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Journal Articles

Role of tungsten disulfide quantum dots in specific protein–protein interactions at air–water interface

Harsharan Kaur, Mayank Garg, Deepak Tomar, Suman Singh, Kailash C. Jena
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 084705 (2024)
https://doi.org/10.1063/5.0187563
Published: February 2024
View article titled, Role of tungsten disulfide quantum dots in specific protein–protein interactions at air–water interface
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Includes: Supplementary data
Journal Articles

Effects of flexibility in coarse-grained models for bovine serum albumin and immunoglobulin G

Frank Hirschmann, Hender Lopez, Felix Roosen-Runge, Tilo Seydel, Frank Schreiber, Martin Oettel
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 084112 (2023)
https://doi.org/10.1063/5.0132493
Published: February 2023
View article titled, Effects of flexibility in coarse-grained models for bovine serum albumin and immunoglobulin G
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Includes: Supplementary data
Journal Articles

Discrete stochastic models of SELEX: Aptamer capture probabilities and protocol optimization

Yue Wang, Bhaven A. Mistry, Tom Chou
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 244103 (2022)
https://doi.org/10.1063/5.0094307
Published: June 2022
View article titled, Discrete stochastic models of SELEX: Aptamer capture probabilities and protocol optimization
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Journal Articles

Understanding the bonding mechanisms of organic molecules deposited on graphene for biosensing applications

Elizabeth J. Legge, Muhammad M. Ali, Hina Y. Abbasi, Benjamen P. Reed, Barry Brennan, Lidija Matjačić, Zari Tehrani, Vlad Stolojan, S. Ravi P. Silva, Owen J. Guy, Andrew J. Pollard
Journal: The Journal of Chemical Physics
J. Chem. Phys. 155, 174703 (2021)
https://doi.org/10.1063/5.0064136
Published: November 2021
View article titled, Understanding the bonding mechanisms of organic molecules deposited on graphene for biosensing applications
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Includes: Supplementary data
Journal Articles

Atomistic insight towards the impact of polymer architecture and grafting density on structure-dynamics of PEGylated bovine serum albumin and their applications

Aravinda Munasinghe, Akash Mathavan, Akshay Mathavan, Ping Lin, Coray M. Colina
Journal: The Journal of Chemical Physics
J. Chem. Phys. 154, 075101 (2021)
https://doi.org/10.1063/5.0038306
Published: February 2021
View article titled, Atomistic insight towards the impact of polymer architecture and grafting density on structure-dynamics of PEGylated bovine serum albumin and their applications
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Includes: Supplementary data
Journal Articles

The effects of antigen size, binding site valency, and flexibility on fab-antigen binding near solid surfaces

Derek B. Bush, Thomas A. Knotts, IV
Journal: The Journal of Chemical Physics
J. Chem. Phys. 149, 165102 (2018)
https://doi.org/10.1063/1.5045356
Published: October 2018
View article titled, The effects of antigen size, binding site valency, and flexibility on fab-antigen binding near solid surfaces
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Journal Articles

Modeling antigen-antibody nanoparticle bioconjugates and their polymorphs

Caroline Desgranges, Jerome Delhommelle
Journal: The Journal of Chemical Physics
J. Chem. Phys. 148, 124507 (2018)
https://doi.org/10.1063/1.5018855
Published: March 2018
View article titled, Modeling antigen-antibody nanoparticle bioconjugates and their polymorphs
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Journal Articles

Binding free energy analysis of protein-protein docking model structures by evERdock

Kazuhiro Takemura, Nobuyuki Matubayasi, Akio Kitao
Journal: The Journal of Chemical Physics
J. Chem. Phys. 148, 105101 (2018)
https://doi.org/10.1063/1.5019864
Published: March 2018
View article titled, Binding free energy analysis of protein-protein docking model structures by evERdock
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Journal Articles

Forced-rupture of cell-adhesion complexes reveals abrupt switch between two brittle states

Scilight
Ngo Minh Toan, D. Thirumalai
Journal: The Journal of Chemical Physics
J. Chem. Phys. 148, 123332 (2018)
https://doi.org/10.1063/1.5011056
Published: March 2018
View article titled, Forced-rupture of cell-adhesion complexes reveals abrupt switch between two brittle states
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Journal Articles

Force feedback effects on single molecule hopping and pulling experiments

M. Rico-Pasto, I. Pastor, F. Ritort
Journal: The Journal of Chemical Physics
J. Chem. Phys. 148, 123327 (2018)
https://doi.org/10.1063/1.5010303
Published: February 2018
View article titled, Force feedback effects on single molecule hopping and pulling experiments
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Journal Articles

Phasor based single-molecule localization microscopy in 3D (pSMLM-3D): An algorithm for MHz localization rates using standard CPUs

Koen J. A. Martens, Arjen N. Bader, Sander Baas, Bernd Rieger, Johannes Hohlbein
Journal: The Journal of Chemical Physics
J. Chem. Phys. 148, 123311 (2018)
https://doi.org/10.1063/1.5005899
Published: December 2017
View article titled, Phasor based single-molecule localization microscopy in 3D (pSMLM-3D): An algorithm for MHz localization rates using standard CPUs
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Includes: Supplementary data
Journal Articles

Two states or not two states: Single-molecule folding studies of protein L

Scilight
Haim Yuval Aviram, Menahem Pirchi, Yoav Barak, Inbal Riven, Gilad Haran
Journal: The Journal of Chemical Physics
J. Chem. Phys. 148, 123303 (2018)
https://doi.org/10.1063/1.4997584
Published: October 2017
View article titled, Two states or not two states: Single-molecule folding studies of protein L
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Includes: Supplementary data
Journal Articles

The effects of tether placement on antibody stability on surfaces

Rebecca W. Grawe, Thomas A. Knotts, IV
Journal: The Journal of Chemical Physics
J. Chem. Phys. 146, 215102 (2017)
https://doi.org/10.1063/1.4983705
Published: June 2017
View article titled, The effects of tether placement on antibody stability on surfaces
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Journal Articles

Probing the effects of surface hydrophobicity and tether orientation on antibody-antigen binding

Derek B. Bush, Thomas A. Knotts, IV
Journal: The Journal of Chemical Physics
J. Chem. Phys. 146, 155103 (2017)
https://doi.org/10.1063/1.4980083
Published: April 2017
View article titled, Probing the effects of surface hydrophobicity and tether orientation on antibody-antigen binding
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Journal Articles

The phase behavior study of human antibody solution using multi-scale modeling

Gang Sun, Ying Wang, Aleksey Lomakin, George B. Benedek, H. Eugene Stanley, Limei Xu, Sergey V. Buldyrev
Journal: The Journal of Chemical Physics
J. Chem. Phys. 145, 194901 (2016)
https://doi.org/10.1063/1.4966972
Published: November 2016
View article titled, The phase behavior study of human antibody solution using multi-scale modeling
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Includes: Supplementary data
Journal Articles

Evaluation of effects of pH and ionic strength on colloidal stability of IgG solutions by PEG-induced liquid-liquid phase separation

Ronald W. Thompson, Jr., Ramil F. Latypov, Ying Wang, Aleksey Lomakin, Julie A. Meyer, Suresh Vunnum, George B. Benedek
Journal: The Journal of Chemical Physics
J. Chem. Phys. 145, 185101 (2016)
https://doi.org/10.1063/1.4966708
Published: November 2016
View article titled, Evaluation of effects of pH and ionic strength on colloidal stability of IgG solutions by PEG-induced liquid-liquid phase separation
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Includes: Supplementary data
Journal Articles

Sensitivity measurement of a cantilever-based surface stress sensor

Ann-Lauriene Haag, Zeno Schumacher, Peter Grutter
Journal: The Journal of Chemical Physics
J. Chem. Phys. 145, 154704 (2016)
https://doi.org/10.1063/1.4964922
Published: October 2016
View article titled, Sensitivity measurement of a cantilever-based surface stress sensor
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Journal Articles

Miming the cancer-immune system competition by kinetic Monte Carlo simulations

Carlo Bianca, Annie Lemarchand
Journal: The Journal of Chemical Physics
J. Chem. Phys. 145, 154108 (2016)
https://doi.org/10.1063/1.4964778
Published: October 2016
View article titled, Miming the cancer-immune system competition by kinetic Monte Carlo simulations
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Journal Articles

Accelerating rejection-based simulation of biochemical reactions with bounded acceptance probability

Vo Hong Thanh, Corrado Priami, Roberto Zunino
Journal: The Journal of Chemical Physics
J. Chem. Phys. 144, 224108 (2016)
https://doi.org/10.1063/1.4953559
Published: June 2016
View article titled, Accelerating rejection-based simulation of biochemical reactions with bounded acceptance probability
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Journal Articles

Transitions in genetic toggle switches driven by dynamic disorder in rate coefficients

Hang Chen, Peter Thill, Jianshu Cao
Journal: The Journal of Chemical Physics
J. Chem. Phys. 144, 175104 (2016)
https://doi.org/10.1063/1.4948461
Published: May 2016
View article titled, Transitions in genetic toggle switches driven by dynamic disorder in rate coefficients
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