(50)
Massa J. Shoura, R. J. K. Udayana Ranatunga, Sarah A. Harris, Steven O. Nielsen, and Stephen D. Levene
Contribution of fluorophore dynamics and solvation to resonant energy transfer in protein-DNA complexes: a molecular-dynamics study
Biophysical Journal 107 700-710 (2014).
(49)
Jingbo Wu, Blake A. Wilson, Dennis W. Smith Jr., and Steven O. Nielsen
Towards an understanding of structure-nonlinearity relationships in triarylamine-based push-pull electro-optic chromophores: the influence of substituent and molecular conformation on molecular hyperpolarizabilities
Journal of Materials Chemistry C 2 2591-2599 (2014).
(48)
Steven O. Nielsen
Nested sampling in the canonical ensemble: Direct calculation of the partition function from NVT trajectories
Journal of Chemical Physics 139 124104 (2013).
(47)
Shuhei Kawamoto, Takenobu Nakamura, Steven O. Nielsen, and Wataru Shinoda
A guiding potential method for evaluating the bending rigidity of tensionless lipid membranes from molecular simulation
Journal of Chemical Physics 139 034108 (2013).
(46)
Jing Hao, Yixing Cheng, R. J. K. Udayana Ranatunga, Suchithra Senevirathne, Michael C. Biewer, Steven O. Nielsen, Qian Wang, and Mihaela C. Stefan
A combined experimental and computational study of the substituent effect on micellar behavior of γ-substituted thermoresponsive amphiphilic poly(ε-caprolactone)s
Macromolecules 46 4829-4838 (2013).
(Book Chapter)
Bernd Ensing, Alessandro Laio, and Steven O. Nielsen
Hamiltonian adaptive hybrid atomistic/coarse-grain molecular dynamics
page 95-110 in
Hybrid Particle-Continuum Methods in Computational Materials Physics
M. H. Muser, G. Sutmann, and R. G. Winkler (editors), John von Neumann Institute for Computing (NIC Series) Volume 46 (2013) isbn13: 9783893368495.
(45)
Dinushi R. Samarajeewa, Gregg R. Dieckmann, Steven O. Nielsen, and Inga H. Musselman
Doping single-walled carbon nanotubes with surfactant peptides containing electron-donor substituents and nitrogen heterocycles
Carbon 57 88-98 (2013).
(44)
Chi-cheng Chiu, Russell H. DeVane, Michael L. Klein, Wataru Shinoda, Preston B. Moore, and Steven O. Nielsen
Effect of carboxylation on carbon nanotube aqueous dispersibility: a predictive coarse-grained molecular dynamics approach
Journal of Physical Chemistry C 116 23102-23106 (2012).
(43)
Chi-cheng Chiu, Wataru Shinoda, Russell H. DeVane, and Steven O. Nielsen
Effects of spherical fullerene nanoparticles on a dipalmitoyl phosphatidylcholine lipid monolayer: a coarse grain molecular dynamics approach
Soft Matter 8 9610-9616 (2012).
(42)
Dinushi R. Samarajeewa, Gregg R. Dieckmann, Steven O. Nielsen, and Inga H. Musselman
Modifying the electronic properties of single-walled carbon nanotubes using designed surfactant peptides
Nanoscale 4 4544-4554 (2012).
(Book Chapter)
R. J. K. Udayana Ranatunga, Chuong T. Nguyen, Chi-cheng Chiu, Wataru Shinoda, and Steven O. Nielsen
Molecular dynamics simulations of nanoparticles and surfactants at oil/water interfaces
Chapter 18 in
Amphiphiles: Molecular Assembly and Applications
R. Nagarajan (editor), ACS Symposium Series Volume 1070 (2011) isbn13: 9780841226500.
(41)
R. J. K. Udayana Ranatunga and Steven O. Nielsen
Application of a continuum mean field approximation to fullerenes in lipid bilayers
Current Nanoscience 7 667-673 (2011).
(40)
Steven O. Nielsen, Preston B. Moore, and Bernd Ensing
Comment on "Adaptive multiscale molecular dynamics of macromolecular fluids" -- Reply
Physical Review Letters 107 099802 (2011).
(39)
Wataru Shinoda, Takenobu Nakamura, and Steven O. Nielsen
Free energy analysis of vesicle-to-bicelle transformation
Soft Matter 7 9012-9020 (2011).
(38)
R. J. K. Udayana Ranatunga, Chuong T. Nguyen, Blake A. Wilson, Wataru Shinoda, and Steven O. Nielsen
Molecular dynamics study of nanoparticles and non-ionic surfactant at an oil-water interface
Soft Matter 7 6942-6952 (2011).
(37)
Steven O. Nielsen, Preston B. Moore, and Bernd Ensing
Adaptive multiscale molecular dynamics of macromolecular fluids
Physical Review Letters 105 237802 (2010).
(36)
Russell DeVane, Arben Jusufi, Wataru Shinoda, Chi-cheng Chiu, Steven O. Nielsen, Preston B. Moore, and Michael L. Klein
Parameterization and application of a coarse grained force field for benzene/fullerene interactions with lipids
Journal of Physical Chemistry B 114 16364-16372 (2010).
(35)
Steven O. Nielsen, Rosa E. Bulo, Preston B. Moore, and Bernd Ensing
Recent progress in adaptive multiscale molecular dynamics simulations of soft matter
Physical Chemistry Chemical Physics 12 12401-12414 (2010).
inside cover article (issue 39)
(34)
R. J. K. Udayana Ranatunga, Robert J. B. Kalescky, Chi-cheng Chiu, and Steven O. Nielsen
Molecular dynamics simulations of surfactant functionalized nanoparticles in the vicinity
of an oil/water interface
Journal of Physical Chemistry C 114 12151-12157 (2010).
(33)
Chi-cheng Chiu, Marie C. Maher, Gregg R. Dieckmann, and Steven O. Nielsen
Molecular dynamics study of a carbon nanotube binding reversible cyclic peptide
ACS Nano 4 2539-2546 (2010).
(32)
Chi-cheng Chiu, Russell DeVane, Michael L. Klein, Wataru Shinoda, Preston B. Moore, and Steven O. Nielsen
Coarse-grained potential models for phenyl-based molecules: II. Application to fullerenes
Journal of Physical Chemistry B 114 6394-6400 (2010).
(31)
Russell DeVane, Michael L. Klein, Chi-cheng Chiu, Steven O. Nielsen, Wataru Shinoda, and Preston B. Moore
Coarse-grained potential models for phenyl-based molecules: I. Parametrization using experimental data
Journal of Physical Chemistry B 114 6386-6393 (2010).
(Book Chapter)
Bernd Ensing and Steven O. Nielsen
Multiscale molecular dynamics and the reverse mapping problem
Chapter 2 in
Trends in Computational Nanomechanics: Transcending Length and Time Scales
T. Dumitrica (editor), Springer Series: Challenges and Advances in Computational Chemistry and Physics. Vol. 9 (2010) isbn: 9781402097843.
(30)
Chi-cheng Chiu, R. J. K. Udayana Ranatunga, David Torres Flores, D. Vladimir Pérez, Preston B. Moore, Wataru Shinoda, and Steven O. Nielsen
A mean field approach for computing solid-liquid surface tension
for nanoscale interfaces
Journal of Chemical Physics 132 054706 (2010).
selected for the February 15, 2010 issue of Virtual Journal of Nanoscale Science & Technology.
(29)
Chi-cheng Chiu, Preston B. Moore, Wataru Shinoda, and Steven O. Nielsen
Size-dependent hydrophobic to hydrophilic transition for nanoparticles:
a molecular dynamics study
Journal of Chemical Physics 131 244706 (2009).
selected for the January 1, 2010 issue of Virtual Journal of Biological Physics Research.
(28)
Chi-cheng Chiu, Gregg R. Dieckmann, and Steven O. Nielsen
Role of peptide-peptide interactions in stabilizing peptide-wrapped single-walled carbon nanotubes: a molecular dynamics study
Biopolymers: Peptide Science 92 156-163 (2009).
(27)
Robert J. B. Kalescky, Wataru Shinoda, Preston B. Moore, and Steven O. Nielsen
Area per ligand as a function of nanoparticle radius: a theoretical and computer simulation approach
Langmuir 25 1352-1359 (2009).
(26)
Uriel Octavio Moreles Vázquez, Wataru Shinoda, Preston B. Moore, Chi-cheng Chiu, and Steven O. Nielsen
Calculating the surface tension between a flat solid and a liquid:
a theoretical and computer simulation study of three
topologically different methods
Journal of Mathematical Chemistry 45 161-174 (2009).
(25)
Chi-cheng Chiu, Gregg R. Dieckmann, and Steven O. Nielsen
Molecular dynamics study of a nanotube-binding amphiphilic helical peptide at different water/hydrophobic interfaces
Journal of Physical Chemistry B 112 16326-16333 (2008).
(Book Chapter)
Steven O. Nielsen, Bernd Ensing, Preston B. Moore, and Michael L. Klein
Coarse grained-to-atomistic mapping algorithm: a tool for multiscale simulations
page 73-88 in
Multiscale Simulation Methods for Nanomaterials
R. B. Ross and S. Mohanty (editors)
Wiley (2008)
isbn: 9780470105283
(24)
Bernd Ensing, Steven O. Nielsen , Preston B. Moore, Michael L. Klein, and Michele Parrinello
Energy conservation in adaptive hybrid atomistic/coarse-grain molecular dynamics
Journal of Chemical Theory and Computation 3 1100-1105 (2007).
(23)
Ekta Khurana, Steven O. Nielsen , and Michael L. Klein
Gemini surfactants at the air/water interface: a fully atomistic molecular dynamics study
Journal of Physical Chemistry B 110 22136-22142 (2006).
(22)
Vanessa Ortiz, Steven O. Nielsen, Michael L. Klein, and Dennis E. Discher
Computer simulation of aqueous block copolymer assemblies: Length scales and methods
Journal of Polymer Science: Part B: Polymer Physics 44 1907-1918 (2006).
(21)
Ekta Khurana, Steven O. Nielsen , Bernd Ensing, and Michael L. Klein
Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents
Journal of Physical Chemistry B 110 18965-18972 (2006).
(20)
Carlos F. Lopez, Steven O. Nielsen , Goundla Srinivas, William F. DeGrado, and Michael L. Klein
Probing membrane insertion activity of antimicrobial polymers via coarse-grain molecular dynamics
Journal of Chemical Theory and Computation 2 649-655 (2006).
(19)
Goundla Srinivas, Steven O Nielsen, Preston B Moore, and Michael L Klein
Molecular dynamics simulations of surfactant
self-organization at a solid-liquid interface
Journal of the American Chemical Society 128 848-853 (2006).
(18)
Steven O Nielsen, Goundla Srinivas, and Michael L Klein
Incorporating a hydrophobic solid into a coarse grain liquid framework:
graphite in an aqueous amphiphilic environment
Journal of Chemical Physics 123 124907 (2005).
(17)
Vanessa Ortiz, Steven O Nielsen, Dennis E Discher, Michael L Klein, Reinhard Lipowsky, and Julian Shillcock
Dissipative particle dynamics simulations of polymersomes
Journal of Physical Chemistry B 109 17708-17714 (2005).
(16)
Steve O Nielsen, Goundla Srinivas, Carlos F. Lopez, and Michael L Klein
Modeling surfactant adsorption on hydrophobic surfaces
Physical Review Letters 94 228301 (2005).
selected for the June 20, 2005 issue of Virtual Journal of Nanoscale Science & Technology.
selected for the June 15, 2005 issue of Virtual Journal of Biological Physics Research.
(15)
Vanessa Ortiz, Steven O Nielsen, Michael L Klein, and Dennis E Discher
Unfolding a linker between helical repeats
Journal of Molecular Biology 349 638-647 (2005).
(14)
Steve O Nielsen, Bernd Ensing, Vanessa Ortiz, Preston B Moore, and Michael L. Klein
Lipid bilayer perturbations around a transmembrane nanotube: a coarse grain molecular dynamics study
Biophysical Journal 88 3822-3828 (2005).
Cover article (June issue)
(13)
Carlos F Lopez, Steve O Nielsen, Bernd Ensing, Preston B Moore, and Michael L Klein
Structure and dynamics of model pore insertion into a membrane
Biophysical Journal 88 3083-3094 (2005).
Cover article (May issue)
(12)
Steve O Nielsen, Carlos F Lopez, Ivaylo Ivanov, Preston B Moore, John C Shelley, and Michael L. Klein
Transmembrane peptide-induced lipid sorting and mechanism of Lα-to-inverted phase transition using coarse-grain molecular dynamics
Biophysical Journal 87 2107-2115 (2004).
(11)
Goundla Srinivas, John C Shelley, Steve O Nielsen, Dennis E. Discher, and Michael L. Klein
Simulation of diblock copolymer self-assembly, using a coarse-grain model
Journal of Physical Chemistry B 108 8153-8160 (2004).
(10)
Steve O. Nielsen, Carlos F. Lopez, Goundla Srinivas, and Michael L. Klein
Coarse grain models and the computer simulation of soft materials
Journal of Physics: Condensed Matter 16 R481-R512 (2004).
Cover article (April 21 issue)
(9)
Carlos F Lopez, Steve O Nielsen, Preston B Moore, and Michael L Klein
Understanding nature's design for a nanosyringe
Proceedings of the National Academy of Sciences 101 4431-4434 (2004).
Mentioned on the cover (March 30 issue)
Featured in the commentary:
A. Aksimentiev and K. Schulten PNAS 101 4337-4338 (2004).
(8)
Carlos F Lopez, Steve O Nielsen, Michael L Klein, and Preston B Moore
Hydrogen Bonding Structure and Dynamics of Water at the
Dimyristoylphosphatidylcholine Lipid Bilayer Surface from a Molecular Dynamics Simulation
Journal of Physical Chemistry B 108 6603-6610 (2004).
(7)
Steve O Nielsen, Carlos F Lopez, Preston B Moore, John C Shelley, and Michael L Klein
Molecular dynamics investigations of lipid Langmuir monolayers using a coarse grain model
Journal of Physical Chemistry B 107 13911-13917 (2003).
(6)
Steve O Nielsen, Carlos F Lopez, Goundla Srinivas, and Michael L Klein
A coarse grain model for n-alkanes parameterized from surface tension data
Journal of Chemical Physics 119 7043-7049 (2003).
(Book Chapter) (postscript file)
Steve O. Nielsen and Michael L. Klein
A coarse grain model for lipid monolayer and bilayer studies
page 27-63 in
Bridging the Time Scales: Molecular Simulations for the Next Decade
P. Nielaba, M. Mareschal, and G. Ciccotti (editors)
Springer (2002)
isbn: 3540443177
(5)
Carlos F Lopez, Steve O Nielsen, Preston B Moore, John C Shelley, and
Michael L Klein
Self-assembly of a phospholipid Langmuir monolayer using
coarse-grained molecular dynamics simulations
Journal of Physics: Condensed Matter 14 9431-9444 (2002).
(4)
Steve Nielsen, Raymond Kapral, and Giovanni Ciccotti
Statistical mechanics of quantum-classical systems
Journal of Chemical Physics
115 5805-5815 (2001).
(3)
Steve Nielsen, Raymond Kapral, and Giovanni Ciccotti
Non-adiabatic dynamics in mixed quantum-classical systems
Journal of Statistical Physics
101 225-242 (2000).
(2)
Steve Nielsen, Raymond Kapral, and Giovanni Ciccotti
Mixed quantum-classical surface hopping dynamics
Journal of Chemical Physics
112 6543-6553 (2000).
(1)
Steve Nielsen and Raymond Kapral
Coloring a Lorentz Gas
Journal of Chemical Physics
109 6460-6468 (1998).