Celeste Sagui

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

JOURNAL OF MOLECULAR BIOLOGY, 435(10).

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

COMPUTERS IN BIOLOGY AND MEDICINE, 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 10). NUCLEIC ACIDS RESEARCH.

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

ACS OMEGA, 7(43), 38728–38743.

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

BIO-PROTOCOL, 11(18).

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

[Review of ]. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 19, 2819–2832.

The F19W mutation reduces the binding affinity of the transmembrane A beta(11-40) trimer to the membrane bilayer

RSC ADVANCES, 11(5), 2664–2676.

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

NUCLEIC ACIDS RESEARCH, 48(17), 9899–9917.

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

NUCLEIC ACIDS RESEARCH, 46(2), 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

ACS CHEMICAL NEUROSCIENCE, 9(5), 1104–1117.

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

JOURNAL OF PHYSICAL CHEMISTRY B, 122(16), 4491–4512.

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

ACS CHEMICAL NEUROSCIENCE, 8(3), 578–591.

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

BIOPHYSICAL JOURNAL, 113(1), 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

JOURNAL OF CHEMICAL PHYSICS, 144(14).

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

PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18(17), 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.

Calculating transition and reaction rates with nonequilibrium work measurements

XXVI IUPAP CONFERENCE ON COMPUTATIONAL PHYSICS (CCP2014), Vol. 640.

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

JOURNAL OF CHEMICAL PHYSICS, 143(15).

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

PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17(41), 27275–27280.

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

JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 55, 72–84.

Structural Determinants of Polyglutamine Protofibrils and Crystallites

ACS CHEMICAL NEUROSCIENCE, 6(4), 632–645.

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

XXVI IUPAP CONFERENCE ON COMPUTATIONAL PHYSICS (CCP2014), Vol. 640.

Classical Electrostatics for Biomolecular Simulations

[Review of ]. CHEMICAL REVIEWS, 114(1), 779–814.

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. I. Nonequilibrium transition path probabilities (vol 140, 034114, 2014)

Moradi, M., Sagui, C., & Roland, C. (2014, February 14). JOURNAL OF CHEMICAL PHYSICS, Vol. 140.

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

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

Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates (vol 140, 034115, 2014)

Moradi, M., Sagui, C., & Roland, C. (2014, February 14). JOURNAL OF CHEMICAL PHYSICS, Vol. 140.

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

NUCLEIC ACIDS RESEARCH, 42(22), 13981–13996.

The gp41(659-671) HIV-1 Antibody Epitope: A Structurally Challenging Small Peptide

JOURNAL OF PHYSICAL CHEMISTRY B, 118(1), 69–80.

Binding Polymorphism in the DNA Bound State of the Pdx1 Homeodomain

PLOS COMPUTATIONAL BIOLOGY, 9(8).

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

NUCLEIC ACIDS RESEARCH, 41(1), 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

CHEMICAL PHYSICS LETTERS, 518, 109–113.

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

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

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

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

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

JOURNAL OF CHEMICAL PHYSICS, 133(12).

Conformational free energies of methyl-alpha-L-iduronic and methyl-beta-D-glucuronic acids in water

JOURNAL OF CHEMICAL PHYSICS, 132(10).

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.

Adaptively Biased Molecular Dynamics: An Umbrella Sampling Method With a Time-Dependent Potential

Babin, V., Karpusenka, V., Moradi, M., Roland, C., & Sagui, C. (2009, December). INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Vol. 109, pp. 3666–3678.

Conformations and free energy landscapes of polyproline peptides

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106(49), 20746–20751.

Adaptively biased molecular dynamics for free energy calculations

Journal of Chemical Physics, 128(13).

Amino acid adsorption on the Si(100) surface: The case of glycine

JOURNAL OF PHYSICAL CHEMISTRY C, 112(7), 2640–2648.

Electrostatics in biomolecular simulations: Where are we now and where are we heading?

COMPUTATIONAL MODELING OF MEMBRANE BILAYERS, Vol. 60, pp. 49–89.

Theoretical investigation of the interaction of glycine with diamond C(100) and C(111) (2x1) surfaces

JOURNAL OF PHYSICAL CHEMISTRY C, 111(34), 12760–12767.

Deprotonation of solvated formic acid: Car-Parrinello and metadynamics simulations

JOURNAL OF PHYSICAL CHEMISTRY B, 110(5), 2325–2331.

Molecular dynamics simulations of DNA with polarizable force fields: Convergence of an ideal B-DNA structure to the crystallographic structure

JOURNAL OF PHYSICAL CHEMISTRY B, 110(23), 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

JOURNAL OF CHEMICAL PHYSICS, 125(20).

Exploring intramolecular reactions in complex systems with metadynamics: The case of the malonate anions

JOURNAL OF PHYSICAL CHEMISTRY A, 109(34), 7682–7687.

New and exotic self-organized patterns for modulated nanoscale systems

NANO LETTERS, 5(2), 389–395.

Quantum simulations of the structure and binding of glycopeptide antibiotic aglycons to cell wall analogues

JOURNAL OF PHYSICAL CHEMISTRY B, 109(43), 20588–20596.

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

PHYSICAL REVIEW E, 72(2).

Surface solvation for an ion in a water cluster

JOURNAL OF CHEMICAL PHYSICS, 122(2).

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

JOURNAL OF CHEMICAL PHYSICS, 120(9), 4530–4544.

First principles investigation of vancomycin and teicoplanin binding to bacterial cell wall termini

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 126(27), 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

JOURNAL OF CHEMICAL PHYSICS, 121(14), 6998–7008.

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

JOURNAL OF CHEMICAL PHYSICS, 120(1), 73–87.

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

Journal of Chemical Physics, 119(15), 7621–7632.

Liquid-crystal phases of capped carbon nanotubes

PHYSICAL REVIEW B, 63(8).