Andricioaei, Ioan - University of California, Irvine

研究领域

Chemical Biology/Physical Chemistry and Chemical Physics/Theoretical and Computational

近期论文

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D. Jeong and I. Andricioaei, "Reconstructing equilibrium entropy and enthalpy profiles from non-equilibrium pulling," J. Chem. Phys. 138, 114110 (2013) link A. D. Hirsh, M. Taranova, T. A. Lionberger, T. D. Lillian, I. Andricioaei* and N. Perkins*, "Structural Ensemble and Dynamics of Toroidal-like DNA Shapes in Bacteriophage Phi29 Exit Cavity," Biophys. J. 104, 2058-2067 (2013) link Loïc Salmon, Gavin Bascom, Ioan Andricioaei, and Hashim M. Al-Hashimi, "A General Method for Constructing Atomic-Resolution RNA Ensembles using NMR Residual Dipolar Couplings: The Basis for Interhelical Motions Revealed," J. Am. Chem. Soc. 135, 5457-5466 (2013) link A. T. Frank and S. Horowitz and I. Andricioaei* and H.M. Al-Hashimi*, "Utility of 1H NMR Chemical Shifts in Determining RNA Structure and Dynamics," J. Phys. Chem. B, 117, 2045-2052 (2013). link M. Mills, B. Orr, M.M. Banaszak Holl and I. Andricioaei, "Attractive hydration forces in DNA-dendrimer Interactions at the nanometer scale," J. Phys. Chem. B, 117, 973-981 (2013). link E. N. Nikolova, G. Bascom, I. Andricioaei and H. M. Al-Hashimi, "Probing sequence-specific DNA flexibility in A-tracts and pyrimidine-purine steps by NMR 13C relaxation and MD simulations," Biochemistry 51, 8654 (2012) link. P. P. Jose and I. Andricioaei, Similarities between protein folding and granular jamming, Nature Communications 3, 1161 (2012) link. N. K. Preketes, J. D. Biggs, H. Ren, I. Andricioaei and S. Mukamel, Simulations of two-dimensional infrared and stimulated resonance Raman spectra of photoactive yellow protein, Chemical Physics, (2012) link. A. Boughton, K. Nguyen, I. Andricioaei* and Z. Chen*, Interfacial Orientation and Secondary Structure Change in Tachyplesin I: Molecular Dynamics and Sum Frequency Generation Spectroscopy Studies, Langmuir 27, 14343-14351 (2011) link. T. D. Lillian, M. Taranova, J. Wereszczynski, I. Andricioaei*, and N. C. Perkins*. "A multiscale dynamic model of DNA supercoil relaxation by topoisomerase IB," Biophys. J., 100, 2016–2023 (2011) link. A.C. Stelzer, A.T. Frank, J.D. Kratz, M.D. Swanson, M.J. Gonzalez-Hernandez, J. Lee, I. Andricioaei, D.M. Markovitz and H.M. Al-Hashimi, "Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble," Nature Chem. Biol. 7, 553–559 (2011) link. E. Nikolova, E. Kim, A. Wise, P. O’Brien, I. Andricioaei and H.M. Al-Hashimi, "Transient Hoogsteen Base-pairs in Canonical Duplex DNA," Nature 470, 498–502 (2011) link. A.T. Frank, I. Andricioaei, "A Comparative Study on the Ability of Two Implicit Solvent Lipid Models to Predict Transmembrane Helix Tilt Angles," J. Membrane Biol. 239, 57-62 (2011) pdf. A.P. Boughton, I. Andricioaei and Z. Chen, "Surface Orientation of Magainin 2: Molecular Dynamics Simulation and Sum Frequency Generation Vibrational Spectroscopic Studies," Langmuir, 26, 16031-16036 (2010) pdf. J. Wereszczynski and I. Andricioaei, "Free Energy Calculations Reveal Rotating-Ratchet Mechanism for DNA Supercoil Relaxation by Topoisomerase IB and its Inhibition," Biophys. J. 99, 869–878 (2010) pdf. J. Wereszczynski and I. Andricioaei, "Conformational and Solvent Entropy Contributions to the Thermal Response of Nucleic Acid-Based Nanothermometers," J. Phys. Chem. B 114, 2076-2082 (2010) pdf. M. Mills, B. Orr, M.M. Banaszak Holl and I. Andricioaei, "Microscopic Basis for the Mesoscopic Extensibility of Dendrimer-Compacted DNA," Biophys. J. 98, 834-842 (2010) pdf. C. Musselman, Q. Zhang, H.M. Al-Hashimi and I. Andricioaei, "Referencing strategy for the direct comparison of nuclear magnetic resonance and molecular dynamics motional parameters in RNA," J. Phys. Chem. B 114, 929-939 (2010) pdf. A.C. Stelzer, A.T. Frank, M. Bailor, H.M. Al-Hashimi and I. Andricioaei, "Constructing Atomic-Resolution RNA Structural Ensembles Using MD and Motionally Decoupled NMR RDCs," Methods 49, 167-173 (2009). A.T. Frank, A.C. Stelzer, H.M. Al-Hashimi and I. Andricioaei, "Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: New insights into RNA dynamics and adaptive ligand recognition," Nucleic Acids Res. 37, 3670-3679 (2009) pdf. J. Nummela and I. Andricioaei, "Energy landscape for DNA rotation and sliding through a phage portal," Biophys.J. (Letter) 96, L29-L31 (2009) pdf. M. Mills and I. Andricioaei, "An experimentally guided umbrella sampling protocol for biomolecules," J. Chem. Phys. 129,114101 (2008) pdf. E. Dethoff, A. Hansen, C. Musselman, E. Watt, I. Andricioaei, and H.M. Al-Hashimi, "Characterizing Complex Dynamics in the TAR Apical Loop and Motional Correlations with the Bulge by NMR, MD and Mutagenesis," Biophys. J. 95, 3906-3915 (2008). C.V. Kelly, P. R. Leroueil, E.K. Nett, J. M. Wereszczynski, J.R. Baker, B. G. Orr, M.M. Banaszak Holl and I. Andricioaei, "Poly(amidoamine) Dendrimers on Lipid Bilayers I: Free Energy and Conformation of Binding," J. Phys. Chem. B 112, 9337-9345 (2008) pdf. C.V. Kelly, P. R. Leroueil, B. G. Orr, M.M. Banaszak Holl and I. Andricioaei, "Poly(amidoamine) Dendrimers on Lipid Bilayers II: Effects of Bilayer Phase and Dendrimer Termination," J. Phys. Chem. B 112, 9346-9353 (2008) pdf. J. Nummela, F. Yassin and I. Andricioaei, "Entropy-energy decomposition from nonequilibrium work trajectories," J. Chem. Phys. 128, 024104 (2008) pdf. J. MacFadyen, J. Wereszczynski and I. Andricioaei, "Directionally negative friction: A method for enhanced sampling of rare events," J. Chem. Phys. 128, 114112 (2008) pdf. J. Nummela and I. Andricioaei, "Exact low-force kinetics from high-force single-molecule unfolding events," Biophys. J. 93, 3373-3381 (2007) pdf. C. Musselman, H.M. Al-Hashimi and I. Andricioaei, "iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge," Biophys. J. 93, 411-422 (2007) pdf. D.M. Jordan, M. Mills, I. Andricioaei, K. Palmo and E.R.P. Zuiderweg, "Parameterization of peptide 13C carbonyl chemical shielding anisotropy in molecular dynamics simulations: Effects of dynamic local distortions on 13C carbonyl NMR relaxation," Chem. Phys. Chem. 8, 1375-1385 (2007). I. Andricioaei, "Specialized methods for improving ergodic sampling using molecular dynamics and Monte Carlo simulations" in Free Energy Calculations: Theory and Applications in Chemistry and Biology, pp. 277-322, eds. A. Pohorille and C. Chipot, Springer Series in Chemical Physics, (2007).