Equilibrium binding energies from fluctuation theorems and force spectroscopy simulations

Brownian dynamics simulations are used to study the detachment of a particle from a substrate. Although the model is simple and generic, we attempt to map its energy, length and time scales onto a specific experimental system, namely a bead that is weakly bound to a cell and then removed by an optical tweezer. The external driving force arises from the combined optical tweezer and substrate potentials, and thermal fluctuations are taken into account by a Brownian force. The Jarzynski equality and Crooks' fluctuation theorem are applied to obtain the equilibrium free energy difference between the final and initial states. To this end, we sample non--equilibrium work trajectories for various tweezer pulling rates. We argue that this methodology should also be feasible experimentally for the envisioned system. Furthermore, we outline how the measurement of a whole free energy profile would allow the experimentalist to retrieve the unknown substrate potential by means of a suitable deconvolution. The influence of the pulling rate on the accuracy of the results is investigated, and umbrella sampling is used to obtain the equilibrium probability of particle escape for a variety of trap potentials.Comment: 21 pages, 11 figures, To appear in Soft Matte

First-principles calculation of phase equilibrium of V-Nb, V-Ta, and Nb-Ta alloys

In this paper, we report the calculated phase diagrams of V-Nb, V-Ta, and Nb-Ta alloys computed by combining the total energies of 40–50 configurations for each system (obtained using density functional theory) with the cluster expansion and Monte Carlo techniques. For V-Nb alloys, the phase diagram computed with conventional cluster expansion shows a miscibility gap with consolute temperature T_c=1250 K. Including the constituent strain to the cluster expansion Hamiltonian does not alter the consolute temperature significantly, although it appears to influence the solubility of V- and Nb-rich alloys. The phonon contribution to the free energy lowers T_c to 950 K (about 25%). Our calculations thus predicts an appreciable miscibility gap for V-Nb alloys. For bcc V-Ta alloy, this calculation predicts a miscibility gap with T_c=1100 K. For this alloy, both the constituent strain and phonon contributions are found to be significant. The constituent strain increases the miscibility gap while the phonon entropy counteracts the effect of the constituent strain. In V-Ta alloys, an ordering transition occurs at 1583 K from bcc solid solution phase to the V_(2)Ta Laves phase due to the dominant chemical interaction associated with the relatively large electronegativity difference. Since the current cluster expansion ignores the V_(2)Ta phase, the associated chemical interaction appears to manifest in making the solid solution phase remain stable down to 1100 K. For the size-matched Nb-Ta alloys, our calculation predicts complete miscibility in agreement with experiment

Selection bias in the M_BH-sigma and M_BH-L correlations and its consequences

It is common to estimate black hole abundances by using a measured correlation between black hole mass and another more easily measured observable such as the velocity dispersion or luminosity of the surrounding bulge. The correlation is used to transform the distribution of the observable into an estimate of the distribution of black hole masses. However, different observables provide different estimates: the Mbh-sigma relation predicts fewer massive black holes than does the Mbh-L relation. This is because the sigma-L relation in black hole samples currently available is inconsistent with that in the SDSS sample, from which the distributions of L or sigma are based: the black hole samples have smaller L for a given sigma or have larger sigma for a given L. This is true whether L is estimated in the optical or in the NIR. If this is a selection rather than physical effect, then the Mbh-sigma and Mbh-L relations currently in the literature are also biased from their true values. We provide a framework for describing the effect of this bias. We then combine it with a model of the bias to make an estimate of the true intrinsic relations. While we do not claim to have understood the source of the bias, our simple model is able to reproduce the observed trends. If we have correctly modeled the selection effect, then our analysis suggests that the bias in the relation is likely to be small, whereas the relation is biased towards predicting more massive black holes for a given luminosity. In addition, it is likely that the Mbh-L relation is entirely a consequence of more fundamental relations between Mbh and sigma, and between sigma and L. The intrinsic relation we find suggests that at fixed luminosity, older galaxies tend to host more massive black holes.Comment: 12 pages, 7 figures. Accepted by ApJ. We have added a figure showing that a similar bias is also seen in the K-band. A new appendix describes the BH samples as well as the fits used in the main tex

NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures

Software packages NUFARM and NUCGEN, are described, which can be used to understand sequence directed structural variations in nucleic acids, by analysis and generation of non-uniform structures. A set of local inter basepair parameters (viz, tilt, roll, twist, shift, slide and rise) have been defined, which use geometry and coordinates of two successive basepairs only and can be used to generate polymeric structures with varying geometries for each of the 16 possible dinucleotide steps. Intra basepair parameters, propeller, buckle, opening and the C6...C8 distance can also be varied, if required, while the sugar phosphate backbone atoms are fixed in some standard conformation in each of the nucleotides. NUPARM can be used to analyse both DNA and RNA structures, with single as well as double stranded helices. The NUCGEN software generates double helical models with the backbone fixed in B-form DNA, but with appropriate modifications in the input data, it can also generate A-form DNA and RNA duplex structures

FUSE Detection of Galactic OVI Emission in the Halo above the Perseus Arm

Background observations obtained with the Far Ultraviolet Spectroscopic Explorer (FUSE) toward l=95.4, b=36.1 show OVI 1032,1038 in emission. This sight line probes a region of stronger-than-average soft X-ray emission in the direction of high-velocity cloud Complex C above a part of the disk where Halpha filaments rise into the halo. The OVI intensities, 1600+/-300 ph/s/cm^2/sr (1032A) and 800+/-300 ph/s/cm^2/sr (1038A), are the lowest detected in emission in the Milky Way to date. A second sight line nearby (l=99.3, b=43.3) also shows OVI 1032 emission, but with too low a signal-to-noise ratio to obtain reliable measurements. The measured intensities, velocities, and FWHMs of the OVI doublet and the CII* line at 1037A are consistent with a model in which the observed emission is produced in the Galactic halo by hot gas ejected by supernovae in the Perseus arm. An association of the observed gas with Complex C appears unlikely.Comment: accepted for publication in ApJL, 11 pages including 3 figure

Dynamic instabilities of fracture under biaxial strain using a phase field model

We present a phase field model of the propagation of fracture under plane strain. This model, based on simple physical considerations, is able to accurately reproduce the different behavior of cracks (the principle of local symmetry, the Griffith and Irwin criteria, and mode-I branching). In addition, we test our model against recent experimental findings showing the presence of oscillating cracks under bi-axial load. Our model again reproduces well observed supercritical Hopf bifurcation, and is therefore the first simulation which does so

Dynamic crossover scaling in polymer solutions

The crossover region in the phase diagram of polymer solutions, in the regime above the overlap concentration, is explored by Brownian Dynamics simulations, to map out the universal crossover scaling functions for the gyration radius and the single-chain diffusion constant. Scaling considerations, our simulation results, and recently reported data on the polymer contribution to the viscosity obtained from rheological measurements on DNA systems, support the assumption that there are simple relations between these functions, such that they can be inferred from one another.Comment: 4 pages, 6 figures, 1 Table. Revised version to appear in Physical Review Letters. Includes supplemental material