Hsu-Chun successfully defended her thesis and got a job offer from Tandem AI, on the same day! 

Yujun Tao successfully defended her thesis and passed her final examination into becoming a PhD, and York Lab was ready to celebrate!

Erika wins 2024 Van Dyke Award, excellence in PhD research in the Chemistry and Chemical Biology department.

Jinzhe Zeng has won the Reid Award, highest honors in PhD research in the Chemistry and Chemical Biology department.

York Lab is looking for GPU programmers for an exciting joint project with NVIDIA and TandemAI
This is an exciting opportunity for a talented scientist to gain valuable experience developing software at the interface of modern free energy simulation and quantum mechanical/artificial intelligence methods. The successful candidate will develop new GPU-accelerated software for alchemical free energy and new AI-enhanced quantum mechanical force fields built using integrated semiempirical density-functional tight-binding and deep-learning neural networks. These methods will be...

Graduate student Erika McCarthy was recognized for her outstanding achievements in training and mentorship with the IQB Inclusive Leadership Award.

Darrin's review on "Modern Alchemical Free Energy Methods for Drug Discovery" is out and featured on the cover of ACS Phys. Chem. Au!
The gorgeous cover image has been created by Yujun Tao.

Jinzhe 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.
The beautiful cover, designed by Yujun Tao, depicts the fusion of density functional electronic structure theory and neural network potentials trained to achieve high accuracy for drug-like molecules to create a first-generation Quantum Deep Potential Interaction (QDπ) model for drug discovery.
To appreciate all the beautiful subtle details the cover really...

No 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.

Congratulations 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.

This 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!

Photo left to right: Frances Arnold, Lauren Lerew, Gayatri Ganeshan, Yujun Tao, Hsu-Chun Tsai, Erika McCarthy

The 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.

You can read more about this award from the media excerpts below:


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One 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!
We congratulate the brave couple for getting married *during* grad school wtih two theses in the future! And wish them all the best!

Şölen 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.

Graduate 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.

The Reid award comes from a chemistry fellowship fund established by the late Dr. Thomas Reid, a Rutgers undergraduate alumnus, who went on to obtain a Ph.D. in Biochemistry and a very successful career as an organic chemist at the 3M Corporation, where he developed the material that is the basis of the ScotchgardTM treatment used in many products.

The Van Dyke Award recognizes full-time graduate students that show excellence in their Ph.D. research. Francis C. Van Dyke was appointed Professor...

York 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.

Graduate 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!

Ken 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.

Timothy 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.

The image is the depiction of an extended variational free energy profile method (vFEP) to compute high-dimensional free energy surfaces for chemical reactions and processes. The analytic representation of the surface enables minimum free energy pathways to be determined and...

Timothy 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.

Congratulations 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). 

The Van Dyke Award recognizes full-time graduate students that show excellence in their Ph.D. research.

Emily 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!

Colin 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.

The 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. 

Emily 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...

Graduate 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...

The 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.

Darrin 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...

The 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 (
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Abir 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 
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Graduate 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...

Congratulations to Yujun and Hsu-Chun on passing their Out-of-Field Research Proposals!

Abir 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.

Interdisciplinary 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...

Graduate 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. 

Şölen 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.

A 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.

Dr. 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.

Colin 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!  

Graduate 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?!

George 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. 

Fourth 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.

Graduate 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.

Abir 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...

After 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...

The 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:

Timothy 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).

Graduate 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.

Graduate 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."

Emily 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.

Graduate 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...

Darrin 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.

Darrin 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. 

New in the AMBER pipeline: GPU-accelerated Thermodynamic Integration free energy method for fast and accurate protein-ligand binding affinity prediction.

Emily 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:

Darrin 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/

Graduate 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.

York Graduate Student Colin Gaines was recently awarded the Rutgers Van Dyke Excellence in Research Award.

Professor 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,...

The 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.

Erich 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.

Graduate 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"

Congratulations 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

Professor 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.

Members 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.

A 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.

Changes 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...

This paper marks the second major milestone in the development of a new linear-scaling force fields for mutliscale modeling applications

Boom. 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.

The 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....

Professor 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.

The 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.