Some formal results for the valence bond basis

In a system with an even number of SU(2) spins, there is an overcomplete set of states--consisting of all possible pairings of the spins into valence bonds--that spans the S=0 Hilbert subspace. Operator expectation values in this basis are related to the properties of the closed loops that are formed by the overlap of valence bond states. We construct a generating function for spin correlation functions of arbitrary order and show that all nonvanishing contributions arise from configurations that are topologically irreducible. We derive explicit formulas for the correlation functions at second, fourth, and sixth order. We then extend the valence bond basis to include triplet bonds and discuss how to compute properties that are related to operators acting outside the singlet sector. These results are relevant to analytical calculations and to numerical valence bond simulations using quantum Monte Carlo, variational wavefunctions, or exact diagonalization.Comment: 22 pages, 14 figure

Ajami : spaces between the street and the privacy of home

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Architecture, 2003.Includes bibliographical references (leaf 48).The thesis investigates, by research and design, spaces which are located between the street and the privacy of home, focusing on the case-study of Ajami; a mixed Palestinian-Israeli and Jewish-Israeli neighborhood in Jaffa, lying on the seashore of the Mediterranean. The houses in Ajami are separated from the street with a sequence of semi-inside spaces, steps and turns in which the privacy of the house is reached gradually as the in-between spaces unfold. While these spaces separate the house from the street they also open, at points, a space for communication between the private and the public. The houses in Ajami reflect a long process of additions, modifications and subdivisions of a once one-family villa surrounded by a courtyard-garden and a wall. The qualities of spaces and movement within the existent buildings were used in the thesis to inspire a building type that was employed in the design of two houses, comprising of thirteen units overall. Behind the relatively simple envelopes of the buildings a variety of in-between spaces are interweaved in the design to form each unit its distinct story of arrival and inhabitation.by Noa Havilio.S.M

Evidence for abundant transcription of non-coding regions in the Saccharomyces cerevisiae genome

Background: Recent studies in a growing number of organisms have yielded accumulating evidence that a significant portion of the non-coding region in the genome is transcribed. We address this issue in the yeast Saccharomyces cerevisiae. Results: Taking into account the absence of a significantly large yeast EST database, we use microarray expression data collected for genomic regions erroneously believed to be coding to study the expression pattern of non-coding regions in the Saccharomyces cerevisiae genome. We find that at least 164 out of 589 (28%) such regions are expressed under specific biological conditions. In particular, looking at the probes that are located opposing other known genes at the same genomic locus, we find that 88 out of 341 (26%) of these genes support antisense transcription. The expression patterns of these antisense genes are positively correlated. We validate these results using RT-PCR on a sample of 6 non-coding transcripts. Conclusions: 1. The yeast genome is transcribed on a scale larger than previously assumed. 2. Correlated transcription of antisense genes is abundant in the yeast genome. 3. Antisense genes in yeast are non-coding.Comment: Journal version available at http://www.biomedcentral.com/1471-2164/6/93/abstrac

Superconductivity and Quantum Spin Disorder in Cuprates

A fundamental connection between superconductivity and quantum spin fluctuations in underdoped cuprates, is revealed. A variational calculation shows that {\em Cooper pair hopping} strongly reduces the local magnetization $m_0$. This effect pertains to recent neutron scattering and muon spin rotation measurements in which $m_0$ varies weakly with hole doping in the poorly conducting regime, but drops precipitously above the onset of superconductivity

Excitation spectrum of the homogeneous spin liquid

We discuss the excitation spectrum of a disordered, isotropic and translationally invariant spin state in the 2D Heisenberg antiferromagnet. The starting point is the nearest-neighbor RVB state which plays the role of the vacuum of the theory, in a similar sense as the Neel state is the vacuum for antiferromagnetic spin wave theory. We discuss the elementary excitations of this state and show that these are not Fermionic spin-1/2 `spinons' but spin-1 excited dimers which must be modeled by bond Bosons. We derive an effective Hamiltonian describing the excited dimers which is formally analogous to spin wave theory. Condensation of the bond-Bosons at zero temperature into the state with momentum (pi,pi) is shown to be equivalent to antiferromagnetic ordering. The latter is a key ingredient for a microscopic interpretation of Zhang's SO(5) theory of cuprate superconductivityComment: RevTex-file, 16 PRB pages with 13 embedded eps figures. Hardcopies of figures (or the entire manuscript) can be obtained by e-mail request to: [email protected]

Local Magnetic Order vs. Superconductivity in a Layered Cuprate

We report on the phase diagram for charge-stripe order in La(1.6-x)Nd(0.4)Sr(x)CuO(4), determined by neutron and x-ray scattering studies and resistivity measurements. From an analysis of the in-plane resistivity motivated by recent nuclear-quadrupole-resonance studies, we conclude that the transition temperature for local charge ordering decreases monotonically with x, and hence that local antiferromagnetic order is uniquely correlated with the anomalous depression of superconductivity at x = 1/8. This result is consistent with theories in which superconductivity depends on the existence of charge-stripe correlations.Comment: 4 pages, 4 figures; introduction revised, Fig. 3 removed, last figure replace

Computational refinement of post-translational modifications predicted from tandem mass spectrometry

Motivation: A post-translational modification (PTM) is a chemical modification of a protein that occurs naturally. Many of these modifications, such as phosphorylation, are known to play pivotal roles in the regulation of protein function. Henceforth, PTM perturbations have been linked to diverse diseases like Parkinson's, Alzheimer's, diabetes and cancer. To discover PTMs on a genome-wide scale, there is a recent surge of interest in analyzing tandem mass spectrometry data, and several unrestrictive (so-called ‘blind’) PTM search methods have been reported. However, these approaches are subject to noise in mass measurements and in the predicted modification site (amino acid position) within peptides, which can result in false PTM assignments

Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification

Motivation: Tandem mass spectrometry (MS/MS) is an indispensable technology for identification of proteins from complex mixtures. Proteins are digested to peptides that are then identified by their fragmentation patterns in the mass spectrometer. Thus, at its core, MS/MS protein identification relies on the relative predictability of peptide fragmentation. Unfortunately, peptide fragmentation is complex and not fully understood, and what is understood is not always exploited by peptide identification algorithms

SAMPI: Protein Identification with Mass Spectra Alignments

BACKGROUND: Mass spectrometry based peptide mass fingerprints (PMFs) offer a fast, efficient, and robust method for protein identification. A protein is digested (usually by trypsin) and its mass spectrum is compared to simulated spectra for protein sequences in a database. However, existing tools for analyzing PMFs often suffer from missing or heuristic analysis of the significance of search results and insufficient handling of missing and additional peaks. RESULTS: We present an unified framework for analyzing Peptide Mass Fingerprints that offers a number of advantages over existing methods: First, comparison of mass spectra is based on a scoring function that can be custom-designed for certain applications and explicitly takes missing and additional peaks into account. The method is able to simulate almost every additive scoring scheme. Second, we present an efficient deterministic method for assessing the significance of a protein hit, independent of the underlying scoring function and sequence database. We prove the applicability of our approach using biological mass spectrometry data and compare our results to the standard software Mascot. CONCLUSION: The proposed framework for analyzing Peptide Mass Fingerprints shows performance comparable to Mascot on small peak lists. Introducing more noise peaks, we are able to keep identification rates at a similar level by using the flexibility introduced by scoring schemes

A mass accuracy sensitive probability based scoring algorithm for database searching of tandem mass spectrometry data

<p>Abstract</p> <p>Background</p> <p>Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) has become one of the most used tools in mass spectrometry based proteomics. Various algorithms have since been developed to automate the process for modern high-throughput LC-MS/MS experiments.</p> <p>Results</p> <p>A probability based statistical scoring model for assessing peptide and protein matches in tandem MS database search was derived. The statistical scores in the model represent the probability that a peptide match is a random occurrence based on the number or the total abundance of matched product ions in the experimental spectrum. The model also calculates probability based scores to assess protein matches. Thus the protein scores in the model reflect the significance of protein matches and can be used to differentiate true from random protein matches.</p> <p>Conclusion</p> <p>The model is sensitive to high mass accuracy and implicitly takes mass accuracy into account during scoring. High mass accuracy will not only reduce false positives, but also improves the scores of true positive matches. The algorithm is incorporated in an automated database search program MassMatrix.</p