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Ioan Andricioaei - Publications

Chemistry University of California, Irvine, Irvine, CA 
Theoretical Chemistry and Biophysics

69 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
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  0.6
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  0.6
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  0.6
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  0.6
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  0.96
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2013 Preketes NK, Biggs JD, Ren H, Andricioaei I, Mukamel S. Simulations of Two-dimensional Infrared and Stimulated Resonance Raman Spectra of Photoactive Yellow Protein. Chemical Physics. 422. PMID 24244064 DOI: 10.1016/j.chemphys.2012.09.002  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2012 Jose PP, Andricioaei I. Similarities between protein folding and granular jamming. Nature Communications. 3: 1161. PMID 23093180 DOI: 10.1038/ncomms2177  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2008 Kelly CV, Liroff MG, Leroueil PR, Mullen DG, Erickson BW, Orr BG, Andricioaei I, Holl MMB. Poly(amidoamine) dendrimer binding, pore formation. and supramolecular structure with phospholipids American Chemical Society, Polymer Preprints, Division of Polymer Chemistry. 49: 870-871.  1
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  1
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  1
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  1
2007 Andricioaei I. Specialized methods for improving ergodic sampling using molecular dynamics and Monte Carlo simulations Springer Series in Chemical Physics. 86: 277-322. DOI: 10.1007/978-3-540-38448-9_8  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2004 Jin M, Andricioaei I, Springer TA. Conversion between three conformational states of integrin I domains with a C-terminal pull spring studied with molecular dynamics. Structure (London, England : 1993). 12: 2137-47. PMID 15576028 DOI: 10.1016/j.str.2004.10.005  1
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  1
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  1
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  1
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  1
2001 Andricioaei I, Straub JE, Voter AF. Smart darting Monte Carlo Journal of Chemical Physics. 114: 6994-7000. DOI: 10.1063/1.1358861  1
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  1
1999 Van der Kloot W, Andricioaei I, Balezina OP. Examining the timing of miniature endplate potential releases at the frog and mouse neuromuscular junctions for deviations from Poisson expectations. PflüGers Archiv : European Journal of Physiology. 438: 578-86. PMID 10555553  1
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.  1
1998 Andricioaei I, Straub JE. Global optimization using bad derivatives: Derivative-free method for molecular energy minimization Journal of Computational Chemistry. 19: 1445-1455.  1
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.  1
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  1
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  1
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