Modeling single-molecule stretching experiments using statistical thermodynamics

Buche, Michael R.; Rimsza, Jessica M.

doi:10.1103/physreve.108.064503

Modeling single-molecule stretching experiments using statistical thermodynamics

Journal Article · Mon Dec 25 23:00:00 EST 2023 · Physical Review. E

DOI:https://doi.org/10.1103/physreve.108.064503· OSTI ID:2311285

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Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)

Single-molecule stretching experiments are widely utilized within the fields of physics and chemistry to characterize the mechanics of individual bonds or molecules, as well as chemical reactions. Analytic relations describing these experiments are valuable, and these relations can be obtained through the statistical thermodynamics of idealized model systems representing the experiments. Since the specific thermodynamic ensembles manifested by the experiments affect the outcome, primarily for small molecules, the stretching device must be included in the idealized model system. Though the model for the stretched molecule might be exactly solvable, including the device in the model often prevents analytic solutions. In the limit of large or small device stiffness, the isometric or isotensional ensembles can provide effective approximations, but the device effects are missing. Here a dual set of asymptotically correct statistical thermodynamic theories are applied to develop accurate approximations for the full model system that includes both the molecule and the device. In conclusion, the asymptotic theories are first demonstrated to be accurate using the freely jointed chain model and then using molecular dynamics calculations of a single polyethylene chain.

View Accepted Manuscript (DOE)

Research Organization:: Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA); USDOE Laboratory Directed Research and Development (LDRD) Program

Grant/Contract Number:: NA0003525

OSTI ID:: 2311285

Report Number(s):: SAND--2024-00081J

Journal Information:: Physical Review. E, Journal Name: Physical Review. E Journal Issue: 6 Vol. 108; ISSN 2470-0045

Publisher:: American Physical Society (APS)Copyright Statement

Country of Publication:: United States

Language:: English

References (65)

Experimental Polymer Mechanochemistry and its Interpretational Frameworks Akbulatov, Sergey; Boulatov, Roman ChemPhysChem, Vol. 18, Issue 11 https://doi.org/10.1002/cphc.201601354	journal	March 2017
Methods for Exerting and Sensing Force in Polymer Materials Using Mechanophores Stratigaki, Maria; Göstl, Robert ChemPlusChem, Vol. 85, Issue 6 https://doi.org/10.1002/cplu.201900737	journal	January 2020
Polymer mechanochemistry: the design and study of mechanophores: Polymer mechanochemistry Brantley, Johnathan N.; Wiggins, Kelly M.; Bielawski, Christopher W. Polymer International, Vol. 62, Issue 1 https://doi.org/10.1002/pi.4350	journal	September 2012
Stretching a Macromolecule in an Atomic Force Microscope: Statistical Mechanical Analysis Kreuzer, H. J.; Payne, S. H.; Livadaru, L. Biophysical Journal, Vol. 80, Issue 6 https://doi.org/10.1016/S0006-3495(01)76222-4	journal	June 2001
On the Precise Meaning of Extension in the Interpretation of Polymer-Chain Stretching Experiments Neumann, Richard M. Biophysical Journal, Vol. 85, Issue 5 https://doi.org/10.1016/S0006-3495(03)74760-2	journal	November 2003
A Temperature-Jump Optical Trap for Single-Molecule Manipulation de Lorenzo, Sara; Ribezzi-Crivellari, Marco; Arias-Gonzalez, J. Ricardo Biophysical Journal, Vol. 108, Issue 12 https://doi.org/10.1016/j.bpj.2015.05.017	journal	June 2015
Synthesis and anticorrosive properties of epoxy polymer for CS in [1 M] HCl solution: Electrochemical, AFM, DFT and MD simulations Hsissou, Rachid; Abbout, Said; Safi, Zaki Construction and Building Materials, Vol. 270 https://doi.org/10.1016/j.conbuildmat.2020.121454	journal	February 2021
LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales Thompson, Aidan P.; Aktulga, H. Metin; Berger, Richard Computer Physics Communications, Vol. 271 https://doi.org/10.1016/j.cpc.2021.108171	journal	February 2022
Chain breaking in the statistical mechanical constitutive theory of polymer networks Buche, Michael R.; Silberstein, Meredith N. Journal of the Mechanics and Physics of Solids, Vol. 156 https://doi.org/10.1016/j.jmps.2021.104593	journal	November 2021
A statistical mechanics framework for polymer chain scission, based on the concepts of distorted bond potential and asymptotic matching Mulderrig, Jason; Talamini, Brandon; Bouklas, Nikolaos Journal of the Mechanics and Physics of Solids, Vol. 174 https://doi.org/10.1016/j.jmps.2023.105244	journal	May 2023
On the equivalence of thermodynamics ensembles for flexible polymer chains Manca, Fabio; Giordano, Stefano; Palla, Pier Luca Physica A: Statistical Mechanics and its Applications, Vol. 395 https://doi.org/10.1016/j.physa.2013.10.042	journal	February 2014
Polymer single chain imaging, molecular forces, and nanoscale processes by Atomic Force Microscopy: The ultimate proof of the macromolecular hypothesis Liu, Yan; Vancso, G. Julius Progress in Polymer Science, Vol. 104 https://doi.org/10.1016/j.progpolymsci.2020.101232	journal	May 2020
Probing of miniPEGγ-PNA–DNA Hybrid Duplex Stability with AFM Force Spectroscopy Dutta, Samrat; Armitage, Bruce A.; Lyubchenko, Yuri L. Biochemistry, Vol. 55, Issue 10 https://doi.org/10.1021/acs.biochem.5b01250	journal	March 2016
Tuning the Mechanical Properties of Metallopolymers via Ligand Interactions: A Combined Experimental and Theoretical Study Vidavsky, Yuval; Buche, Michael R.; Sparrow, Zachary M. Macromolecules, Vol. 53, Issue 6 https://doi.org/10.1021/acs.macromol.9b02756	journal	March 2020
Mechanochemistry: A Force of Synthesis Do, Jean-Louis; Friščić, Tomislav ACS Central Science, Vol. 3, Issue 1 https://doi.org/10.1021/acscentsci.6b00277	journal	December 2016
Single Molecule Study of Force-Induced Rotation of Carbon–Carbon Double Bonds in Polymers Huang, Wenmao; Zhu, Zhenshu; Wen, Jing ACS Nano, Vol. 11, Issue 1 https://doi.org/10.1021/acsnano.6b07119	journal	November 2016
Force-Rate Characterization of Two Spiropyran-Based Molecular Force Probes Gossweiler, Gregory R.; Kouznetsova, Tatiana B.; Craig, Stephen L. Journal of the American Chemical Society, Vol. 137, Issue 19 https://doi.org/10.1021/jacs.5b02492	journal	May 2015
Substituent Effects and Mechanism in a Mechanochemical Reaction Barbee, Meredith H.; Kouznetsova, Tatiana; Barrett, Scott L. Journal of the American Chemical Society, Vol. 140, Issue 40 https://doi.org/10.1021/jacs.8b09263	journal	September 2018
Spatially Selective and Density-Controlled Activation of Interfacial Mechanophores Sulkanen, Audrey R.; Sung, Jaeuk; Robb, Maxwell J. Journal of the American Chemical Society, Vol. 141, Issue 9 https://doi.org/10.1021/jacs.8b10257	journal	February 2019
Enabling Room-Temperature Mechanochromic Activation in a Glassy Polymer: Synthesis and Characterization of Spiropyran Polycarbonate Vidavsky, Yuval; Yang, Steven J.; Abel, Brooks A. Journal of the American Chemical Society, Vol. 141, Issue 25 https://doi.org/10.1021/jacs.9b04229	journal	June 2019
Application of the ReaxFF Reactive Force Field to Reactive Dynamics of Hydrocarbon Chemisorption and Decomposition Mueller, Jonathan E.; van Duin, Adri C. T.; Goddard, William A. The Journal of Physical Chemistry C, Vol. 114, Issue 12 https://doi.org/10.1021/jp9089003	journal	January 2010
Characterization of Single- and Double-Stranded DNA on Gold Surfaces Moses, Selina; Brewer, Scott H.; Lowe, Lisa B. Langmuir, Vol. 20, Issue 25 https://doi.org/10.1021/la0492815	journal	November 2004
Entropic Elasticity of Single Polymer Chains of Poly(methacrylic acid) Measured by Atomic Force Microscopy Ortiz, C.; Hadziioannou, G. Macromolecules, Vol. 32, Issue 3 https://doi.org/10.1021/ma981245n	journal	February 1999
Mechanochemistry: One Bond at a Time Liang, Jian; Fernández, Julio M. ACS Nano, Vol. 3, Issue 7 https://doi.org/10.1021/nn900294n	journal	June 2009
A revolution in optical manipulation Grier, David G. Nature, Vol. 424, Issue 6950 https://doi.org/10.1038/nature01935	journal	August 2003
Inducing and quantifying forbidden reactivity with single-molecule polymer mechanochemistry Wang, Junpeng; Kouznetsova, Tatiana B.; Niu, Zhenbin Nature Chemistry, Vol. 7, Issue 4 https://doi.org/10.1038/nchem.2185	journal	February 2015
Multi-modal mechanophores based on cinnamate dimers Zhang, Huan; Li, Xun; Lin, Yangju Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-01412-8	journal	October 2017
Steering chemical reactions with force Garcia-Manyes, Sergi; Beedle, Amy E. M. Nature Reviews Chemistry, Vol. 1, Issue 11 https://doi.org/10.1038/s41570-017-0083	journal	November 2017
The many flavours of mechanochemistry and its plausible conceptual underpinnings O’Neill, Robert T.; Boulatov, Roman Nature Reviews Chemistry, Vol. 5, Issue 3 https://doi.org/10.1038/s41570-020-00249-y	journal	February 2021
The role of polymer mechanochemistry in responsive materials and additive manufacturing Ghanem, Maroun Abi; Basu, Amrita; Behrou, Reza Nature Reviews Materials, Vol. 6, Issue 1 https://doi.org/10.1038/s41578-020-00249-w	journal	October 2020
Unveiling the influence of device stiffness in single macromolecule unfolding Florio, G.; Puglisi, G. Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-41330-x	journal	March 2019
Optical tweezers in single-molecule biophysics Bustamante, Carlos J.; Chemla, Yann R.; Liu, Shixin Nature Reviews Methods Primers, Vol. 1, Issue 1 https://doi.org/10.1038/s43586-021-00021-6	journal	March 2021
From molecular mechanochemistry to stress-responsive materials Black, Ashley L.; Lenhardt, Jeremy M.; Craig, Stephen L. J. Mater. Chem., Vol. 21, Issue 6 https://doi.org/10.1039/C0JM02636K	journal	January 2011
Inequivalence of fixed-force and fixed-extension statistical ensembles for a flexible polymer tethered to a planar substrate Dutta, Sandipan; Benetatos, Panayotis Soft Matter, Vol. 14, Issue 33 https://doi.org/10.1039/C8SM01321G	journal	January 2018
The influence of device handles in single-molecule experiments Bellino, Luca; Florio, Giuseppe; Puglisi, Giuseppe Soft Matter, Vol. 15, Issue 43 https://doi.org/10.1039/C9SM01376H	journal	January 2019
Mechanochemical tools for polymer materials Chen, Yinjun; Mellot, Gaëlle; van Luijk, Diederik Chemical Society Reviews, Vol. 50, Issue 6 https://doi.org/10.1039/D0CS00940G	journal	January 2021
Force-mediated molecule release from double network hydrogels Jayathilaka, Pavithra Bhakthi; Molley, Thomas Gregory; Huang, Yuwan Chemical Communications, Vol. 57, Issue 68 https://doi.org/10.1039/D1CC02726C	journal	January 2021
Novel optical approach to atomic force microscopy Meyer, Gerhard; Amer, Nabil M. Applied Physics Letters, Vol. 53, Issue 12 https://doi.org/10.1063/1.100061	journal	September 1988
High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases Zwanzig, Robert W. The Journal of Chemical Physics, Vol. 22, Issue 8 https://doi.org/10.1063/1.1740409	journal	August 1954
Theory, analysis, and interpretation of single-molecule force spectroscopy experiments Dudko, O. K.; Hummer, G.; Szabo, A. Proceedings of the National Academy of Sciences, Vol. 105, Issue 41 https://doi.org/10.1073/pnas.0806085105	journal	October 2008
Rate-dependent force–extension models for single-molecule force spectroscopy experiments Benedito, Manon; Manca, Fabio; Palla, Pier Luca Physical Biology, Vol. 17, Issue 5 https://doi.org/10.1088/1478-3975/ab97a8	journal	August 2020
Roadmap for optical tweezers Volpe, Giovanni; Maragò, Onofrio M.; Rubinsztein-Dunlop, Halina Journal of Physics: Photonics, Vol. 5, Issue 2 https://doi.org/10.1088/2515-7647/acb57b	journal	April 2023
Polymer Physics Rubinstein, Michael; Colby, Ralph H. https://doi.org/10.1093/oso/9780198520597.001.0001	book	June 2003
Statistical mechanical constitutive theory of polymer networks: The inextricable links between distribution, behavior, and ensemble Buche, Michael R.; Silberstein, Meredith N. Physical Review E, Vol. 102, Issue 1 https://doi.org/10.1103/PhysRevE.102.012501	journal	July 2020
Freely jointed chain models with extensible links Buche, Michael R.; Silberstein, Meredith N.; Grutzik, Scott J. Physical Review E, Vol. 106, Issue 2 https://doi.org/10.1103/PhysRevE.106.024502	journal	August 2022
Inequivalence of statistical ensembles in single molecule measurements Sinha, Supurna; Samuel, Joseph Physical Review E, Vol. 71, Issue 2 https://doi.org/10.1103/PhysRevE.71.021104	journal	February 2005
Ensemble inequivalence in single-molecule experiments Süzen, M.; Sega, M.; Holm, C. Physical Review E, Vol. 79, Issue 5 https://doi.org/10.1103/PhysRevE.79.051118	journal	May 2009
Dissociation rates from single-molecule pulling experiments under large thermal fluctuations or large applied force Abkenar, Masoud; Gray, Thomas H.; Zaccone, Alessio Physical Review E, Vol. 95, Issue 4 https://doi.org/10.1103/PhysRevE.95.042413	journal	April 2017
Isotensional and isometric force-extension response of chains with bistable units and Ising interactions Benedito, Manon; Giordano, Stefano Physical Review E, Vol. 98, Issue 5 https://doi.org/10.1103/PhysRevE.98.052146	journal	November 2018
Acceleration and Trapping of Particles by Radiation Pressure Ashkin, A. Physical Review Letters, Vol. 24, Issue 4 https://doi.org/10.1103/PhysRevLett.24.156	journal	January 1970
Atomic-Beam Deflection by Resonance-Radiation Pressure Ashkin, A. Physical Review Letters, Vol. 25, Issue 19 https://doi.org/10.1103/PhysRevLett.25.1321	journal	November 1970
Three-dimensional viscous confinement and cooling of atoms by resonance radiation pressure Chu, Steven; Hollberg, L.; Bjorkholm, J. E. Physical Review Letters, Vol. 55, Issue 1 https://doi.org/10.1103/PhysRevLett.55.48	journal	July 1985
Atomic Force Microscope Binnig, G.; Quate, C. F.; Gerber, Ch. Physical Review Letters, Vol. 56, Issue 9 https://doi.org/10.1103/PhysRevLett.56.930	journal	March 1986
Experimental Observation of Optically Trapped Atoms Chu, Steven; Bjorkholm, J. E.; Ashkin, A. Physical Review Letters, Vol. 57, Issue 3 https://doi.org/10.1103/PhysRevLett.57.314	journal	July 1986
Advances in atomic force microscopy Giessibl, Franz J. Reviews of Modern Physics, Vol. 75, Issue 3 https://doi.org/10.1103/RevModPhys.75.949	journal	July 2003
Direct Measurement of the Full, Sequence-Dependent Folding Landscape of a Nucleic Acid Woodside, M. T.; Anthony, P. C.; Behnke-Parks, W. M. Science, Vol. 314, Issue 5801 https://doi.org/10.1126/science.1133601	journal	November 2006
Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules Smith, S. B.; Cui, Y.; Bustamante, C. Science, Vol. 271, Issue 5250 https://doi.org/10.1126/science.271.5250.795	journal	February 1996
Single-Molecule Biomechanics with Optical Methods Mehta, A. D. Science, Vol. 283, Issue 5408 https://doi.org/10.1126/science.283.5408.1689	journal	March 1999
Optical trapping and manipulation of viruses and bacteria Ashkin, A.; Dziedzic, J. Science, Vol. 235, Issue 4795 https://doi.org/10.1126/science.3547653	journal	March 1987
Direct measurement of the forces between complementary strands of DNA Lee, G.; Chrisey, L.; Colton, R. Science, Vol. 266, Issue 5186 https://doi.org/10.1126/science.7973628	journal	November 1994
Adhesion forces between individual ligand-receptor pairs Florin, E.; Moy, V.; Gaub, H. Science, Vol. 264, Issue 5157 https://doi.org/10.1126/science.8153628	journal	April 1994
Single-Molecule Studies of Protein Folding with Optical Tweezers Bustamante, Carlos; Alexander, Lisa; Maciuba, Kevin Annual Review of Biochemistry, Vol. 89, Issue 1 https://doi.org/10.1146/annurev-biochem-013118-111442	journal	June 2020
Reconstructing Folding Energy Landscapes by Single-Molecule Force Spectroscopy Woodside, Michael T.; Block, Steven M. Annual Review of Biophysics, Vol. 43, Issue 1 https://doi.org/10.1146/annurev-biophys-051013-022754	journal	May 2014
Probing the Relation Between Force—Lifetime—and Chemistry in Single Molecular Bonds Evans, Evan Annual Review of Biophysics and Biomolecular Structure, Vol. 30, Issue 1 https://doi.org/10.1146/annurev.biophys.30.1.105	journal	June 2001
Optical tweezers — from calibration to applications: a tutorial Gieseler, Jan; Gomez-Solano, Juan Ruben; Magazzù, Alessandro Advances in Optics and Photonics, Vol. 13, Issue 1 https://doi.org/10.1364/AOP.394888	journal	March 2021

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