Fluctuation symmetries for work and heat

We consider a particle dragged through a medium at constant temperature as described by a Langevin equation with a time-dependent potential. The time-dependence is specified by an external protocol. We give conditions on potential and protocol under which the dissipative work satisfies an exact symmetry in its fluctuations for all times. We also present counter examples to that exact fluctuation symmetry when our conditions are not satisfied. Finally, we consider the dissipated heat which differs from the work by a temporal boundary term. We explain when and why there can be a correction to the standard fluctuation theorem due to the unboundedness of that temporal boundary. However, the corrected fluctuation symmetry has again a general validity.Comment: 10 pages, 4 figures (v2: minor typographic corrections

Stochastic thermodynamics of chemical reaction networks

For chemical reaction networks described by a master equation, we define energy and entropy on a stochastic trajectory and develop a consistent nonequilibrium thermodynamic description along a single stochastic trajectory of reaction events. A first-law like energy balance relates internal energy, applied (chemical) work and dissipated heat for every single reaction. Entropy production along a single trajectory involves a sum over changes in the entropy of the network itself and the entropy of the medium. The latter is given by the exchanged heat identified through the first law. Total entropy production is constrained by an integral fluctuation theorem for networks arbitrarily driven by time-dependent rates and a detailed fluctuation theorem for networks in the steady state. Further exact relations like a generalized Jarzynski relation and a generalized Clausius inequality are discussed. We illustrate these results for a three-species cyclic reaction network which exhibits nonequilibrium steady states as well as transitions between different steady states.Comment: 14 pages, 2 figures, accepted for publication in J. Chem. Phy

Performance grading and motivational functioning and fear in physical education : a self-determination theory perspective

Grounded in self-determination theory, the present study examines the explanatory role of students' perceived need satisfaction and need frustration in the relationship between performance grading (versus non-grading) and students' motivation and fear in a real-life educational physical education setting. Grading consisted of teacher judgments of students' performances through observations, based on pre-defined assessment criteria. Thirty-one classes with 409 students (M-age = 14.7) from twenty-seven Flemish (Belgian) secondary schools completed questionnaires measuring students' perceived motivation, fear and psychological need satisfaction and frustration, after two lessons: one with and one without performance grading. After lessons including performance grading, students reported less intrinsic motivation and identified regulation, and more external regulation, amotivation and fear. As expected, less need satisfaction accounted for (i.e., mediated) the relationship between performance grading and self-determined motivational outcomes. Need frustration explained the relationship between performance grading and intrinsic motivation, as well as less self-determined motivational outcomes. Theoretical and practical implications are discusse

Diagnosis of sub-clinical coccidiosis in fast growing broiler chickens by MicroRNA profiling

Coccidiosis in broiler chickens, caused by infection with Eimeria spp. remains one of the most economically important production diseases. Development of a genetic biomarker panel of sub-clinical infection would be an important biological tool for the management of broiler flocks. We analysed expression of MicroRNAs (miRNAs) to determine the potential for these in diagnosing coccidiosis in broiler flocks. miRNA expression, in the ilea of Ross 308 broilers, was compared between chickens naturally clinically or sub-clinically infected with Eimeria maxima and Eimeria acervulina using NextSeq 500 sequencing. 50 miRNAs with greatest coefficient of variance were determined and principal component analysis showed that these miRNAs clustered within the clinical and sub-clinical groups much more closely than uninfected controls. Following false detection rate analysis and quantitative PCR we validated 3 miRNAs; Gallus gallus (gga)-miR-122-5p, gga-miR-205b and gga-miR-144-3p, which may be used to diagnose sub-clinical coccidiosis

Evaluation of amplified rDNA restriction analysis (ARDRA) for the identification of Mycoplasma species

BACKGROUND: Mycoplasmas are present worldwide in a large number of animal hosts. Due to their small genome and parasitic lifestyle, Mycoplasma spp. require complex isolation media. Nevertheless, already over 100 different species have been identified and characterized and their number increases as more hosts are sampled. We studied the applicability of amplified rDNA restriction analysis (ARDRA) for the identification of all 116 acknowledged Mycoplasma species and subspecies. METHODS: Based upon available 16S rDNA sequences, we calculated and compared theoretical ARDRA profiles. To check the validity of these theoretically calculated profiles, we performed ARDRA on 60 strains of 27 different species and subspecies of the genus Mycoplasma. RESULTS: In silico digestion with the restriction endonuclease AluI (AG^CT) was found to be most discriminative and generated from 3 to 13 fragments depending on the Mycoplasma species. Although 73 Mycoplasma species could be differentiated using AluI, other species gave undistinguishable patterns. For these, an additional restriction digestion, typically with BfaI (C^TAG) or HpyF10VI (GCNNNNN^NNGC), was needed for a final identification. All in vitro obtained restriction profiles were in accordance with the calculated fragments based on only one 16S rDNA sequence, except for two isolates of M. columbinum and two isolates of the M. mycoides cluster, for which correct ARDRA profiles were only obtained if the sequences of both rrn operons were taken into account. CONCLUSION: Theoretically, restriction digestion of the amplified rDNA was found to enable differentiation of all described Mycoplasma species and this could be confirmed by application of ARDRA on a total of 27 species and subspecies

Entropy production for mechanically or chemically driven biomolecules

Entropy production along a single stochastic trajectory of a biomolecule is discussed for two different sources of non-equilibrium. For a molecule manipulated mechanically by an AFM or an optical tweezer, entropy production (or annihilation) occurs in the molecular conformation proper or in the surrounding medium. Within a Langevin dynamics, a unique identification of these two contributions is possible. The total entropy change obeys an integral fluctuation theorem and a class of further exact relations, which we prove for arbitrarily coupled slow degrees of freedom including hydrodynamic interactions. These theoretical results can therefore also be applied to driven colloidal systems. For transitions between different internal conformations of a biomolecule involving unbalanced chemical reactions, we provide a thermodynamically consistent formulation and identify again the two sources of entropy production, which obey similar exact relations. We clarify the particular role degenerate states have in such a description