Celeste Sagui

Works (48)

2018 journal article

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

Nucleic Acids Research, 46(2), 942–955.

By: F. Pan, Y. Zhang, V. Man, C. Roland & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2018 journal article

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.

By: Y. Zhang, C. Roland & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2018 journal article

Structure and dynamics of DNA and RNA double helices obtained from the CCG and GGC trinucleotide repeats

Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 122(16), 4491–4512.

By: F. Pan, V. Man, C. Roland & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2017 journal article

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.

By: Y. Zhang, C. Roland & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2017 journal article

Structure and dynamics of DNA and RNA double helices of CAG and GAC trinucleotide repeats

Biophysical Journal, 113(1), 19–36.

By: F. Pan, V. Man, C. Roland & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2016 journal article

Amyloid properties of asparagine and glutamine in prion-like proteins

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

By: Y. Zhang, V. Man, C. Roland & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2016 journal article

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

Journal of Chemical Physics, 144(14).

By: V. Man, F. Pan, C. Sagui & C. Roland

Source: NC State University Libraries
Added: August 6, 2018

2016 journal article

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

Physical Chemistry Chemical Physics, 18(17), 11951–11958.

By: V. Man, N. Van-Oanh, P. Derreumaux, M. Li, C. Roland, C. Sagui, P. Nguyen

Source: NC State University Libraries
Added: August 6, 2018

2015 conference paper

Calculating transition and reaction rates with nonequilibrium work measurements

In Xxvi iupap conference on computational physics (ccp2014) (Vol. 640).

By: M. Moradi, C. Sagui & C. Roland

Source: NC State University Libraries
Added: August 6, 2018

2015 journal article

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

Journal of Chemical Physics, 143(15).

By: M. Viet, P. Derreumaux, M. Li, C. Roland, C. Sagui & P. Nguyen

Source: NC State University Libraries
Added: August 6, 2018

2015 journal article

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

Physical Chemistry Chemical Physics, 17(41), 27275–27280.

By: M. Viet, P. Truong, P. Derreumaux, M. Li, C. Roland, C. Sagui, P. Nguyen

Source: NC State University Libraries
Added: August 6, 2018

2015 journal article

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

Journal of Molecular Graphics & Modelling, 55, 72–84.

By: Y. Zhang & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2015 journal article

Structural determinants of polyglutamine protofibrils and crystallites

ACS Chemical Neuroscience, 6(4), 632–645.

By: V. Man, C. Roland & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2015 conference paper

The The adaptively biased molecular dynamics method revisited: New capabilities and an application

In Xxvi iupap conference on computational physics (ccp2014) (Vol. 640).

By: M. Moradi, V. Babin, C. Roland & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2014 review

Classical electrostatics for biomolecular simulations

Chemical Reviews.

By: G. Cisneros, M. Karttunen, P. Ren & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2014 article

Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities (vol 140, 034114, 2014)

Journal of Chemical Physics.

By: M. Moradi, C. Sagui & C. Roland

Source: NC State University Libraries
Added: August 6, 2018

2014 article

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

Journal of Chemical Physics.

By: M. Moradi, C. Sagui & C. Roland

Source: NC State University Libraries
Added: August 6, 2018

2014 journal article

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

Nucleic Acids Research, 42(22), 13981–13996.

By: F. Pan, C. Roland & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2014 journal article

The The gp41(659-671) HIV-1 antibody epitope: A structurally challenging small peptide

Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 118(1), 69–80.

By: Y. Zhang & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2013 journal article

Binding polymorphism in the DNA bound state of the Pdx1 Homeodomain

PLoS Computational Biology, 9(8).

By: V. Babin, D. Wang, R. Rose & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2013 journal article

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

Nucleic Acids Research, 41(1), 33–43.

By: M. Moradi, V. Babin, C. Roland & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2011 journal article

A A Statistical analysis of the PPII propensity of amino acid guests in proline-rich peptides

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

By: M. Moradi, V. Babin, C. Sagui & C. Roland

Source: NC State University Libraries
Added: August 6, 2018

2011 journal article

Calculating relative transition rates with driven nonequilibrium simulations

Chemical Physics Letters, 518, 109–113.

By: M. Moradi, C. Sagui & C. Roland

Source: NC State University Libraries
Added: August 6, 2018

2011 journal article

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

Proteins, 79(3), 937–946.

By: V. Babin, C. Roland & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2010 journal article

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

Journal of Chemical Physics, 133(12).

By: M. Moradi, V. Babin, C. Roland & C. Saguia

Source: NC State University Libraries
Added: August 6, 2018

2010 journal article

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

Journal of Chemical Physics, 132(10).

By: V. Babin & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2010 journal article

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

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

By: J. Lee, C. Sagui & C. Roland

Source: NC State University Libraries
Added: August 6, 2018

2010 journal article

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

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

By: M. Moradi, J. Lee, V. Babin, C. Roland & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2009 conference paper

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

In International Journal of Quantum Chemistry (Vol. 109, pp. 3666–3678).

Source: NC State University Libraries
Added: August 6, 2018

2009 journal article

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.

By: M. Moradi, V. Babin, C. Roland, T. Darden & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2008 journal article

Adaptively biased molecular dynamics for free energy calculations

Journal of Chemical Physics, 128(13).

By: V. Babin, C. Roland & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2008 journal article

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

Journal of Physical Chemistry. C, 112(7), 2640–2648.

By: X. Luo, G. Qian, C. Sagui & C. Roland

Source: NC State University Libraries
Added: August 6, 2018

2008 review

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

Computational modeling of membrane bilayers.

By: M. Karttunen, J. Rottler, I. Vattulainen & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2007 journal article

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.

By: K. Odbadrakh, X. Luo, J. Lee, C. Sagui & C. Roland

Source: NC State University Libraries
Added: August 6, 2018

2006 journal article

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

Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 110(5), 2325–2331.

By: J. Lee, E. Asciutto, V. Babin, C. Sagui, T. Darden & C. Roland

Source: NC State University Libraries
Added: August 6, 2018

2006 journal article

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, Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 110(23), 11571–11581.

By: V. Babin, J. Baucom, T. Darden & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2006 journal article

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

Journal of Chemical Physics, 125(20).

By: V. Babin, C. Roland, T. Darden & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2005 journal article

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

Journal of Physical Chemistry. A, Molecules, Spectroscopy, Kinetics, Environment & General Theory, 109(34), 7682–7687.

By: E. Asciutto & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2005 journal article

New and exotic self-organized patterns for modulated nanoscale systems

Nano Letters, 5(2), 389–395.

By: C. Sagui, E. Asciutto & C. Roland

Source: NC State University Libraries
Added: August 6, 2018

2005 journal article

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

Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 109(43), 20588–20596.

By: J. Lee, C. Sagui & C. Roland

Source: NC State University Libraries
Added: August 6, 2018

2005 journal article

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

Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 72(2).

By: E. Asciutto, C. Roland & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2005 journal article

Surface solvation for an ion in a water cluster

Journal of Chemical Physics, 122(2).

By: D. Herce, L. Perera, T. Darden & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2004 journal article

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

Journal of Chemical Physics, 120(9), 4530–4544.

By: C. Sagui, P. Pomorski, T. Darden & C. Roland

Source: NC State University Libraries
Added: August 6, 2018

2004 journal article

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

Journal of the American Chemical Society, 126(27), 8384–8385.

By: J. Lee, C. Sagui & C. Roland

Source: NC State University Libraries
Added: August 6, 2018

2004 journal article

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.

By: J. Baucom, T. Transue, M. Fuentes-Cabrera, J. Krahn, T. Darden & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2004 journal article

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.

By: C. Sagui, L. Pedersen & T. Darden

Source: NC State University Libraries
Added: August 6, 2018

2003 journal article

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

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

By: H. Herce, T. Darden & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2001 journal article

Liquid-crystal phases of capped carbon nanotubes - art. no.081403

Physical Review. B, Condensed Matter and Materials Physics, 6308(8), 1403.

By: A. Somoza, C. Sagui & C. Roland

Source: NC State University Libraries
Added: August 6, 2018