Thermodynamics of accuracy in kinetic proofreading: Dissipation and efficiency trade-offs

The high accuracy exhibited by biological information transcription processes is due to kinetic proofreading, i.e., by a mechanism which reduces the error rate of the information-handling process by driving it out of equilibrium. We provide a consistent thermodynamic description of enzyme-assisted assembly processes involving competing substrates, in a Master Equation framework. We introduce and evaluate a measure of the efficiency based on rigorous non-equilibrium inequalities. The performance of several proofreading models are thus analyzed and the related time, dissipation and efficiency vs. error trade-offs exhibited for different discrimination regimes. We finally introduce and analyze in the same framework a simple model which takes into account correlations between consecutive enzyme-assisted assembly steps. This work highlights the relevance of the distinction between energetic and kinetic discrimination regimes in enzyme-substrate interactions.Comment: IOP Class, 20 pages, 9 figure

Conservation Laws shape Dissipation

Starting from the most general formulation of stochastic thermodynamics---i.e. a thermodynamically consistent nonautonomous stochastic dynamics describing systems in contact with several reservoirs---, we define a procedure to identify the conservative and the minimal set of nonconservative contributions in the entropy production. The former is expressed as the difference between changes caused by time-dependent drivings and a generalized potential difference. The latter is a sum over the minimal set of flux--force contributions controlling the dissipative flows across the system. When the system is initially prepared at equilibrium (e.g. by turning off drivings and forces), a finite-time detailed fluctuation theorem holds for the different contributions. Our approach relies on identifying the complete set of conserved quantities and can be viewed as the extension of the theory of generalized Gibbs ensembles to nonequilibrium situations.Comment: 24 pages, 11 figures, 3 tables. Published version in double column forma

Spoken Thesaurus: Sorrow

The Hindi Thesaurus addresses such questions in a series of lively, unscripted Hindi-medium conversations about groups of words of related meaning. Concentrating on selected mainstream words and phrases, we help you to broaden your active vocabulary by encountering styles of language appropriate for everyday speech. The conversations are between Rupert Snell (Hindi teacher and perpetual Hindi learner) and Neha Ladha (mother-tongue speaker of Hindi). Glossaries for each podcast can be read online or downloaded in PDF format. (Length: 7:49)Asian Studie

Thermodynamic Efficiency in Dissipative Chemistry

Chemical processes in closed systems are poorly controllable since they always relax to equilibrium. Living systems avoid this fate and give rise to a much richer diversity of phenomena by operating under nonequilibrium conditions. Recent experiments in dissipative self-assembly also demonstrated that by opening reaction vessels and steering certain concentrations, an ocean of opportunities for artificial synthesis and energy storage emerges. To navigate it, thermodynamic notions of energy, work and dissipation must be established for these open chemical systems. Here, we do so by building upon recent theoretical advances in nonequilibrium statistical physics. As a central outcome, we show how to quantify the efficiency of such chemical operations and lay the foundation for performance analysis of any dissipative chemical process.Comment: revtex format: 11 pages (4 + 7 for appendices), 6 figures (4 + 2

Thermodynamically Consistent Coarse Graining of Biocatalysts beyond Michaelis--Menten

Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. This procedure provides stoichiometries, reaction fluxes (rate laws), and reaction forces (Gibbs energies of reaction) for the coarse-grained level. It can treat active transporters and molecular machines, and thus extends the applicability of ideas that originated in enzyme kinetics. Our results lay the foundations for systematic studies of the thermodynamics of large-scale biochemical reaction networks. Moreover, we identify the conditions under which a relation between one-way fluxes and forces holds at the coarse-grained level as it holds at the detailed level. In doing so, we clarify the speculations and broad claims made in the literature about such a general flux--force relation. As a further consequence we show that, in contrast to common belief, the second law of thermodynamics does not require the currents and the forces of biochemical reaction networks to be always aligned.Comment: 14 pages, 5 figure

Proprietà allodiale civica e formazione del distretto urbano nella fondazione dei borghi nuovi vercellesi (prima metà del XIII secolo)

Con questo contributo si cercherà di sviluppare il rapporto tra proprietà allodiale cittadina e istituzione di borghi nuovi. Il ruolo degli acquisti e dei patrimoni civici nelle fondazioni comunali non ha ricevuto grandi attenzioni da parte della medievistica, sebbene il ricorso ad estensioni appartenenti ai comuni urbani per la creazione di insediamenti fosse abbastanza usuale. In particolare nel caso vercellese, esso sembra essere stato utilizzato dall'amministrazione civica con particolare consapevolezza: fu, infatti, un momento importante per la creazione del districtus nella prima metà del XIII secolo. L’opportunità di un suo studio può dunque essere suggerita, più che dalla volontà di descrivere una situazione eccezionale, dal proposito di mettere in rilievo motivazioni e modalità di una prassi assai diffusa presso le autonomie cittadine italiane: l'acquisizione del suolo su cui venivano eretti i borghi nuovi

Detailed Fluctuation Theorems: A Unifying Perspective

We present a general method to identify an arbitrary number of fluctuating quantities which satisfy a detailed fluctuation theorem for all times within the framework of time-inhomogeneous Markovian jump processes. In doing so we provide a unified perspective on many fluctuation theorems derived in the literature. By complementing the stochastic dynamics with a thermodynamic structure (i.e. using stochastic thermodynamics), we also express these fluctuating quantities in terms of physical observables.Comment: revtex format: 17 pages (12 + 5 for appendices), 7 figures, 3 tables. v2: published version, added an exampl