Dynamic force spectroscopy of DNA hairpins: II. Irreversibility and dissipation

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

doi:10.1088/1742-5468/2009/02/p02061

Cited by 42 publications

(54 citation statements)

References 55 publications

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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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“…Conventional thermodynamics at or near equilibrium needs serious modification to accommodate the events of single molecular processes as well as nano-systems which are generally in states far away from equilibrium [1][2][3][4][5][6][7][8][9][10] . The single molecule study is very important in biological systems because most of the processes in cell are taking place on the level of a single or a few molecules.…”

Section: Introductionmentioning

confidence: 99%

Entropic estimate of cooperative binding of substrate on a single oligomeric enzyme: An index of cooperativity

Banerjee

Das

Gangopadhyay

2012

The Journal of Chemical Physics

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Here we have systematically studied the cooperative binding of substrate molecules on the active sites of a single oligomeric enzyme in a chemiostatic condition. The average number of bound substrate and the net velocity of the enzyme catalyzed reaction are studied by the formulation of stochastic master equation for the cooperative binding classified here as spatial and temporal. We have estimated the entropy production for the cooperative binding schemes based on single trajectory analysis using a kinetic Monte Carlo technique. It is found that the total as well as the medium entropy production show the same generic diagnostic signature for detecting the cooperativity, usually characterized in terms of the net velocity of the reaction. This feature is also found to be valid for the total entropy production rate at the nonequilibrium steady state. We have introduced an index of cooperativity, C, defined in terms of the ratio of the surprisals or equivalently, the stochastic system entropy associated with the fully bound state of the cooperative and non-cooperative cases. The criteria of cooperativity in terms of C is compared with that of the Hill coefficient and gives a microscopic insight on the cooperative binding of substrate on a single oligomeric enzyme which is usually characterized by macroscopic reaction rate.

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Dynamic force spectroscopy of DNA hairpins: II. Irreversibility and dissipation

Cited by 42 publications

References 55 publications

Toward Physical Realizations of Thermodynamic Resource Theories

Toward Physical Realizations of Thermodynamic Resource Theories

Recent progress in fluctuation theorems and free energy recovery

Entropic estimate of cooperative binding of substrate on a single oligomeric enzyme: An index of cooperativity

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