1,391 research outputs found
Detection of Functional Modes in Protein Dynamics
Proteins frequently accomplish their biological function by collective atomic motions. Yet the identification of collective motions related to a specific protein function from, e.g., a molecular dynamics trajectory is often non-trivial. Here, we propose a novel technique termed “functional mode analysis” that aims to detect the collective motion that is directly related to a particular protein function. Based on an ensemble of structures, together with an arbitrary “functional quantity” that quantifies the functional state of the protein, the technique detects the collective motion that is maximally correlated to the functional quantity. The functional quantity could, e.g., correspond to a geometric, electrostatic, or chemical observable, or any other variable that is relevant to the function of the protein. In addition, the motion that displays the largest likelihood to induce a substantial change in the functional quantity is estimated from the given protein ensemble. Two different correlation measures are applied: first, the Pearson correlation coefficient that measures linear correlation only; and second, the mutual information that can assess any kind of interdependence. Detecting the maximally correlated motion allows one to derive a model for the functional state in terms of a single collective coordinate. The new approach is illustrated using a number of biomolecules, including a polyalanine-helix, T4 lysozyme, Trp-cage, and leucine-binding protein
Synergy between trastuzumab and pertuzumab for human epidermal growth factor 2 (Her2) from colocalization: an in silico based mechanism
10.1186/bcr2888Breast Cancer Research133-BCRR
Measurement of B(t->Wb)/B(t->Wq) at the Collider Detector at Fermilab
We present a measurement of the ratio of top-quark branching fractions R= B(t
-> Wb)/B(t -> Wq), where q can be a b, s or a d quark, using lepton-plus-jets
and dilepton data sets with integrated luminosity of ~162 pb^{-1} collected
with the Collider Detector at Fermilab during Run II of the Tevatron. The
measurement is derived from the relative numbers of t-tbar events with
different multiplicity of identified secondary vertices. We set a lower limit
of R > 0.61 at 95% confidence level.Comment: 7 pages, 2 figures, published in Physical Review Letters; changes
made to be consistent with published versio
Measurement of the Dipion Mass Spectrum in X(3872) -> J/Psi Pi+ Pi- Decays
We measure the dipion mass spectrum in X(3872)--> J/Psi Pi+ Pi- decays using
360 pb-1 of pbar-p collisions at 1.96 TeV collected with the CDF II detector.
The spectrum is fit with predictions for odd C-parity (3S1, 1P1, and 3DJ)
charmonia decaying to J/Psi Pi+ Pi-, as well as even C-parity states in which
the pions are from Rho0 decay. The latter case also encompasses exotic
interpretations, such as a D0-D*0Bar molecule. Only the 3S1 and J/Psi Rho
hypotheses are compatible with our data. Since 3S1 is untenable on other
grounds, decay via J/Psi Rho is favored, which implies C=+1 for the X(3872).
Models for different J/Psi-Rho angular momenta L are considered. Flexibility in
the models, especially the introduction of Rho-Omega interference, enable good
descriptions of our data for both L=0 and 1.Comment: 7 pages, 4 figures -- Submitted to Phys. Rev. Let
Search for Higgs Boson Decaying to b-bbar and Produced in Association with W Bosons in p-pbar Collisions at sqrt{s}=1.96 TeV
We present a search for Higgs bosons decaying into b-bbar and produced in
association with W bosons in p-pbar collisions at sqrt{s}=1.96 TeV. This search
uses 320 pb-1 of the dataset accumulated by the upgraded Collider Detector at
Fermilab. Events are selected that have a high-transverse momentum electron or
muon, missing transverse energy, and two jets, one of which is consistent with
a hadronization of a b quark. Both the number of events and the dijet mass
distribution are consistent with standard model background expectations, and we
set 95% confidence level upper limits on the production cross section times
branching ratio for the Higgs boson or any new particle with similar decay
kinematics. These upper limits range from 10 pb for mH=110 GeV/c2 to 3 pb for
mH=150 GeV/c2.Comment: 7 pages, 3 figures; updated title to published versio
Search for ZZ and ZW Production in ppbar Collisions at sqrt(s) = 1.96 TeV
We present a search for ZZ and ZW vector boson pair production in ppbar
collisions at sqrt(s) = 1.96 TeV using the leptonic decay channels ZZ --> ll nu
nu, ZZ --> l l l' l' and ZW --> l l l' nu. In a data sample corresponding to an
integrated luminosity of 194 pb-1 collected with the Collider Detector at
Fermilab, 3 candidate events are found with an expected background of 1.0 +/-
0.2 events. We set a 95% confidence level upper limit of 15.2 pb on the cross
section for ZZ plus ZW production, compared to the standard model prediction of
5.0 +/- 0.4 pb.Comment: 7 pages, 2 figures. This version is accepted for publication by Phys.
Rev. D Rapid Communication
Measurement of the Inclusive Jet Cross Section using the Kt algorithm in pp-bar Collisions at sqrt(s) = 1.96 TeV
We report on a measurement of the inclusive jet production cross section in
pp-bar collisions at sqrt{s} = 1.96 TeV using data collected with the upgraded
Collider Detector at Fermilab in Run II (CDF II) corresponding to an integrated
luminosity of 385 pb^-1. Jets are reconstructed using the kt algorithm. The
measurement is carried out for jets with rapidity 0.1 < | yjet | < 0.7 and
transverse momentum in the range 54 < ptjet < 700 GeV/c. The measured cross
section is in good agreement with next-to-leading order perturbative QCD
predictions after the necessary non-perturbative parton-to-hadron corrections
are included.Comment: Submitted to Phys. Rev. Let
Search for Second-Generation Scalar Leptoquarks in Collisions at =1.96 TeV
Results on a search for pair production of second generation scalar
leptoquark in collisions at =1.96 TeV are reported. The
data analyzed were collected by the CDF detector during the 2002-2003 Tevatron
Run II and correspond to an integrated luminosity of 198 pb. Leptoquarks
(LQ) are sought through their decay into (charged) leptons and quarks, with
final state signatures represented by two muons and jets and one muon, large
transverse missing energy and jets. We observe no evidence for production
and derive 95% C.L. upper limits on the production cross sections as well
as lower limits on their mass as a function of , where is the
branching fraction for .Comment: 9 pages (3 author list) 5 figure
Measurement of the Cross Section for Prompt Diphoton Production in p-pbar Collisions at sqrt(s) = 1.96 TeV
We report a measurement of the rate of prompt diphoton production in
collisions at using a data sample of 207
pb collected with the upgraded Collider Detector at Fermilab (CDF II).
The background from non-prompt sources is determined using a statistical method
based on differences in the electromagnetic showers. The cross section is
measured as a function of the diphoton mass, the transverse momentum of the
diphoton system, and the azimuthal angle between the two photons and is found
to be consistent with perturbative QCD predictions.Comment: 7 pages, 3 figures,revtex4. Version accepted by PRL, but with cross
section tables i
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