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Our Mission
We develop computational tools for probing various quantum mechanical phenomena in complex environments. Currently, we are especially interested in (1) free energy simulation of enzyme and solution-phase reactions; and (2) the modeling of photochemical and photophysical processes in solution, macromolecular environment, and photon cavities.
Group News
December 2024, A warm welcome to Alberto dos Santos, a talented new postdoc, to our group.
December 2024, Congratulations to Richard Van on the the publication of his Biochemistry paper on Cas9 HNH catalysis with Dr. Rajan and other collaborators.
December 2024, Congratulations to Xinwei Ji (a former visiting undergraduate student), Zheng Pei, and our collaborators, Mr. Junjie Yang, Dr. Binju Wang and Dr. Yuezhi Mao, on the acceptance of a manuscript on "On the Entanglement of Chromophore and Solvent Orbitals" by the Journal of Chemical Physics. The paper was selected as the Editor's Pick.
September 2024, A warm welcome to Dr. Ye Mei, who visits our group again after a 5-year break.
July 2024, A warm welcome to Sanghita Sengupta, a talented new postdoc, to our group.
June 2024, We are fortunate to receive an NIH R35 grant to continue our study of enzyme reactions and bioimaging probes.
April 2024, Congratulations to Xiaoliang Pan, who just joined Vilya. He did 7 years of remarkable postdoctoral work at our group!
December 2023, A warm welcome to Samitha Ranasinghe, a talented graduate student, to our group.
November 2023, Congratulations to Zhu Zou, a joint PhD student with Dr. Zhibo Yang's lab, on passing his PhD defense!
November 2023, Congratulations to Xiaoliang Pan, Chance Lander, Carly Wickizer, Richard Van, and our collaborators, Dr. Yuezhi Mao, Dr. Ye Mei, and Dr. Jingzhi Pu, for the acceptance of a manuscript on our Colab Tutorial on Machine Learning Potential by the Journal of Computational Chemistry.
October 2023, Congratutions to Xiaoliang Pan and our collaborators, whose manuscript on enzyme reaction free energy barrier decomposition was accepted by the Journal of Chemical Theory and Computation.
July 2023, Our joint project with Dr. Pengfei Huo's group at the University of Rochester on polariton chemistry software development is funded by NSF.
April 2023, Congratulations to Songyuan Yao, who successfully defensed his Ph.D. dissertation. Two very productive years!
April 2023, Congratulations to Carly Wickizer on receiving the NSF Graduate Research Fellowship Program award.
April 2023, Congratulation to our collaborators, Xintian Feng of Q-Chem, Kwangho Nam of UT Arlington, and Dan Major of Bar Ilan University on receiving a joint NIH SBIR Phase II grant with our group.
March 2023, Congratulations to Carly Wickizer and Chance Lander on the passing of their general examinations.
January 2023, Welcome back, Zheng Pei, to become a postdoc in the group.
January 2023, Congratulations to Songyuan Yao, Richard Van, Xiaoliang Pan, and our collaborators on the publication of our work on the training of machine learning potentials for use as implicit solvent models in RSC Advances. This work started a few years ago in one of Dr. Ye Mei's visits.
October 2022, Kudos to Richard Van on the release of our tutorial on AlphaFold, RoseTTAFold, and OmegaFold on the Software section of our webpage.
October 2022, Congratulations to Zheng Pei, a former visiting student from our collaborator Wanzhen Liang's group, on the publication of the analytical calculation of DIM/QM Raman spectra of molecules adsorbed to metal nanoclusters on the Journal of Chemical Physics.
September 2022, Congratulations to Ryan Snyder and Byrant Kim, both from our collaborator Jingzhi Pu's group, for their excellent work on the use of Gaussian process regression to faciliate ai-QM/MM-quality reaction free energy simulations, which appeared in an article in Physical Chemistry Chemical Physics. It was designated as a 2022 HOT PCCP article!
August 2022, Congratulations to Ken Nicholas (our colleague at OU) and Chance Lander on the acceptance of a paper on potential organometallic catalysts for nitrous oxide decomposition by Inorganic Chemistry.
August 2022, Congratulations to Chance Lander, Vardhan Satalkar, Junjie Yang and our collaborators on the acceptance of a paper on the electron density changes in chemical reactions by Molecular Physics. It will be part of a Special Issue dedicated to Prof. Peter Gill.
July 2022, Yihan was promoted to Associate Professor of Chemistry and Biochemistry with tenure.
Spring 2022, We would like to invite you to listen to presentations from the seminar series on "Theory and Simulation of Electronic and Optical Processes in Molecules and Materials".
May 2022, Congratulations to Xiaoliang Pan,Richard Van and our collaborators (Evgeny Epifanovsky, Jian Liu, Jingzhi Pu, and Kwangho Nam) on the acceptance of a paper on multiple timestep simulations by the Journal of Physical Chemistry.
May 2022, Congratulations to Vardhan Satalkar and other many collaborators (Enrico Benassi, Yuezhi Mao, Chongzhao Ran, and Xiaoyuan Chen) on the acceptance of a paper on the modeling of oxyluciferin analogs by the Journal of Photochemistry & Photobiology, A.
March 2022, Congratulations to Junjie Yang, Zheng Pei, Erick Calderon Leon, and Carly Wickizer on the acceptance of our cQED-TDDFT gradient paper by the Journal of Chemical Physics. Go Polaritons!
February 2022, Congratulations to George Richter-Addo and Jennifer Londono, our collaborators on their publication on the study of a unique intermolecular H-bond between N-hydroxyaminphetamine with iron porphyrin.
January 2022, Welcome to Carly Wickizer and Chance Lander, two very talented graduate student to the group.
October 2021, Congratulations to Qi Ou, our collaborator whose paper on triplet exciton-photon coupling has been published by JACS.
September 3, 2021, Farewell to Junjie Yang, who is transferring to Caltech. Two very productive years! Among other achievements, Junjie laid down the QED-TDDFT theoretical framework for studying molecular polarities and assisted Xiaoliang with the development of machine-learning potential of enzyme systems.
September 2, 2021, Congratulations to Vardhan Satalkar, who successfully defended his PhD thesis. Five very productive years! Among other achievements, Vardhan substantially enhanced our understanding of the substituent effect on the spectroscopic properties of chromophores and on the energetics of chemical reactions.
September 1, 2021, Our joint project with Dr. Zhibo Yang's group on the study of spin-crossing reactions has started with NSF funding. It builds on solid progresses made previously by Yunwen Tao, Zheng Pei, and Zhu Zou.
August 2021, Congratulations to Xiaoliang Pan on the acceptance of his paper on machine learning modeling of enzyme simulations by JCTC.
August 2021, Congratulations to Junjie Yang, whose paper on QED-TDDFT method for studying polariton chemistry has been published by JCP and designated as Editor's Pick.
June 2021, Welcome to Chance Lander, an incoming graduate student, to carry out Computational Chemistry research on Ken Nicholas scholarship.
June 2021, Welcome to Syed Aslam, a high-school student in Norman, to carry out summer research in our lab.
June 2021, Welcome to Catherine Hill to join our lab as an undergraduate researcher.
March 2021, Congratulations to Zheng Pei, Junjie Yang and our collaborators on the new JPCL publication on our first work on TADF molecules.
February 2021, Congratulations to our collaborator Bin Wang on the new JPCC publication on the modeling of plasmon-induced CO2 conversion.
February 2021, Congratulations to our collaborator Ye Mei on the new JCTC publication on adaptive QM/MM free energy simulations.
January 2021, Congratulations to Xiaoliang Pan on the new JCP publication of a fast QM/MM electrostatics algorithm.
October 2020, Farewell to Zheng Pei, who returns to Xiamen University after a productive two-year visit.
October 2020. Congratulations to Junjie Yangand Zheng Pei, for the acceptance of two manuscripts on the energy density in LR-TDDFTand RT-TDDFT calculations by PCCP.
September 2020: Congratulations to Chongzhao Ran, our collaborator, for the publication of a report on a chemiluminescence probe for AD research in Nat. Commun.
February 2020: Congratulations to Richard Van, who won OU Provost's Certificate in Teaching. Only the top 10% of graduate teaching assistants across the campus are honored with the award.
February 2020: We welcome Vale Cofer-Shabica, who visits us from the Subotnik group at UPenn.
December 2019: Congratulations to our collaborators, Drs. Ville Kaila, Dage Sundholm, and Ye Mei, on the publication of our TDDFT benchmarking paper.
November 2019: Congratulations to Yunwen Tao (a former postdoc), Zheng Pei (a visiting student from Xiamen University) and Yuezhi Mao (a collaborator at Stanford), whose paper on the modeling of spin-crossing reactions was accepted by IJQC.
October 2019: Dr. Ulrich Hansmann, Dr. Bin Wang and Yihan hosted the 2019 Southwestern Theoretical and Computational Chemistry meeting from October 25 to 27. Thirty-two speakers and over thirty poster presenters shared their latest breakthroughs at the meeting.
October 2019: Xiaoliang Pan's recent paper was selected as one of the 2019 PCCP HOT Articles.
August 2019: Congratulations to Xiaoliang Pan, whose paper on accelerated enzyme reaction free energy calculations was accepted by PCCP.
August 2019: Congratulations to Dr. David Colby (our collaborator at the University of Mississippi) and Erica Luong (an undergraduate student) on the publication of a JOC paper on the amazing selective C--C bond cleavage in pentafluoro aryl geminal diols.
May 2019: Farewell to Yunwen Tao, who returns to SMU to work with Elfi Kraka, a leading quantum chemist.
April 2019: Congratulations to Zheng Pei, who won the best student poster award at the ACS National Meeting at Orlando.
January 2019: Our paper on the computation of absorption/emission spectra of CRANAD molecules (fluorophores for AD research) was accepted by Theoretical Chemistry Accounts. Congratulations to co-first-authors, Vardhan Satalkar and (former rotation student) Theo Rusmore.
January 2019: Welcome to Yunwen Tao, who will be a postdoc in our group in the next five months.
December 2018: Farewell to Genwei Zhang, who has been super productive in our group. Genwei will join the Pentelute group at MIT as a postdoc.
September 2018: Three papers were published in the QM/MM special issue of Molecules. Congratulations to Xiaoliang Pan and our collaborators, Ye Mei and Junming Ho.
September 2018: Our paper on the substitution effect on frontier orbitals of conjugated moleculeswas accepted by Chemical Science. Congratulations to our collaborators, Yuezhi Mao and Martin Head-Gordon.
September 2018: Farewell to Junjie Yang (an undergraduate student from Nanjing University), who had a very productive visit to our group for two months.
September 2018: Congratulations to Vardhan Satalkar, who passed his general exam!
September 2018: Welcome to Micheal Nguyenand Richard Van, two undergraduate students, to our group.
September 2018: Welcome to Zheng Pei (a PhD student from Xiamen University), who will visit us for one year.
June 2018: Yihan was selected as one of the 2018 Ralph E. Powe Junior Faculty Enhancement Award Winners.
May 2018: Congratulations to Nathaniel and Jacobwho made excellent poster presentations on their FYRE (first-year research experience) research! Jacob won one of the best FYRE posters award.
March 2018: Jingheng, Xiaoliang, and Vardhanmade poster presentations at the Austin Symposium.
February 2018: A joint paper with Dr. Zhibo Yang's group on "Towards Enhanced Metabolomic Data Analysis of Mass Spectrometry Image: Multivariate Curve Resolution and Machine Learning" was accepted by Analytica Chimica Acta. Congratulations to Xiang Tian (from Dr. Yang's lab) and Genwei for their great work.
February 2018: Welcome to Prof. Jing Huang, who visits us from Westlake University in China.
January 2018: Welcome to Dr. Yuezhi Mao, who visits us from UC Berkeley.
January 2018: Welcome to new FYRE students, Harsh Bhakta, Nathaniel Gunter, and Jacob Moser!
December 2017: Welcome to new graduate students, Jingheng Deng and Zhu Zou! Zhu is a joint student with Dr. Zhibo Yang's group.
October 2017: Congratulations to our collaborator, Dr. Chongzhao Ran of Massachusetts General Hospital, for a new PNAS publication on near-infrared fluorescence probes for studying reactive oxygen species in Alzheimer's diseases.
September 2017: Welcome to Prof. Ye Mei, who visits us from East China Normal University.
June 2017: Welcome to Dr. Genwei Zhang, a joint master student with Dr. Zhibo Yang's group.
May 2017: Congratulations to Erica Luong and John Alberse who have completed (fabulous!) research within the OU First-Year Research Experience (FYRE) program. Each presented a poster to the department faculty/students.
April 2017: Our paper on an analysis of energy components in DFT/AMOEBA calculations was accepted by JCTC.
March 2017: We welcomed Dr. Enrico Benassi from Scuola Normale Superiore (Pizza, Italy) for a 4-month visit.
February 2017: We welcomed Alex Zech from the University of Geneva for a 2-week visit.
January 2017: We welcomed John Alberse, Erica Luong (Undergraduate Students), Xiaoliang Pan(Postdoctoral Fellow) and Vardhan Satalkar (Graduate Student) to our group.
January 2017: Our paper on QM/MM polarization energy was accepted by JCTC.
August 2016: Yihan Shao moved to OU.
Our Mission
We develop computational tools for probing various quantum mechanical phenomena in complex environments. Currently, we are especially interested in (1) free energy simulation of enzyme and solution-phase reactions; and (2) the modeling of photochemical and photophysical processes in solution, macromolecular environment, and photon cavities.
2022 GROUP NEWS
August 2022, Congratulations to Ken Nicholas (our colleague at OU) and Chance Lander on the acceptance of a paper on potential organometallic catalysts for nitrous oxide decomposition by Inorganic Chemistry.
August 2022, Congratulations to Chance Lander, Vardhan Satalkar, Junjie Yang and our collaborators on the acceptance of a paper on the electron density changes in chemical reactions by Molecular Physics. It will be part of a Special Issue dedicated to Prof. Peter Gill.
July 2022, Yihan was promoted to Associate Professor of Chemistry and Biochemistry with tenure.
Spring 2022, We would like to invite you to listen to presentations from the seminar series on "Theory and Simulation of Electronic and Optical Processes in Molecules and Materials".
May 2022, Congratulations to Xiaoliang Pan,Richard Van and our collaborators (Evgeny Epifanovsky, Jian Liu, Jingzhi Pu, and Kwangho Nam) on the acceptance of a paper on multiple timestep simulations by the Journal of Physical Chemistry.
May 2022, Congratulations to Vardhan Satalkar and other many collaborators (Enrico Benassi, Yuezhi Mao, Chongzhao Ran, and Xiaoyuan Chen) on the acceptance of a paper on the modeling of oxyluciferin analogs by the Journal of Photochemistry & Photobiology, A.
March 2022, Congratulations to Junjie Yang, Zheng Pei, Erick Calderon Leon, and Carly Wickizer on the acceptance of our cQED-TDDFT gradient paper by the Journal of Chemical Physics. Go Polaritons!
February 2022, Congratulations to George Richter-Addo and Jennifer Londono, our collaborators on their publication on the study of a unique intermolecular H-bond between N-hydroxyaminphetamine with iron porphyrin.
January 2022, Welcome to Carly Wickizer and Chance Lander, two very talented graduate student to the group.
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