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Ioan Andricioaei - Publications

Affiliations: 
Chemistry University of California, Irvine, Irvine, CA 
Area:
Theoretical Chemistry and Biophysics
Website:
http://www.faculty.uci.edu/profile.cfm?faculty_id=5491
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100 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Bogetti AT, Leung JMG, Russo JD, Zhang S, Thompson JP, Saglam AS, Ray D, Mostofian B, Pratt AJ, Abraham RC, Harrison PO, Dudek M, Torrillo PA, DeGrave AJ, Adhikari U, ... ... Andricioaei I, et al. A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0]. Living Journal of Computational Molecular Science. 5. PMID 37200895 DOI: 10.33011/livecoms.5.1.1655  0.74
2023 Prabhakar PR, Ray D, Andricioaei I. Predicting residue cooperativity during protein folding: A combined, molecular dynamics and unsupervised learning approach. The Journal of Chemical Physics. 158: 134108. PMID 37031148 DOI: 10.1063/5.0140113  0.735
2022 Stone SE, Ray D, Andricioaei I. Force-Field-Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA. Journal of Chemical Information and Modeling. PMID 36049242 DOI: 10.1021/acs.jcim.2c00519  0.77
2022 Ray D, Quijano RN, Andricioaei I. Point mutations in SARS-CoV-2 variants induce long-range dynamical perturbations in neutralizing antibodies. Chemical Science. 13: 7224-7239. PMID 35799828 DOI: 10.1039/d2sc00534d  0.682
2021 Ray D, Stone SE, Andricioaei I. Markovian Weighted Ensemble Milestoning (M-WEM): Long-Time Kinetics from Short Trajectories. Journal of Chemical Theory and Computation. PMID 34910499 DOI: 10.1021/acs.jctc.1c00803  0.723
2021 Ray D, Le L, Andricioaei I. Distant residues modulate conformational opening in SARS-CoV-2 spike protein. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34615730 DOI: 10.1073/pnas.2100943118  0.705
2020 Ray D, Gokey T, Mobley DL, Andricioaei I. Kinetics and free energy of ligand dissociation using weighted ensemble milestoning. The Journal of Chemical Physics. 153: 154117. PMID 33092382 DOI: 10.1063/5.0021953  0.72
2020 Ray D, Andricioaei I. Free Energy Landscape and Conformational Kinetics of Hoogsteen Base Pairing in DNA vs. RNA. Biophysical Journal. PMID 32946766 DOI: 10.1016/J.Bpj.2020.08.031  0.785
2020 Ray D, Andricioaei I. Weighted ensemble milestoning (WEM): A combined approach for rare event simulations. The Journal of Chemical Physics. 152: 234114. PMID 32571033 DOI: 10.1063/5.0008028  0.761
2020 Ray D, Andricioaei I. Hoogsteen Base Pairing in DNA vs RNA: Thermodynamics and Kinetics from Enhanced Sampling Simulation and Markov State Modeling Biophysical Journal. 118: 299a-300a. DOI: 10.1016/J.Bpj.2019.11.1697  0.761
2019 Maghsoodi A, Chatterjee A, Andricioaei I, Perkins NC. How the phage T4 injection machinery works including energetics, forces, and dynamic pathway. Proceedings of the National Academy of Sciences of the United States of America. PMID 31767752 DOI: 10.1073/Pnas.1909298116  0.352
2019 Chatterjee A, Maghsoodi A, Perkins NC, Andricioaei I. Elastic continuum stiffness of contractile tail sheaths from molecular dynamics simulations. The Journal of Chemical Physics. 151: 185103. PMID 31731851 DOI: 10.1063/1.5125807  0.405
2018 Grazioli G, Andricioaei I. Advances in milestoning. I. Enhanced sampling via wind-assisted reweighted milestoning (WARM). The Journal of Chemical Physics. 149: 084103. PMID 30193480 DOI: 10.1063/1.5029954  0.349
2018 Grazioli G, Andricioaei I. Advances in milestoning. II. Calculating time-correlation functions from milestoning using stochastic path integrals. The Journal of Chemical Physics. 149: 084104. PMID 30193477 DOI: 10.1063/1.5037482  0.398
2018 Xu Y, McSally J, Andricioaei I, Al-Hashimi HM. Modulation of Hoogsteen dynamics on DNA recognition. Nature Communications. 9: 1473. PMID 29662229 DOI: 10.1038/S41467-018-03516-1  0.455
2017 Grazioli G, Butts CT, Andricioaei I. Automated placement of interfaces in conformational kinetics calculations using machine learning. The Journal of Chemical Physics. 147: 152727. PMID 29055331 DOI: 10.1063/1.4989857  0.327
2017 Maghsoodi A, Chatterjee A, Andricioaei I, Perkins NC. Dynamic Model Exposes the Energetics and Dynamics of the Injection Machinery for Bacteriophage T4. Biophysical Journal. 113: 195-205. PMID 28700918 DOI: 10.1016/J.Bpj.2017.05.029  0.35
2017 Ficici E, Jeong D, Andricioaei I. Electric-Field-Induced Protein Translocation via a Conformational Transition in SecDF: An MD Study. Biophysical Journal. 112: 2520-2528. PMID 28636909 DOI: 10.1016/J.Bpj.2017.04.034  0.367
2016 Zhou H, Kimsey IJ, Nikolova EN, Sathyamoorthy B, Grazioli G, McSally J, Bai T, Wunderlich CH, Kreutz C, Andricioaei I, Al-Hashimi HM. m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs. Nature Structural & Molecular Biology. PMID 27478929 DOI: 10.1038/Nsmb.3270  0.386
2016 Frank AT, Andricioaei I. A Reaction Coordinate-Free Approach to Recovering Kinetics from Potential-Scaled Simulations: Application of Kramers' Rate Theory. The Journal of Physical Chemistry. B. PMID 27220565 DOI: 10.1021/Acs.Jpcb.6B02654  0.673
2016 Maghsoodi A, Chatterjee A, Andricioaei I, Perkins NC. A first model of the dynamics of the bacteriophage T4 injection machinery Journal of Computational and Nonlinear Dynamics. 11. DOI: 10.1115/1.4033554  0.383
2016 Andricioaei I. The Role of Entropy in Explaining Tightly Bend DNA Propensity and Kinetic Barriers to Base Pair Unzipping Biophysical Journal. 110: 566a. DOI: 10.1016/J.Bpj.2015.11.3028  0.486
2016 McSally J, Andricioaei I. Entropy Calculations of Hoogsteen and Watson-Crick Conformations Biophysical Journal. 110: 405a. DOI: 10.1016/J.Bpj.2015.11.2186  0.467
2016 Grazioli G, Andricioaei I. Calculating Watson-Crick to Hoogsteen Transition Kinetics in DNA with Langevin Dynamics and Fokker-Planck Diffusion in Reduced Configuration Space Biophysical Journal. 110: 404a-405a. DOI: 10.1016/J.Bpj.2015.11.2184  0.35
2015 Roy M, Grazioli G, Andricioaei I. Rate turnover in mechano-catalytic coupling: A model and its microscopic origin. The Journal of Chemical Physics. 143: 045105. PMID 26233168 DOI: 10.1063/1.4926664  0.57
2015 Frank AT, Zhang Q, Al-Hashimi HM, Andricioaei I. Slowdown of Interhelical Motions Induces a Glass Transition in RNA. Biophysical Journal. 108: 2876-85. PMID 26083927 DOI: 10.1016/J.Bpj.2015.04.041  0.676
2015 Cournia Z, Allen TW, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete NV, Deckman JT, Delemotte L, Del Val C, Friedman R, Gkeka P, Hege HC, Hénin J, Kasimova MA, et al. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. The Journal of Membrane Biology. 248: 611-40. PMID 26063070 DOI: 10.1007/S00232-015-9802-0  0.728
2015 Ficici E, Andricioaei I, Howorka S. Dendrimers in Nanoscale Confinement: The Interplay between Conformational Change and Nanopore Entrance. Nano Letters. PMID 26053678 DOI: 10.1021/Acs.Nanolett.5B01960  0.347
2015 Ficici E, Andricioaei I. On the Possibility of Facilitated Diffusion of Dendrimers Along DNA. The Journal of Physical Chemistry. B. 119: 6894-904. PMID 25989627 DOI: 10.1021/Acs.Jpcb.5B02090  0.465
2015 Mentes A, Florescu AM, Brunk E, Wereszczynski J, Joyeux M, Andricioaei I. Free-energy landscape and characteristic forces for the initiation of DNA unzipping. Biophysical Journal. 108: 1727-38. PMID 25863064 DOI: 10.1016/J.Bpj.2015.01.025  0.718
2015 Grazioli G, Andricioaei I. A Smoluchowski Equation for Force-Modulated Chemistry in Single Molecule Pulling Experiments Biophysical Journal. 108: 161a. DOI: 10.1016/J.Bpj.2014.11.887  0.334
2014 Bascom G, Andricioaei I. Single-Walled Carbon Nanotubes Modulate the B- to A-DNA Transition. The Journal of Physical Chemistry. C, Nanomaterials and Interfaces. 118: 29441-29447. PMID 25553205 DOI: 10.1021/Jp5081274  0.793
2014 Taranova M, Hirsh AD, Perkins NC, Andricioaei I. Role of microscopic flexibility in tightly curved DNA. The Journal of Physical Chemistry. B. 118: 11028-36. PMID 25155114 DOI: 10.1021/Jp502233U  0.764
2014 Mereuta L, Roy M, Asandei A, Lee JK, Park Y, Andricioaei I, Luchian T. Slowing down single-molecule trafficking through a protein nanopore reveals intermediates for peptide translocation. Scientific Reports. 4: 3885. PMID 24463372 DOI: 10.1038/Srep03885  0.539
2014 Lionberger TA, Vahia A, Hirsh AD, Taranova M, Andricioaei I, Perkins NC, Meyhöfer E, Martin CT. Mechanical Strain Generated by RNA Polymerase during Transcription Initiation can Drive Structural Changes in DNA Topology that Relieve Repression Biophysical Journal. 106: 488a. DOI: 10.1016/J.Bpj.2013.11.4478  0.744
2013 Ucuncuoglu N, Andricioaei I, Sari L. Insights from simulations into the mechanism of human topoisomerase I: explanation for a seeming controversy in experiments. Journal of Molecular Graphics & Modelling. 44: 286-96. PMID 23933704 DOI: 10.1016/J.Jmgm.2013.07.003  0.395
2013 Hirsh AD, Taranova M, Lionberger TA, Lillian TD, Andricioaei I, Perkins NC. Structural ensemble and dynamics of toroidal-like DNA shapes in bacteriophage ϕ29 exit cavity. Biophysical Journal. 104: 2058-67. PMID 23663849 DOI: 10.1016/J.Bpj.2013.03.032  0.763
2013 Jeong D, Andricioaei I. Reconstructing equilibrium entropy and enthalpy profiles from non-equilibrium pulling. The Journal of Chemical Physics. 138: 114110. PMID 23534630 DOI: 10.1063/1.4795236  0.354
2013 Salmon L, Bascom G, Andricioaei I, Al-Hashimi HM. A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed. Journal of the American Chemical Society. 135: 5457-66. PMID 23473378 DOI: 10.1021/Ja400920W  0.782
2013 Frank AT, Horowitz S, Andricioaei I, Al-Hashimi HM. Utility of 1H NMR chemical shifts in determining RNA structure and dynamics. The Journal of Physical Chemistry. B. 117: 2045-52. PMID 23320790 DOI: 10.1021/Jp310863C  0.672
2013 Mills M, Orr BG, Banaszak Holl MM, Andricioaei I. Attractive hydration forces in DNA-dendrimer interactions on the nanometer scale. The Journal of Physical Chemistry. B. 117: 973-81. PMID 23234339 DOI: 10.1021/Jp309616T  0.42
2013 Hirsh AD, Lillian TD, Lionberger TA, Taranova M, Andricioaei I, Perkins NC. A model for highly strained DNA compressed inside a protein cavity Journal of Computational and Nonlinear Dynamics. 8. DOI: 10.1115/1.4007535  0.71
2013 Taranova M, Lionberger TA, Hirsh AD, Perkins NC, Andricioaei I. Transcription on Tangled DNA Biophysical Journal. 104: 585a. DOI: 10.1016/J.Bpj.2012.11.3252  0.751
2013 Roy M, Andricioaei I. A Comparative Study of Mechanical Stability of Circular Permutants during Co-Translocational Unfolding of Proteins through Mitochondrial Pore Biophysical Journal. 104: 399a-400a. DOI: 10.1016/J.Bpj.2012.11.2229  0.573
2013 Ficici E, Andricioaei I. Biomimetic Strategy for Nanoparticle Sliding on DNA Tracks Biophysical Journal. 104: 255a-256a. DOI: 10.1016/J.Bpj.2012.11.1435  0.438
2013 Andricioaei I. Conformational Transitions of Nucleic Acids under External Forces: Computer Simulations and a Stochastic Theory for their Kinetics Biophysical Journal. 104: 16a. DOI: 10.1016/J.Bpj.2012.11.120  0.463
2012 Jose PP, Andricioaei I. Similarities between protein folding and granular jamming. Nature Communications. 3: 1161. PMID 23093180 DOI: 10.1038/Ncomms2177  0.772
2012 Nikolova EN, Bascom GD, Andricioaei I, Al-Hashimi HM. Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations. Biochemistry. 51: 8654-64. PMID 23035755 DOI: 10.1021/Bi3009517  0.804
2012 Mentes A, Kim E, Andricioaei I. Structural and Energetic Details of the DNA-Binding and Cleavage Core of Saccharomyces Cerevisiae Topoisomerases II Linked to DNA through its Active Site Tyrosine Biophysical Journal. 102: 447a. DOI: 10.1016/J.Bpj.2011.11.2448  0.701
2012 Hirsh AD, Taranova M, Lillian TD, Lionberger TA, Andricioaei I, Perkins NC. The Structure and Function of Highly Bent Toroidal DNA in Bacteriophage φ29 Biophysical Journal. 102: 421a-422a. DOI: 10.1016/J.Bpj.2011.11.2305  0.762
2012 Taranova M, Lionberger TA, Hirsh AD, Perkins NC, Andricioaei I. Impact of Bending and Torsional Deformations of DNA on the Function of T7-RNA Polymerase Biophysical Journal. 102: 285a. DOI: 10.1016/J.Bpj.2011.11.1578  0.751
2011 Boughton AP, Nguyen K, Andricioaei I, Chen Z. Interfacial orientation and secondary structure change in tachyplesin I: molecular dynamics and sum frequency generation spectroscopy studies. Langmuir : the Acs Journal of Surfaces and Colloids. 27: 14343-51. PMID 22054114 DOI: 10.1021/La203192C  0.362
2011 Stelzer AC, Frank AT, Kratz JD, Swanson MD, Gonzalez-Hernandez MJ, Lee J, Andricioaei I, Markovitz DM, Al-Hashimi HM. Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble. Nature Chemical Biology. 7: 553-9. PMID 21706033 DOI: 10.1038/Nchembio.596  0.653
2011 Lillian TD, Taranova M, Wereszczynski J, Andricioaei I, Perkins NC. A multiscale dynamic model of DNA supercoil relaxation by topoisomerase IB. Biophysical Journal. 100: 2016-23. PMID 21504738 DOI: 10.1016/J.Bpj.2011.03.003  0.768
2011 Nikolova EN, Kim E, Wise AA, O'Brien PJ, Andricioaei I, Al-Hashimi HM. Transient Hoogsteen base pairs in canonical duplex DNA. Nature. 470: 498-502. PMID 21270796 DOI: 10.1038/Nature09775  0.432
2011 Frank A, Andricioaei I. A comparative study on the ability of two implicit solvent lipid models to predict transmembrane helix tilt angles. The Journal of Membrane Biology. 239: 57-62. PMID 21152910 DOI: 10.1007/S00232-010-9325-7  0.678
2011 Hirsh AD, Taranova M, Lillian TD, Lionberger TA, Andricioaei I, Perkins NC. Investigating a Novel Toroid-Shaped DNA Structure Found in Mature Bacteriophage φ29 Biophysical Journal. 100: 401a. DOI: 10.1016/J.Bpj.2010.12.2384  0.746
2011 Mills M, Orr BG, Holl MMB, Andricioaei I. Contributions of Ordered Solvent to Long-Range DNA-Dendrimer Interactions Biophysical Journal. 100: 356a-357a. DOI: 10.1016/J.Bpj.2010.12.2140  0.372
2010 Boughton AP, Andricioaei I, Chen Z. Surface orientation of magainin 2: molecular dynamics simulation and sum frequency generation vibrational spectroscopic studies. Langmuir : the Acs Journal of Surfaces and Colloids. 26: 16031-6. PMID 20857957 DOI: 10.1021/La1024394  0.347
2010 Wereszczynski J, Andricioaei I. Free energy calculations reveal rotating-ratchet mechanism for DNA supercoil relaxation by topoisomerase IB and its inhibition. Biophysical Journal. 99: 869-78. PMID 20682265 DOI: 10.1016/J.Bpj.2010.04.077  0.485
2010 Mills M, Orr B, Banaszak Holl MM, Andricioaei I. Microscopic basis for the mesoscopic extensibility of dendrimer-compacted DNA. Biophysical Journal. 98: 834-42. PMID 20197037 DOI: 10.1016/J.Bpj.2009.11.020  0.461
2010 Wereszczynski J, Andricioaei I. Conformational and solvent entropy contributions to the thermal response of nucleic acid-based nanothermometers. The Journal of Physical Chemistry. B. 114: 2076-82. PMID 20088545 DOI: 10.1021/Jp911681N  0.402
2010 Musselman C, Zhang Q, Al-Hashimi H, Andricioaei I. Referencing strategy for the direct comparison of nuclear magnetic resonance and molecular dynamics motional parameters in RNA. The Journal of Physical Chemistry. B. 114: 929-39. PMID 20039757 DOI: 10.1021/Jp905286H  0.379
2010 Lillian TD, Taranova M, Andricioaei I, Perkins NC. Simulating the Relaxation of DNA Supercoils By Topoisomerase I Biophysical Journal. 98: 74a. DOI: 10.1016/J.Bpj.2009.12.417  0.761
2010 Mills KM, Guzman D, Guan Z, Andricioaei I. Sources of Heterogeneity in the Forced Unfolding Pathway of Streptokinase Beta Revealed through High-Temperature Steered MD Simulations Biophysical Journal. 98: 752a. DOI: 10.1016/J.Bpj.2009.12.4123  0.368
2009 Stelzer AC, Frank AT, Bailor MH, Andricioaei I, Al-Hashimi HM. Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs. Methods (San Diego, Calif.). 49: 167-73. PMID 19699798 DOI: 10.1016/J.Ymeth.2009.08.006  0.681
2009 Frank AT, Stelzer AC, Al-Hashimi HM, Andricioaei I. Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition. Nucleic Acids Research. 37: 3670-9. PMID 19369218 DOI: 10.1093/Nar/Gkp156  0.68
2009 Nummela J, Andricioaei I. Energy landscape for DNA rotation and sliding through a phage portal. Biophysical Journal. 96: L29-31. PMID 19217842 DOI: 10.1016/J.Bpj.2008.12.3761  0.45
2009 Frank AT, Stelzer A, Andricioaei I, Al-Hashimi H. An RNA Structural Ensemble Derived by Combining MD and Elongated NMR RDCs Provides Evidence for Adaptive Recognition via Conformational Selection Biophysical Journal. 96: 579a. DOI: 10.1016/J.Bpj.2008.12.3026  0.673
2009 Mills KM, Orr B, Holl MB, Andricioaei I. Force Calculations for DNA-PAMAM Dendrimer Interactions from Molecular Dynamics Simulations Biophysical Journal. 96: 366a. DOI: 10.1016/J.Bpj.2008.12.1969  0.457
2009 Bascom GD, Guinn T, Andricioaei I. Simulated Single-Molecule FRET Trajectories: A Comparative Analysis Between Three Telomeric G-quadruplexes Biophysical Journal. 96: 344a. DOI: 10.1016/J.Bpj.2008.12.1728  0.795
2009 Preketes NK, Andricioaei I. Multidimensional Optical Spectroscopy Of Proteins Out Of Thermal Equilibrium Biophysical Journal. 96: 313a. DOI: 10.1016/J.Bpj.2008.12.1564  0.327
2008 Mills M, Andricioaei I. An experimentally guided umbrella sampling protocol for biomolecules. The Journal of Chemical Physics. 129: 114101. PMID 19044944 DOI: 10.1063/1.2976440  0.399
2008 Dethoff EA, Hansen AL, Musselman C, Watt ED, Andricioaei I, Al-Hashimi HM. Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis. Biophysical Journal. 95: 3906-15. PMID 18621815 DOI: 10.1529/Biophysj.108.140285  0.37
2008 Kelly CV, Leroueil PR, Nett EK, Wereszczynski JM, Baker JR, Orr BG, Banaszak Holl MM, Andricioaei I. Poly(amidoamine) dendrimers on lipid bilayers I: Free energy and conformation of binding. The Journal of Physical Chemistry. B. 112: 9337-45. PMID 18620450 DOI: 10.1021/Jp801377A  0.312
2008 MacFadyen J, Wereszczynski J, Andricioaei I. Directionally negative friction: a method for enhanced sampling of rare event kinetics. The Journal of Chemical Physics. 128: 114112. PMID 18361559 DOI: 10.1063/1.2841102  0.367
2008 Nummela J, Yassin F, Andricioaei I. Entropy-energy decomposition from nonequilibrium work trajectories. The Journal of Chemical Physics. 128: 024104. PMID 18205440 DOI: 10.1063/1.2817332  0.341
2007 Nummela J, Andricioaei I. Exact low-force kinetics from high-force single-molecule unfolding events. Biophysical Journal. 93: 3373-81. PMID 17704183 DOI: 10.1529/Biophysj.107.111658  0.381
2007 Jordan DM, Mills KM, Andricioaei I, Bhattacharya A, Palmo K, Zuiderweg ER. Parameterization of peptide 13C carbonyl chemical shielding anisotropy in molecular dynamics simulations. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 8: 1375-85. PMID 17526036 DOI: 10.1002/Cphc.200700003  0.393
2007 Musselman C, Al-Hashimi HM, Andricioaei I. iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge. Biophysical Journal. 93: 411-22. PMID 17449677 DOI: 10.1529/Biophysj.107.104620  0.376
2006 Musselman C, Pitt SW, Gulati K, Foster LL, Andricioaei I, Al-Hashimi HM. Impact of static and dynamic A-form heterogeneity on the determination of RNA global structural dynamics using NMR residual dipolar couplings. Journal of Biomolecular Nmr. 36: 235-49. PMID 17077936 DOI: 10.1007/S10858-006-9087-9  0.407
2006 Wereszczynski J, Andricioaei I. On structural transitions, thermodynamic equilibrium, and the phase diagram of DNA and RNA duplexes under torque and tension. Proceedings of the National Academy of Sciences of the United States of America. 103: 16200-5. PMID 17060631 DOI: 10.1073/Pnas.0603850103  0.444
2006 Luo G, Andricioaei I, Xie XS, Karplus M. Dynamic distance disorder in proteins is caused by trapping. The Journal of Physical Chemistry. B. 110: 9363-7. PMID 16686476 DOI: 10.1021/Jp057497P  0.591
2006 Tian P, Andricioaei I. Size, motion, and function of the SecY translocon revealed by molecular dynamics simulations with virtual probes. Biophysical Journal. 90: 2718-30. PMID 16461399 DOI: 10.1529/Biophysj.105.073304  0.347
2006 Xing C, Andricioaei I. On the calculation of time correlation functions by potential scaling. The Journal of Chemical Physics. 124: 034110. PMID 16438570 DOI: 10.1063/1.2159476  0.349
2005 Sari L, Andricioaei I. Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative supercoil relaxation. Nucleic Acids Research. 33: 6621-34. PMID 16314322 DOI: 10.1093/Nar/Gki935  0.474
2005 MacFadyen J, Andricioaei I. A skewed-momenta method to efficiently generate conformational-transition trajectories. The Journal of Chemical Physics. 123: 074107. PMID 16229559 DOI: 10.1063/1.2000242  0.358
2005 Tian P, Andricioaei I. Repetitive pulling catalyzes co-translocational unfolding of barnase during import through a mitochondrial pore. Journal of Molecular Biology. 350: 1017-34. PMID 15979642 DOI: 10.1016/J.Jmb.2005.05.035  0.358
2004 Andricioaei I, Goel A, Herschbach D, Karplus M. Dependence of DNA polymerase replication rate on external forces: a model based on molecular dynamics simulations. Biophysical Journal. 87: 1478-97. PMID 15345530 DOI: 10.1529/Biophysj.103.039313  0.664
2003 Petrella RJ, Andricioaei I, Brooks BR, Karplus M. An improved method for nonbonded list generation: rapid determination of near-neighbor pairs. Journal of Computational Chemistry. 24: 222-31. PMID 12497601 DOI: 10.1002/Jcc.10123  0.652
2003 Andricioaei I, Dinner AR, Karplus M. Self-guided enhanced sampling methods for thermodynamic averages Journal of Chemical Physics. 118: 1074-1084. DOI: 10.1063/1.1528893  0.703
2001 Andricioaei I, Karplus M. On the calculation of entropy from covariance matrices of the atomic fluctuations Journal of Chemical Physics. 115: 6289-6292. DOI: 10.1063/1.1401821  0.529
2001 Andricioaei I, Straub JE, Voter AF. Smart darting Monte Carlo Journal of Chemical Physics. 114: 6994-7000. DOI: 10.1063/1.1358861  0.658
2001 Andricioaei I, Straub JE, Karplus M. Simulation of quantum systems using path integrals in a generalized ensemble Chemical Physics Letters. 346: 274-282. DOI: 10.1016/S0009-2614(01)00965-4  0.729
1999 Straub JE, Andricioaei I. Computational methods inspired by Tsallis statistics: Monte Carlo and molecular dynamics algorithms for the simulation of classical and quantum systems Brazilian Journal of Physics. 29: 179-186. DOI: 10.1590/S0103-97331999000100016  0.685
1998 Andricioaei I, Straub JE. Global optimization using bad derivatives: Derivative-free method for molecular energy minimization Journal of Computational Chemistry. 19: 1445-1455. DOI: 10.1002/(Sici)1096-987X(199810)19:13<1445::Aid-Jcc2>3.0.Co;2-Q  0.642
1997 Andricioaei I, Straub JE. On Monte Carlo and molecular dynamics methods inspired by Tsallis statistics: Methodology, optimization, and application to atomic clusters The Journal of Chemical Physics. 107: 9117-9124. DOI: 10.1063/1.475203  0.68
1997 Andricioaei I, Straub JE. An efficient Monte Carlo algorithm for overcoming broken ergodicity in the simulation of spin systems Physica a: Statistical Mechanics and Its Applications. 247: 553-558. DOI: 10.1016/S0378-4371(97)00421-4  0.664
1996 Andricioaei I, Straub JE. Generalized simulated annealing algorithms using Tsallis statistics: Application to conformational optimization of a tetrapeptide. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 53: R3055-R3058. PMID 9964765 DOI: 10.1103/Physreve.53.R3055  0.677
1996 Andricioaei I, Straub JE. Finding the needle in the Haystack: algorithms for conformal optimization Computers in Physics. 10: 449-454. DOI: 10.1063/1.168582  0.62
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