Fluctuation relations for molecular motors

This review is focused on the application of specific fluctuation relations, such as the Gallavotti-Cohen relation, to ratchet models of a molecular motor. A special emphasis is placed on two-states models such as the flashing ratchet model. We derive the Gallavotti-Cohen fluctuation relation for these models and we discuss some of its implications.Comment: 27 pages, 11 figure

Handling qualities aspects of NASA YF-12 flight experience

The handling qualities of the YF-12 airplane as observed during NASA research flights over the past five years were reviewed. Aircraft behavior during takeoff, acceleration, climb, cruise, descent, and landing are discussed. Pilot comments on the various flight phases and tasks are presented. Handling qualities parameters such as period, damping, amplitude ratios, roll-yaw coupling, and flight path response sensitivity are compared to existing and proposed handling qualities criteria. The influence of the propulsion systems, stability augmentation, autopilot systems, atmospheric gusts, and temperature changes are also discussed. YF-12 experience correlates well with flying qualities criteria, except for longitudinal short period damping, where existing and proposed criteria appear to be more stringent than necessary

Non-equilibrium fluctuations and mechanochemical couplings of a molecular motor

We investigate theoretically the violations of Einstein and Onsager relations, and the efficiency for a single processive motor operating far from equilibrium using an extension of the two-state model introduced by Kafri {\em et al.} [Biophys. J. {\bf 86}, 3373 (2004)]. With the aid of the Fluctuation Theorem, we analyze the general features of these violations and this efficiency and link them to mechanochemical couplings of motors. In particular, an analysis of the experimental data of kinesin using our framework leads to interesting predictions that may serve as a guide for future experiments.Comment: 4 pages, 4 figures, accepted to Phys. Rev. Let

Multi-parameter deformed and nonstandard Y(glM)Y(gl_M) Yangian symmetry in integrable variants of Haldane-Shastry spin chain

By using `anyon like' representations of permutation algebra, which pick up nontrivial phase factors while interchanging the spins of two lattice sites, we construct some integrable variants of Haldane-Shastry (HS) spin chain. Lax equations for these spin chains allow us to find out the related conserved quantities. However, it turns out that such spin chains also possess a few additional conserved quantities which are apparently not derivable from the Lax equations. Identifying these additional conserved quantities, and the usual ones related to Lax equations, with different modes of a monodromy matrix, it is shown that the above mentioned HS like spin chains exhibit multi-parameter deformed and `nonstandard' variants of $Y(gl_M)$ Yangian symmetry.Comment: 18 pages, latex, no figure

Multi-lectin Affinity Chromatography and Quantitative Proteomic Analysis Reveal Differential Glycoform Levels between Prostate Cancer and Benign Prostatic Hyperplasia Sera.

Currently prostate-specific antigen is used for prostate cancer (PCa) screening, however it lacks the necessary specificity for differentiating PCa from other diseases of the prostate such as benign prostatic hyperplasia (BPH), presenting a clinical need to distinguish these cases at the molecular level. Protein glycosylation plays an important role in a number of cellular processes involved in neoplastic progression and is aberrant in PCa. In this study, we systematically interrogate the alterations in the circulating levels of hundreds of serum proteins and their glycoforms in PCa and BPH samples using multi-lectin affinity chromatography and quantitative mass spectrometry-based proteomics. Specific lectins (AAL, PHA-L and PHA-E) were used to target and chromatographically separate core-fucosylated and highly-branched protein glycoforms for analysis, as differential expression of these glycan types have been previously associated with PCa. Global levels of CD5L, CFP, C8A, BST1, and C7 were significantly increased in the PCa samples. Notable glycoform-specific alterations between BPH and PCa were identified among proteins CD163, C4A, and ATRN in the PHA-L/E fraction and among C4BPB and AZGP1 glycoforms in the AAL fraction. Despite these modest differences, substantial similarities in glycoproteomic profiles were observed between PCa and BPH sera

Spectral gap of the totally asymmetric exclusion process at arbitrary filling

We calculate the spectral gap of the Markov matrix of the totally asymmetric simple exclusion process (TASEP) on a ring of L sites with N particles. Our derivation is simple and self-contained and extends a previous calculation that was valid only for half-filling. We use a special property of the Bethe equations for TASEP to reformulate them as a one-body problem. Our method is closely related to the one used to derive exact large deviation functions of the TASEP

Mitochondrial DNA analysis of eneolithic trypillians from Ukraine reveals neolithic farming genetic roots

The agricultural revolution in Eastern Europe began in the Eneolithic with the Cucuteni-Trypillia culture complex. In Ukraine, the Trypillian culture (TC) existed for over two millennia (ca. 5,400–2,700 BCE) and left a wealth of artifacts. Yet, their burial rituals remain a mystery and to date almost nothing is known about the genetic composition of the TC population. One of the very few TC sites where human remains can be found is a cave called Verteba in western Ukraine. This report presents four partial and four complete mitochondrial genomes from nine TC individuals uncovered in the cave. The results of this analysis, combined with the data from previous reports, indicate that the Trypillian population at Verteba carried, for the most part, a typical Neolithic farmer package of mitochondrial DNA (mtDNA) lineages traced to Anatolian farmers and Neolithic farming groups of central Europe. At the same time, the find of two specimens belonging to haplogroup U8b1 at Verteba can be viewed as a connection of TC with the Upper Paleolithic European populations. At the level of mtDNA haplogroup frequencies, the TC population from Verteba demonstrates a close genetic relationship with population groups of the Funnel Beaker/ Trichterbecker cultural complex from central and northern Europe (ca. 3,950–2,500 BCE)