Dynamic force spectroscopy of DNA hairpins: I. Force kinetics and free energy landscapes

Mossa, Alessandro; Manosas, Maria; Forns, Nuria; Huguet, Josep Maria; Ritort, Fèlix

doi:10.1088/1742-5468/2009/02/p02060

Cited by 62 publications

(110 citation statements)

References 50 publications

(98 reference statements)

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“…Many TRT results concern quasiclassical systems, whose density operators ρ commute with their Hamiltonians H: [ρ, H] = 0 (e.g., [2, 28-31, 63, 72, 73]). Such quasiclassical results might be realized more easily than quantum results: Classical platforms, such as DNA and colloidal particles, have been used to test small-scale statistical mechanics such as fluctuation relations [6][7][8][9][10][11][12][13]. These classical platforms might be recycled to realize TRTs.…”

Section: How Should Trts Model Continuous Spectra?mentioning

confidence: 99%

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Toward Physical Realizations of Thermodynamic Resource Theories

Halpern

2016

Information and Interaction

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Conventional statistical mechanics describes large systems and averages over many particles or over many trials. But work, heat, and entropy impact the small scales that experimentalists can increasingly control, e.g., in single-molecule experiments. The statistical mechanics of small scales has been quantified with two toolkits developed in quantum information theory: resource theories and one-shot information theory. The field has boomed recently, but the theorems amassed have hardly impacted experiments. Can thermodynamic resource theories be realized experimentally? Via what steps can we shift the theory toward physical realizations? Should we care? I present eleven opportunities in physically realizing thermodynamic resource theories.

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Section: How Should Trts Model Continuous Spectra?mentioning

confidence: 99%

“…I could have advocated for bounding, with idealizations, efficiencies achievable in labs. I should have invoked the connections being developed with fluctuation relations [3][4][5], statistical mechanical theorems that have withstood experimental tests [6][7][8][9][10][11][12][13].…”

Section: Introductionmentioning

confidence: 99%

Toward Physical Realizations of Thermodynamic Resource Theories

Halpern

2016

Information and Interaction

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“…In Figure 4 we summarize recent results obtained in the Small Biosystems lab in Barcelona for the mechanical unfolding/refolding of DNA hairpins [21,22] using a dualbeam miniaturized optical tweezers [23]. DNA hairpins are versatile structures formed by a stem of a few tens of base pairs that end in loop.…”

Section: The Crooks Fluctuation Relation and Free Energy Recoverymentioning

confidence: 99%

Recent progress in fluctuation theorems and free energy recovery

Alemany

Ribezzi

Ritort

2011

AIP Conference Proceedings

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Abstract. In this note we review recent progress about fluctuation relations and their applicability to free energy recovery in single molecule experiments. We underline the importance of the operational definition for the mechanical work and the non-invariance of fluctuation relations under Galilean transformations, both aspects currently amenable to experimental test. Finally we describe a generalization of the Crooks fluctuation relation useful to recover free energies of partially equilibrated states and thermodynamic branches. NONEQUILIBRIUM SMALL SYSTEMSIn 1944 Erwin Schrödinger published the classic monography What is life? where he pointed out the importance of physical and chemistry laws to understand living systems [1]. The notion that genetic information should be encoded in an "aperiodic crystal" seeded the subsequent discovery of the double helix structure of DNA. Chapter 7 of Schrödinger's monography contains an interesting discussion about the similarities and differences between a clockwork motion and the functioning of an organism. According to Schrödinger the regular motion of a clock must be secured by a weak spring. Yet, whatever the weakness of the spring is, it will produce frictional effects that do compensate for the external driving of the clock (e.g. the battery) in order to secure its regular motion. Being friction a statistical phenomenon he concludes that the regular motion of the clock cannot be understood without statistical mechanics. Then he further states: For it must not believed that the driving mechanism really does away with the statistical nature of the process. The true physical picture includes the possibility that even a regularly going clock should all at once invert its motion and, working backward, rewind its own spring -at the expense of the heat of the environment. The event is just 'still a little less likely' than a 'Brownian fit' of a clock without driving mechanism.Recent advances in microfabrication techniques, detection systems and instrumentation have made possible the measurement of such "inverted motions" referred by Schrödinger. The controlled manipulation and detection of very small objects makes possible to exert and measure tiny forces applied on them and follow their trajectories in space-time with resolution of piconewtons, nanometers and microseconds respectively.

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“…non-equilibrium) experiment and measuring the work done during the process. The identity has been recently experimentally tested (Mossa et al, 2009;Ritort, 2003). In the present Chapter we discuss four illustrative, exactly solvable models in non-equilibrium thermodynamics of small systems.…”

Section: Introductionmentioning

confidence: 99%