Lower bounds on dissipation upon coarse graining

By different coarse-graining procedures we derive lower bounds on the total mean work dissipated in Brownian systems driven out of equilibrium. With several analytically solvable examples we illustrate how, when, and where the information on the dissipation is captured.Comment: 11 pages, 8 figure

Efficiency of Free Energy Transduction in Autonomous Systems

We consider the thermodynamics of chemical coupling from the viewpoint of free energy transduction efficiency. In contrast to an external parameter-driven stochastic energetics setup, the dynamic change of the equilibrium distribution induced by chemical coupling, adopted, for example, in biological systems, is inevitably an autonomous process. We found that the efficiency is bounded by the ratio between the non-symmetric and the symmetrized Kullback-Leibler distance, which is significantly lower than unity. Consequences of this low efficiency are demonstrated in the simple two-state case, which serves as an important minimal model for studying the energetics of biomolecules.Comment: 4 pages, 4 figure

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

Single-molecule experiments in biological physics: methods and applications

I review single-molecule experiments (SME) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SME it is possible to: manipulate molecules one at a time and measure distributions describing molecular properties; characterize the kinetics of biomolecular reactions and; detect molecular intermediates. SME provide the additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SME it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level emphasizing the importance of SME to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SME from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOT), magnetic tweezers (MT), biomembrane force probe (BFP) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation), proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SME to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.Comment: Latex, 60 pages, 12 figures, Topical Review for J. Phys. C (Cond. Matt

Face recognition and visual search strategies in autism spectrum disorders: Amending and extending a recent review by Weigelt et al.

The purpose of this review was to build upon a recent review by Weigelt et al. which examined visual search strategies and face identification between individuals with autism spectrum disorders (ASD) and typically developing peers. Seven databases, CINAHL Plus, EMBASE, ERIC, Medline, Proquest, PsychInfo and PubMed were used to locate published scientific studies matching our inclusion criteria. A total of 28 articles not included in Weigelt et al. met criteria for inclusion into this systematic review. Of these 28 studies, 16 were available and met criteria at the time of the previous review, but were mistakenly excluded; and twelve were recently published. Weigelt et al. found quantitative, but not qualitative, differences in face identification in individuals with ASD. In contrast, the current systematic review found both qualitative and quantitative differences in face identification between individuals with and without ASD. There is a large inconsistency in findings across the eye tracking and neurobiological studies reviewed. Recommendations for future research in face recognition in ASD were discussed

The CMS High Level Trigger

At the Large Hadron Collider at CERN the proton bunches cross at a rate of 40MHz. At the Compact Muon Solenoid experiment the original collision rate is reduced by a factor of O (1000) using a Level-1 hardware trigger. A subsequent factor of O(1000) data reduction is obtained by a software-implemented High Level Trigger (HLT) selection that is executed on a multi-processor farm. In this review we present in detail prototype CMS HLT physics selection algorithms, expected trigger rates and trigger performance in terms of both physics efficiency and timing.Comment: accepted by EPJ Nov 200

PRODUCTION AND DECAY PROPERTIES OF THE D(1285) MESON IN K-P INTERACTIONS AT 4.2 GEV-C

We have studied the production and decay of the D(1285) meson in the reaction K-p→ ΛD at an incident K- momentum of 4.2 GeV/c. The cross section for this reaction is 11 ± 3 μb and the branching ratios D→ KKπ/D → ηππ and D → 4π/D → ηππ are found to be 0.42 ± 0.15 and 0.7 ± 0.5, respectively. The proportion of D → ηπ+π- going through the intermediate δ±π∓ states is 0.72 ± 0.15. Forward and backward exchange mechanisms are found to contribute in the ratio 3 : 2. © 1979

Production and decay properties of the D(1285) meson in K-p interactions at 4.2 GeV/c

We have studied the production and decay of the D(1285) meson in the reaction K-p→ ΛD at an incident K- momentum of 4.2 GeV/c. The cross section for this reaction is 11 ± 3 μb and the branching ratios D→ KKπ/D → ηππ and D → 4π/D → ηππ are found to be 0.42 ± 0.15 and 0.7 ± 0.5, respectively. The proportion of D → ηπ+π- going through the intermediate δ±π∓ states is 0.72 ± 0.15. Forward and backward exchange mechanisms are found to contribute in the ratio 3 : 2. © 1979