AI+Science hackathon. Code Slides Certificate

May 8-9 - I participated in the Large Language Model (LLM) Hackathon for applications in chemistry and materials science. Link

May 6-9 - I participated in the AI+Science Hackathon organized by the Data Science Institute (DSI) at the University of Chicago. Link

Apr 30 - Our working paper "Deep Learning for Molecular Orbitals" was posted on ChemRxiv. Link

Apr 22 - May 6 - I participated in MLMR's annual materials informatics competition 2024.

April 22-26 - I attended the "Learning Collective Variables and Coarse-Grained Models" workshop organized by the Institute for Mathematical and Statistical Innovation (IMSI) at the University of Chicago. Link

April 8-12 - I attended the "Machine Learning Force Fields" workshop organized by the Institute for Mathematical and Statistical Innovation (IMSI) at the University of Chicago. Link

Mar 29 - Our team placed sixth in the Bayesian Optimization Hackathon. We found that Thompson sampling was twice as efficient in finding high-performing metal-organic framework (MOF) candidates compared to random sampling. Code Link

Mar 27-29 - I participated in the Bayesian Optimization Hackathon for Chemistry and Materials organized by the Acceleration Consortium at the University of Toronto. Link GitHub YouTube Slides

Mar 25-29 - I attended the "Machine Learning in Electronic-Structure Theory" workshop organized by the Institute for Mathematical and Statistical Innovation (IMSI) at the University of Chicago. Link

Mar 11-15 - I attended the "Materials Informatics: Tutorials and Hands-On" workshop organized by the Institute for Mathematical and Statistical Innovation (IMSI) at the University of Chicago. Link

Mar 1 - I presented my Classical Molecular and Materials Modeling term project. YouTube

Feb 14 - I presented a poster at the PME admitted student visit weekend.

Feb 14 - Our work on isoreticular design of pcu MOFs for CO2 capture was published in Nature Communications Chemistry. Link Behind the paper

Feb 9 - Our Argonne team won HPCwire’s Editors’ Choice Award for Best Use of High-Performance Data Analysis & Artificial Intelligence. Link

Feb 9 - I made a poster for the PME Lunar New Year celebration. Link

Feb 7 - Our work on MOF+AI was featured in Argonne News. Link

Jan 5 - I joined the Gagliardi group at the University of Chicago. Link

2023

Oct 17 - I delivered a talk at the CD4DC All Hands Meeting at the University of Chicago. Link

Sept 26 - I started my PhD at the Pritzker School of Molecular Engineering (PME) at the University of Chicago.

July 27 - I delivered a talk at the group meeting at LLNL.

July 27 - I delivered a talk at the 2023 Artificial Intelligence for Materials Science (AIMS) meeting. LinkPresentation

July 18 - I made a YouTube video about Yosemite. Link

July 13 - I delivered a talk at the Computational Chemistry and Materials Science Summer Institute student meeting.

July 4 - I made a YouTube video about San Francisco. Link

June 29 - Our paper "End-to-end AI framework for interpretable prediction of molecular and crystal properties" was published in Machine Learning: Science and Technology. Link

June 28 - The code for GHP-MOFassemble was released on GitHub. Link

June 14 - Our paper "GHP-MOFassemble: Diffusion modeling, high throughput screening, and molecular dynamics for rational discovery of novel metal-organic frameworks for carbon capture at scale" was posted on arXiv. Link

June 5 - I started my internship as a Computational Chemistry and Materials Science (CCMS) Summer Institute Fellow at Lawrence Livermore National Laboratory.

May 31 - I completed my Predoctoral Appointee position at Argonne National Laboratory.

May 22 - The Science Olympiad varsity team I coached at Marie Murphy School finished in sixth place at the national competition. Congrats!

April 25 - The Science Olympiad varsity team I coached at Marie Murphy School advanced to the national competition. Congrats!

April 12 - I delivered a talk at the AIChE Midwest Regional Conference.

April 5 - Our code for our diffusion-model-based metal-organic framework (MOF) generation algorithm for carbon capture was released on GitLab. Link

April 3 - I accepted a PhD offer from the UChicago Pritzker School of Molecular Engineering.

April 3 - I started as a Predoctoral Appointee at Argonne National Laboratory.

April 2 - I posted my first YouTube video on half marathon training preparation. Video

Mar 12 - The Science Olympiad varsity team I coached at Marie Murphy School advanced to the state competition. Congrats!

Mar 2-4 - I visited the Materials Science department at Carnegie Mellon University.

Feb 23-25 - I visited the UChicago Pritzker School of Molecular Engineering. Photo

Feb 23 - I submitted an abstract to the AIChE Midwest Regional Conference. Abstract

Feb 21-23 - I presented a poster at the MaRDA Annual Meeting. Poster

Feb 7 - I wrote a blog post about my experience participating in iQuHack 2023. Blog

Jan 27-29 - I participated in the iQuHack Quantum Computing Hackathon hosted by MIT iQuISE. Website GitHub Blog

Jan 22 - I passed JLPT N1. Certificate

Jan 19-21 - I participated in the Solid-state Materials Chemistry and Data Science Hackathon (SSMCDST) hosted by Lehigh University. Final PresentationWebsite

Jan 17 - I wrote a blog post on my experience as a master’s student in Materials Engineering at Northwestern. Blog

Jan 2 - I wrote a blog post on my recent work on i-MAX phases. Blog

2022

Dec 27 - I shared a blog post about computational materials science.

Dec 22 - Our paper "End-to-end AI Framework for Interpretable Prediction of Molecular and Crystal Properties" was posted on arXiv. Paper

Dec 10 - I graduated from Northwestern University with a master’s degree in Materials Science and Engineering.

Dec 4 - I took the Japanese Language Proficiency Test (JLPT) N1.

Nov 27-Dec 1 - I participated in the Battery Informatics & ML Competition hosted by NIST and TRI.

Nov 24 - I started coaching Science Olympiad at Marie Murphy School.

Oct 8 - I finished in 99th place in Abbott Chicago 5k. Certificate Result

Oct 6 - I started mentoring students at Nichols Middle School. Morning Mentor

Sept 28 - I contributed to XSEDE and NERSC proposals that were awarded high-performance computing resources.

Sept 28 - I presented a rapid-fire research talk at the QMT Journal Club meeting. Slide

Aug 31 - I delivered a group presentation at a Wolverton group meeting. Slide

Aug 11 - I developed code for calculating site-specific chemical similarity of materials. GitHub link

Aug 8-12 - I attended the Machine Learning for Materials Research (MLMR) Seminar 2022 hosted by UMD. Group Picture

Aug 4 - I wrote two extractor scripts for materials data visualization on Clowder. Slide

Aug 1-5 - I attended the 2022 MaRDA Summer Hackathon at Georgia Tech. GitHub Photo

July 18 - I finished in 38th place in Under Armour Chicago 10K. Result

July 14 - I presented a poster at the Artificial Intelligence for Materials Science (AIMS) Meeting. Poster Presentation

July 13 - I presented a poster at the C3S Symposium. Poster

June 13 - I attended the Argonne Quantum Computing Tutorial.

June 13 - I started my summer internship as a Research Aide Technical at Argonne National Lab.

May 26-27 - I attended the Computational Representation of Materials Workshop hosted by TRI.

May 15 - Our team placed fourth in the Stanford Cleantech Challenge. Slides

Feb 22 - I presented a research poster at the Materials Data Alliance (MaRDA) Meeting. Page

Jan 28 - Our team won first place in the ALCF AI Hackathon.