28 research outputs found
Entropically Driven Helix Formation
The helix is a ubiquitous motif for biopolymers. We propose a heuristic,
entropically based model that predicts helix formation in a system of hard
spheres and semiflexible tubes. We find that the entropy of the spheres is
maximized when short stretches of the tube form a helix with a geometry close
to that found in natural helices. Our model could be directly tested with
wormlike micelles as the tubes, and the effect could be used to self-assemble
supramolecular helices.Comment: 5 pages, one included figur
Helical Tubes in Crowded Environments
When placed in a crowded environment, a semi-flexible tube is forced to fold
so as to make a more compact shape. One compact shape that often arises in
nature is the tight helix, especially when the tube thickness is of comparable
size to the tube length. In this paper we use an excluded volume effect to
model the effects of crowding. This gives us a measure of compactness for
configurations of the tube, which we use to look at structures of the
semi-flexible tube that minimize the excluded volume. We focus most of our
attention on the helix and which helical geometries are most compact. We found
that helices of specific pitch to radius ratio 2.512 to be optimally compact.
This is the same geometry that minimizes the global curvature of the curve
defining the tube. We further investigate the effects of adding a bending
energy or multiple tubes to begin to explore the more complete space of
possible geometries a tube could form.Comment: 10 page
The First Hour of Extra-galactic Data of the Sloan Digital Sky Survey Spectroscopic Commissioning: The Coma Cluster
On 26 May 1999, one of the Sloan Digital Sky Survey (SDSS) fiber-fed
spectrographs saw astronomical first light. This was followed by the first
spectroscopic commissioning run during the dark period of June 1999. We present
here the first hour of extra-galactic spectroscopy taken during these early
commissioning stages: an observation of the Coma cluster of galaxies. Our data
samples the Southern part of this cluster, out to a radius of 1.5degrees and
thus fully covers the NGC 4839 group. We outline in this paper the main
characteristics of the SDSS spectroscopic systems and provide redshifts and
spectral classifications for 196 Coma galaxies, of which 45 redshifts are new.
For the 151 galaxies in common with the literature, we find excellent agreement
between our redshift determinations and the published values. As part of our
analysis, we have investigated four different spectral classification
algorithms: spectral line strengths, a principal component decomposition, a
wavelet analysis and the fitting of spectral synthesis models to the data. We
find that a significant fraction (25%) of our observed Coma galaxies show signs
of recent star-formation activity and that the velocity dispersion of these
active galaxies (emission-line and post-starburst galaxies) is 30% larger than
the absorption-line galaxies. We also find no active galaxies within the
central (projected) 200 h-1 Kpc of the cluster. The spatial distribution of our
Coma active galaxies is consistent with that found at higher redshift for the
CNOC1 cluster survey. Beyond the core region, the fraction of bright active
galaxies appears to rise slowly out to the virial radius and are randomly
distributed within the cluster with no apparent correlation with the potential
merger of the NGC 4839 group. [ABRIDGED]Comment: Accepted in AJ, 65 pages, 20 figures, 5 table
The Sloan Digital Sky Survey Quasar Catalog I. Early Data Release
We present the first edition of the Sloan Digital Sky Survey (SDSS) Quasar
Catalog. The catalog consists of the 3814 objects (3000 discovered by the SDSS)
in the initial SDSS public data release that have at least one emission line
with a full width at half maximum larger than 1000 km/s, luminosities brighter
than M_i^* = -23, and highly reliable redshifts. The area covered by the
catalog is 494 square degrees; the majority of the objects were found in SDSS
commissioning data using a multicolor selection technique. The quasar redshifts
range from 0.15 to 5.03. For each object the catalog presents positions
accurate to better than 0.2" rms per coordinate, five band (ugriz) CCD-based
photometry with typical accuracy of 0.05 mag, radio and X-ray emission
properties, and information on the morphology and selection method. Calibrated
spectra of all objects in the catalog, covering the wavelength region 3800 to
9200 Angstroms at a spectral resolution of 1800-2100, are also available. Since
the quasars were selected during the commissioning period, a time when the
quasar selection algorithm was undergoing frequent revisions, the sample is not
homogeneous and is not intended for statistical analysis.Comment: 27 pages, 4 figures, 4 tables, accepted by A
Galaxy Clustering in Early SDSS Redshift Data
We present the first measurements of clustering in the Sloan Digital Sky
Survey (SDSS) galaxy redshift survey. Our sample consists of 29,300 galaxies
with redshifts 5,700 km/s < cz < 39,000 km/s, distributed in several long but
narrow (2.5-5 degree) segments, covering 690 square degrees. For the full,
flux-limited sample, the redshift-space correlation length is approximately 8
Mpc/h. The two-dimensional correlation function \xi(r_p,\pi) shows clear
signatures of both the small-scale, ``fingers-of-God'' distortion caused by
velocity dispersions in collapsed objects and the large-scale compression
caused by coherent flows, though the latter cannot be measured with high
precision in the present sample. The inferred real-space correlation function
is well described by a power law, \xi(r)=(r/6.1+/-0.2 Mpc/h)^{-1.75+/-0.03},
for 0.1 Mpc/h < r < 16 Mpc/h. The galaxy pairwise velocity dispersion is
\sigma_{12} ~ 600+/-100 km/s for projected separations 0.15 Mpc/h < r_p < 5
Mpc/h. When we divide the sample by color, the red galaxies exhibit a stronger
and steeper real-space correlation function and a higher pairwise velocity
dispersion than do the blue galaxies. The relative behavior of subsamples
defined by high/low profile concentration or high/low surface brightness is
qualitatively similar to that of the red/blue subsamples. Our most striking
result is a clear measurement of scale-independent luminosity bias at r < 10
Mpc/h: subsamples with absolute magnitude ranges centered on M_*-1.5, M_*, and
M_*+1.5 have real-space correlation functions that are parallel power laws of
slope ~ -1.8 with correlation lengths of approximately 7.4 Mpc/h, 6.3 Mpc/h,
and 4.7 Mpc/h, respectively.Comment: 51 pages, 18 figures. Replaced to match accepted ApJ versio
Colors of 2625 Quasars at 0<z<5 Measured in the Sloan Digital Sky Survey Photometric System
We present an empirical investigation of the colors of quasars in the Sloan
Digital Sky Survey (SDSS) photometric system. The sample studied includes 2625
quasars with SDSS photometry. The quasars are distributed in a 2.5 degree wide
stripe centered on the Celestial Equator covering square degrees.
Positions and SDSS magnitudes are given for the 898 quasars known prior to SDSS
spectroscopic commissioning. New SDSS quasars represent an increase of over
200% in the number of known quasars in this area of the sky. The ensemble
average of the observed colors of quasars in the SDSS passbands are well
represented by a power-law continuum with (). However, the contributions of the bump
and other strong emission lines have a significant effect upon the colors. The
color-redshift relation exhibits considerable structure, which may be of use in
determining photometric redshifts for quasars. The range of colors can be
accounted for by a range in the optical spectral index with a distribution
(95% confidence), but there is a red tail in the
distribution. This tail may be a sign of internal reddening. Finally, we show
that there is a continuum of properties between quasars and Seyfert galaxies
and we test the validity of the traditional division between the two classes of
AGN.Comment: 66 pages, 15 figures (3 color), accepted by A
Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma
Multiple myeloma, a plasma cell malignancy, is the second most common blood cancer. Despite extensive research, disease heterogeneity is poorly characterized, hampering efforts for early diagnosis and improved treatments. Here, we apply single cell RNA sequencing to study the heterogeneity of 40 individuals along the multiple myeloma progression spectrum, including 11 healthy controls, demonstrating high interindividual variability that can be explained by expression of known multiple myeloma drivers and additional putative factors. We identify extensive subclonal structures for 10 of 29 individuals with multiple myeloma. In asymptomatic individuals with early disease and in those with minimal residual disease post-treatment, we detect rare tumor plasma cells with molecular characteristics similar to those of active myeloma, with possible implications for personalized therapies. Single cell analysis of rare circulating tumor cells allows for accurate liquid biopsy and detection of malignant plasma cells, which reflect bone marrow disease. Our work establishes single cell RNA sequencing for dissecting blood malignancies and devising detailed molecular characterization of tumor cells in symptomatic and asymptomatic patients
Compact tube geometries in crowded environments
We study the effects of crowding on a hard semi-flexible tube. We use the tube, to model polymers such as proteins, in the regime where its width is comparable to its length. In this regime the polymer does not form a coiled ball. We use the depletion volume interaction between the tube and a solution of small hard spheres to model the effects of crowding. The tube bends into a compact configuration in order to maximize the entropy of the spheres. We analyze these compact geometries for various size crowding spheres. We find that at some tube lengths a tight helix reminiscent of α-helices in proteins can be formed. We then elaborate on the crowding effect by constraining the system in a tight cylinder. The tight boundaries increases the drive toward helix formation and there is now an interplay between the two relevant length scales: the sphere sizes and the cylinder width. We apply the model to tight tunnels seen in the cell, such as the ribosomal exit tunnel. The tunnel has a width comparable to the α-helices which form as the nascent protein traverses the tunnel. In our simplified model the tight boundaries in the tunnel show a large free energy gain with helix formation. We compare the entropic drive towards helix formation with an electrostatic repulsion between the tube and cylinder walls. This allows us to compare two of the dominant forces in the tunnel. We do this in a simplified model where the helical tube is approximated s a straight cylinder that is concentric with the tunnel. We also smooth out the charges to give a homogeneous charge distribution along the cylinder walls. Using numerical solutions of the Poisson-Boltzmann equation we see that in the tight tunnel the counter-ions screen most of the charge so that in our model the charge would not be enough to overcome the entropic drive towards helix formation. The screening in the tight confines of the tunnel causes the electrostatic potential in the tunnel to depend logarithmically on the charges on the tunnel walls
Biocompatibility of a Marine Collagen-Based Scaffold In Vitro and In Vivo
Scaffold material is essential in providing mechanical support to tissue, allowing stem cells to improve their function in the healing and repair of trauma sites and tissue regeneration. The scaffold aids cell organization in the damaged tissue. It serves and allows bio mimicking the mechanical and biological properties of the target tissue and facilitates cell proliferation and differentiation at the regeneration site. In this study, the developed and assayed bio-composite made of unique collagen fibers and alginate hydrogel supports the function of cells around the implanted material. We used an in vivo rat model to study the scaffold effects when transplanted subcutaneously and as an augment for tendon repair. Animals’ well-being was measured by their weight and daily activity post scaffold transplantation during their recovery. At the end of the experiment, the bio-composite was histologically examined, and the surrounding tissues around the implant were evaluated for inflammation reaction and scarring tissue. In the histology, the formation of granulation tissue and fibroblasts that were part of the inclusion process of the implanted material were noted. At the transplanted sites, inflammatory cells, such as plasma cells, macrophages, and giant cells, were also observed as expected at this time point post transplantation. This study demonstrated not only the collagen-alginate device biocompatibility, with no cytotoxic effects on the analyzed rats, but also that the 3D structure enables cell migration and new blood vessel formation needed for tissue repair. Overall, the results of the current study proved for the first time that the implantable scaffold for long-term confirms the well-being of these rats and is correspondence to biocompatibility ISO standards and can be further developed for medical devices application