Publications

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2022

D. Ray, R. N. Quijano, and I. Andricioaei, “Point Mutations in SARS-CoV-2 Variants Induce Long-Range Dynamical Perturbations in Neutralizing Antibodies”, bioRxiv (2022)

D. Ray, S. E. Stone, and I. Andricioaei, “Markovian Weighted Ensemble Milestoning (M-WEM): Long-time Kinetics from Short Trajectories”, J. Chem. Theory Comput. 18, 1, 79–95 (2022)

S. E. Stone, D. Ray, and I. Andricioaei, “Studying the Association and Dissociation of Trypsin-Benzamidine Complex Using Enhanced Sampling Molecular Dynamics”, Revue Roumaine de Chimie (Romanian Journal of Chemistry), Just Accepted (2022)

2021

D. Ray, L. Le, and I. Andricioaei, “Distant Residues Modulate the Conformational Opening in SARS-CoV-2 Spike Protein”, Proc. Nat. Acad. Sci. USA. 118 (43) e2100943118 (2021)

2020

D. Ray, T. Gokey, D. L. Mobley, and I. Andricioaei,”Kinetics and free energy of ligand dissociation using weighted ensemble milestoning”, J. Chem. Phys. 153, 154117 (2020)

D. Ray and I. Andricioaei, “Free Energy Landscape and Conformational Kinetics of Hoogsteen Base-Pairing in DNA vs RNA”, Biophys. J. 119, 1568–1579 (2020)

D. Ray and I. Andricioaei, “Weighted ensemble milestoning (WEM): A combined approach for rare event simulations”, J. Chem. Phys. 152, 234114 (2020)

2019

A. Maghsoodi, A. Chatterjee, I. Andricioaei and N. Perkins, “How the phage T4 injection machinery works including energetics, forces, and dynamic pathway”, Proc. Nat. Acad. Sci. 201909298 (2019)

A. Chatterjee, A. Maghsoodi, N. Perkins and I. Andricioaei, “Elastic Continuum Stiffness of Contractile Tail Sheaths from Molecular Dynamics Simulations”, J. Chem. Phys. 151, 185103 (2019)

2018

G. Grazioli and I. Andricioaei, “Advancements in milestoning: II Calculating time-correlation functions from milestoning data using stochastic path integrals in milestone space”, J. Chem. Phys. 149, 084103 (2018).

G. Grazioli and I. Andricioaei, “Advancements in milestoning: I. Accelerated milestoning using wind assisted re-weighted trajectories”, J. Chem. Phys. 149, 084104 (2018).

Y. Xu, J. McSally, I. Andricioaei, H.M. Al-Hashimi, “Modulation of Hoogsteen Dynamics on DNA Recognition”, Nature Commun. 9, 1473 (2018).

2017

G. Grazioli, C.T. Butts, I. Andricioaei, “Automated placement of interfaces in conformational kinetics calculations using machine learning”, J. Chem. Phys. 147, 152727 (2017).

A. Maghsoodi, A. Chatterjee, I. Andricioaei, NC. Perkins., “Dynamic Model Exposes the Energetics andDynamics of the Injection Machinery for Bacteriophage T4”, Biophys. J. 113, 195-205 (2017).

E. Ficici and I. Andricioaei, “Electric-field induced protein translocation via a conformational transition in SecDF: A molecular dynamics study”, Biophys. J. 112, 2520-2528 (2017).

2016

A. Maghsoodi, A. Chatterjee, I. Andricioaei, NC. Perkins., “A First Model of the Dynamics of the Bacteriophage T4 Injection Machinery”, J. Comput. Nonlinear Dynam. 11(4), 041026 (2016).

H. Zhou, I.J. Kimsey, E.N. Nikolova, B. Sathyamoorthy, G. Grazioli, J. McSally, T. Bai, C.H. Wunderlich, C. Kreutz, I. Andricioaei* and H. M Al-Hashimi*, “m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs”, Nature Structural & Molecular Biology, 23, 803–810 (2016).

A.T. Frank and I. Andricioaei, “Reaction coordinate-free approach to recovering kinetics from potential-scaled simulations: Application of Kramers’ rate theory”, J. Phys. Chem. B, 120 (33), 8600–8605 (2016).

2015

Z. Cournia, T.W. Allen, I. Andricioaei, et al., Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory, J. Membrane Biol., 248, 611 (2015).

M. Roy, G. Grazioli, I. Andricioaei, “Rate turnover in mechano-catalytic coupling: A model and its microscopic origin,” J. Chem. Phys., 143, 045105 (2015).

E. Ficici, I. Andricioaei and S. Howorka, “Dendrimers in nanoscale confinement: The interplay between conformational change and nanopore entrance,” Nano Letters 15, 4822-4828 (2015).

A.T. Frank, Q. Zhang, H.M. Al-Hashimi, I. Andricioaei, “Slowdown of Interhelical motions induces a glass transition in RNA” Biophys. J. 108, 2876-2885 (2015).

E. Ficici and I. Andricioaei, “On the possibility of facilitated diffusion of dendrimers along DNA,” J. Phys. Chem. B 119, 6894-6904 (2015).

A. Mentes, A.M. Florescu, E. Brunk, J. Wereszczynski, M. Joyeux and I. Andricioaei, “Free energy landscape and characteristic forces for the initiation of DNA unzipping,” Biophys. J. 108, 1727-1738 (2015).

2014

M. Taranova, A. Hirsh, N. Perkins and I. Andricioaei, “Role of microscopic flexibility in tightly curved DNA,” J. Phys. Chem. B, 118, 11028–11036 (2014).

G. Bascom, I. Andricioaei, “Single-walled carbon nanotubes modulate the B- to A-DNA transition,” J. Phys. Chem. C 118, 29441-29447 (2014).

L. Mereuta, M. Roy, A. Asandei, J.K. Lee, Y. Park, I. Andricioaei and T. Luchian, “Slowing down single-molecule trafficking through a protein nanopore reveals intermediates for peptide translocation,” Nature Sci. Rep. 4, 3885 (2014).

2013

A. D. Hirsch, M. Taranova, T. Lionberger, T. Lillian, I. Andricioaei and N. C. Perkins, “Structural ensemble and dynamics of toroidal-like DNA shapes in bacteriophage φ29 exit cavity,” Biophys. J. 104, 2058-2067 (2013).

L. Salmon, G. Bascom, I. Andricioaei and H. 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 (14), 5457–5466 (2013).

A.T. Frank , S. Horowitz, I. Andricioaei and H. M. Al-Hashimi “Utility of H-1 NMR chemical shifts in determining RNA structure and dynamics, J. Phys. Chem. B 117 (7), 2045-2052 (2013).

N. Ucuncuoglu, I. Andricioaei and L. Sari, “Insights from simulations into the mechanism of human topoisomerase I: Explanation for a seeming controversy in experiments,” Journal of Mollecular Graphics and Modeling, 44, 286-296 (2013).

A. D. Hirsh, T. D. Lillian, T. A. Lionberger, M. Taranova, I. Andricioaei, N. C. Perkins, “A model for highly strained DNA compressed inside a protein cavity,” J. Comput. Nonlinear Dynam. 8, 031001 (2013).

D. Jeong and I. Andricioaei, “Reconstructing equilibrium entropy and enthalpy profiles from non-equilibrium pulling,” J. Chem. Phys. 138, 114110 (2013).

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, 422, 63-72 (2013).

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,” Biophysical Journal 104, 2058-2067 (2013)

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,” Journal of the American Chemical Society 135, 5457-5466 (2013)

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,” Journal of Physical Chemistry B, 117, 2045-2052 (2013).

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).

2012

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).

P. P. Jose and I. Andricioaei, “Similarities between protein folding and granular jamming,” Nature Communications 3, 1161 (2012).

Prior to 2012

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).

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).

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).

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).

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).

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).

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).

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).

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).

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).

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).

J. Nummela and I. Andricioaei, “Energy landscape for DNA rotation and sliding through a phage portal,” Biophys.J. (Letter) 96, L29-L31 (2009).

M. Mills and I. Andricioaei, “An experimentally guided umbrella sampling protocol for biomolecules,” J. Chem. Phys. 129,114101 (2008).

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).

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).

J. Nummela, F. Yassin and I. Andricioaei, “Entropy-energy decomposition from nonequilibrium work trajectories,” J. Chem. Phys. 128, 024104 (2008).

J. MacFadyen, J. Wereszczynski and I. Andricioaei, “Directionally negative friction: A method for enhanced sampling of rare events,” J. Chem. Phys. 128, 114112 (2008).

J. Nummela and I. Andricioaei, “Exact low-force kinetics from high-force single-molecule unfolding events,” Biophys. J. 93, 3373-3381 (2007).

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).

J. Wereszczynski and I. Andricioaei, “On structural transitions, thermodynamic equilibrium and the phase diagram of DNA and RNA duplexes under external tension and torque,” Proc. Natl. Acad. Sci. U.S.A. 103, 16200-16205 (2006).

C. Musselman, S. Pitt, K. Gulati, L. Foster, I. Andricioaei and H. Al-Hashimi, “Impact of static and dynamic A-form heterogeneity on the determination of RNA global structural dynamics using NMR residual dipolar couplings,” J. Biomol. NMR, 36, 235-249 (2006).

P. Tian and I. Andricioaei, “Size, motion and function of the SecY translocon revealed by molecular dynamics simulations with virtual probes,” Biophys. J., 90, 2718-2730 (2006).

C. Xing and I. Andricioaei, “On the calculation of time-correlation functions by potential scaling,” J. Chem. Phys. 124, 034110 (2006).

G. Luo, I. Andricioaei, X.S. Xie and M. Karplus, “Distance disorder in proteins is caused by trapping,” (Letter) J. Phys. Chem. B 110, 9363-9367 (2006).

J. MacFadyen and I. Andricioaei, “A Skewed-Momenta method to efficiently generate conformational-transition trajectories,” J. Chem. Phys. 123, 074107 (2005).

L. Sari and I. Andricioaei, “Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative DNA supercoil relaxation” Nucleic Acids Research 33, 6621-6634 (2005).

P. Tian and I. Andricioaei, “Repetitive pulling catalyzes co-translocational unfolding of barnase during import through a mitochondrial pore,” J. Mol. Biol. 350, 1017-1034 (2005).

M. Jin, I. Andricioaei, T.A. Springer, “Conversion between three conformational states of integrin I domains with a C-terminal pull spring studied with molecular dynamics,” Structure 12, 2137-2147 (2004).