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Colin successfully defended his thesis, congratulations!

September 10, 2020Colin Gaines

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.


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Emily is Ph.inisheD. after a successful thesis defense! Congratulations!

August 27, 2020Emily Atieh

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...
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York Lab "Hat-Trick" of new free energy papers published!

August 27, 2020Tai-Sung Lee, Timothy Giese, Hsu-Chun Tsai, Yujun Tao

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. 


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Emily's paper on Peer Leader Learning Attitudes published in J. Chem. Ed.!

July 29, 2020Emily Atieh

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...
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York Lab awarded intramural research grant from the Center for COVID-19 Response and Pandemic Preparedness (CCRP2)

July 15, 2020Darrin York, Abir Ganguly

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.


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Darrin is the recipient of the second annual Grossman Innovation Prize

May 28, 2020Darrin York, Tai-Sung Lee, Timothy Giese

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...
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York lab among first cohort of researchers to gain access to the fastest academic supercomputer in the world

April 10, 2020Darrin York

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's paper on VS ribozyme published in Nature Chemistry!

January 20, 2020Abir Ganguly

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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Colin's paper on RNA enzyme design published in RNA!

December 18, 2019Colin Gaines

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...
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Yujun and Hsu pass their OFRP... Congratulations!

December 4, 2019Hsu-Chun Tsai, Yujun Tao

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


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Abir's paper has been selected as an ACS Editor's Choice article

October 30, 2019Abir Ganguly

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.


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Darrin organizes an ACS symposium on integrating theory and experiment

August 19, 2019Darrin York

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...
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Ken's Paper On The Pistol Ribozyme Accepted

July 30, 2019Kenneth Kostenbader

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. 


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Şölen's crystal paper featured on cover of J. Phys. Chem. B

June 7, 2019Şölen Ekesan

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.


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York group leads new Ontology for discussion of RNA-cleavage reactions in ACS Chem. Biol.

June 5, 2019Darrin York, Abir Ganguly, Şölen Ekesan, Kenneth Kostenbader, Colin Gaines

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.


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Şölen selected to receive "Promise in COMP" award

June 3, 2019Şölen Ekesan

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.


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Colin Wins Poster Award at Nucleic Acids Conference

February 15, 2019Colin Gaines

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!  


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York Group at the Nucleic Acids Conference!

February 13, 2019Darrin York, Şölen Ekesan, Emily Atieh, Kenneth Kostenbader, Colin Gaines

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?!


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George's JACS paper on Molecular Solvation Theory is now available!

January 30, 2019George Giambaşu

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. 


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Emily Wins Rieman Award for Excellence in Teaching

January 18, 2019Emily Atieh

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.


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Ken Selected to Receive BASF Corporation Catalysts Division Fellowship

September 14, 2018Kenneth Kostenbader

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.


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Abir wins Best Poster at the Rutgers Postdoctoral Symposium!

April 14, 2018Abir Ganguly

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...
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York Group Takes Retreat in Florida Following ACS Meeting

March 20, 2018Darrin York, Şölen Ekesan, Emily Atieh, Kenneth Kostenbader

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...
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LBSR Makes a Big Impact at the 255th ACS Meeting in New Orleans

March 17, 2018Darrin York, Tai-Sung Lee, Abir Ganguly, Şölen Ekesan, Emily Atieh, Kenneth Kostenbader, Colin Gaines

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:


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New GPU-accelerated free energy method in JCTC

February 7, 2018Darrin York, Timothy Giese

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).


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Colin wins Reid Award for Outstanding Accomplishments in Doctoral Research

January 11, 2018Colin Gaines

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."


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Ken and Emily Win Van Dyke Award for Excellence in Research

January 11, 2018Emily Atieh, Kenneth Kostenbader

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.


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Emily Atieh Publishes Book Chapter in ACS Symposium Series

November 20, 2017Emily Atieh

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.


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Colin Gaines has paper accepted into Angewandte Chemie

August 7, 2017Colin Gaines

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...
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Darrin York to give Closing Plenary Talk at QM/MM Methods and Applications conference At University of Manchester

July 21, 2017Darrin York

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.


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Darrin York attends CHARMM Developers Meeting at Harvard University

July 16, 2017Darrin York

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


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New GPU-accelerated pmemdGTI module offers over 2 orders of magnitude speedup in free energy calculations

July 5, 2017Darrin York, Tai-Sung Lee, Brad Sherborne, Yuan Hu, Zhuyan Guo

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


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Emily Atieh Presents at the Chemistry Education Research Conference at Miami University

July 3, 2017Emily Atieh

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:


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Darrin York Gives Opening Plenary Lecture at TheoBio17 in San Sebastian, Spain

June 30, 2017Darrin York

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/


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Ken Kostenbader Wins Duff Travel Award

May 25, 2017Kenneth Kostenbader
Graduate 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.
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Emily Atieh attends AAAS-CASE Workshop in Washington D.C.

April 5, 2017Emily Atieh

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.


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Colin Gaines wins Van Dyke Award for Excellence in Research

January 19, 2017Colin Gaines

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


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Emily Atieh Awarded Duff Travel Award

December 12, 2016Emily Atieh
Graduate 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.
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5th Zing Nucleic Acids Conference

December 5, 2016Darrin York, Kenneth Kostenbader, Colin Gaines, Junjie Ouyang
Professor 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...
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Darrin York Transforms Teaching in Active Learning Classrooms

November 7, 2016Darrin York, Emily Atieh

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,...
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Darrin York's Attendance at Solvay Conference in Brussels

October 19, 2016Darrin York

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.


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JCP Editor's Pick

May 16, 2016Erich Kuechler

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.


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Colin's Paper on Twister Ribozyme Featured in C&EN

February 26, 2016Colin Gaines

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"


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Haoyuan Chen Receives Reid Award for Outstanding Accomplishments in Doctoral Research

January 27, 2016Haoyuan Chen

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


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Maria Panteva Successfully Defends Thesis!

November 11, 2015Maria Panteva
Maria Panteva has successfully defended her thesis, titled "Development and Application of Computational Models to Study Ion-Nucleic Acid Interactions"
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Erich Kuechler Successfully Defends Thesis!

October 21, 2015Erich Kuechler
Erich 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."
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Thakshila Dissanayake Successfully Defends Thesis!

September 22, 2015Thakshila Dissanayake
Thakshila Dissanayake successfully defends thesis, titled "A multiscale computational approach to study RNase A catalysis"
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Darrin York Named New Jersey Professor of the Year!

November 20, 2014Darrin York

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.


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Brian Radak Successfully Defends Thesis!

September 23, 2014Brian Radak
Brian 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."
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Ming Huang Successfully Defends Thesis!

August 4, 2014Ming Huang
Ming 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"
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Faculty Honored for Teaching, Research, Service, and Diversity Initiatives

May 7, 2014Darrin York

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.


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Ming's Sugar Pucker Profile Paper Featured on April Cover of JCTC!

April 8, 2014Ming Huang

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.


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Major Changes to Rutgers General Chemistry Course - First Page Headlines!

April 7, 2014Darrin York

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...
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High Achiever Recognition Ceremony

February 21, 2014Darrin York

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Publication: "Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions"

February 19, 2014Darrin York, Timothy Giese, Haoyuan Chen, Ming Huang

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


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Darrin York's Talk at the Gordon Research Conference

February 7, 2014Darrin York

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Bringing the "Wow" Factor to Chemistry Class

January 9, 2014Darrin York

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.



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Nobel Prize Winner Martin Karplus was Advisor to Three CCB Faculty

October 9, 2013Martin Karplus

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....
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20 Years of PME: Symposium Honoring Professor Darrin York, Tom Darden, and Lee G Pedersen

September 9, 2013Darrin York, Lee Pedersen, Tom Darden
2013 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...
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Professor Darrin York honored with SAS Award for Distinguished Contribution to Undergraduate Education

May 9, 2013Darrin York

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.


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Introducing a Novel E-Learning System Targeting Better Education for Students in the Science Industries

February 19, 2013Darrin York

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.


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Reaction Path and Transition States for RNA Transphosphorylation Models

January 16, 2012Darrin York, Joseph Piccirilli, Kin-Yiu Wong, Michael Harris
Understanding 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.
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Molecules of RNA Form Biological Catalysts

January 1, 2011Darrin York, Tai-Sung Lee
It 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.
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