Celeste Sagui

Comparative Study of the Bending Free Energies of C- and G-Based DNA: A-, B-, and Z-DNA and Associated Mismatched Trinucleotide Repeats

Fakharzadeh, A., Moradi, M., Sagui, C., & Roland, C. (2025, May 16). Journal of Chemical Information and Modeling, Vol. 5.

Structural and Dynamical Properties of Nucleic Acid Hairpins Implicated in Trinucleotide Repeat Expansion Diseases

Pan, F., Xu, P., Roland, C., Sagui, C., & Weninger, K. (2024, October 10). Biomolecules, Vol. 14.

Conformationally Restricted Glycopeptide Backbone Inhibits Gas-Phase H/D Scrambling between Glycan and Peptide Moieties

Code, C., Qiu, D., Solov’yov, I. A., Lee, J.-G., Shin, H.-C., Roland, C., … Jørgensen, T. J. D. (2023, October 26). Journal of the American Chemical Society, Vol. 10.

Frustration Between Preferred States of Complementary Trinucleotide Repeat DNA Hairpins Anticorrelates with Expansion Disease Propensity

Xu, P., Zhang, J., Pan, F., Mahn, C., Roland, C., Sagui, C., & Weninger, K. (2023, April 5). Journal of Molecular Biology, Vol. 435.

Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal

Kandola, T., Venkatesan, S., Zhang, J., Lerbakken, B. T., Schulze, A. V., Blanck, J. F., … Halfmann, R. (2023, June 13). ELife, Vol. 12.

Structure and Dynamics of DNA and RNA Double Helices Formed by d(CTG), d(GTC), r(CUG), and r(GUC) Trinucleotide Repeats and Associated DNA–RNA Hybrids

Fakharzadeh, A., Qu, J., Pan, F., Sagui, C., & Roland, C. (2023, September 8). The Journal of Physical Chemistry B, Vol. 9.

Unpolarized laser method for infrared spectrum calculation of amide I C O bonds in proteins using molecular dynamics simulation

Man, V. H., He, X., Nguyen, P. H., Sagui, C., Roland, C., Xie, X.-Q., & Wang, J. (2023, April 13). Computers in Biology and Medicine, Vol. 159.

Novel eGZ-motif formed by regularly extruded guanine bases in a left-handed Z-DNA helix as a major motif behind CGG trinucleotide repeats

Fakharzadeh, A., Zhang, J., Roland, C., & Sagui, C. (2022, May 6). Nucleic Acids Research, Vol. 5.

RNA as a Major-Groove Ligand: RNA–RNA and RNA–DNA Triplexes Formed by GAA and UUC or TTC Sequences

Zhang, J., Fakharzadeh, A., Roland, C., & Sagui, C. (2022, October 24). ACS Omega, Vol. 7, pp. 38728–38743.

Construction of DNA/RNA Triplex Helices Based on GAA/TTC Trinucleotide Repeats

Zhang, J., Fakharzadeh, A., Pan, F., Roland, C., & Sagui, C. (2021, January 1). BIO-PROTOCOL, Vol. 11.

Molecular conformations and dynamics of nucleotide repeats associated with neurodegenerative diseases: double helices and CAG hairpin loops

Pan, F., Zhang, Y., Xu, P., Man, V. H., Roland, C., Weninger, K., & Sagui, C. (2021, January 1). Computational and Structural Biotechnology Journal, Vol. 19, pp. 2819–2832.

The F19W mutation reduces the binding affinity of the transmembrane Aβ_11–40 trimer to the membrane bilayer

Tran, T. T., Pan, F., Tran, L., Roland, C., & Sagui, C. (2021, January 1). RSC Advances, Vol. 11, pp. 2664–2676.

Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich’s ataxia: DNA triplexes and RNA/DNA hybrids

Zhang, J., Fakharzadeh, A., Pan, F., Roland, C., & Sagui, C. (2020, August 5). Nucleic Acids Research, Vol. 48, pp. 9899–9917.

Structure and Dynamics of DNA and RNA Double Helices Obtained from the CCG and GGC Trinucleotide Repeats

Pan, F., Man, V. H., Roland, C., & Sagui, C. (2018, April 4). The Journal of Physical Chemistry B, Vol. 122, pp. 4491–4512.

E-motif formed by extrahelical cytosine bases in DNA homoduplexes of trinucleotide and hexanucleotide repeats

Pan, F., Zhang, Y., Man, V. H., Roland, C., & Sagui, C. (2017, November 13). Nucleic Acids Research, Vol. 46, pp. 942–955.

Structural and Dynamical Characterization of DNA and RNA Quadruplexes Obtained from the GGGGCC and GGGCCT Hexanucleotide Repeats Associated with C9FTD/ALS and SCA36 Diseases

Zhang, Y., Roland, C., & Sagui, C. (2017, December 27). ACS Chemical Neuroscience, Vol. 9, pp. 1104–1117.

Structure and Dynamics of DNA and RNA Double Helices of CAG and GAC Trinucleotide Repeats

Pan, F., Man, V. H., Roland, C., & Sagui, C. (2017, July 1). Biophysical Journal, Vol. 113, pp. 19–36.

Amyloid Properties of Asparagine and Glutamine in Prion-like Proteins

ACS Chemical Neuroscience, 7(5), 576–587.

Comparative melting and healing of B-DNA and Z-DNA by an infrared laser pulse

Man, V. H., Pan, F., Sagui, C., & Roland, C. (2016, April 12). The Journal of Chemical Physics, Vol. 144.

Contrasting Roles of Asparagine and Glutamine in the Aggregation of Prion-Like Proteins

Biophysical Journal, 110(3), 214a–215a.

Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses

Man, V. H., Van-Oanh, N.-T., Derreumaux, P., Li, M. S., Roland, C., Sagui, C., & Nguyen, P. H. (2016, January 1). Physical Chemistry Chemical Physics, Vol. 18, pp. 11951–11958.

Stability and Ion Distributions Around Left- and Right-Handed DNA and RNA Duplexes: A Comparative Study

Biophysical Journal, 110(3), 407a.

Structural Determinants of Polyqlutamine Protofibrils and Crystallites

Biophysical Journal, 110(3), 215a.

Structure and Dynamics of DNA and RNA Double Helices Obtained from the GGGGCC and CCCCGG Hexanucleotide Repeats That Are the Hallmark of C9FTD/ALS Diseases

Zhang, Y., Roland, C., & Sagui, C. (2016, December 9). ACS Chemical Neuroscience, Vol. 8, pp. 578–591.

Calculating transition and reaction rates with nonequilibrium work measurements

Moradi, M., Sagui, C., & Roland, C. (2015, September 28). Journal of Physics Conference Series, Vol. 640.

Picosecond dissociation of amyloid fibrils with infrared laser: A nonequilibrium simulation study

Viet, M. H., Derreumaux, P., Li, M. S., Roland, C., Sagui, C., & Nguyen, P. H. (2015, October 20). The Journal of Chemical Physics, Vol. 143.

Picosecond melting of peptide nanotubes using an infrared laser: a nonequilibrium simulation study

Viet, M. H., Truong, P. M., Derreumaux, P., Li, M. S., Roland, C., Sagui, C., & Nguyen, P. H. (2015, January 1). Physical Chemistry Chemical Physics, Vol. 17, pp. 27275–27280.

Structural Determinants of Polyglutamine Protofibrils and Crystallites

Man, V. H., Roland, C., & Sagui, C. (2015, January 21). ACS Chemical Neuroscience, Vol. 6, pp. 632–645.

The Adaptively Biased Molecular Dynamics method revisited: New capabilities and an application

Moradi, M., Babin, V., Roland, C., & Sagui, C. (2015, September 28). Journal of Physics Conference Series, Vol. 640.

Correction to Classical Electrostatics for Biomolecular Simulations

Chemical Reviews, 114(9), 5116–5116.

Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities

The Journal of Chemical Physics, 140(3), 034114.

Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates

The Journal of Chemical Physics, 140(3), 034115.

Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study

Pan, F., Roland, C., & Sagui, C. (2014, November 26). Nucleic Acids Research, Vol. 42, pp. 13981–13996.

Publisher's Note: “Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities” [J. Chem. Phys. 140, 034114 (2014)]

Moradi, M., Sagui, C., & Roland, C. (2014, February 10). The Journal of Chemical Physics, Vol. 140.

Publisher's Note: “Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates” [J. Chem. Phys. 140, 034115 (2014)]

Moradi, M., Sagui, C., & Roland, C. (2014, February 12). The Journal of Chemical Physics, Vol. 140.

Secondary structure assignment for conformationally irregular peptides: Comparison between DSSP, STRIDE and KAKSI

Zhang, Y., & Sagui, C. (2014, November 6). Journal of Molecular Graphics and Modelling, Vol. 55, pp. 72–84.

Binding Polymorphism in the DNA Bound State of the Pdx1 Homeodomain

Babin, V., Wang, D., Rose, R. B., & Sagui, C. (2013, August 8). PLoS Computational Biology, Vol. 9.

Classical Electrostatics for Biomolecular Simulations

Cisneros, G. A., Karttunen, M., Ren, P., & Sagui, C. (2013, August 27). Chemical Reviews, Vol. 114, pp. 779–814.

The gp41_659–671 HIV-1 Antibody Epitope: A Structurally Challenging Small Peptide

Zhang, Y., & Sagui, C. (2013, December 13). The Journal of Physical Chemistry B, Vol. 118, pp. 69–80.

Reaction path ensemble of the B–Z-DNA transition: a comprehensive atomistic study

Moradi, M., Babin, V., Roland, C., & Sagui, C. (2012, October 25). Nucleic Acids Research, Vol. 41, pp. 33–43.

A Statistical Analysis of the PPII Propensity of Amino Acid Guests in Proline-Rich Peptides

Biophysical Journal, 100(4), 1083–1093.

Calculating relative transition rates with driven nonequilibrium simulations

Moradi, M., Sagui, C., & Roland, C. (2011, November 3). Chemical Physics Letters, Vol. 518, pp. 109–113.

PPII Propensity of Multiple-Guest Amino Acids in a Proline-Rich Environment

The Journal of Physical Chemistry B, 115(26), 8645–8656.

A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers

Moradi, M., Babin, V., Roland, C., & Sagui, C. (2010, September 24). The Journal of Chemical Physics, Vol. 133.

Conformational free energies of methyl-α-L-iduronic and methyl-β-D-glucuronic acids in water

Babin, V., & Sagui, C. (2010, March 11). The Journal of Chemical Physics, Vol. 132.

Dimerization free energy of vancomycin-group antibiotics and the cooperative effect: A density functional approach

International Journal of Quantum Chemistry, 110(15), 2894–2902.

Free energy and structure of polyproline peptides: An ab initio and classical molecular dynamics investigation

International Journal of Quantum Chemistry, 110(15), 2865–2879.

The α-sheet: A missing-in-action secondary structure?

Proteins: Structure, Function, and Bioinformatics, 79(3), 937–946.

Adaptively biased molecular dynamics: An umbrella sampling method with a time‐dependent potential

Babin, V., Karpusenka, V., Moradi, M., Roland, C., & Sagui, C. (2009, August 27). International Journal of Quantum Chemistry, Vol. 109, pp. 3666–3678.

Conformations and free energy landscapes of polyproline peptides

Moradi, M., Babin, V., Roland, C., Darden, T. A., & Sagui, C. (2009, November 18). Proceedings of the National Academy of Sciences, Vol. 106, pp. 20746–20751.

Adaptively biased molecular dynamics for free energy calculations

Babin, V., Roland, C., & Sagui, C. (2008, April 1). The Journal of Chemical Physics, Vol. 128.

Amino Acid Adsorption on the Si(100) Surface:  The Case of Glycine

Luo, X., Qian, G., Sagui, C., & Roland, C. (2008, January 31). The Journal of Physical Chemistry C, Vol. 112, pp. 2640–2648.

Chapter 2 Electrostatics in Biomolecular Simulations: Where Are We Now and Where Are We Heading?

Karttunen, M., Rottler, J., Vattulainen, I., & Sagui, C. (2008, January 1). Current Topics in Membranes, Vol. 60, pp. 49–89.

Theoretical Investigation of the Interaction of Glycine with Diamond C(100) and C(111) (2 × 1) Surfaces

Odbadrakh, K., Luo, X., Lee, J.-G., Sagui, C., & Roland, C. (2007, August 1). The Journal of Physical Chemistry C, Vol. 111, pp. 12760–12767.

Deprotonation of Solvated Formic Acid:  Car−Parrinello and Metadynamics Simulations

Lee, J.-G., Asciutto, E., Babin, V., Sagui, C., Darden, T., & Roland, C. (2006, January 14). The Journal of Physical Chemistry B, Vol. 110, pp. 2325–2331.

Molecular Dynamics Simulations of DNA with Polarizable Force Fields:  Convergence of an Ideal B-DNA Structure to the Crystallographic Structure

Babin, V., Baucom, J., Darden, T. A., & Sagui, C. (2006, May 19). The Journal of Physical Chemistry B, Vol. 110, pp. 11571–11581.

Molecular dynamics simulations of polarizable DNA in crystal environment

International Journal of Quantum Chemistry, 106(15), 3260–3269.

The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections

Babin, V., Roland, C., Darden, T. A., & Sagui, C. (2006, November 28). The Journal of Chemical Physics, Vol. 125.

Exploring Intramolecular Reactions in Complex Systems with Metadynamics:  The Case of the Malonate Anions

Asciutto, E., & Sagui, C. (2005, August 6). The Journal of Physical Chemistry A, Vol. 109, pp. 7682–7687.

New and Exotic Self-Organized Patterns for Modulated Nanoscale Systems

Sagui, C., Asciutto, E., & Roland, C. (2005, January 22). Nano Letters, Vol. 5, pp. 389–395.

Quantum Simulations of the Structure and Binding of Glycopeptide Antibiotic Aglycons to Cell Wall Analogues

Lee, J.-G., Sagui, C., & Roland, C. (2005, October 12). The Journal of Physical Chemistry B, Vol. 109, pp. 20588–20596.

Self-assembled patterns and strain-induced instabilities for modulated systems

Asciutto, E., Roland, C., & Sagui, C. (2005, August 15). Physical Review E, Vol. 72.

Ab initio calculation of electrostatic multipoles with Wannier functions for large-scale biomolecular simulations

Sagui, C., Pomorski, P., Darden, T. A., & Roland, C. (2004, February 20). The Journal of Chemical Physics, Vol. 120, pp. 4530–4544.

First Principles Investigation of Vancomycin and Teicoplanin Binding to Bacterial Cell Wall Termini

Lee, J.-G., Sagui, C., & Roland, C. (2004, June 18). Journal of the American Chemical Society, Vol. 126, pp. 8384–8385.

Molecular dynamics simulations of the d(CCAACGTTGG)2 decamer in crystal environment: Comparison of atomic point-charge, extra-point, and polarizable force fields

Baucom, J., Transue, T., Fuentes-Cabrera, M., Krahn, J. M., Darden, T. A., & Sagui, C. (2004, October 5). The Journal of Chemical Physics, Vol. 121, pp. 6998–7008.

Surface solvation for an ion in a water cluster

Herce, D. H., Perera, L., Darden, T. A., & Sagui, C. (2004, December 23). The Journal of Chemical Physics, Vol. 122.

Calculation of ionic charging free energies in simulation systems with atomic charges, dipoles, and quadrupoles

Herce, D. H., Darden, T., & Sagui, C. (2003, October 15). The Journal of Chemical Physics, Vol. 119, pp. 7621–7632.

Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations

Sagui, C., Pedersen, L. G., & Darden, T. A. (2003, December 22). The Journal of Chemical Physics, Vol. 120, pp. 73–87.

Liquid-crystal phases of capped carbon nanotubes

Somoza, A. M., Sagui, C., & Roland, C. (2001, February 1). Physical Review. B, Condensed Matter, Vol. 63.