A charged particle in a magnetic field - Jarzynski Equality

We describe some solvable models which illustrate the Jarzynski theorem and related fluctuation theorems. We consider a charged particle in the presence of magnetic field in a two dimensional harmonic well. In the first case the centre of the harmonic potential is translated with a uniform velocity, while in the other case the particle is subjected to an ac force. We show that Jarzynski identity complements Bohr-van Leeuwen theorem on the absence of diamagnetism in equilibrium classical system.Comment: 5 pages, minor corrections made and journal reference adde

Single molecule experiments in biophysics: exploring the thermal behavior of nonequilibrium small systems

Biomolecules carry out very specialized tasks inside the cell where energies involved are few tens of k_BT, small enough for thermal fluctuations to be relevant in many biomolecular processes. In this paper I discuss a few concepts and present some experimental results that show how the study of fluctuation theorems applied to biomolecules contributes to our understanding of the nonequilibrium thermal behavior of small systems.Comment: Proceedings of the 22nd Statphys Conference 2004 (Bangalore,India). Invited contributio

Phase diagram for unzipping DNA with long-range interactions

We present a critique and extension of the mean-field approach to the mechanical pulling transition in bound polymer systems. Our model is motivated by the theoretically and experimentally important examples of adsorbed polymers and double-stranded DNA, and we focus on the case in which quenched disorder in the sequence of monomers is unimportant for the statistical mechanics. We show how including excluded volume interactions in the model affects the phase diagram for the critical pulling force, and we predict a re-entrancy phase at low temperatures which has not been previously discussed. We also consider the case of non-equilibrium pulling, in which the external force probes the local, rather than the global structure of the dsDNA or adsorbed polymer. The dynamics of the pulling transition in such experiments could illuminate the polymer's loop structure, which depends on the nature of excluded volume interactions.Comment: 4 pages, 2 figures; this version clarifies Eq. 8, and corrects errors in Fig.

Inferring DNA sequences from mechanical unzipping data: the large-bandwidth case

The complementary strands of DNA molecules can be separated when stretched apart by a force; the unzipping signal is correlated to the base content of the sequence but is affected by thermal and instrumental noise. We consider here the ideal case where opening events are known to a very good time resolution (very large bandwidth), and study how the sequence can be reconstructed from the unzipping data. Our approach relies on the use of statistical Bayesian inference and of Viterbi decoding algorithm. Performances are studied numerically on Monte Carlo generated data, and analytically. We show how multiple unzippings of the same molecule may be exploited to improve the quality of the prediction, and calculate analytically the number of required unzippings as a function of the bandwidth, the sequence content, the elasticity parameters of the unzipped strands

Two enzymes catalyze vitamin K 2,3-epoxide reductase activity in mouse: VKORC1 is highly expressed in exocrine tissues while VKORC1L1 is highly expressed in brain

AbstractVKORC1 and VKORC1L1 are enzymes that both catalyze the reduction of vitamin K2,3-epoxide via vitamin K quinone to vitamin K hydroquinone. VKORC1 is the key enzyme of the classical vitamin K cycle by which vitamin K-dependent (VKD) proteins are γ-carboxylated by the hepatic γ-glutamyl carboxylase (GGCX). In contrast, the VKORC1 paralog enzyme, VKORC1L1, is chiefly responsible for antioxidative function by reduction of vitamin K to prevent damage by intracellular reactive oxygen species. To investigate tissue-specific vitamin K 2,3-epoxide reductase (VKOR) function of both enzymes, we quantified mRNA levels for VKORC1, VKORC1L1, GGCX, and NQO1 and measured VKOR enzymatic activities in 29 different mouse tissues. VKORC1 and GGCX are highly expressed in liver, lung and exocrine tissues including mammary gland, salivary gland and prostate suggesting important extrahepatic roles for the vitamin K cycle. Interestingly, VKORC1L1 showed highest transcription levels in brain. Due to the absence of detectable NQO1 transcription in liver, we assume this enzyme has no bypass function with respect to activation of VKD coagulation proteins. Our data strongly suggest diverse functions for the vitamin K cycle in extrahepatic biological pathways

A quantum version of free energy - irreversible work relations

We give a quantum version of the Jarzynski relation between the distribution of work done over a certain time-interval on a system and the difference of equilibrium free energies. The main new ingredient is the identification of work depending on the quantum history of the system and the proper definition of various quantum ensembles over which the averages should be made. We also discuss a number of different regimes that have been considered by other authors and which are unified in the present set-up. In all cases, and quantum or classical, it is a general relation between heat and time-reversal that makes the Jarzynski relation so universally valid

Probing complex RNA structures by mechanical force

RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by solely invoking successive openings of native helices. Indeed, typical force-extension responses of complex RNA molecules are largely shaped by stretching-induced, long-lived intermediates including non-native helices. This is first shown for a set of generic structural motifs found in larger RNA structures, and then for Escherichia coli's 1540-base long 16S ribosomal RNA, which exhibits a surprisingly well-structured and reproducible unfolding pathway under mechanical stretching. Using out-of-equilibrium stochastic simulations, we demonstrate that these experimental results reflect the slow relaxation of RNA structural rearrangements. Hence, micromanipulations of single RNA molecules probe both their native structures and long-lived intermediates, so-called "kinetic traps", thereby capturing -at the single molecular level- the hallmark of RNA folding/unfolding dynamics.Comment: 9 pages, 9 figure

Nanowire assembly, e.g. for optical probes, comprises optically trapping high aspect ratio semiconductor nanowire with infrared single-beam optical trap and attaching nanowire to organic or inorganic structure

NOVELTY - A nanowire assembly method comprises optically trapping a semiconductor nanowire with an infrared single-beam optical trap and attaching the nanowire to an organic or inorganic structure by laser fusing. The nanowire is further trapped in a fluid environment. The optical trap has a beam wavelength of 1064 nm. The nanowire has an aspect ratio greater than 100 and a diameter less than 100 (preferably less than 80) nm. The nanowire and the organic or inorganic structure form a heterostructure. USE - For fabricating a nanowire assembly for use as e.g. active photonic devices, passive photonic devices, optical probes, subwavelength microscopy. ADVANTAGE - Nanowires with diameters as small as 20 nm and aspect ratios of above one hundred can be trapped and transported in three dimensions, enabling the construction of nanowire architectures which may function in various capacities. Nanowire structures can now be assembled in physiological environments, offering new forms of chemical, mechanical and optical stimulation of living cells. DETAILED DESCRIPTION - An INDEPENDENT CLAIM is included for a nanowire assembly comprising a nanowire and an organic or inorganic structure or an arbitrary structure. DESCRIPTION OF DRAWING(S) - The figure shows a schematic diagram of an optical tweezers instrument for nanowire trapping

Extracting Structural Information of a Heteropolymer from Force-Extension Curves

We present a theory for the reverse analysis on the sequence information of a single H/P two-letter random hetero-polymer (RHP) from its force-extension(f-z) curves during quasi static stretching. Upon stretching of a self-assembled RHP, it undergoes several structural transitions. The typical elastic response of a hetero-polymeric globule is a set of overlapping saw-tooth patterns. With consideration of the height and the position of the overlapping saw-tooth shape, we analyze the possibility of extracting the binding energies of the internal domains and the corresponding block sizes of the contributing conformations.Comment: 5 figures 7 page

Fabrication of 10 nm diameter hydrocarbon nanopores

The addition of carbon to samples, during transmission electron microscope imaging, presents a barrier to accurate analysis; the controlled deposition of hydrocarbons by a focused electron beam can be a useful technique for local nanometer-scale sculpting of material. Here we use hydrocarbon deposition to form nanopores from larger focused ion beam holes in silicon nitride membranes. Using this method, we close 100–200 nm diameter holes to diameters of 10 nm and below, with deposition rates of 0.6 nm/min. I-V characteristics of electrolytic flow through these nanopores agree quantitatively with a one dimensional model at all examined salt concentrations