477 research outputs found
Identification of Amino Acid Sequences with Good Folding Properties in an Off-Lattice Model
Folding properties of a two-dimensional toy protein model containing only two
amino-acid types, hydrophobic and hydrophilic, respectively, are analyzed. An
efficient Monte Carlo procedure is employed to ensure that the ground states
are found. The thermodynamic properties are found to be strongly sequence
dependent in contrast to the kinetic ones. Hence, criteria for good folders are
defined entirely in terms of thermodynamic fluctuations. With these criteria
sequence patterns that fold well are isolated. For 300 chains with 20 randomly
chosen binary residues approximately 10% meet these criteria. Also, an analysis
is performed by means of statistical and artificial neural network methods from
which it is concluded that the folding properties can be predicted to a certain
degree given the binary numbers characterizing the sequences.Comment: 15 pages, 8 Postscript figures. Minor change
Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products
We developed a low-cost, high-throughput microbiome profiling method that
uses combinatorial sequence tags attached to PCR primers that amplify the rRNA
V6 region. Amplified PCR products are sequenced using an Illumina paired-end
protocol to generate millions of overlapping reads. Combinatorial sequence
tagging can be used to examine hundreds of samples with far fewer primers than
is required when sequence tags are incorporated at only a single end. The
number of reads generated permitted saturating or near-saturating analysis of
samples of the vaginal microbiome. The large number of reads al- lowed an
in-depth analysis of errors, and we found that PCR-induced errors composed the
vast majority of non-organism derived species variants, an ob- servation that
has significant implications for sequence clustering of similar high-throughput
data. We show that the short reads are sufficient to assign organisms to the
genus or species level in most cases. We suggest that this method will be
useful for the deep sequencing of any short nucleotide region that is
taxonomically informative; these include the V3, V5 regions of the bac- terial
16S rRNA genes and the eukaryotic V9 region that is gaining popularity for
sampling protist diversity.Comment: 28 pages, 13 figure
Two-Way Quantum Time Transfer: A Method for Daytime Space-Earth Links
Remote clock synchronization is crucial for many classical and quantum
network applications. Current state-of-the-art remote clock synchronization
techniques achieve femtosecond-scale clock stability utilizing frequency combs,
which are supplementary to quantum-networking hardware. Demonstrating an
alternative, we synchronize two remote clocks across our freespace testbed
using a method called two-way quantum time transfer (QTT). In one second we
reach picosecond-scale timing precision under very lossy and noisy channel
conditions representative of daytime space-Earth links with commercial
off-the-shelf quantum-photon sources and detection equipment. This work
demonstrates how QTT is potentially relevant for daytime space-Earth quantum
networking and/or providing high-precision secure timing in GPS-denied
environments.Comment: arXiv admin note: text overlap with arXiv:2211.0073
Quick and Clean Cloning: A Ligation-Independent Cloning Strategy for Selective Cloning of Specific PCR Products from Non-Specific Mixes
We have developed an efficient strategy for cloning of PCR products that contain an unknown region flanked by a known sequence. As with ligation-independent cloning, the strategy is based on homology between sequences present in both the vector and the insert. However, in contrast to ligation-independent cloning, the cloning vector has homology with only one of the two primers used for amplification of the insert. The other side of the linearized cloning vector has homology with a sequence present in the insert, but nested and non-overlapping with the gene-specific primer used for amplification. Since only specific products contain this sequence, but none of the non-specific products, only specific products can be cloned. Cloning is performed using a one-step reaction that only requires incubation for 10 minutes at room temperature in the presence of T4 DNA polymerase to generate single-stranded extensions at the ends of the vector and insert. The reaction mix is then directly transformed into E. coli where the annealed vector-insert complex is repaired and ligated. We have tested this method, which we call quick and clean cloning (QC cloning), for cloning of the variable regions of immunoglobulins expressed in non-Hodgkin lymphoma tumor samples. This method can also be applied to identify the flanking sequence of DNA elements such as T-DNA or transposon insertions, or be used for cloning of any PCR product with high specificity
Search for Neutral Higgs Bosons in Events with Multiple Bottom Quarks at the Tevatron
The combination of searches performed by the CDF and D0 collaborations at the
Fermilab Tevatron Collider for neutral Higgs bosons produced in association
with b quarks is reported. The data, corresponding to 2.6 fb-1 of integrated
luminosity at CDF and 5.2 fb-1 at D0, have been collected in final states
containing three or more b jets. Upper limits are set on the cross section
multiplied by the branching ratio varying between 44 pb and 0.7 pb in the Higgs
boson mass range 90 to 300 GeV, assuming production of a narrow scalar boson.
Significant enhancements to the production of Higgs bosons can be found in
theories beyond the standard model, for example in supersymmetry. The results
are interpreted as upper limits in the parameter space of the minimal
supersymmetric standard model in a benchmark scenario favoring this decay mode.Comment: 10 pages, 2 figure
Single hadron response measurement and calorimeter jet energy scale uncertainty with the ATLAS detector at the LHC
The uncertainty on the calorimeter energy response to jets of particles is
derived for the ATLAS experiment at the Large Hadron Collider (LHC). First, the
calorimeter response to single isolated charged hadrons is measured and
compared to the Monte Carlo simulation using proton-proton collisions at
centre-of-mass energies of sqrt(s) = 900 GeV and 7 TeV collected during 2009
and 2010. Then, using the decay of K_s and Lambda particles, the calorimeter
response to specific types of particles (positively and negatively charged
pions, protons, and anti-protons) is measured and compared to the Monte Carlo
predictions. Finally, the jet energy scale uncertainty is determined by
propagating the response uncertainty for single charged and neutral particles
to jets. The response uncertainty is 2-5% for central isolated hadrons and 1-3%
for the final calorimeter jet energy scale.Comment: 24 pages plus author list (36 pages total), 23 figures, 1 table,
submitted to European Physical Journal
Search for the standard model Higgs boson decaying to a pair in events with no charged leptons and large missing transverse energy using the full CDF data set
We report on a search for the standard model Higgs boson produced in
association with a vector boson in the full data set of proton-antiproton
collisions at TeV recorded by the CDF II detector at the
Tevatron, corresponding to an integrated luminosity of 9.45 fb. We
consider events having no identified charged lepton, a transverse energy
imbalance, and two or three jets, of which at least one is consistent with
originating from the decay of a quark. We place 95% credibility level upper
limits on the production cross section times standard model branching fraction
for several mass hypotheses between 90 and . For a Higgs
boson mass of , the observed (expected) limit is 6.7
(3.6) times the standard model prediction.Comment: Accepted by Phys. Rev. Let
Search for the standard model Higgs boson decaying to a bb pair in events with one charged lepton and large missing transverse energy using the full CDF data set
We present a search for the standard model Higgs boson produced in
association with a W boson in sqrt(s) = 1.96 TeV p-pbar collision data
collected with the CDF II detector at the Tevatron corresponding to an
integrated luminosity of 9.45 fb-1. In events consistent with the decay of the
Higgs boson to a bottom-quark pair and the W boson to an electron or muon and a
neutrino, we set 95% credibility level upper limits on the WH production cross
section times the H->bb branching ratio as a function of Higgs boson mass. At a
Higgs boson mass of 125 GeV/c2 we observe (expect) a limit of 4.9 (2.8) times
the standard model value.Comment: Submitted to Phys. Rev. Lett (v2 contains clarifications suggested by
PRL
Search for the standard model Higgs boson decaying to a bb pair in events with two oppositely-charged leptons using the full CDF data set
We present a search for the standard model Higgs boson produced in
association with a Z boson in data collected with the CDF II detector at the
Tevatron, corresponding to an integrated luminosity of 9.45/fb. In events
consistent with the decay of the Higgs boson to a bottom-quark pair and the Z
boson to electron or muon pairs, we set 95% credibility level upper limits on
the ZH production cross section times the H -> bb branching ratio as a function
of Higgs boson mass. At a Higgs boson mass of 125 GeV/c^2 we observe (expect) a
limit of 7.1 (3.9) times the standard model value.Comment: To be submitted to Phys. Rev. Let
Broadband Reconfiguration of OptoMechanical Filters
We demonstrate broad-band reconfiguration of coupled photonic crystal
nanobeam cavities by using optical gradient force induced mechanical actuation.
Propagating waveguide modes that exist over wide wavelength range are used to
actuate the structures and in that way control the resonance of localized
cavity mode. Using this all-optical approach, more than 18 linewidths of tuning
range is demonstrated. Using on-chip temperature self-referencing method that
we developed, we determined that 20 % of the total tuning was due to
optomechanical reconfiguration and the rest due to thermo-optic effects.
Independent control of mechanical and optical resonances of our structures, by
means of optical stiffening, is also demonstrated
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