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Journal Articles

Coarse-grained dynamics of transiently bound fast linkers

Sophie Marbach, Christopher E. Miles
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 214117 (2023)
https://doi.org/10.1063/5.0139036
Published: June 2023
View article titled, Coarse-grained dynamics of transiently bound fast linkers
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Includes: Supplementary data
Journal Articles

Emulsion imaging of a DNA nanostar condensate phase diagram reveals valence and electrostatic effects

Nathaniel Conrad, Grace Chang, Deborah K. Fygenson, Omar A. Saleh
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 234203 (2022)
https://doi.org/10.1063/5.0130808
Published: December 2022
View article titled, Emulsion imaging of a DNA nanostar condensate phase diagram reveals valence and electrostatic effects
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Includes: Supplementary data
Journal Articles

Investigation into the mechanism and dynamics of DNA association and dissociation utilizing kinetic Monte Carlo simulations

Ryan J. Menssen, Gregory J. Kimmel, Andrei Tokmakoff
Journal: The Journal of Chemical Physics
J. Chem. Phys. 154, 045101 (2021)
https://doi.org/10.1063/5.0035187
Published: January 2021
View article titled, Investigation into the mechanism and dynamics of DNA association and dissociation utilizing kinetic Monte Carlo simulations
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Journal Articles

A mean-field model of linker-mediated colloidal interactions

W. Benjamin Rogers
Journal: The Journal of Chemical Physics
J. Chem. Phys. 153, 124901 (2020)
https://doi.org/10.1063/5.0020578
Published: September 2020
View article titled, A mean-field model of linker-mediated colloidal interactions
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Includes: Supplementary data
Journal Articles

A lattice model for the interpretation of oligonucleotide hybridization experiments

Paul J. Sanstead, Andrei Tokmakoff
Journal: The Journal of Chemical Physics
J. Chem. Phys. 150, 185104 (2019)
https://doi.org/10.1063/1.5092526
Published: May 2019
View article titled, A lattice model for the interpretation of oligonucleotide hybridization experiments
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Journal Articles

Mechanisms of DNA hybridization: Transition path analysis of a simulation-informed Markov model

Raymond Jin, Lutz Maibaum
Journal: The Journal of Chemical Physics
J. Chem. Phys. 150, 105103 (2019)
https://doi.org/10.1063/1.5054593
Published: March 2019
View article titled, Mechanisms of DNA hybridization: Transition path analysis of a simulation-informed Markov model
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Includes: Supplementary data
Journal Articles

Forward-flux sampling with jumpy order parameters

Amir Haji-Akbari
Journal: The Journal of Chemical Physics
J. Chem. Phys. 149, 072303 (2018)
https://doi.org/10.1063/1.5018303
Published: May 2018
View article titled, Forward-flux sampling with jumpy order parameters
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Journal Articles

Surface energy fluctuation effects in single crystals of DNA-functionalized nanoparticles

Ting I. N. G. Li, Monica Olvera de la Cruz
Journal: The Journal of Chemical Physics
J. Chem. Phys. 143, 243156 (2015)
https://doi.org/10.1063/1.4938533
Published: December 2015
View article titled, Surface energy fluctuation effects in single crystals of DNA-functionalized nanoparticles
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Journal Articles

Coarse-grained modeling of DNA oligomer hybridization: Length, sequence, and salt effects

Daniel M. Hinckley, Joshua P. Lequieu, Juan J. de Pablo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 141, 035102 (2014)
https://doi.org/10.1063/1.4886336
Published: July 2014
View article titled, Coarse-grained modeling of DNA oligomer hybridization: Length, sequence, and salt effects
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Includes: Supplementary data
Journal Articles

Sequence-dependent theory of oligonucleotide hybridization kinetics

Karthikeyan Marimuthu, Raj Chakrabarti
Journal: The Journal of Chemical Physics
J. Chem. Phys. 140, 175104 (2014)
https://doi.org/10.1063/1.4873585
Published: May 2014
View article titled, Sequence-dependent theory of oligonucleotide hybridization kinetics
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Includes: Supplementary data
Journal Articles

Exploring the mechanisms of DNA hybridization on a surface

Terry J. Schmitt, J. Brandon Rogers, Thomas A. Knotts, IV
Journal: The Journal of Chemical Physics
J. Chem. Phys. 138, 035102 (2013)
https://doi.org/10.1063/1.4775480
Published: January 2013
View article titled, Exploring the mechanisms of DNA hybridization on a surface
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Journal Articles

A coarse-grained model for DNA-functionalized spherical colloids, revisited: Effective pair potential from parallel replica simulations

Panagiotis E. Theodorakis, Christoph Dellago, Gerhard Kahl
Journal: The Journal of Chemical Physics
J. Chem. Phys. 138, 025101 (2013)
https://doi.org/10.1063/1.4773920
Published: January 2013
View article titled, A coarse-grained model for DNA-functionalized spherical colloids, revisited: Effective pair potential from parallel replica simulations
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Journal Articles

Stability of DNA-linked nanoparticle crystals: Effect of number of strands, core size, and rigidity of strand attachment

Olivia Padovan-Merhar, Fernando Vargas Lara, Francis W. Starr
Journal: The Journal of Chemical Physics
J. Chem. Phys. 134, 244701 (2011)
https://doi.org/10.1063/1.3596745
Published: June 2011
View article titled, Stability of DNA-linked nanoparticle crystals: Effect of number of strands, core size, and rigidity of strand attachment
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Journal Articles

Thermodynamics of DNA hybridization on surfaces

Terry J. Schmitt, Thomas A. Knotts, IV
Journal: The Journal of Chemical Physics
J. Chem. Phys. 134, 205105 (2011)
https://doi.org/10.1063/1.3592557
Published: May 2011
View article titled, Thermodynamics of DNA hybridization on surfaces
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Journal Articles

Packing structures of single-stranded DNA and double-stranded DNA thiolates on Au(111): A molecular simulation study

Liqun Yao, Jim Sullivan, Jason Hower, Yi He, Shaoyi Jiang
Journal: The Journal of Chemical Physics
J. Chem. Phys. 127, 195101 (2007)
https://doi.org/10.1063/1.2786984
Published: November 2007
View article titled, Packing structures of single-stranded DNA and double-stranded DNA thiolates on Au(111): A molecular simulation study
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