Bayesian field theoretic reconstruction of bond potential and bond mobility in single molecule force spectroscopy

Quantifying the forces between and within macromolecules is a necessary first step in understanding the mechanics of molecular structure, protein folding, and enzyme function and performance. In such macromolecular settings, dynamic single-molecule force spectroscopy (DFS) has been used to distort bonds. The resulting responses, in the form of rupture forces, work applied, and trajectories of displacements, have been used to reconstruct bond potentials. Such approaches often rely on simple parameterizations of one-dimensional bond potentials, assumptions on equilibrium starting states, and/or large amounts of trajectory data. Parametric approaches typically fail at inferring complex-shaped bond potentials with multiple minima, while piecewise estimation may not guarantee smooth results with the appropriate behavior at large distances. Existing techniques, particularly those based on work theorems, also do not address spatial variations in the diffusivity that may arise from spatially inhomogeneous coupling to other degrees of freedom in the macromolecule, thereby presenting an incomplete picture of the overall bond dynamics. To solve these challenges, we have developed a comprehensive empirical Bayesian approach that incorporates data and regularization terms directly into a path integral. All experiemental and statistical parameters in our method are estimated empirically directly from the data. Upon testing our method on simulated data, our regularized approach requires fewer data and allows simultaneous inference of both complex bond potentials and diffusivity profiles.Comment: In review - Python source code available on github. Abridged abstract on arXi

Slowdown and splitting of gap solitons in apodized Bragg gratings

We study the motion of gap solitons in two models of apodized nonlinear fiber Bragg gratings (BGs), with the local reflectivity (LR) varying along the fiber. A single step of LR, and a periodic array of alternating steps with opposite signs (a "Bragg superstructure") are considered. A challenging possibility is to slow down and eventually halt the soliton by passing it through the step of increasing reflectivity, thus capturing a pulse of standing light. First, we develop an analytical approach, assuming adiabatic evolution of the soliton, and making use of the energy conservation and balance equation for the momentum. Comparison with simulations shows that the analytical approximation is quite accurate (unless the inhomogeneity is too steep): the soliton is either transmitted across the step or bounces back. If the step is narrow, systematic simulations demontrate that the soliton splits into transmitted and reflected pulses (splitting of a BG soliton which hits a chirped grating was observed in experiments). Moving through the periodic "superstructure", the soliton accummulates distortion and suffers radiation loss if the structure is composed of narrow steps. The soliton moves without any loss or irreversible deformation through the array of sufficiently broad steps.Comment: to appear in a special issue on Wave-Optical Engineering, Journal of Modern Optic

Profiles of inflated surfaces

We study the shape of inflated surfaces introduced in \cite{B1} and \cite{P1}. More precisely, we analyze profiles of surfaces obtained by inflating a convex polyhedron, or more generally an almost everywhere flat surface, with a symmetry plane. We show that such profiles are in a one-parameter family of curves which we describe explicitly as the solutions of a certain differential equation.Comment: 13 pages, 2 figure

Medium Resolution Near-Infrared Spectra of the Host Galaxies of Nearby Quasars

We present medium resolution near-infrared host galaxy spectra of low redshift quasars, PG 0844 + 349 (z=0.064), PG 1226 + 023 (z=0.158), and PG 1426+015 (z=0.086). The observations were done by using the Infrared Camera and Spectrograph (IRCS) at the Subaru 8.2 m telescope. The full width at half maximum of the point spread function was about 0.3 arcsec by operations of an adaptive optics system, which can effectively resolve the quasar spectra from the host galaxy spectra. We spent up to several hours per target and developed data reduction methods to reduce the systematic noises of the telluric emissions and absorptions. From the obtained spectra, we identified absorption features of Mg I (1.503 um), Si I (1.589 um) and CO (6-3) (1.619 um), and measured the velocity dispersions of PG 0844 + 349 to be 132+/-110 km s-1 and PG 1426 + 015 to be 264+/-215 km s-1. By using an M_BH-sigma relation of elliptical galaxies, we derived the black hole (BH) mass of PG 0844+349, log(M_BH/M_SUN) = 7.7+/-5.5 and PG 1426+015, log(M_BH/M_SUN) = 9.0+/-7.5. These values are consistent with the BH mass values from broad emission lines with an assumption of a virial factor of 5.5.Comment: 16 pages, 5 figure

A Study of a Mini-drift GEM Tracking Detector

A GEM tracking detector with an extended drift region has been studied as part of an effort to develop new tracking detectors for future experiments at RHIC and for the Electron Ion Collider that is being planned for BNL or JLAB. The detector consists of a triple GEM stack with a small drift region that was operated in a mini TPC type configuration. Both the position and arrival time of the charge deposited in the drift region were measured on the readout plane which allowed the reconstruction of a short vector for the track traversing the chamber. The resulting position and angle information from the vector could then be used to improve the position resolution of the detector for larger angle tracks, which deteriorates rapidly with increasing angle for conventional GEM tracking detectors using only charge centroid information. Two types of readout planes were studied. One was a COMPASS style readout plane with 400 micron pitch XY strips and the other consisted of 2x10mm2 chevron pads. The detector was studied in test beams at Fermilab and CERN, along with additional measurements in the lab, in order to determine its position and angular resolution for incident track angles up to 45 degrees. Several algorithms were studied for reconstructing the vector using the position and timing information in order to optimize the position and angular resolution of the detector for the different readout planes. Applications for large angle tracking detectors at RHIC and EIC are also discussed.Comment: Submitted to the IEEE Transactions on Nuclear Scienc

Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes

Genetics and “omics” studies designed to uncover genotype to phenotype relationships often identify large numbers of potential candidate genes, among which the causal genes are hidden. Scientists generally lack the time and technical expertise to review all relevant information available from the literature, from key model species and from a potentially wide range of related biological databases in a variety of data formats with variable quality and coverage. Computational tools are needed for the integration and evaluation of heterogeneous information in order to prioritise candidate genes and components of interaction networks that, if perturbed through potential interventions, have a positive impact on the biological outcome in the whole organism without producing negative side effects. Here we review several bioinformatics tools and databases that play an important role in biological knowledge discovery and candidate gene prioritization. We conclude with several key challenges that need to be addressed in order to facilitate biological knowledge discovery in the future.&nbsp