Free energy calculations of glycosaminoglycan - Protein interactions

Glycosaminoglycans (GAGs) are complex highly charged linear polysaccharides that have a variety of roles in biological processes. We report the first use of molecular dynamics (MD) free energy calculations using the MM/PBSA method to investigate the binding of GAGs to protein molecules, namely the platelet endothelial cell adhesion molecule 1 (PECAM-1) and annexin A2. Calculations of the free energy of the binding of heparin fragments of different sizes reveal the existence of a region of low GAG-binding affinity in domains 5-6 of PECAM-1 and a region of high affinity in domains 2-3, consistent with experimental data and ligand-protein docking studies. A conformational hinge movement between domains 2 and 3 was observed, which allows the binding of heparin fragments of increasing size (pentasaccharides to octasaccharides) with an increasingly higher binding affinity. Similar simulations of the binding of a heparin fragment to annexin A2 reveal the optimization of electrostatic and hydrogen bonding interactions with the protein and protein-bound calcium ions. In general, these free energy calculations reveal that the binding of heparin to protein surfaces is dominated by strong electrostatic interactions for longer fragments, with equally important contributions from van der Waals interactions and vibrational entropy changes, against a large unfavorable desolvation penalty due to the high charge density of these molecules.

In situ transmission electron microscope study of single asperity sliding contacts

Direct observation of events taking place at the contacting interfaces is important to understand many tribological phenomena. Transmission electron microscope (TEM) has the ability to look through materials at very high magnifications. Most of the TEM observations are done long after the deforming loads and stresses have been relaxed and the material state is further disturbed during the specimen preparation. We have developed a specimen holder in which two electron transparent surfaces can be brought in contact and moved relative to each other in JEOL 2000FX microscope. This holder enables visualization of not only the contacting surfaces at nanoscale but also the subsurface deformation resulting from the contact interaction. Sliding experimentS have been carried out mimicking a single asperity sliding contact. A sharp tungsten probe is moved laterally against a tip mounted on a cantilever. Magnitude of the contact instability, when the contact is broken is found to be dependent on the local geometry of the contact.(C) 2009 Elsevier Ltd. All rights reserved.

Search for Higgs bosons predicted in two-Higgs-doublet models via decays to tau lepton pairs in 1.96 TeV proton-antiproton collisions

We present the results of a search for Higgs bosons predicted in two-Higgs-doublet models, in the case where the Higgs bosons decay to tau lepton pairs, using 1.8 inverse fb of integrated luminosity of proton-antiproton collisions recorded by the CDF II experiment at the Fermilab Tevatron. Studying the observed mass distribution in events where one or both tau leptons decay leptonically, no evidence for a Higgs boson signal is observed. The result is used to infer exclusion limits in the two-dimensional parameter space of tan beta versus m(A).

Measurement of particle production and inclusive differential cross sections in pp̅ collisions at √s=1.96 TeV

We report a set of measurements of particle production in inelastic pbar{p} collisions collected with a minimum-bias trigger at the Tevatron Collider with the CDF II experiment. The inclusive charged particle transverse momentum differential cross section is measured, with improved precision, over a range about ten times wider than in previous measurements. The former modeling of the spectrum appears to be incompatible with the high particle momenta observed. The dependence of the charged particle transverse momentum on the event particle multiplicity is analyzed to study the various components of hadron interactions. This is one of the observable variables most poorly reproduced by the available Monte Carlo generators. A first measurement of the event transverse energy sum differential cross section is also reported. A comparison with a Pythia prediction at the hadron level is performed. The inclusive charged particle differential production cross section is fairly well reproduced only in the transverse momentum range available from previous measurements. At higher momentum the agreement is poor. The transverse energy sum is poorly reproduced over the whole spectrum. The dependence of the charged particle transverse momentum on the particle multiplicity needs the introduction of more sophisticated particle production mechanisms, such as multiple parton interactions, in order to be better explained.

Search for the Higgs boson produced in association with Z→ℓ+ℓ- using the matrix element method at CDF II

We present a search for associated production of the standard model (SM) Higgs boson and a $Z$ boson where the $Z$ boson decays to two leptons and the Higgs decays to a pair of $b$ quarks in $p\bar{p}$ collisions at the Fermilab Tevatron. We use event probabilities based on SM matrix elements to construct a likelihood function of the Higgs content of the data sample. In a CDF data sample corresponding to an integrated luminosity of 2.7 fb$^{-1}$ we see no evidence of a Higgs boson with a mass between 100 GeV$/c^2$ and 150 GeV$/c^2$. We set 95% confidence level (C.L.) upper limits on the cross-section for $ZH$ production as a function of the Higgs boson mass $m_H$; the limit is 8.2 times the SM prediction at $m_H = 115$ GeV$/c^2$.

Measurement of the WW+WZ production cross section using a matrix element technique in lepton+jets events

We present a measurement of the $WW+WZ$ production cross section observed in a final state consisting of an identified electron or muon, two jets, and missing transverse energy. The measurement is carried out in a data sample corresponding to up to 4.6~fb$^{-1}$ of integrated luminosity at $\sqrt{s} = 1.96$ TeV collected by the CDF II detector. Matrix element calculations are used to separate the diboson signal from the large backgrounds. The $WW+WZ$ cross section is measured to be $17.4\pm3.3$~pb, in agreement with standard model predictions. A fit to the dijet invariant mass spectrum yields a compatible cross section measurement.

Search for Maximal Flavor Violating Scalars in Same-Charge Lepton Pairs in pp̅ Collisions at √s=1.96 TeV

Models of Maximal Flavor Violation (MxFV) in elementary particle physics may contain at least one new scalar SU$(2)$ doublet field $\Phi_{FV} = (\eta^0,\eta^+)$ that couples the first and third generation quarks ($q_1,q_3$) via a Lagrangian term $\mathcal{L}_{FV} = \xi_{13} \Phi_{FV} q_1 q_3$. These models have a distinctive signature of same-charge top-quark pairs and evade flavor-changing limits from meson mixing measurements. Data corresponding to 2 fb$^{-1}$ collected by the CDF II detector in $p\bar{p}$ collisions at $\sqrt{s} = 1.96$ TeV are analyzed for evidence of the MxFV signature. For a neutral scalar $\eta^0$ with $m_{\eta^0} = 200$ GeV/$c^2$ and coupling $\xi_{13}=1$, $\sim$ 11 signal events are expected over a background of $2.1 \pm 1.8$ events. Three events are observed in the data, consistent with background expectations, and limits are set on the coupling $\xi_{13}$ for $m_{\eta^0} = 180-300$ GeV/$c^2$.

Combination of Tevatron Searches for the Standard Model Higgs Boson in the W+W- Decay Mode

We combine searches by the CDF and D0 collaborations for a Higgs boson decaying to W+W-. The data correspond to an integrated total luminosity of 4.8 (CDF) and 5.4 (D0) fb-1 of p-pbar collisions at sqrt{s}=1.96 TeV at the Fermilab Tevatron collider. No excess is observed above background expectation, and resulting limits on Higgs boson production exclude a standard-model Higgs boson in the mass range 162-166 GeV at the 95% C.L.

Combined Tevatron upper limit on gg->H->W+W- and constraints on the Higgs boson mass in fourth-generation fermion models

We combine results from searches by the CDF and D0 collaborations for a standard model Higgs boson (H) in the process gg->H->W+W- in p=pbar collisions at the Fermilab Tevatron Collider at sqrt{s}=1.96 TeV. With 4.8 fb-1 of integrated luminosity analyzed at CDF and 5.4 fb-1 at D0, the 95% Confidence Level upper limit on \sigma(gg->H) x B(H->W+W-) is 1.75 pb at m_H=120 GeV, 0.38 pb at m_H=165 GeV, and 0.83 pb at m_H=200 GeV. Assuming the presence of a fourth sequential generation of fermions with large masses, we exclude at the 95% Confidence Level a standard-model-like Higgs boson with a mass between 131 and 204 GeV.

Inclusive Search for Standard Model Higgs Boson Production in the WW Decay Channel using the CDF II Detector

We present a search for standard model (SM) Higgs boson production using ppbar collision data at sqrt(s) = 1.96 TeV, collected with the CDF II detector and corresponding to an integrated luminosity of 4.8 fb-1. We search for Higgs bosons produced in all processes with a significant production rate and decaying to two W bosons. We find no evidence for SM Higgs boson production and place upper limits at the 95% confidence level on the SM production cross section (sigma(H)) for values of the Higgs boson mass (m_H) in the range from 110 to 200 GeV. These limits are the most stringent for m_H > 130 GeV and are 1.29 above the predicted value of sigma(H) for mH = 165 GeV.

Exclusion of an Exotic Top Quark with -4/3 Electric Charge Using Soft Lepton Tagging

We present a measurement of the electric charge of the top quark using $\ppbar$ collisions corresponding to an integrated luminosity of 2.7~fb$^{-1}$ at the CDF II detector. We reconstruct $\ttbar$ events in the lepton+jets final state and use kinematic information to determine which $b$-jet is associated with the leptonically- or hadronically-decaying $t$-quark. Soft lepton taggers are used to determine the $b$-jet flavor. Along with the charge of the $W$ boson decay lepton, this information permits the reconstruction of the top quark's electric charge. Out of 45 reconstructed events with $2.4\pm0.8$ expected background events, 29 are reconstructed as $\ttbar$ with the standard model $+$2/3 charge, whereas 16 are reconstructed as $\ttbar$ with an exotic $-4/3$ charge. This is consistent with the standard model and excludes the exotic scenario at 95\% confidence level. This is the strongest exclusion of the exotic charge scenario and the first to use soft leptons for this purpose.

First Measurement of the b-Jet Cross Section in Events with a W Boson in pp̅ Collisions at √s=1.96 TeV

The cross section for jets from b quarks produced with a W boson has been measured in ppbar collision data from 1.9/fb of integrated luminosity recorded by the CDF II detector at the Tevatron. The W+b-jets process poses a significant background in measurements of top quark production and prominent searches for the Higgs boson. We measure a b-jet cross section of 2.74 +- 0.27(stat.) +- 0.42(syst.) pb in association with a single flavor of leptonic W boson decay over a limited kinematic phase space. This measured result cannot be accommodated in several available theoretical predictions.

Direct Top-Quark Width Measurement at CDF

We present a measurement of the top-quark width using $t\bar{t}$ events produced in $p\bar{p}$ collisions at Fermilab's Tevatron collider and collected by the CDF II detector. In the mode where the top quark decays to a $W$ boson and a bottom quark, we select events in which one $W$ decays leptonically and the other hadronically~(lepton + jets channel) . From a data sample corresponding to 4.3~fb$^{-1}$ of integrated luminosity, we identify 756 candidate events. The top-quark mass and the mass of $W$ boson that decays hadronically are reconstructed for each event and compared with templates of different top-quark widths~($\Gamma_t$) and deviations from nominal jet energy scale~($\Delta_{JES}$) to perform a simultaneous fit for both parameters, where $\Delta_{JES}$ is used for the {\it in situ} calibration of the jet energy scale. By applying a Feldman-Cousins approach, we establish an upper limit at 95$\%$ confidence level~(CL) of $\Gamma_t $

Measurement of W-Boson Polarization in Top-Quark Decay in pp̅ Collisions at √s=1.96 TeV

We report measurements of the polarization of W bosons from top-quark decays using 2.7 fb^-1 of ppbar collisions collected by the CDF II detector. Assuming a top-quark mass of 175 GeV/c^2, three measurements are performed. A simultaneous measurement of the fraction of longitudinal (f_0) and right-handed (f_+) W bosons yields the model-independent results f_0 = 0.88 \pm 0.11 (stat) \pm 0.06 (syst) and f_+ = -0.15 \pm 0.07 (stat) \pm 0.06 (syst) with a correlation coefficient of -0.59. A measurement of f_0 (f_+) constraining f_+ (f_0) to its standard model value of 0.0 (0.7) yields f_0 = 0.70 \pm 0.07 (stat) \pm 0.04 (syst) (f_+ = -0.01 \pm 0.02 (stat) \pm 0.05 (syst)). All these results are consistent with standard model expectations.

Measurement of the WW+WZ Production Cross Section Using the lepton+jets Final State at CDF II

We report two complementary measurements of the WW+WZ cross section in the final state consisting of an electron or muon, missing transverse energy, and jets, performed using p\bar{p} collision data at sqrt{s} = 1.96 TeV collected by the CDF II detector. The first method uses the dijet invariant mass distribution while the second more sensitive method uses matrix-element calculations. The result from the second method has a signal significance of 5.4 sigma and is the first observation of WW+WZ production using this signature. Combining the results gives sigma_{WW+WZ} = 16.0 +/- 3.3 pb, in agreement with the standard model prediction.