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Journal Articles

Molecular dynamics studies of knotted polymers

Mark DelloStritto, Cristian Micheletti, Michael L. Klein
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 244904 (2024)
https://doi.org/10.1063/5.0237773
Published: December 2024
View article titled, Molecular dynamics studies of knotted polymers
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Journal Articles

Adaptive resolution force probe simulations: Coarse graining in the ideal gas approximation

Marco Oestereich, Jürgen Gauss, Gregor Diezemann
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 154903 (2024)
https://doi.org/10.1063/5.0228198
Published: October 2024
View article titled, Adaptive resolution force probe simulations: Coarse graining in the ideal gas approximation
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Journal Articles

Quantification of van der Waals forces in bimodal and trimodal AFM

Sergio Santos, Karim Gadelrab, Lamiaa Elsherbiny, Xaver Drexler, Tuza Olukan, Josep Font, Victor Barcons, Matteo Chiesa
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 204703 (2023)
https://doi.org/10.1063/5.0154196
Published: May 2023
View article titled, Quantification of van der Waals forces in bimodal and trimodal AFM
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Journal Articles

Assessing models of force-dependent unbinding rates via infrequent metadynamics

Willmor J. Peña Ccoa, Glen M. Hocky
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 125102 (2022)
https://doi.org/10.1063/5.0081078
Published: March 2022
View article titled, Assessing models of force-dependent unbinding rates via infrequent metadynamics
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Includes: Supplementary data
Journal Articles

Identification and correction of miscalibration artifacts based on force noise for optical tweezers experiments

Marvin Freitag, Dieter Kamp, Marie Synakewicz, Johannes Stigler
Journal: The Journal of Chemical Physics
J. Chem. Phys. 155, 175101 (2021)
https://doi.org/10.1063/5.0063690
Published: November 2021
View article titled, Identification and correction of miscalibration artifacts based on force noise for optical tweezers experiments
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Includes: Supplementary data
Journal Articles

Simulation of protein pulling dynamics on second time scale with boxed molecular dynamics

Sarah Mapplebeck, Jonathan Booth, Dmitrii Shalashilin
Journal: The Journal of Chemical Physics
J. Chem. Phys. 155, 085101 (2021)
https://doi.org/10.1063/5.0059321
Published: August 2021
View article titled, Simulation of protein pulling dynamics on second time scale with boxed molecular dynamics
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Journal Articles

Detection of single DNA mismatches by force spectroscopy in short DNA hairpins

F. Landuzzi, X. Viader-Godoy, F. Cleri, I. Pastor, F. Ritort
Journal: The Journal of Chemical Physics
J. Chem. Phys. 152, 074204 (2020)
https://doi.org/10.1063/1.5139284
Published: February 2020
View article titled, Detection of single DNA mismatches by force spectroscopy in short DNA hairpins
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Includes: Supplementary data
Journal Articles

Non-Markov bond model for dynamic force spectroscopy

Jakob Tómas Bullerjahn, Sebastian Sturm, Klaus Kroy
Journal: The Journal of Chemical Physics
J. Chem. Phys. 152, 064104 (2020)
https://doi.org/10.1063/1.5134742
Published: February 2020
View article titled, Non-Markov bond model for dynamic force spectroscopy
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Journal Articles

Single molecule force spectroscopy of a streptomycin-binding RNA aptamer: An out-of-equilibrium molecular dynamics study

Luis A. Baptista, Paulo A. Netz
Journal: The Journal of Chemical Physics
J. Chem. Phys. 151, 195102 (2019)
https://doi.org/10.1063/1.5128126
Published: November 2019
View article titled, Single molecule force spectroscopy of a streptomycin-binding RNA aptamer: An out-of-equilibrium molecular dynamics study
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Includes: Supplementary data
Journal Articles

Thermal versus mechanical unfolding in a model protein

Rafael Tapia-Rojo, Juan J. Mazo, Fernando Falo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 151, 185105 (2019)
https://doi.org/10.1063/1.5126071
Published: November 2019
View article titled, Thermal versus mechanical unfolding in a model protein
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Journal Articles

On the forward/backward symmetry of transition path time distributions in nonequilibrium systems

Alexander M. Berezhkovskii, Dmitrii E. Makarov
Journal: The Journal of Chemical Physics
J. Chem. Phys. 151, 065102 (2019)
https://doi.org/10.1063/1.5109293
Published: August 2019
View article titled, On the forward/backward symmetry of transition path time distributions in nonequilibrium systems
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Journal Articles

Diffusion in a rough potential: Dual-scale structure and regime crossovers

Carlos E. Colosqui
Journal: The Journal of Chemical Physics
J. Chem. Phys. 150, 181102 (2019)
https://doi.org/10.1063/1.5096552
Published: May 2019
View article titled, Diffusion in a rough potential: Dual-scale structure and regime crossovers
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Journal Articles

Goodness of fit testing in dynamic single-molecule force spectroscopy

Ana E. Bergues-Pupo, Melis Goktas, Isabell Tunn, Patricia Lopez-Garcia, Ana Vila Verde, Kerstin G. Blank, Angelo Valleriani
Journal: The Journal of Chemical Physics
J. Chem. Phys. 149, 244120 (2018)
https://doi.org/10.1063/1.5055071
Published: December 2018
View article titled, Goodness of fit testing in dynamic single-molecule force spectroscopy
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Includes: Supplementary data
Journal Articles

Absolute cross section for DNA damage induced by low-energy (10 eV) electrons: Experimental refinements and sample characterization by AFM

Editor’s Pick
N. Brodeur, P. Cloutier, A. D. Bass, G. Bertrand, D. J. Hunting, M. Grandbois, L. Sanche
Journal: The Journal of Chemical Physics
J. Chem. Phys. 149, 164904 (2018)
https://doi.org/10.1063/1.5041805
Published: October 2018
View article titled, Absolute cross section for DNA damage induced by low-energy (10 eV) electrons: Experimental refinements and sample characterization by AFM
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Journal Articles

Transition-path properties for folding reactions in the limit of small barriers

Andrew G. T. Pyo, Noel Q. Hoffer, Krishna Neupane, Michael T. Woodside
Journal: The Journal of Chemical Physics
J. Chem. Phys. 149, 115101 (2018)
https://doi.org/10.1063/1.5046692
Published: September 2018
View article titled, Transition-path properties for folding reactions in the limit of small barriers
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Journal Articles

Communication: Transition-path velocity as an experimental measure of barrier crossing dynamics

Alexander M. Berezhkovskii, Dmitrii E. Makarov
Journal: The Journal of Chemical Physics
J. Chem. Phys. 148, 201102 (2018)
https://doi.org/10.1063/1.5030427
Published: May 2018
View article titled, Communication: Transition-path velocity as an experimental measure of barrier crossing dynamics
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Journal Articles

Preface: Special Topic on Single-Molecule Biophysics

Dmitrii E. Makarov, Benjamin Schuler
Journal: The Journal of Chemical Physics
J. Chem. Phys. 148, 123001 (2018)
https://doi.org/10.1063/1.5028275
Published: March 2018
View article titled, Preface: Special Topic on Single-Molecule Biophysics
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Journal Articles

History, rare, and multiple events of mechanical unfolding of repeat proteins

Fidan Sumbul, Arin Marchesi, Felix Rico
Journal: The Journal of Chemical Physics
J. Chem. Phys. 148, 123335 (2018)
https://doi.org/10.1063/1.5013259
Published: March 2018
View article titled, History, rare, and multiple events of mechanical unfolding of repeat proteins
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Includes: Supplementary data
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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