RC
R. I. Cukier
Molecular Dynamics SimulationComputer SimulationModels, ChemicalModels, MolecularQuantum TheoryBase Pairingcs.LGElectronsElectron TransportEntropy
On Valency
published · living versionsW_pywrvmmj·v1 · currentpublished
Preprints & journals
79 papers in the corpus · 1967–2024Increasing transformer token length with a Maximum Entropy Principle Method2408.10277v1 · R. I. Cukier2024 · 0 citationsarXiv
Resetting a fixed broken ELBO2312.06828v1 · Robert I. Cukier2023 · 0 citationsarXiv
Machine learning can be used to distinguish protein families and generate new proteins belonging to those families.31703505 · Jin, Chi, Cukier, Robert I2019 · 3 citationsThe Journal of chemical physics. 2019;151(17):175102
Reweighting ensemble probabilities with experimental histogram data constraints using a maximum entropy principle.30579321 · Lou, Hongfeng, Cukier, Robert I2019 · 6 citationsThe Journal of chemical physics. 2018;149(23):234106
Generating Intrinsically Disordered Protein Conformational Ensembles from a Database of Ramachandran Space Pair Residue Probabilities Using a Markov Chain.30204435 · Cukier, Robert I2019 · 17 citationsThe journal of physical chemistry. B. 2018;122(39):9087-9101
Conformational Ensembles Exhibit Extensive Molecular Recognition Features.31459119 · Cukier, Robert I2020 · 3 citationsACS omega. 2018;3(8):9907-9920
Generating intrinsically disordered protein conformational ensembles from a Markov chain.29544285 · Cukier, Robert I2018 · 3 citationsThe Journal of chemical physics. 2018;148(10):105102
Molecular Dynamics of Oxazole Yellow Dye in its Ground and First Excited Electronic States in Solution and when Intercalated in dsDNA.29022340 · Jin, Chi, Cerutti, David, Cukier, Robert I2018 · 3 citationsThe journal of physical chemistry. B. 2017;121(44):10242-10248
Hinge action versus grip in translocation by RNA polymerase.28853995 · Nedialkov, Yuri A, Opron, Kristopher, Caudill, Hailey L et al.2018 · 10 citationsTranscription. 2018;9(1):1-16
A Trigger Sequence in a Leucine Zipper Aids its Dimerization; Simulation Results1708.08093v1 · Robert I. Cukier2017 · 0 citationsarXiv
Conformational transition in signal transduction: metastable states and transition pathways in the activation of a signaling protein.25945797 · Banerjee, Rahul, Yan, Honggao, Cukier, Robert I2016 · 9 citationsThe journal of physical chemistry. B. 2015;119(22):6591-602
Dihedral angle entropy measures for intrinsically disordered proteins.25679039 · Cukier, Robert I2015 · 18 citationsThe journal of physical chemistry. B. 2015;119(9):3621-34
Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details.25550432 · Wang, Beibei, Opron, Kristopher, Burton, Zachary F et al.2015 · 28 citationsNucleic acids research. 2015;43(2):1133-46
Glucose-Promoted Localization Dynamics of Excess Electrons in Aqueous Glucose Solution Revealed by Ab Initio Molecular Dynamics Simulation.26588118 · Liu, Jinxiang, Cukier, Robert I, Bu, Yuxiang et al.2015 · 9 citationsJournal of chemical theory and computation. 2014;10(10):4189-97
Simulations of potentials of mean force for separating a leucine zipper dimer and the basic region of a basic region leucine zipper dimer.25124233 · Cukier, Robert I2015 · 2 citationsThe journal of physical chemistry. B. 2014;118(35):10341-54
Conformational transition of response regulator RR468 in a two-component system signal transduction process.24731214 · Banerjee, Rahul, Yan, Honggao, Cukier, Robert I2015 · 6 citationsThe journal of physical chemistry. B. 2014;118(18):4727-42
Transition paths of Met-enkephalin from Markov state modeling of a molecular dynamics trajectory.24571787 · Banerjee, Rahul, Cukier, Robert I2014 · 9 citationsThe journal of physical chemistry. B. 2014;118(11):2883-95
Variance of a potential of mean force obtained using the weighted histogram analysis method.24175967 · Cukier, Robert I2014 · 5 citationsThe journal of physical chemistry. B. 2013;117(47):14785-96
Bending Vibration-Governed Solvation Dynamics of an Excess Electron in Liquid Acetonitrile Revealed by Ab Initio Molecular Dynamics Simulation.26583391 · Liu, Jinxiang, Cukier, Robert I, Bu, Yuxiang2015 · 10 citationsJournal of chemical theory and computation. 2013;9(11):4727-34
Computational simulation strategies for analysis of multisubunit RNA polymerases.23987500 · Wang, Beibei, Feig, Michael, Cukier, Robert I et al.2014 · 24 citationsChemical reviews. 2013;113(11):8546-66
Excess dielectron in an ionic liquid as a dynamic bipolaron.23521297 · Liu, Jinxiang, Wang, Zhiping, Zhang, Meng et al.2013 · 20 citationsPhysical review letters. 2013;110(10):107602
The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation.23202476 · Nedialkov, Yuri A, Opron, Kristopher, Assaf, Fadi et al.2013 · 38 citationsBiochimica et biophysica acta. 2013;1829(2):187-98
Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase.22676913 · Kireeva, Maria L, Opron, Kristopher, Seibold, Steve A et al.2013 · 39 citationsBMC biophysics. 2012;5:11
Simulations of temperature and salt concentration effects on bZIP, a basic region leucine zipper.22559083 · Cukier, Robert I2012 · 7 citationsThe journal of physical chemistry. B. 2012;116(21):6071-86
Solvation and evolution dynamics of an excess electron in supercritical CO2.23003186 · Wang, Zhiping, Liu, Jinxiang, Zhang, Meng et al.2012 · 20 citationsPhysical review letters. 2012;108(20):207601
Ferreting out correlations from trajectory data.22168728 · Cukier, Robert I2012 · 5 citationsThe Journal of chemical physics. 2011;135(22):225103
A hamiltonian replica exchange method for building protein-protein interfaces applied to a leucine zipper.21280805 · Cukier, Robert I2011 · 7 citationsThe Journal of chemical physics. 2011;134(4):045104
How many atoms are required to characterize accurately trajectory fluctuations of a protein?20590215 · Cukier, Robert I2010 · 1 citationThe Journal of chemical physics. 2010;132(24):245101
Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase.20478425 · Seibold, Steve A, Singh, Badri Nath, Zhang, Chunfen et al.2010 · 39 citationsBiochimica et biophysica acta. 2010;1799(8):575-87
Exploration of the biological micro-surrounding effect on the excited states of the size-expanded fluorescent base x-cytosine in DNA.20175554 · Zhang, Laibin, Chen, Xiaohua, Liu, Haiying et al.2010 · 14 citationsThe journal of physical chemistry. B. 2010;114(10):3726-34
States and migration of an excess electron in a pyridinium-based, room-temperature ionic liquid: an ab initio molecular dynamics simulation exploration.20145852 · Wang, Zhiping, Zhang, Liang, Cukier, Robert I et al.2010 · 29 citationsPhysical chemistry chemical physics : PCCP. 2010;12(8):1854-61
Hamiltonian replica exchange method study of Escherichia coli and Yersinia pestis HPPK.19924845 · Su, Li, Cukier, Robert I2010 · 7 citationsThe journal of physical chemistry. B. 2009;113(50):16197-208
Effect of metal ions on radical type and proton-coupled electron transfer channel: sigma-radical vs pi-radical and sigma-channel vs pi-channel in the imide units.19399771 · Chen, Xiaohua, Xing, Dianxiang, Zhang, Liang et al.2010 · 12 citationsJournal of computational chemistry. 2009;30(16):2694-705
Hamiltonian replica exchange method studies of a leucine zipper dimer.19586073 · Su, Li, Cukier, Robert I2009 · 14 citationsThe journal of physical chemistry. B. 2009;113(28):9595-605
Excess electron solvation in an imidazolium-based room-temperature ionic liquid revealed by ab initio molecular dynamics simulations.19469567 · Wang, Zhiping, Zhang, Liang, Chen, Xiaohua et al.2009 · 39 citationsThe journal of physical chemistry. B. 2009;113(24):8222-6
Hetero-ring-expansion design for adenine-based DNA motifs: evidence from DFT calculations and molecular dynamics simulations.19245224 · Han, Li, Li, Huifang, Cukier, Robert I et al.2009 · 28 citationsThe journal of physical chemistry. B. 2009;113(13):4407-12
An enhanced molecular dynamics study of HPPK-ATP conformation space exploration and ATP binding to HPPK.19191740 · Su, Li, Cukier, Robert I2010 · 9 citationsThe journal of physical chemistry. A. 2009;113(10):2025-35
Apo adenylate kinase encodes its holo form: a principal component and varimax analysis.19159290 · Cukier, Robert I2009 · 24 citationsThe journal of physical chemistry. B. 2009;113(6):1662-72
Absorption and fluorescence emission spectroscopic characters of size-expanded yDNA bases and effect of deoxyribose and base pairing.19159339 · Zhang, Laibin, Li, Huifang, Chen, Xiaohua et al.2009 · 24 citationsThe journal of physical chemistry. B. 2009;113(4):1173-81
Remarkable metal counterion effect on the internucleotide J-couplings and chemical shifts of the N-H...N hydrogen bonds in the W-C base pairs.18598072 · Li, Huifang, Cukier, Robert I, Bu, Yuxiang2008 · 10 citationsThe journal of physical chemistry. B. 2008;112(30):9174-81
Solvation of excess electrons in LiF ionic pair matrix: evidence for a solvated dielectron from ab initio molecular dynamics simulations and calculations.18314971 · Zhang, Liang, Yan, Shihai, Cukier, R I et al.2008 · 20 citationsThe journal of physical chemistry. B. 2008;112(12):3767-72
A molecular dynamics study comparing a wild-type with a multiple drug resistant HIV protease: differences in flap and aspartate 25 cavity dimensions.17623840 · Seibold, Steve A, Cukier, Robert I2007 · 19 citationsProteins. 2007;69(3):551-65
Hamiltonian and distance replica exchange method studies of Met-enkephalin.17918879 · Su, Li, Cukier, Robert I2007 · 20 citationsThe journal of physical chemistry. B. 2007;111(42):12310-21
Ca2+ selectivity of the sarcoplasmic reticulum Ca2+-ATPase at the enzyme-water interface and in the Ca2+ entrance channel.17914795 · Xiang, Feng, Cukier, Robert I, Bu, Yuxiang2007 · 5 citationsThe journal of physical chemistry. B. 2007;111(42):12282-93
Rational design of hetero-ring-expanded guanine analogs with enhanced properties for modified DNA building blocks.17580864 · Zhang, Jinmei, Cukier, Robert I, Bu, Yuxiang2007 · 35 citationsThe journal of physical chemistry. B. 2007;111(28):8335-41
Prostaglandin endoperoxide H synthases: peroxidase hydroperoxide specificity and cyclooxygenase activation.17462992 · Liu, Jiayan, Seibold, Steve A, Rieke, Caroline J et al.2007 · 52 citationsThe Journal of biological chemistry. 2007;282(25):18233-18244
Exploration on regulating factors for proton transfer along hydrogen-bonded water chains.17387667 · Yan, Shihai, Zhang, Liang, Cukier, Robert I et al.2007 · 19 citationsChemphyschem : a European journal of chemical physics and physical chemistry. 2007;8(6):944-54
Theoretical prediction of the p53 gene mutagenic mechanism induced by trans-4-hydroxy-2-nonenal.17439265 · Xing, Dianxiang, Sun, Lixiang, Cukier, Robert I et al.2007 · 10 citationsThe journal of physical chemistry. B. 2007;111(19):5362-71
Catalytic mechanism of guanine deaminase: an ONIOM and molecular dynamics study.17394305 · Yao, Lishan, Cukier, Robert I, Yan, Honggao2007 · 31 citationsThe journal of physical chemistry. B. 2007;111(16):4200-10
Exploration of the Ca2+ interaction modes of the nifedipine calcium channel antagonist.17177225 · Liu, Huichun, Zhang, Liang, Li, Ping et al.2007 · 5 citationsChemphyschem : a European journal of chemical physics and physical chemistry. 2007;8(2):304-14
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