Şölen Ekesan

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Position: Assistant Research Professor
Education:
BS and MS in Chemical Engineering - Boğaziçi University, Turkey
PhD in Chemistry - Brandeis University, MA
Email: solen.ekesan[at]rutgers.edu
Office: CIPR-308H


About Me:

I'm interested in developing and applying a broad range of advanced models for molecular simulations of biocatalysis, including new hybrid molecular mechanical/quantum mechanical and deep-learning force fields that can be used to aid the interpretation of experiments and make predictions about biological mechanisms. My development work has focused on creation of improved methods for robust determination of free energy surfaces and reaction paths for catalytic mechanisms.  My applied work has been wide-ranging, and included work on simulating molecular crystals of nucleic acids, as well as computational enzymology studies of catalytic nucleic acids such as naturally occurring RNA enzymes (e.g., hammerhead, pistol and HDV ribozymes), and artificially engineered RNA and DNA enzymes (e.g., MTR1 and SAR ribozymes and the 8-17 DNAzyme).  Insight gained from mechanistic studies these systems has allowed me to uncover general principles about the architecture and role of electrostatics in ribozyme active sites that may aid in the design of new nucleic acid biotechnology and therapeutics.




Selected Publications:

RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis


(2022) 126, 5982-5990
DOI: 10.1021/acs.jpcb.2c03727
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Who stole the proton? Suspect general base guanine found with a smoking gun in the pistol ribozyme


(2022) 20, 6216-6230
DOI: 10.1039/d2ob00234e
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Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8–17 DNAzyme in solution


(2019) 47, 10282-10295
DOI: 10.1093/nar/gkz773
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Full Publications:

Surface-Accelerated String Method for Locating Minimum Free Energy Paths

(2024)
DOI: 10.1021/acs.jctc.3c01401
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Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology

(2023) 51, 4508-4518
DOI: 10.1093/nar/gkad260
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Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis

(2023) 145, 2830-2839
DOI: 10.1021/jacs.2c10079
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RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis

(2022) 126, 5982-5990
DOI: 10.1021/acs.jpcb.2c03727
Read More   View Full Article   Download PDF   
Combined QM/MM, Machine Learning Path Integral Approach to Compute Free Energy Profiles and Kinetic Isotope Effects in RNA Cleavage Reactions

(2022) 18, 4304-4317
DOI: 10.1021/acs.jctc.2c00151
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Who stole the proton? Suspect general base guanine found with a smoking gun in the pistol ribozyme

(2022) 20, 6216-6230
DOI: 10.1039/d2ob00234e
Read More   View Full Article   Download PDF   
Development of Range-Corrected Deep Learning Potentials for Fast, Accurate Quantum Mechanical/molecular Mechanical Simulations of Chemical Reactions in Solution

(2021) 17, 6993-7009
DOI: 10.1021/acs.jctc.1c00201
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Extension of the Variational Free Energy Profile and Multistate Bennett Acceptance Ratio Methods for High-Dimensional Potential of Mean Force Profile Analysis

(2021) 125, 4216-4232
DOI: 10.1021/acs.jpca.1c00736
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Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8–17 DNAzyme in solution

(2019) 47, 10282-10295
DOI: 10.1093/nar/gkz773
Read More   View Full Article   Download PDF   
An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes

(2019) 14, 1068-1076
DOI: 10.1021/acschembio.9b00202
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Framework for Conducting and Analyzing Crystal Simulations of Nucleic Acids to Aid in Modern Force Field Evaluation

(2019) 123, 4611-4624
DOI: 10.1021/acs.jpcb.8b11923
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Exchange potentials for semi-classical electrons

(2016) 18, 30748-30753
DOI: 10.1039/C6CP06100A
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Magnetism and Bond Order in Diatomic Molecules Described by Semiclassical Electrons

(2016) 120, 6264-6269
DOI: 10.1021/acs.jpcb.6b02576
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Pointillist rendering of electron charge and spin density suffices to replicate trends in atomic properties

(2015) 471, 20150370
DOI: 10.1098/rspa.2015.0370
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Transferable pseudoclassical electrons for aufbau of atomic ions

(2014) 35, 1159-1164
DOI: 10.1002/jcc.23612
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