Celeste Sagui

Physics

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 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 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

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

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

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

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

2010 | journal article

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

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 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

2019 | 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

2019 | 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