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York Lab leads an Amber Free Energy Workhsop at San Diego!August 19, 2024 Darrin York, Timothy Giese, Şölen Ekesan, Jinzhe Zeng, Erika McCarthy, Lauren Lerew, Ryan Snyder, Zeke PiskulichLast week Darrin and collaborators Andreas Goetz, Metin Aktulga and Kenny Merz held an Amber Free Energy Workshop in San Diego Supercomputer Center on UCSD campus. | ![]() |
Yujun's paper featured on the cover of JCP!June 13, 2024 Yujun TaoYujun Tao's paper "Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials" got featured on the cover of the volume 160 issue 22 of Journal of Chemical Phsyics. (https://pubs.aip.org/aip/jcp/issue/160/22). Read More | ![]() |
Lauren and Erika present at the RNA Society Meeting in Scotland!June 3, 2024 Erika McCarthy, Lauren LerewLauren Lerew and Erika McCharthy presented their ribozyme work at the RNA Society annual meeting in Edinburgh, Scotland. Read More | ![]() |
Darrin gives an SBGrid webinar at Harvard Medical School!May 21, 2024 Darrin YorkDarrin York gave a virtual talk entitled "Free energy methods in Amber" as part of the SBGrid webinar series of Fall 2024. Read More | ![]() |
Hsu-Chun successfully defended her thesis. Congrats Dr. Tsai!March 13, 2024 Hsu-Chun TsaiHsu-Chun Tsai successfully defended her thesis and got a job offer from Tandem AI, on the same day! Read More | ![]() |
Yujun successfully defends her thesis. Congrats Dr. Tao!March 12, 2024 Yujun TaoYujun Tao successfully defended her thesis and passed her final examination into becoming a PhD, and York Lab was ready to celebrate! Read More | ![]() |
Erika wins 2024 Van Dyke Award. Congratulations Erika!January 12, 2024Erika McCarthy won the 2024 Van Dyke Award, excellence in PhD research in the Chemistry and Chemical Biology department. Read More | ![]() |
Jinzhe wins Reid Award. Congratulations Jinzhe!January 12, 2024Jinzhe Zeng has won the Reid Award, highest honors in PhD research in the Chemistry and Chemical Biology department. Read More | ![]() |
Erika wins 2024 IQB Inclusive Leadership Award!December 11, 2023 Erika McCarthyGraduate student Erika McCarthy was recognized for her outstanding achievements in training and mentorship with the IQB Inclusive Leadership Award. Read More | ![]() |
Darrin's review AFE Methods review is out and featured on the cover (THANKS YUJUN!)November 22, 2023 Darrin York, Yujun TaoDarrin's review on "Modern Alchemical Free Energy Methods for Drug Discovery" is out and featured on the cover of ACS Phys. Chem. Au! Read More | ![]() |
Yujun makes the cover of ACS Environmental Au!September 20, 2023 Yujun Tao
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Yujun and Jinzhe's paper featured on the cover of JCTC!March 10, 2023 Yujun Tao, Jinzhe ZengJinzhe and Yujun's paper "QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery" got featured on the cover of the most recent issue of JCTC. Read More | ![]() |
YorkLab set of "fantastic 4" drug discovery papers just out!January 27, 2023No need to fear, they're here. Just call for four (drug discovery papers), fantastic four: optimized alchemical pathways framework; ACES enhanced sampling; ProFESSA workflow and QDπ machine learning potential. Read More | ![]() |
Jinzhe won 2022-2023 Van Dyke Award for excellence in research!January 10, 2023 Jinzhe ZengCongratulations Jinzhe Zeng on winning the Van Dyke Award for excellence for the 2022-2023 academic year. This $1000 award recognizes graduate students for excellence in research. Read More | ![]() |
York Group graduate students meet Nobel Laureate Frances Arnold!November 16, 2022 Hsu-Chun Tsai, Yujun Tao, Erika McCarthy, Lauren Lerew, Gayatri GaneshanThis year's Aaron J. Shatkin Memorial Lecture at Rutgers University was given by Professor Frances Arnold from Cal Tech, who won the 2018 Nobel Prize in Chemistry for discovering and developing methods of “directed evolution.” York Group members, especially the female graduate students, attended which turned out to be a spectacular lecture, and were super excited to have gotten a chance to meet with and talk to Prof Arnold at the end. Looking forward to meeting many more female chemistry Nobel Laureates! Read More | ![]() |
York Lab shares NSF Cyberinfrastructure for Sustained Scientific Innovation (CSSI)!October 31, 2022 Darrin YorkThe Cyberinfrastructure for Sustained Scientific Innovation (CSSI) program provides funding opportunities for projects that propose to address evolving and emerging needs in cyberinfrastructure. This $3.8 million grant by the National Science Foundation (NSF) will catalyze the work of York Lab at Rutgers University, along with Kenny Merz (MSU), H. Metin Aktulga (MSU), Andreas Goetz (SDSC). Together, the cutting-edge computational expertise and cyberinfrastructure will enable software testing. | ![]() |
Shi got married! Congratulations to Shi & JaiqiSeptember 30, 2022 Shi ZhangOne fall day graduate student Shi Zhang left little red boxes on all York Group members' desks, which to our surprise turned out to be wedding favors. York Group couldn't let Shi get away without the proper York Group outing and ordering ALL the appetizers on the menu! We made sure Shi & Jaiqi were properly celebrated and everyone had a wonderful evening of lots of smiles! Read More | ![]() |
Şölen's best article EVER makes the JPC B cover!August 18, 2022 Şölen Ekesan, Erika McCarthyŞölen Ekesan's work, with contributions by Erika McCarthy, on RNA electrostatics is published in JPC B and featured on the cover of the current issue. The work is going to be part of a forthcoming "Biomolecular Electrostatic Phenomena" special issue, and focuses on electrostatics of nucleic acid enzyme active sites and interactions with metal ions. Read More | ![]() |
Hsu-Chun and Yujun win Reid and van Dyke awards for excellence in researchJanuary 13, 2022 Hsu-Chun Tsai, Yujun TaoGraduate students Hsu-Chun Tsai and Yujun Tao were awarded this year's Reid and Van Dyke Award for Excellence in Research. Both Hsu and Yujun are forth year Ph.D. candidates. Read More | ![]() |
York group book chapter on AMBER drug discovery boost is published!November 19, 2021 Darrin York, Tai-Sung Lee, Timothy Giese, Abir Ganguly, Hsu-Chun TsaiYork group article "Robust, Efficient and Automated Methods for Accurate Prediction of Protein-Ligand Binding Affinities in AMBER Drug Discovery Boost" published in Free Energy Methods in Drug Discovery: Current State and Future Directions. Read More | ![]() |
Jinzhe's first paper with the York Lab is out in JCTC!November 9, 2021 Jinzhe ZengGraduate student Jinzhe Zeng's paper titled "Development of Range-Corrected Deep Learning Potentials for Fast, Accurate Quantum Mechanical/Molecular Mechanical Simulations of Chemical Reactions in Solution", depicting a machine learning procedure to train one QM model to reproduce another (target) QM model is now published in Journal of Chemical Theory and Computation. Jinzhe already has a few other publications but this was his first one with York Lab! Congratulations Jinzhe! Read More | ![]() |
Ken successfully defended his thesis and survived pistols and hammerheads! Congratulations!September 15, 2021 Kenneth KostenbaderKen Kostenbader has defended his thesis in the first ever in-person AND virtual thesis defense by the York Group (thanks again Covid 19!). Ken's public defense was virtually attended by people from around the country and the world, and even included a minute of surprise Swedish. Read More | ![]() |
Tim and Şölen's new paper is featured as the cover of JPC A!May 20, 2021 Timothy Giese, Şölen EkesanTimothy Giese and Şölen's Ekesan's new paper entitled "Extension of the Variational Free Energy Profile and Multistate Bennett Acceptance Ratio Methods for High-Dimensional Potential of Mean Force Profile Analysis" is the cover of the latest issue of The Journal of Physical Chemistry A. Read More | ![]() |
Tim's new paper solves all your relative binding free energies at once!February 2, 2021 Timothy GieseTimothy Giese's latest paper "Variational Method for Networkwide Analysis of Relative Ligand Binding Free Energies with Loop Closure and Experimental Constraints" is published online at JCTC. In this paper Tim lays out the detailed procedure of network-wide free energy calculation. Tim also implemented these methods into FE-ToolKit, which can be downloaded from gitlab. Read More | ![]() |
Hsu receives the Van Dyke Research Award!January 14, 2021 Hsu-Chun TsaiCongratulations to Hsu-Chun for winning the Van Dyke Research Award! She's been carrying out excellent research on alchemical free energy calculations and has co-authored 3 papers in the last year (see our highight on Free Energy Hat Trick). Read More | ![]() |
Emily has a new paper out!December 29, 2020 Emily AtiehEmily Atieh, PhD's latest paper "Beneath the Surface: An Investigation of General Chemistry Students’ Study Skills to Predict Course Outcomes" just came out as ASAP (as soon as publishable) in Journal of Chemical Education Research. Pandemic didn't stop Emily from graduating, moving to a new state and starting her postdoc all the while finishing up manuscripts and publishing papers! Read More | ![]() |
Colin successfully defended his thesis, congratulations!September 10, 2020 Colin GainesColin Gaines has successfully defended his thesis in virtual thesis defense. His research focuses on investigating the structure, dynamics, and reaction mechanism of the twister ribozyme through the use of a variety of computation tools including MD, QM/MM, and Constant pH MD simulations. Read More | ![]() |
York Lab "Hat-Trick" of new free energy papers published!August 27, 2020 Tai-Sung Lee, Timothy Giese, Hsu-Chun Tsai, Yujun TaoThe York Lab, in a series of three recently published papers, have made breakthroughs in the development, validation, and establishment of best practices for GPU-accelerated free energy simulation methods in AMBER. Read More | ![]() |
Emily is Ph.inisheD. after a successful thesis defense! Congratulations!August 27, 2020 Emily AtiehEmily Atieh has successfully defended her thesis in the first ever virtual thesis defense by the York Group (thanks Covid 19!). She gave her public defense to an audience of over 30 people from around the state (and country). Emily's chemistry education research, aside from producing many publications, has also resulted in the development of the Chem-TI Program that provides undergraduates with experience in helping students in General Chemistry, which Emily developed, taught and oversaw throughout her PhD. Emily will be continuing her research efforts as a postdoctoral researcher with... Read More | ![]() |
Emily's paper on Peer Leader Learning Attitudes published in J. Chem. Ed.!July 29, 2020 Emily AtiehGraduate student Emily Atieh's paper, titled "Through the Looking CLASS: When Peer Leader Learning Attitudes Are Not What They Seem", has been published in J. Chem. Educ., and is now available through J. Chem. Educ. website. This paper talks about Teaching Internship which is a credit-bearing program composed of undergraduate near peer instructors (teaching interns, or TIs) that offers supplemental assistance for students in the General Chemistry courses. TIs develop a dual role of student and instructor over time, they afford a unique... Read More | ![]() |
York Lab awarded intramural research grant from the Center for COVID-19 Response and Pandemic Preparedness (CCRP2)July 15, 2020 Darrin York, Abir GangulyThe Center for COVID-19 Response and Pandemic Preparedness announced the biomedical and social science research awardees for COVID-related research at Rutgers University. These 35 COVID-related projects were competitively selected from a diverse pool of over 150 applications across all Chancellor’s Units and are being generously supported by the Offices of the Senior Vice Chancellor for Academic Affairs and Research at RBHS; Provost & Executive Vice Chancellor for Research & Academic Affairs at Rutgers-New Brunswick; Provost & Executive Vice Chancellor for Research & Academic Affairs at Rutgers-Newark; and Senior Vice President for Research and Economic Development. Read More | ![]() |
Darrin is the recipient of the second annual Grossman Innovation PrizeMay 28, 2020 Darrin York, Tai-Sung Lee, Timothy GieseDarrin York, has received the second annual Grossman Innovation Prize from the School of Arts and Sciences. Read the news release to learn how York Lab's research could improve drug development, including for COVID-19, and learn also about Rutgers alumnus Alan Grossman and his support for innovative research. The York team, which also includes Associate Research Professors Timothy Giese and Tai-Sung Lee, will use the Grossman Prize to investigate the use of quantum mechanical force fields... Read More | ![]() |
York lab among first cohort of researchers to gain access to the fastest academic supercomputer in the worldApril 10, 2020 Darrin YorkThe York Lab project was among an elite set of 49 chosen to be awarded allocations on the new NSF-funded Leadership-class computer system designed to be used by the most experienced academic computational scientists in the nation. This recent allocation award provides the York Lab access to the world's most powerful academic supercomputer, Frontera ( | ![]() |
Abir's paper on VS ribozyme published in Nature Chemistry!January 20, 2020 Abir GangulyAbir Ganguly's paper titled "Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme" (or as we like to call it "Abir vs VS") has been published in Nature Chemistry. This collaborative work where theory and experiment team up to tackle down important scientific questions will surely be exemplery. Congratulations to York and Piccirilli Labs, and Abir Ganguly specifically! This paper has also been highlighted in Expert Pitch section of | ![]() |
Colin's paper on RNA enzyme design published in RNA!December 18, 2019 Colin GainesGraduate student Colin Gaines's paper, titled "The L-platform/L-scaffold framework: a blueprint for RNA-cleaving nucleic acid enzyme design", has been published in RNA, and is now available on our Publication page as well as through RNA journal website. This paper develops a framework to serve as a blueprint to facilitate site-specific RNA-cleaving nucleic acid enzyme design. The L-platform/L-scaffold is illustrated to be common to 5 of the 9 currently known naturally occurring ribozyme classes (Twr, HPr, VSr, HHr, Psr), and... Read More | ![]() |
Yujun and Hsu pass their OFRP... Congratulations!December 4, 2019 Hsu-Chun Tsai, Yujun TaoCongratulations to Yujun and Hsu-Chun on passing their Out-of-Field Research Proposals! Read More | ![]() |
Abir's paper has been selected as an ACS Editor's Choice articleOctober 30, 2019 Abir GangulyAbir Ganguly's new paper titled "Evidence for a Catalytic Strategy to Promote Nucleophile Activation in Metal-Dependent RNA-Cleaving Ribozymes and 8-17 DNAzyme" was selected as an ACS Editor's Choice article. This work published in ACS Catalysis compares four nucleic acid enzymes in their way of nucleophile activiation. Read More | ![]() |
Darrin organizes an ACS symposium on integrating theory and experimentAugust 19, 2019 Darrin YorkInterdisciplinary research holds key advantages in addressing modern scientific grand challenges. Funding agencies and institutions recognize the growing need to promote research at the interface of traditional disciplines, and are creating incentives to engage in interdisciplinary research, education and training. However, building effective research strategies and collaborations that span disciplines is not easy. The gap between theory and experiment is one of the most difficult and most vital to bridge. This challenge is particularly important in advancing objectives in biocatalysis. Experiments provide essential information about structure and... Read More | ![]() |
Ken's Paper On The Pistol Ribozyme AcceptedJuly 30, 2019 Kenneth KostenbaderGraduate student Kenneth Kostenbader's paper, titled "Molecular simulations of the pistol ribozyme: unifying the interpretation of experimental data and establishing functional links with the hammerhead ribozyme" has been accepted for publication for the upcoming issue of RNA. Read More | ![]() |
Şölen's crystal paper featured on cover of J. Phys. Chem. BJune 7, 2019 Şölen EkesanŞölen Ekesan’s paper "Framework for Conducting and Analyzing Crystal Simulations of Nucleic Acids to Aid in Modern Force Field Evaluation" is featured on the cover of the June 6th issue of the Journal of Physical Chemistry B. Her paper introduces a framework for B-factor decomposition into additive intramolecular, rotational, and translational atomic fluctuation components, and applies it to a benchmark set of A-DNA, Z-DNA, and B-DNA double helix systems. Read More | ![]() |
York group leads new Ontology for discussion of RNA-cleavage reactions in ACS Chem. Biol.June 5, 2019 Darrin York, Abir Ganguly, Şölen Ekesan, Kenneth Kostenbader, Colin GainesA new ontology for discussion of RNA-cleavage reactions is now available online at the ACS Chemical Biology website. This new ontology, developed by a group of leaders in the field and lead by the York group, aims to clarify conversations on these reactions carried out by protein, RNA, and DNA enzymes by providing a standardized vocabulary. Utilization of this ontology would enable more precise interpretations of mechanisms in the context of structure and bonding. Read More | ![]() |
Şölen selected to receive "Promise in COMP" awardJune 3, 2019 Şölen EkesanDr. Şölen Ekesan was selected as one of the eight young women scientists to receive "Promise in COMP" award at the first ever "Women Make COMP" symposium at the ACS Fall 2019 National Meeting in San Diego, CA. Şölen will be giving a 15-minute talk at the symposium. Read More | ![]() |
Colin Wins Poster Award at Nucleic Acids ConferenceFebruary 15, 2019 Colin GainesColin Gaines was one of the award recipients during the Gala and Poster Awards Ceremony at the 6th Nucleic Acids Conference in the Bahamas. His poster utilized Augmented Reality to display some of his most recent work with ribozymes. Congratulations, Colin! Read More | ![]() |
York Group at the Nucleic Acids Conference!February 13, 2019 Darrin York, Şölen Ekesan, Emily Atieh, Kenneth Kostenbader, Colin GainesGraduate students Colin, Ken, and Emily and post-doc Solen accompanied Professor York to the 6th Nucleic Acids Conference in the Bahamas, hosted by Fusion. Solen gave a fascinating talk on her latest work with DNAzyme, while Colin, Ken, and Emily presented their latest work on their ribozymes. Somehow between all the interesting talks and insightful conversations, the York group managed to get away for a short bit for some much-needed scuba diving! What better way to relieve some stress than to go shark-diving?! Read More | ![]() |
George's JACS paper on Molecular Solvation Theory is now available!January 30, 2019 George GiambaşuGeorge Giambasu's paper, "Predicting Site-Binding Modes of Ions and Water to Nucleic Acids Using Molecular Solvation Theory," has been published in the Journal of the American Chemical Society, and is now available on our Publications page as well as through the JACS website. This paper presents a new means for prediction cation and water site binding to nucleic acids using methods based on the 3D-RISM molecular solvation theory. This site binding plays a role in how nucleic acids fold, react, and function. Read More | ![]() |
Emily Wins Rieman Award for Excellence in TeachingJanuary 18, 2019 Emily AtiehFourth year graduate student Emily L. Atieh was awarded the Rieman Award for Excellence in Teaching during the Rutgers Graduate Student Awards Ceremony. The Rieman Award recognizes exceptional performance in undergraduate teaching, which Emily has demonstrated in running both the Certificate in Chemistry Education program and a Teaching Internship in Chemistry, in addition to her contributions to the implementation of Active Learning recitations in General Chemistry. Read More | ![]() |
Ken Selected to Receive BASF Corporation Catalysts Division FellowshipSeptember 14, 2018 Kenneth KostenbaderGraduate student Ken Kostenbader was selected as the BASF Corporation Catalysts Division Fellow for the 2018-2019 academic year in recognition of his strong academic record, honors, awards, outreach, and other meritorious credentials. Working with the York Group, Ken is engaged in the development of computational methods and molecular simulation tools to study the principles of biocatalysis, with the long-term goal of enabling computational enzyme design for industrially relevant chemical conversions. Read More | ![]() |
Abir wins Best Poster at the Rutgers Postdoctoral Symposium!April 14, 2018 Abir GangulyAbir highlighted his research at the 9th Annual Rutgers Postdoc Symposium, winning "Best Poster" for his presentation titled "Catalysis in Varkud Satellite Ribozyme." It focused on investigating the dynamical structure and catalytic mechanism of the Varkud satellite ribozyme, a catalytic RNA which happens to be by far the largest of the nucleolytic ribozymes. The study was carried out using a variety of advanced computational methods, some of which have been either recently developed or are under active development in the group, that are specifically tailored to study RNA systems. Augmented reality was used to visualize the tertiary structure of the ribozyme and its active site during... Read More | ![]() |
York Group Takes Retreat in Florida Following ACS MeetingMarch 20, 2018 Darrin York, Şölen Ekesan, Emily Atieh, Kenneth KostenbaderAfter the intense activity of the New Orleans ACS meeting, the York group had a retreat to North Florida, near Gainesville, the homes of UFL collaborators Adrian Roitberg and Michael Harris who joined in discussions. As a result, the York lab has initiated new collaborative projects that will be ongoing and require more regular meetings. The retreat itself combined discussions, brainstorming sessions, and team-building activities (AGENDA). The outcome is that the group has developed a strategic plan with specific goals and set... Read More | ![]() |
LBSR Makes a Big Impact at the 255th ACS Meeting in New OrleansMarch 17, 2018 Darrin York, Tai-Sung Lee, Abir Ganguly, Şölen Ekesan, Emily Atieh, Kenneth Kostenbader, Colin GainesThe Laboratory for Biomolecular Simulation Research made a big impact at the recent 255th American Chemical Society National Meeting in New Orleans, LA (Mar. 18-22, 2018). Special highlights include: Read More | ![]() |
New GPU-accelerated free energy method in JCTCFebruary 7, 2018 Darrin York, Timothy GieseTimothy Giese and Darrin York have published a new paper that reports a GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method in the Journal of Chemical Theory and Computation. The method has the practical advantage that no modification of the main MD code is required to propagate the dynamics, enabling all the performance benefits of GPU-acceleration to be realized, in addition to unlocking the full spectrum of features available within the MD software, such as Hamiltonian replica exchange (HREM). Read More | ![]() |
Ken and Emily Win Van Dyke Award for Excellence in ResearchJanuary 11, 2018 Emily Atieh, Kenneth KostenbaderGraduate students Ken Kostenbader and Emily Atieh were both awarded the Van Dyke Award for Excellence in Research during the Rutgers Graduate Student Awards Ceremony. Both Ken and Emily are third year Ph.D. candidates. Read More | ![]() |
Colin wins Reid Award for Outstanding Accomplishments in Doctoral ResearchJanuary 11, 2018 Colin GainesGraduate student Colin Gaines was selected among three other graduate students in the Rutgers Chemistry Department to receive the distinguished Reid Award for Outstanding Accomplishments in Doctoral Research. This award included a talk by Colin, titled "Computational RNA Enzymology: Unraveling the Catalytic Mechanism of the Twister Ribozyme." Read More | ![]() |
Emily Atieh Publishes Book Chapter in ACS Symposium SeriesNovember 20, 2017 Emily AtiehEmily Atieh has her book chapter published in the ACS Symposium Series, "Online Course Development and the Effect on the On-Campus Classroom." The chapter, titled "Creation of Academic Social Networks (ASNs) for Effective Online eLearning Communities," discusses the development and use of our own in-house eLearning system. This eLearning system has been used to deliver individual quizzes, homeworks, practice assignments, and other activities to our chemistry students, along with providing a means for offering online recitations. More recently, it has been used to connect students in a purposeful way to encourage cooperative learning and study group formation. Read More | ![]() |
Colin Gaines has paper accepted into Angewandte ChemieAugust 7, 2017 Colin GainesGraduate student Colin Gaines has his paper accepted into Angewandte Chemie! This paper is titled "Model for the Functional Active State of the TS Ribozyme from Molecular Simulation" and discusses the use of MD simulations and molecular solvation theory to predict a key structural rearrangement of the twister-sister (TS) ribozyme crystal structure. From this rearrangement, two distinct models for the active state of this ribozyme in solution were developed, both of which were consistent with the available functional data. A number of testable predictions for refining the mechanistic model are also discussed, further demonstrating the need for collaboration between computation and... Read More | ![]() |
Darrin York to give Closing Plenary Talk at QM/MM Methods and Applications conference At University of ManchesterJuly 21, 2017 Darrin YorkDarrin York will be delivering the closing Plenary talk at the QM/MM Methods and Applications: Probing complex systems in biology and materials conference at the University of Manchester, UK. The title of this talk is "Insights into the amazing world of RNA catalysis from hybrid quantum mechanical/molecular mechanical simulations." An abstract can be found below. Read More | ![]() |
Darrin York attends CHARMM Developers Meeting at Harvard UniversityJuly 16, 2017 Darrin YorkDarrin York attended the CHARMM Developers Meeting at Harvard University this weekend. CHARMM is maintained by a group of developers, led by 2013 Nobel Prize winner Martin Karplus. Read More | ![]() |
New GPU-accelerated pmemdGTI module offers over 2 orders of magnitude speedup in free energy calculationsJuly 5, 2017 Darrin York, Tai-Sung Lee, Brad Sherborne, Yuan Hu, Zhuyan GuoNew in the AMBER pipeline: GPU-accelerated Thermodynamic Integration free energy method for fast and accurate protein-ligand binding affinity prediction. Read More | ![]() |
Emily Atieh Presents at the Chemistry Education Research Conference at Miami UniversityJuly 3, 2017 Emily AtiehEmily Atieh attended the Graduate Student/Post-Doc Chemistry Education Research Conference at Miami University in Oxford, Ohio. The title of the presentation was "Implementation and Evaluation of an Undergraduate Certificate in Chemistry Education Program." This was the fourth time this conference has been held, and it is hosted by Dr. Stacey Lowery Bretz, a faculty member in the Department of Chemistry and Biochemistry at Miami. The conference included CER students from all around the U.S. and Canada. It featured a series of professional development workshops and plenary talks about current research. More information about the conference can be found here: Read More | ![]() |
Darrin York Gives Opening Plenary Lecture at TheoBio17 in San Sebastian, SpainJune 30, 2017 Darrin YorkDarrin York attended TheoBio17 in Donostia/San Sebastian, Basque Country Spain from June 26-June 30. His plenary talk was titled "Diverse Catalytic Strategies of RNA Enzymes: Recurring Themes and New Twists." The scope of this congress is on the modeling of biological, biochemical and biophysical systems, ranging from electronic structure to mesoscopic coarse grained systems and beyond from both an application and a methodological point of view. More information about this meeting can be found at their website: http://theobio17.dipc.org/ Read More | ![]() |
Ken Kostenbader Wins Duff Travel AwardMay 25, 2017 Kenneth KostenbaderGraduate student Ken Kostenbader has been awarded a Thomas Duff Travel Award to present at the American Chemical Society National Meeting next Spring of 2018. The conference will take place in New Orleans, LA. This research talk will be on his work with Pistol Ribozyme. Read More | ![]() |
Emily Atieh attends AAAS-CASE Workshop in Washington D.C.April 5, 2017 Emily AtiehGraduate Student Emily Atieh attends the CASE Workshop (Catalyzing Advocacy of Science and Engineering) in Washington, D.C., sponsored by the American Association for the Advancement of Science. Two graduate students were selected from several participating universities based on their application and qualifications. This workshop featured a series of talks and training from members of all levels of the federal govnement, including the Office of Management and Budget (OMB) and the Office of Science and Technology Policy (OSTP). One talk featured Illinois Rep. Bill Foster, currently the only Congressman to hold a Ph.D. in Physics. Read More | ![]() |
Colin Gaines wins Van Dyke Award for Excellence in ResearchJanuary 19, 2017 Colin GainesYork Graduate Student Colin Gaines was recently awarded the Rutgers Van Dyke Excellence in Research Award. Read More | ![]() |
Emily Atieh Awarded Duff Travel AwardDecember 12, 2016 Emily AtiehGraduate student Emily Atieh has been awarded a Thomas Duff Travel Award to present at the American Chemical Society National Meeting next Fall of 2017. The conference will take place in Washington, D.C. This research talk will be on her work with our peer instructors in General Chemistry: the Teaching Interns. Read More | ![]() |
5th Zing Nucleic Acids ConferenceDecember 5, 2016 Darrin York, Kenneth Kostenbader, Colin Gaines, Junjie OuyangProfessor York and three graduate students - Colin, Ken, and Junjie - attended the 5th Zing Nucleic Acids Conference. Understanding processes involving DNA and RNA at the molecular and chemical level is the central theme of this conference. DNA is a repository of genetic information and must be accurately copied once and only once in each cell cycle. Its integrity is vital to the cell, and it is the only molecule that is repaired if damage occurs. By contrast RNA is the ‘working substance’ of genetics and an extremely versatile molecule. Of course it is the messenger that passes the information between DNA and protein synthesis, yet it does so much more. It is the key component of the... Read More | ![]() |
Darrin York Transforms Teaching in Active Learning ClassroomsNovember 7, 2016 Darrin York, Emily AtiehProfessor Darrin York is one of several faculty members taking advantage of the new Active Learning Classrooms located on the different campuses of Rutgers University. Currently, Professor York teaches two sections of an active learning recitation for the high-enrollment General Chemistry course. Students work in small groups to solve problems, while Professors York and Guerra assist students, along with the Teaching Interns led by Emily Atieh. The new classrooms come equipped with the latest technology and features to facilitate learning and communication, both within groups and between students and faculty. These classrooms are at the heart of some of the latest research into how large,... Read More | ![]() |
Darrin York's Attendance at Solvay Conference in BrusselsOctober 19, 2016 Darrin YorkThe Solvay Conference is among the most famous conference in chemistry and physics, and has been attended by countless Nobel laureates since its beginnings in 1911. The famous photograph, shown to the side here, was taken at the fifth Solvay Conference in 1927, and includes 17 Nobel laureates or future Nobel laureates, out of the 29 attendants. It is hosted in Brussels, Belgium, and this year it was held from October 19th through the 22nd. Darrin York attended this conference to present a talk. A photo of this year's conference is shown on top. Read More | ![]() |
JCP Editor's PickMay 16, 2016 Erich KuechlerErich Kuechler's paper, VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions, has been selected as a JCP Editor's Pick. It will be highlited on the JCP Homepage during the week of May 16th, 2016. Read More | ![]() |
Colin's Paper on Twister Ribozyme Featured in C&ENFebruary 26, 2016 Colin GainesGraduate student Colin Gaines has had his first paper accepted: "Ribozyme Catalysis With A Twist: The Active State Of The Twister Ribozyme In Solution Predicted From Molecular Simulation" Read More | ![]() |
Haoyuan Chen Receives Reid Award for Outstanding Accomplishments in Doctoral ResearchJanuary 27, 2016 Haoyuan ChenCongratulations to our own graduate student, Haoyuan Chen, for receiving the Reid Award and giving a presentation titled "Multi-scale Computer Simulation of RNA" at the 2015 Rutgers University Department of Chemistry and Chemical Biology's Graduate Student Awards Ceremony Read More | ![]() |
Maria Panteva Successfully Defends Thesis!November 11, 2015 Maria PantevaMaria Panteva has successfully defended her thesis, titled "Development and Application of Computational Models to Study Ion-Nucleic Acid Interactions" Read More | |
Erich Kuechler Successfully Defends Thesis!October 21, 2015 Erich KuechlerErich Kuechler successfully defended his thesis on October 21st 2015. His thesis is titled "Charge-dependent non-bonded interaction methods for use in quantum mechanical modeling of condensed phase reactions." Read More | ![]() |
Thakshila Dissanayake Successfully Defends Thesis!September 22, 2015 Thakshila DissanayakeThakshila Dissanayake successfully defends thesis, titled "A multiscale computational approach to study RNase A catalysis" Read More | ![]() |
Darrin York Named New Jersey Professor of the Year!November 20, 2014 Darrin YorkProfessor Darrin M. York has been named the New Jersey Professor of the Year for his innovative solutions to a problem that has plagued large universities like Rutgers for a long time. His creation and direction of an eLearning team and a new software for hosting online recitations (ChIPS) for general chemistry students has been met with great positivity. Read More | ![]() |
Brian Radak Successfully Defends Thesis!September 23, 2014 Brian RadakBrian Radak successfully defended his thesis on September 23, 2014, graduating from the graduate program in Chemical Physics. His thesis is titled "Computational Methods for Understanding RNA Catalysis: A Molecular Approach." Read More | ![]() |
Ming Huang Successfully Defends Thesis!August 4, 2014 Ming HuangMing Huang successfully defended his thesis on August 4, 2014, graduating from the graduate program in Scientific Computation. His thesis is titled "Assessment and Improvement of Computational Models to Study Biological Catalysis" Read More | ![]() |
Faculty Honored for Teaching, Research, Service, and Diversity InitiativesMay 7, 2014 Darrin YorkMembers of the university community who have made outstanding contributions in the classroom, to their disciplines, or for the benefit of the community or world were honored during a May 7 reception at the Rutgers Visitor Center. The Rutgers Faculty Scholar-Teacher Award honors faculty members who have made outstanding contributions in research and teaching. The award recognizes those who bring together scholarly and classroom activities. The award includes a $1,000 honorarium. Read More | ![]() |
Ming's Sugar Pucker Profile Paper Featured on April Cover of JCTC!April 8, 2014 Ming HuangA graphic from the York Group paper "Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods" has been featured on the April cover of the Journal of Chemical Theory and Computation. Read More | ![]() |
Major Changes to Rutgers General Chemistry Course - First Page Headlines!April 7, 2014 Darrin YorkChanges to the overall structure of the Rutgers University general chemistry course have been implemented over the past two semesters, amid the "General Chemistry Problem." This problem refers primarily to the high rate of dropping or failing of the class as a whole. Course coordinator, Dr. Darrin York, has made it his mission to combat the underlying issues, which have included the creation of an online software for the purposes of recitations, office hours, and review sessions. This has resulted in greater student participation, higher attendance rates for recitation, and the ease with which students may attend the review sessions/office hours, which has proved particularly helpful for... Read More | ![]() |
High Achiever Recognition CeremonyFebruary 21, 2014 Darrin YorkRead More | |
Publication: "Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions"February 19, 2014 Darrin York, Timothy Giese, Haoyuan Chen, Ming HuangThis paper marks the second major milestone in the development of a new linear-scaling force fields for mutliscale modeling applications Read More | ![]() |
Darrin York's Talk at the Gordon Research ConferenceFebruary 7, 2014 Darrin YorkRead More | ![]() |
Bringing the "Wow" Factor to Chemistry ClassJanuary 9, 2014 Darrin YorkBoom. Rutgers chemistry Professor Darrin York and lab support specialist Bob Porcja are using in-class demonstrations to get students more interested in an often intimidating subject. York and Porcja design the demonstrations to turn principles they cover in class into something more tangible. They say connecting with the material this way helps students grasp concepts more easily and retain information longer. Read More | ![]() |
Nobel Prize Winner Martin Karplus was Advisor to Three CCB FacultyOctober 9, 2013 Martin KarplusThe Nobel Prize in Chemistry 2013 was awarded jointly to Martin Karplus, Michael Levitt, and Arieh Warshel "for the development of multiscale models for complex chemical systems". The Rutgers Chemistry and Chemical Biology faculty applaud the accomplishments of these three outstanding scientists and their contributions to the Chemical Sciences. Three of the Rutgers Department of Chemistry faculty, Profs.... Read More | ![]() |
20 Years of PME: Symposium Honoring Professor Darrin York, Tom Darden, and Lee G PedersenSeptember 9, 2013 Darrin York, Lee Pedersen, Tom Darden2013 year marks the 20th anniversary of the publication of the first "Particle-mesh Ewald" (PME) paper, which initiated the use of so-called "Fast Ewald" methods in simulations. These methods have computational costs that scale proportionally (linearly) with the size of the molecular system, and for the first time allowed very large macromolecular systems to be simulated stable on long time scales. This methodology revolutionized the ability of computational simulation techniques to model large scale biological systems, such as proteins and especially nucleic acids, where long-range ionic forces have crucial effects on structure and dynamics. The use of fast Ewald methods has enabled the... Read More | ![]() |
Professor Darrin York honored with SAS Award for Distinguished Contribution to Undergraduate EducationMay 9, 2013 Darrin YorkProfessor Darrin York was one of ten faculty members honored this week with the SAS Award for Distinguished Contributions to Undergraduate Education. These awards are presented to faculty members within the School of Arts and Sciences who are recognized for their accomplishments in the area of undergraduate education, both within and beyond the classroom. Read More | |
Introducing a Novel E-Learning System Targeting Better Education for Students in the Science IndustriesFebruary 19, 2013 Darrin YorkThe Rutgers University Chemistry and Chemical Biology Department is quickly moving forward with a novel e-learning system that could transform the way students learn chemistry at universities and grade schools nationwide, while helping educators fill the void for better trained personnel in the science industries. Read More | ![]() |
Reaction Path and Transition States for RNA Transphosphorylation ModelsJanuary 16, 2012 Darrin York, Joseph Piccirilli, Kin-Yiu Wong, Michael HarrisUnderstanding the mechanisms underlying the catalytic properties of RNA have applications in the design of new biotechnology, and are also implicated in the evolutionary origins of life itself. Isotopic labels provide powerful and sensitive experimental probes to fingerprint the nature of transition states in biochemical reactions, which in turn can characterize different reaction mechanisms, particularly with the aid of first-principles calculations from fundamental physical laws in quantum mechanics. Read More | ![]() |
Molecules of RNA Form Biological CatalystsJanuary 1, 2011 Darrin York, Tai-Sung LeeIt is a fundamental question as to how molecules of RNA, with its limited chemical repertoire of fairly inert nucleotide units, are able to form biological catalysts that can speed up reaction rates by 10 million-fold or more. The answer to these questions have implications into the origins of life itself which may well have started from ribonucleic acids in an RNA world. Read More |