Probabilistic time

The concept of time emerges as an ordering structure in a classical statistical ensemble. Probability distributions $p_\tau(t)$ at a given time $t$ obtain by integrating out the past and future. We discuss all-time probability distributions that realize a unitary time evolution as described by rotations of the real wave function $q_\tau(t)=\pm \sqrt{p_\tau(t)}$. We establish a map to quantum physics and the Schr\"odinger equation. Suitable classical observables are mapped to quantum operators. The non-commutativity of the operator product is traced back to the incomplete statistics of the local-time subsystem. Our investigation of classical statistics is based on two-level observables that take the values one or zero. Then the wave functions can be mapped to elements of a Grassmann algebra. Quantum field theories for fermions arise naturally from our formulation of probabilistic time.Comment: new references, 30 page

Entanglement, Bell Inequalities and Decoherence in Particle Physics

We demonstrate the relevance of entanglement, Bell inequalities and decoherence in particle physics. In particular, we study in detail the features of the ``strange'' $K^0 \bar K^0$ system as an example of entangled meson--antimeson systems. The analogies and differences to entangled spin--1/2 or photon systems are worked, the effects of a unitary time evolution of the meson system is demonstrated explicitly. After an introduction we present several types of Bell inequalities and show a remarkable connection to CP violation. We investigate the stability of entangled quantum systems pursuing the question how possible decoherence might arise due to the interaction of the system with its ``environment''. The decoherence is strikingly connected to the entanglement loss of common entanglement measures. Finally, some outlook of the field is presented.Comment: Lectures given at Quantum Coherence in Matter: from Quarks to Solids, 42. Internationale Universit\"atswochen f\"ur Theoretische Physik, Schladming, Austria, Feb. 28 -- March 6, 2004, submitted to Lecture Notes in Physics, Springer Verlag, 45 page

Vacuum Fluctuations, Geometric Modular Action and Relativistic Quantum Information Theory

A summary of some lines of ideas leading to model-independent frameworks of relativistic quantum field theory is given. It is followed by a discussion of the Reeh-Schlieder theorem and geometric modular action of Tomita-Takesaki modular objects associated with the quantum field vacuum state and certain algebras of observables. The distillability concept, which is significant in specifying useful entanglement in quantum information theory, is discussed within the setting of general relativistic quantum field theory.Comment: 26 pages. Contribution for the Proceedings of a Conference on Special Relativity held at Potsdam, 200

Interferometry with independent Bose-Einstein ondensates: parity as an EPR/Bell quantum variable

When independent Bose-Einstein condensates (BEC), described quantum mechanically by Fock (number) states, are sent into interferometers, the measurement of the output port at which the particles are detected provides a binary measurement, with two possible results $\pm1$. With two interferometers and two BEC's, the parity (product of all results obtained at each interferometer) has all the features of an Einstein-Podolsky-Rosen quantity, with perfect correlations predicted by quantum mechanics when the settings (phase shifts of the interferometers) are the same. When they are different, significant violations of Bell inequalities are obtained. These violations do not tend to zero when the number $N$ of particles increases, and can therefore be obtained with arbitrarily large systems, but a condition is that all particles should be detected. We discuss the general experimental requirements for observing such effects, the necessary detection of all particles in correlation, the role of the pixels of the CCD detectors, and that of the alignments of the interferometers in terms of matching of the wave fronts of the sources in the detection regions. Another scheme involving three interferometers and three BEC's is discussed; it leads to Greenberger Horne Zeilinger (GHZ) sign contradictions, as in the usual GHZ case with three particles, but for an arbitrarily large number of them. Finally, generalizations of the Hardy impossibilities to an arbitrarily large number of particles are introduced. BEC's provide a large versality for observing violations of local realism in a variety of experimental arrangements.Comment: appendix adde

Entanglement and the geometry of two qubits

Two qubits is the simplest system where the notions of separable and entangled states and entanglement witnesses first appear. We give a three dimensional geometric description of these notions. This description however carries no quantitative information on the measure of entanglement. A four dimensional description captures also the entanglement measure. We give a neat formula for the Bell states which leads to a slick proof of the fundamental teleportation identity. We describe optimal distillation of two qubits geometrically and present a simple geometric proof of the Peres-Horodecki separability criterion.Comment: Added one figure and one reference. Added a key idenity for teleportatio

Reproducibility of differential proteomic technologies in CPTAC fractionated xenografts

The NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) employed a pair of reference xenograft proteomes for initial platform validation and ongoing quality control of its data collection for The Cancer Genome Atlas (TCGA) tumors. These two xenografts, representing basal and luminal-B human breast cancer, were fractionated and analyzed on six mass spectrometers in a total of 46 replicates divided between iTRAQ and label-free technologies, spanning a total of 1095 LC-MS/MS experiments. These data represent a unique opportunity to evaluate the stability of proteomic differentiation by mass spectrometry over many months of time for individual instruments or across instruments running dissimilar workflows. We evaluated iTRAQ reporter ions, label-free spectral counts, and label-free extracted ion chromatograms as strategies for data interpretation (source code is available from http://homepages.uc.edu/~wang2x7/Research.htm). From these assessments, we found that differential genes from a single replicate were confirmed by other replicates on the same instrument from 61 to 93% of the time. When comparing across different instruments and quantitative technologies, using multiple replicates, differential genes were reproduced by other data sets from 67 to 99% of the time. Projecting gene differences to biological pathways and networks increased the degree of similarity. These overlaps send an encouraging message about the maturity of technologies for proteomic differentiation

Proteogenomic integration reveals therapeutic targets in breast cancer xenografts

Recent advances in mass spectrometry (MS) have enabled extensive analysis of cancer proteomes. Here, we employed quantitative proteomics to profile protein expression across 24 breast cancer patient-derived xenograft (PDX) models. Integrated proteogenomic analysis shows positive correlation between expression measurements from transcriptomic and proteomic analyses; further, gene expression-based intrinsic subtypes are largely re-capitulated using non-stromal protein markers. Proteogenomic analysis also validates a number of predicted genomic targets in multiple receptor tyrosine kinases. However, several protein/phosphoprotein events such as overexpression of AKT proteins and ARAF, BRAF, HSP90AB1 phosphosites are not readily explainable by genomic analysis, suggesting that druggable translational and/or post-translational regulatory events may be uniquely diagnosed by MS. Drug treatment experiments targeting HER2 and components of the PI3K pathway supported proteogenomic response predictions in seven xenograft models. Our study demonstrates that MS-based proteomics can identify therapeutic targets and highlights the potential of PDX drug response evaluation to annotate MS-based pathway activities

Prototype tests of the Electromagnetic Particle Injector-2 for Fast Time Response Disruption Mitigation in Tokamaks

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