News

April 2025

Parth gave both an oral and a poster presentation at the 5th Annual Biophysics Colloquium at UC Davis.

March 2025

Our new paper is out in Journal of Chemical Information and Modeling! https://pubs.acs.org/doi/10.1021/acs.jcim.4c02272

Siddharth gave a poster presentation at the ACS Spring Meeting 2025 as one of the seven finalists for the NVIDIA GPU Award.

Parth passed his qualifying exam and became a Ph.D. candidate! Congratulations Parth!

Prof. Ahn is featured on the Vagelos Molecular Life Sciences Program website! https://vagelosmls.sas.upenn.edu/

February 2025

Celeste, Maryam, and Parth gave a poster presentation at the Biophysical Society Annual Meeting 2025.

We have a visiting graduate student researcher from Pusan National University, Jaeyoung Kim, for three days. Welcome, Jaeyoung!

January 2025

Prof. Ahn gave an invited talk titled "Bridging timescales between simulations and catalytic and biological processes" at the Center for Predictive Bioresilience at Lawrence Livermore National Laboratory. 

Prof. Ahn is on the JCIM Early Career Board! https://pubs.acs.org/page/jcisd8/editors.html

Congratulations to Siddharth for being awarded the Duke Center for HIV Structural Biology Trainee Travel Award to attend the 2025 ACS Spring Meeting to compete for the NVIDIA GPU Award!

We have two new rotating graduate students this quarter, Eleanor Zhu and Scott O'Shea. Welcome, Eleanor and Scott!

Our new paper is out in iScience! https://www.sciencedirect.com/science/article/pii/S2589004224029687

December 2024

Prof. Ahn gave an invited talk titled "Bridging timescales in protein simulations using Parallelized Gaussian accelerated molecular dynamics (ParGaMD)" in the Department of Biological Sciences at Seoul National University.

Prof. Ahn gave an invited talk titled "Bridging timescales in protein simulations using Parallelized Gaussian accelerated molecular dynamics (ParGaMD)" at the Special Seminar in Molecular Biology and Chemistry and Biochemistry in UCSD.

November 2024

Congratulations to Maryam for being awarded the 2025 Travel Award from the Biophysical Society to attend the 2025 Biophysical Society Annual Meeting!

October 2024

Prof. Ahn gave an invited talk titled "Bridging timescales in protein simulations using Parallelized Gaussian accelerated molecular dynamics (ParGaMD)" at the GaMD Workshop in UNC Chapel hill and at the Duke Center for HIV Structural Biology.

Prof. Ahn joins the COE AI Center Faculty Advisory Board (https://engineering.ucdavis.edu/ai-experts).

Celeste gave an oral presentation and Parth gave a poster presentation at the AICHE Annual Meeting 2024.

Maryam passed her qualifying exam and became a Ph.D. candidate! Congratulations Maryam!

Celeste gave an oral presentation and Parth gave a poster presentation at the CHMS Research Symposium.

September 2024

Our new paper is out in Journal of Chemical Theory and Computation! https://pubs.acs.org/doi/10.1021/acs.jctc.4c00978

August 2024

Our new paper is out in Nature Communications! https://www.nature.com/articles/s41467-024-50976-9

Celeste passed her qualifying exam and became a Ph.D. candidate! Congratulations Celeste!

July 2024

Siddharth and Prof. Ahn gave a talk titled "Stability and Dynamics of Zeolite-confined Au nanoclusters" at the 2024 Computational Chemistry GRS and GRC, respectively.

Our new paper is out in the Journal of Chemical Physics! https://pubs.aip.org/aip/jcp/article/161/4/046101/3303879/Optimization-of-the-resampling-method-in-the

Our new paper is out in the Journal of Chemical Information and Modeling! https://pubs.acs.org/doi/full/10.1021/acs.jcim.4c00344

 June 2024

We have new undergraduate students joining the lab this quarter, Maxen Hamelynck and Anirud Aiyer. Welcome, Maxen and Anirud!

We have three new Young Scholars Program participants Caleb Sobol, Avni Desai, and Valerie Ta joining the lab this summer. Welcome, Caleb, Avni, and Valerie!

Congratulations Dennis, Celine, and Benjamin for graduating from UC Davis! We'll miss you guys.

May 2024

Parth passed his preliminary exam and became a Ph.D. student! Congratulations Parth!

Siddharth gave a contributed talk and poster presentation at the 2nd Annual Scientific Advisory Board Review for Duke Center for HIV Structural Biology. 

Prof. Ahn participated in the NSF Chemistry Early Career Investigator Workshop.

Siddharth gave a contributed talk titled "Elucidating the fluxionality and dynamics of zeolite-confined Au nanoclusters using machine learning potentials" at the West Coast Theoretical Chemistry 2024 Meeting.

April 2024

Prof. Ahn joins the Biomedical Engineering Graduate Group at UC Davis.

We have a new undergraduate student joining the lab this quarter, Aadit Kohli. Welcome, Aadit!

Prof. Ahn gave an invited talk titled "Bridging timescales between simulations and catalytic and biological processes" at the Chemical Sciences, Geosciences, & Biosciences (CSGB) Sandia National Laboratory PI Meeting.

We have a new undergraduate student joining the lab this quarter, Brandon Choi. Welcome, Brandon!

March 2024

Siddharth passed his qualifying exam and became a Ph.D. candidate! Congratulations Siddharth!

Prof. Ahn was awarded the Collaborative Development Award from the Duke Center for HIV Structural Biology as the main PI for the project “Accelerating pathway sampling in molecular dynamics simulations for HIV-1 immunogen design” ($175,000). https://dhvi.duke.edu/programs-and-centers/duke-center-hiv-structural-biology/funding-opportunities-and-awards

February 2024

The Ahn Lab is featured in the UC Davis College of Engineering news article: https://che.engineering.ucdavis.edu/news/innovative-chemical-engineering-simulations-unveil-breakthroughs-pain-therapy-research

Prof. Ahn joins the Materials Science and Engineering Graduate Group at UC Davis.

We have a new undergraduate student joining the lab this quarter, Lana Abujamil. Welcome, Lana!

January 2024

Prof. Ahn gave an invited talk titled "Bridging timescales between simulations and catalytic and biological processes" in the Dept of Materials Science and Engineering at UC Davis. 

Prof. Ahn gave an invited talk titled "Bridging timescales between simulations and biological processes for computer aided drug discovery" in the Advanced Analytics for Drug Discovery and Development Session at the Korean American Society in Biotech and Pharmaceuticals - San Francisco (KASBP-SF) Symposium 2024. Press coverage: https://youtu.be/VLPhWmFW8DA

Prof. Ahn gave an invited talk titled "Bridging timescales between simulations and catalytic and biological processes" in the AMS Special Session on Mathematical Modeling and Simulation of Biomolecular Systems at the Joint Mathematics Meetings (JMM) 2024. 

December 2023

Our new paper is out in the Journal of General Physiology! https://doi.org/10.1085/jgp.202313368

We have a new graduate student joining the lab this quarter, Parth Bandivadekar. Welcome, Parth!

Prof. Ahn gave a seminar titled "Bridging timescales between simulations and catalytic and biological process" in the Dept of Chemical and Biomolecular Engineering at the University of California, Irvine. 

November 2023

Congratulations to Celeste for being awarded the 2024 Travel Award from the Biophysical Society to attend the 2024 Biophysical Society Annual Meeting!

We have a new undergraduate student joining the lab this quarter, Dongkwan So. Welcome, Dongkwan!

Prof. Ahn was awarded 335,000 simulation units by Anton 2 at Pittsburgh Supercomputing Center for the project “Unveiling the mechanism of alpha-synuclein aggregation and prevention with small molecules using molecular dynamics,” which will focus on running long conventional MD simulations to explore alpha-synuclein aggregation and interaction with paramagenetic amyloid ligands (PALs).

October 2023

Congratulations to Tanya, Siddharth, Dennis, and Celeste for giving oral or poster presentations at CHMS Reseon arch Symposium! 

We have a new graduate student rotating from the Dept of Chemistry, Jinho Seo. Welcome, Jinho!

We have a new undergraduate student joining the lab this quarter, Benjamin Arambula Sanchez. Welcome, Benjamin!

August 2023

Prof. Ahn was awarded 9600 GPU node hours by TACC Frontera Pathways for the project “Unveiling the mechanism of alpha-synuclein aggregation and prevention with small molecules using molecular dynamics,” which will focus on enhanced sampling method development and using the new method to explore alpha-synuclein aggregation and interaction with paramagnetic amyloid ligands (PALs).

Prof. Ahn gave a seminar titled "Bridging timescales between simulations and catalytic and biological process" in the Dept of Chemistry at the University of Colorado, Denver. 

Siddharth gave an oral presentation at ACS Fall Meeting 2023 titled "Elucidating the fluxionality and dynamics of zeolite-confined Au nanoclusters using machine learning potentials."

We have a new graduate student from the Dept of Chemistry joining the Ahn Lab, Maryam Foroozmehr. Welcome, Maryam!

July 2023

Siddharth has received 200,000 ACCESS credits from ACCESS Explore for his project titled "Machine learning-based computational methods development to study catalytic and enzyme systems" and Celeste has received 750,000 ACCESS credits from ACCESS Discover for her project titled "Atomic-level molecular dynamics study of paramagnetic amyloid ligands and α-synuclein." Congratulations, Siddharth and Celeste!

June 2023

Prof. Ahn gives a seminar talk titled "Looking through the lens of a computational microscope" at the 2023 University of Science and Technology (UST) Global Mentoring Conference. 

We have two new Young Scholars Program participants Isabella Wu and Alistair King joining the lab this summer. Welcome, Isabella and Alistair!

Congratulations to Tanya for being selected for the AMPAC summer research internship, which will take place in the McDonald-Nandi Lab and the Ahn Lab this summer!

Prof. Ahn participates at the NSF MPS Workshop for Young Investigators.

Prof. Ahn gives a keynote seminar and a career seminar at the 2023 Korean Life Scientists in the Bay Area (KOLIS) Annual Conference.

May 2023

Dennis gives an oral presentation at the WESTPA developers' meeting regarding his equal weight resampler for WE.

Congratulations to Celeste and Siddharth for passing their preliminary exams!

Siddharth gives a 3 minute lightning talk and a poster presentation titled "Elucidating the fluxionality and dynamics of zeolite-confined Au nanoclusters using machine learning potentials" at the CeRCaS Spring Meeting 2023.

Siddharth gives a poster presentation titled "Elucidating the fluxionality and dynamics of zeolite-confined Au nanoclusters using machine learning potentials" at the West Coast Theoretical Chemistry Meeting 2023.

April 2023

Dennis gives a poster presentation at the Undergraduate Research, Scholarship, and Creative Activities Conference at UC Davis regarding his equal weight resampler for WE.

Dennis will start a summer internship at OpenEye, Cadence Molecular Sciences with the Enhanced Sampling team and will work on looking at different integrators for MD simulations! 

Prof. Ahn won the 2023 Synergy Team Research Award with Prof. Qizhi Gong and Prof. John Voss at UC Davis! ($150,000 in total for the team for one year or $50,000 for each PI)

We'll have a new undergraduate student joining the lab this summer, Ethan Vickrey. Welcome, Ethan!

We have a new undergraduate student joining the lab this quarter, Joshua Lew. Welcome, Joshua!

March 2023

Prof. Ahn gives a seminar talk titled "Looking through the lens of a computational microscope" at the K-BioX Global Class Seminar. 

Prof. Ahn gives a seminar talk titled "Building the lens of a computational microscope" at the Mathematical Molecular Biosciences (MMB) Seminar.

Prof. Ahn is featured in the March WISE newsletter from the Biophysics Graduate Group at UC Davis.

Prof. Ahn gives a seminar talk titled "Building the lens of a computational microscope" at the Graduate Group in Applied Mathematics (GGAM) Mini-Conference at UC Davis.

Feb 2023

Prof. Ahn is awarded the UC Davis Research Travel Grant ($800) for the upcoming Biophysical Society 2023 Annual Meeting. Mac Kevin Braza (Amaro lab) will be presenting a poster titled “Full Length APOBEC3B Active Site Opening Mechanism” (Prof. Ahn is a co-first author).

Jan 2023

Our new paper on DeepWEST is out now! https://pubs.acs.org/doi/10.1021/acs.jctc.2c00282

We have a new undergraduate student joining the lab this quarter, Tanya Chettri. Welcome, Tanya!

Workstations have finally arrived for the Ahn lab!

Siddharth gives a talk about the weighted ensemble method (WE) during the weekly Rosetta Brainstorm meetings at UC Davis.

Prof. Ahn gives a seminar talk titled "Looking through the lens of a computational microscope" to the Biophysics Graduate Group at UC Davis.

Dec 2022

Prof. Ahn is featured in an article about new faculty members at the College of Engineering at UC Davis (https://engineering.ucdavis.edu/news/meet-our-new-faculty-0).

Nov 2022

We have two new graduate students joining the lab next quarter, Hung-Yu (Celeste) Wan and Siddharth Sonti. Welcome, Celeste and Siddharth! 

We have a new undergraduate student joining the lab next quarter, Celine Recinos. Welcome, Celine!

Prof. Ahn gives a seminar talk titled "Looking through the lens of a computational microscope" to the Dept of Chemistry at UC Davis.

Prof. Ahn joins the Applied Mathematics Graduate Group at UC Davis (http://appliedmath.ucdavis.edu/blog/welcome-surl-hee-ahn-ggam).

Oct 2022

Our 2021 Gordon Bell Special Prize for COVID-19 Finalist paper is out now! https://journals.sagepub.com/doi/full/10.1177/10943420221128233

We have a new undergraduate student joining the lab this quarter, Dennis Plotnikov. Welcome, Dennis!

Prof. Ahn joins the Biophysics Graduate Group at UC Davis.

Sept 2022

Prof. Ahn, Prof. Jungwon Park and his graduate students are awarded 6674 GPU node hours ($4388.10) by the NSF ACCESS for their project: “Investigating the dissolution of a Pt nanoparticle using molecular dynamics and the weighted ensemble method.”

Prof. Ahn joins the HPC Core Facility Advisory Committee (https://hpc.ucdavis.edu/advisory-committee).

Prof. Ahn gives the keynote lecture at 2022 CHMS Graduate Research Symposium at UC Davis.

Prof. Ahn gives an informal seminar at UCSB to computational groups in the Dept of Chemistry and Dept of Chemical Engineering.

July 2022

Prof. Ahn starts as a new tenure-track assistant professor in the Dept of Chemical Engineering at UC Davis.