7,404 research outputs found
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
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. 
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
- …