News
2023
Nov 12-17, 2023:
I will be attending SC23 in Denver, CO. I will be giving an updated version of my talk on “Important Considerations When Expanding HPC Cyberinfrastructure” at the VA-HPC booth on Wednesday 3:00-3:30PM local time.
Jul 26, 2023:
Our paper demonstrating how quantum tunneling facilitates water motion across phenanthrene (Phe), a planar three-ring polycyclic aromatic hydrocarbon (PAH) has been published at the prestigious Journal of American Chemical Society. As always, I want to thank co-authors Donatella Loru, Amanda L. Steber, Cristóbal Pérez, Daniel A. Obenchain, Juan C. López, and Melanie Schnell, for completing this impressive work with little input from me in the final stages.
Feb 21, 2023:
Our paper showing that hydration of simple sugars mimicks that of pure water clusters and explaining the implications of that observation has been published at the prestigious PNAS - Proceedings of the National Academy of Sciences. I am thankful to my long-time co-authors Amanda L. Steber, Zbigniew Kisiel, Melanie Schnell and Cristóbal Pérez for the impressive collaboration and for getting the impactful study over the finish line.
2022
Nov 13-18, 2022:
I will be attending SC22 in Dallas, TX. I will look forward to having a productive and enjoyable conference and giving a short 30-minute presentations on “Important Considerations When Expanding HPC Cyberinfrastructure” at the VA-HPC booth.
Sept 1, 2022:
Hopper-AMD is open for general campus use after months of configuration and testing
Mar 1, 2022:
Hopper-AMD, an expansion of the Hopper-Intel cluster that has been in production since early 2021, is fully racked and stacked by our technology partners. It will be configured and put into production over the next few months. This expansion includes some 8500 cores, 125 GPUs all interec
- 90 CPU nodes each with up to 4TB of RAM
- 24 GPU nodes each with 4x A100-80GB GPUs
- 7 GPU nodes for OpenStack each with 3x A40
- 1 NVIDIA DGX A100s each with 8x A100-40GB GPUs
- 2 login nodes
- 2 DTNs
- 1 Samba (SMB/CIFS) server
2021
Jul 26, 2021:
Our study on the non-covalent interactions holding together diflouromethane clusters is published at Angewandte Chemie International Edition. Once again, I am grateful to my collaborators for completing the work when I could not contribute much to the finishing stages due to my GMU HPC responsibilities.
June 23, 2021:
Hopper is open for the general use. Since its initial opening for test users, a few improvements and capabilities have been included:
- it now includes GPU-computing capabilities via an NVIDIA DGX A100 server that has been deployed in Feb/March 2021
- it uses a fast all-flash storage for scratch directories, replacing our older BeeGFS storage
- it uses a distributed storage solution with a mix of HDD, SATA SSDs, and NVMe SSDs for /home directories, replacing our older Gluster storage
Apr 06, 2021:
Our paper studying the microsolvation of polycyclic aromatic hydrocarbons (PAHs) using rotational spectroscopy is published at Physical Chemistry Chemical Physics. I had been too busy with my GMU responsibilities for the final push, but the amazing Donatella Loru, Amanda L. Steber, Pablo Pinacho, Sébastien Gruet, Anouk M. Rijs, Cristóbal Pérez, and Melanie Schnell completed the study. Big thanks to them all for the enjoyable and rewarding collaboration.
Jan 15, 2021:
Hopper, our new HPC cluster is open to a group of test users. It has 3500 Intel Cascade Lake cores, an HDR Infiniband and dual 25Gbpbs network backend, and a combination of BeeGFS and Gluster storage. https://orc.gmu.edu/wp-content/uploads/2020/10/MicrosoftTeams-image-1.jpg It’ll be open for general use in the next few months.
2020
Oct 26, 2020:
My collaboration with my dear friend Prof. Jared Pienkos and his student Sarah McDarmont at University of Tennessee at Chattanooga on “Exploiting a C–F Activation Strategy to Generate Novel Tris (pyrazolyl) methane Ligands” is published at ZAAC - the Journal of Inorganic and General Chemistry. Thanks to Jared and his group for doing all the hard synthesis, characterization, crystallography and writing and allowing me to provide computational support.
July 27, 2020:
I have moved to George Mason University (GMU) in Fairfax, VA to support GMU’s expanding research computing infrastructure and services. I am grateful to College of Charleston (CofC) for two impactful years where we were able to establish an HPC cluster as a campus-wide resource. I am especially thankful for people at the Division of Information Technology (IT) and School of Science and Math (SSM) for their contributions to make it all possible.
Feb 25, 2020:
Our paper on the competition between solvation and aggregation of glycoaldehydes is published at Angewandte Chemie International Edition as a communication. Big thanks to Dr. Cristobal Perez, Dr. Amanda Steber, Prof. Zbigniew Kisiel and Prof. Melanie Schnell for the enjoyable and rewarding collaboration.
Feb 17-18, 2020:
I had an enjoyable and productive time visiting friends and colleagues at Furman University. A collaborative Journal of Visualized Experiments (JoVE) article with Prof. George C. Shields Group will be out in print soon.
2019
Nov 17-22, 2019:
I’ll be attending SC19 in Denver, CO. I look forward to a productive and enjoyable conference.
April 22, 2019:
CofC’s new HPC cluster is full operation. Learn more about it at https://hpc.cofc.edu/docs.
CofC faculty and staff can request an account for themselves or their students following the instuctions here.
April 05, 2019:
CofC’s new HPC cluster is open for testing for a select group of users. Learn more about the cluster here.
Feb 14, 2019:
Our paper on 15-Crown-5 ether and its complexation with water is out in print Phys. Chem. Chem. Phys. as a cover article. Big thanks to Prof. Juan Carlos Lopez for pushing the project forward.
2018
Nov 30, 2018:
A comparison of linear assignment problem (LAP) solvers is available. The takeaways from this exercise will be used to improve ArbAlign and use LAP solvers in developing other useful tools.
Nov 10-17, 2018:
I’ll be attending SC18 in Dallas, TX. I look forward to a productive and enjoyable conference.
Oct 28, 2018:
Arbalign’s source code is now in GitHub. Improvements and new features will be implemented and shared there.
Oct 24, 2018:
An early version of our CofC HPC user guide is online. Big thanks to Wendi Sapp (Oak Ridge National Lab/Sustainable Horizons Institute) and the CADES team at ORNL for sharing the template for this documentation.
July 31, 2018:
I’ve signed on as an NSF XSEDE Campus Champion for the College of Charleston to promote XSEDE resources on campus and help onboarding new researchers.
July 02, 2018:
I’m excited to start a new adventure as an HPC sysadmin and facilitator at College of Charleston! Big thanks to friends and colleagues at Furman for making my last two years very memorable.
Feb 16, 2018:
Our paper on the complexity of (H2O)11 strucuture and potential energy surface is out in print at J. Chem. Theory and Comp..
Feb 15, 2018:
Our paper on the effect of mixing ammonia and amines on sulfate aerosol formation is out in print at J. Phys. Chem. A.. It was selected as ACS Editors’ Choice.
2017
Nov 07, 2017:
Our collaboration with Amanda L. Steber, Cristóbal Pérez, Anouk M. Rijs, Brooks H. Pate, Zbigniew Kisiel, and Melanie Schnell on acenaphthene’s complexation with with water clusters is published at J. Phys. Chem. Lett..
June 26, 2017:
Skylight is fully operational and open to all MERCURY consortium members. Please see the quickstart guide here.
May 29, 2017:
Skylight, our new MERCURY HPC cluster, arrived. You can see its specs here. It was purchased through an NSF-MRI grant and hosted at Clemson University’s datacenter. The cluster is expected to go into full production in June 2017.
April 26, 2017:
Our collaboration with Cristobal Perez, Amanda L. Steber, Anouk M. Rijs, Juan Carlos Lopez, Zbigniew Kisiel and Melanie Schnell on corranulene and its complex with water is published here.
April 11, 2017:
Our paper outlining ArbAlign, a tool for aligning arbitrarily ordered molecules, is published here.
March 13, 2017:
Dr. Temelso is named as a 2017 Foresight Fellow in Computational Chemistry.
2016
Dec 15, 2016:
ArbAlign, our tool for aligning molecules is made publicly available here.
August 01, 2016:
After six wonderful years at Bucknell, our group has moved to Furman University. We are grateful to Bucknell University, our chemistry department colleagues and our many great students for making the last six years enjoyable and productive. Please look for us if you are ever in the Greenville area!
March 18, 2016:
Our collaboration with Prof. Brooks H. Pate (Virginia), Prof. Zbigniew Kisiel(Polish Academy of Sciences), Jeremy O. Richardson(Cambridge/Durham), Adam A. Reid(Cambridge), David J. Wales (Cambridge), Stuart C. Althorpe(Cambridge) on quantum tunneling in water hexamers was published in Science.
You can read the paper, and perspective piece and video describing its significance.
March 12 - 17, 2016:
I attended the 251st ACS National Meeting in San Diego, CA and gave talks on
“Optimal superposition of arbitrarily ordered molecules using the Kuhn-Munkres algorithm”
“Effect of single and multiple types of bases on aerosol formation rates”
March 15, 2016:
Our group was awarded 350,000 SU (core-hours) worth of computer time on NSF’s XSEDE facilites at the San Diego Supercomputing Center (SDSC-Comet) and Texas Advanced Computing Center (TACC-Stampede).
2015
Sept 15, 2015:
Our group was awarded a three-year NSF-RUI grant to study the thermodynamics of secondary aerosol formation. You can find the summary here.
July 23 - 25, 2015:
Our group hosted the 14th MERCURY conference for computational chemistry. It featured six lectures by prominent keynote speakers, an undergraduate poster session and a lot more.
July 23-24, 2015:
Our four students (Bobby Cao, Nana Appiah-Padi, Fern Morrison and Grace Kim) concluded their busy summer by presenting their research findings at the Sigma Xi and MERCURY Poster Session held here at Bucknell University.
May 1, 2015:
Our collaboration with Dr. James Swan on the “Formation of deprotonated 2-imidazoline-4(5)-one product ions in the collision-induced dissociation of some serine-containing dipeptides” was published. You can find the article here.
April 16, 2015:
Our article on “The Importance and Reliability of Small Basis Set CCSD(T) Corrections to MP2 Binding and Relative Energies of Water Clusters” came out online.
March 15, 2015:
Our group was awarded 500,000 SU (core-hours) worth of computer time on NSF’s XSEDE facilites at Texas Advanced Computing Center (TACC-Stampede).
2014
Oct 27, 2014:
Our collaboration with Prof. Brooks H. Pate at the University of Virginia and Prof. Zbigniew Kisiel at the Polish Academy of Sciences on the structure of water nonamers and decamers resulted in paper published in Angewandte Chemie. You can read the article here.
Sept 04, 2014:
Our article on the hydration of the sulfuric acid−Methylamine complex and implications for aerosol formation came out online.
July 24 - 26, 2014:
Our group hosted the 13th MERCURY conference for computational chemistry. It featured six lectures by prominent keynote speakers, an undergraduate poster session and a lot more.
July 24-25, 2014:
Our four students (Joel Mabey, Dechen Yangkyi, Bobby Cao and Nana Appiah-Padi) concluded their busy summer by presenting their research findings at the Sigma Xi and MERCURY Poster Session held here at Bucknell University.
May 19, 2014:
Our group’s undergraduate research program gets underway with two Bucknell students (Joel Mabey and Dechen Yangkyi), and Lewisburg Area HS’s Nana Appiah-Padi and an incoming BUcknell freshman, Bobby Cao as part of Bucknell’s NSF-STEP program.
April 22, 2014:
Our paper entitled “Structural Analysis of Alpha-Fetoprotein (AFP)-like Peptides with Anti- Breast-Cancer Properties” got published.
2013
Oct 01, 2013:
Our article on the structure and thermodynamics of H3O+(H2O)8 clusters came out online.
July 25 - 27, 2013:
Our group hosted the 12th MERCURY conference for computational chemistry. It featured six lectures by prominent keynote speakers, an undergraduate poster session and a lot more.
July 25-26, 2013:
Our three students concluded their busy summer by presenting their research findings at the Sigma Xi and MERCURY Poster Session held here at Bucknell University.
July 22, 2013:
Our benchmark data on water clusters got posted at The Benchmark Energy & Geometry Database (BEGDB).
May 20, 2013:
Our new HPC cluster, Marcy, is fully operational and open to all MERCURY consortium members. Please see the quickstart guide here.
May 14, 2013:
A cover article co-authored by Cristóbal Pérez, Simon Lobsiger, Nathan A. Seifert, Daniel P. Zaleski, and Brooks H. Pate at University of Virginia, Zbigniew Kisiel at the Polish Academy of Sciences and our group came out online. It is entitled “Broadband Fourier transform rotational spectroscopy for structure determination: The water heptamer”
Apr 07 - 11, 2013:
I attended the 245th ACS National Meeting and gave a talk entitled “Better Configurational Sampling Methods for Large Water Clusters”
Apr 01, 2013:
Our group was awarded 500,000 SU (core-hours) worth of computer time on NSF’s XSEDE facilites at the San Diego Supercomputing Center (SDSC-Trestles) and Texas Advanced Computing Center (TACC-Stampede).
Jan 01, 2013:
Our group was awarded 200,000 SU (core-hours) worth of computer time at DOE’s NERSC facilites.
2012
Oct 08 - 12, 2012:
I attended the 31st Annual AAAR (American Association for Aerosol Research) conference in Minneapolis, MN.
August 20, 2012:
Our group was awarded a three-year NSF-RUI grant to study the thermodynamics of secondary aerosol formation.
Aug 19 - 23, 2012:
I attended the 244th ACS National Meeting and gave a talk on “Quantum mechanical study of sulfuric acid hydration and its atmospheric implications”.
July 26 - 28, 2012:
Our group hosted the 11th MERCURY conference for computational chemistry. It featured six lectures by prominent keynote speakers, an undergraduate poster session and a lot more.
July 25, 2012:
Our five students concluded their busy summer by presenting their research findings at the Sigma Xi Poster Session held here at Bucknell University.
May 21, 2012:
We started a 10-week summer research session with five Bucknell students. Judy Phan, Kat Klein, Carla Renner and Danielle Bustos will study the thermodynamics of binary and ternary nucleation of sulfuric acid while Matt Szucs will perform a computational rationalization of collision induced fragmentation of some dipeptides.
May 18, 2012:
Our collaboration with Prof. Brooks H. Pate at the University of Virginia and Prof. Zbigniew Kisiel at the Polish Academy of Sciences resulted in a Science paper. You can read the article and a perspective piece describing its significance. A C&EN summary is available here.
May 1, 2012:
Our paper entitled “Hydration of the Bisulfate Ion: Atmospheric Implications” came out in print.
Mar 10, 2012:
Our paper entitled “Quantum Mechanical Study of Sulfuric Acid Hydration: Atmospheric Implications” came out in print.
2011
Oct 29, 2011:
Our paper on “Benchmark Structures and Binding Energies of Small Water Clusters with Anharmonicity Corrections” came out in print.
Sept 26, 2011:
I joined a Bucknell group for a working visit to IBM’s Watson Research Center in Hawthorne, NY.
Aug 28 - Sep 1, 2011:
I attended the 242nd ACS National Meeting and presented a talk on correcting for vibrational anharmonicity in small water clusters.
July 29, 2011:
Devon Husar, Edgardo Parrilla and Judy Phan presented posters the 10th MERCURY conference for computational chemistry held here at Bucknell University.
July 28-30, 2011:
Our group hosted the 10th MERCURY conference for computational chemistry. It featured six lectures by prominent keynote speakers, an undergraduate poster session and a lot more.
July 25, 2011:
Devon Husar, Edgardo Parrilla and Judy Phan presented posters of their summer research at the Sigma Xi Poster Session held here at Bucknell University.
July 15, 2011:
Our paper on “The Effect of Anharmonicity on Hydrogen-Bonded Systems: The Case of Water Clusters” came out in print.
May 18, 2011:
Three Bucknell students (Devon Husar, Edgardo Parrilla and Judy Phan) have joined our group. They will all be doing research on the thermodynamics of aerosol formation this summer.
April 08, 2011:
Dr. Temelso attended a P3 Workshop at Hope College in Holland, Michigan.
March 18, 2011:
Dr. Shields gave a “Highlands in Chemistry” seminar at Virginia Tech. Both Drs. Shields and Temelso had meaningful discussions with the chemistry faculty and students at Virginia Tech.
2010
Dec 01, 2010:
Our group was awarded 10,000 SU (core-hours) worth of computer time at DOE’s NERSC facilites.
Oct 12, 2010:
I gave a talk entitled “Modeling the growth of water clusters and atmospheric aerosols from first principles” to the Bucknell University Chemistry department.
Aug 22, 2010:
I attended the 240th ACS meeting in Boston, MA where a prominent five-day session entitled “Physical Chemistry of Hydrates, Interfaces, and Aerosols and their Relationship to the Climate System” was the main course.
Aug 02, 2010:
Kaye Archer and Arianne Gauthier presented a poster of their research at the 2010 MERCURY conference at Hamilton College in Clinton, NY.
July 01, 2010:
We have moved to Bucknell University in Lewisburg, PA.
May 24, 2010:
Our group’s undergraduate research program gets underway with two AASU students. Kaye Archer is a senior physics and math major who will study the formation of aerosols. Arianne Gauthier is a rising sophomore who will be working on multi-level studies of breast cancer inhibitor derived from AFPs.
Feb 24, 2010:
Our group attended the 50th Sanibel Symposium on Quantum Theory on St. Simons Island in February 24th - March 1st, 2010. Kaye Archer ‘10 presented “Accurate Predictions of the Structure and Energies of Water Decamers” while Dr. Berhane Temelso presented “Benchmark Quality Structures and Energies for Small Water Clusters.”
2009
Oct 20, 2009:
Our group’s SGI Altix 3700 Bx2 was installed on campus. Pictures and specs are available here.
Aug 24, 2009:
Duong Vo and Brian Redden joined our group for the Fall semester as part of their Honors Chemistry class’s research requirement.
Aug 2-4, 2009:
Our group attended the MERCURY conference held at the campus of Hamilton College in Clinton, NY. Kaye Archer and Amber Kay Barnes presented posters. The conference concludes a productive first summer of research for our group.
July 01, 2009:
Our group was awarded a combined 300,000 SU (core-hours) worth of computer time at 13 TeraGrid computing facilites. The allocation is to be used over a three year span.
June 30, 2009:
Our group ordered an SGI Altix 3700 Bx2 shared memory machine with 128 Itanium2 cores, 640GB RAM and 7.2TB of storage. The purchase is funded by an NSF-MRI grant for the MERCURY consortium. The machine should arrive in a month.
June 15, 2009:
Arianne Gauthier joined our group for a five week period as part of the STEP program. She is an incoming freshman from Rutledge, GA planning on being a pre-med major. Her project will involve searching through protein databases for peptides that resembles our AFPeps and their activity and relationship (if any) to breast cancer inhibition.
May 18, 2009:
Our group’s undergraduate research program gets underway with two AASU students. Kaye Archer is a senior physics and math major who will study the formation of aerosols. Amber Kay Barnes is a sophomore rehabilitation sciences major who will be working on breast cancer inhibitors.
April 15, 2009:
Our group was awarded a combined 50,000 SU (core-hours) worth of computer time at 13 TeraGrid computing facilites. A large portion of our computations this summer will be performed on the TeraGrid.