NMR Determination of Oligonucleotide Structure

This unit provides an overview of the use of NMR to determine oligonucleotide structure. It covers basic NMR spectral properties, acquisition of interproton distance restraints and torsion angle restraints, structure refinement, assessment of the quality of the structure obtained. Software programs used in the process are also described.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143742/1/cpnc0702.pd

Feedback control of spin systems

The feedback stabilization problem for ensembles of coupled spin 1/2 systems is discussed from a control theoretic perspective. The noninvasive nature of the bulk measurement allows for a fully unitary and deterministic closed loop. The Lyapunov-based feedback design presented does not require spins that are selectively addressable. With this method, it is possible to obtain control inputs also for difficult tasks, like suppressing undesired couplings in identical spin systems.Comment: 16 pages, 15 figure

Differential loss of chromosome 11q in familial and sporadic parasympathetic paragangliomas detected by comparative genomic hybridization

Parasympathetic paragangliomas (PGLs) represent neuroendocrine tumors arising from chief cells in branchiomeric and intravagal paraganglia, which share several histological features with their sympathetic counterpart sympathoadrenal paragangliomas. In recent years, genetic analyses of the familial form of PGL have attracted considerable interest. However, the majority of paragangliomas occurs sporadically and it remains to be determined whether the pathogenesis of sporadic paraganglioma resembles that of the familial form. Furthermore, data on comparative genetic aberrations are scarce. To provide fundamental cytogenetic data on sporadic and hereditary PGLs, we performed comparative genomic hybridization using directly fluorochrome-conjugated DNA extracted from 12 frozen and 4 paraffin-embedded tumors. The comparative genomic hybridization data were extended by loss of heterozygosity analysis of chromosome 11q. DNA copy number changes were found in 10 (63%) of 16 tumors. The most frequent chromosomal imbalance involved loss of chromosome 11. Six of seven familial tumors and two of nine sporadic tumors showed loss of 11q (86% versus 22%, P = 0.012). Deletions of 11p and 5p were found in two of nine sporadic tumors. We conclude that overall DNA copy number changes are infrequent in PGLs compared to sympathetic paragangliomas and that loss of chromosome 11 may be an important event in their tumorigenesis, particularly in familial paragangliomas

Cosmological Black Holes on Branes

We examined analytically a cosmological black hole domain wall system. Using the C-metric construction we derived the metric for the spacetime describing an infinitely thin domain wall intersecting a cosmological black hole. We studied the behaviour of the scalar field describing a self-interacting cosmological domain wall and find the approximated solution valid for large distances. The thin wall approximation and the back raection problem were elaborated finding that the topological kink solution smoothed out singular behaviour of the zero thickness wall using a core topological and hence thick domain wall. We also analyze the nucleation of cosmological black holes on and in the presence of a domain walls and conclude that the domain wall will nucleate small black holes on it rather than large ones inside.Comment: 13 pages, Revtex, to be published in Phys.Rev. D1

Decoherence and Programmable Quantum Computation

An examination of the concept of using classical degrees of freedom to drive the evolution of quantum computers is given. Specifically, when externally generated, coherent states of the electromagnetic field are used to drive transitions within the qubit system, a decoherence results due to the back reaction from the qubits onto the quantum field. We derive an expression for the decoherence rate for two cases, that of the single-qubit Walsh-Hadamard transform, and for an implementation of the controlled-NOT gate. We examine the impact of this decoherence mechanism on Grover's search algorithm, and on the proposals for use of error-correcting codes in quantum computation.Comment: submitted to Phys. Rev. A 35 double-spaced pages, 2 figures, in LaTe

Operation of universal gates in a DXD superconducting solid state quantum computer

We demonstrate that complete set of gates can be realized in a DXD superconducting solid state quantum computer (quamputer), thereby proving its universality.Comment: 4 pages, 2 figure

Edge magnetoplasmons in periodically modulated structures

We present a microscopic treatment of edge magnetoplasmons (EMP's) within the random-phase approximation for strong magnetic fields, low temperatures, and filling factor $\nu =1(2)$, when a weak short-period superlattice potential is imposed along the Hall bar. The modulation potential modifies both the spatial structure and the dispersion relation of the fundamental EMP and leads to the appearance of a novel gapless mode of the fundamental EMP. For sufficiently weak modulation strengths the phase velocity of this novel mode is almost the same as the group velocity of the edge states but it should be quite smaller for stronger modulation. We discuss in detail the spatial structure of the charge density of the renormalized and the novel fundamental EMP's.Comment: 8 pages, 4 figure

Losses of chromosomes 1p and 3q are early genetic events in the development of sporadic pheochromocytomas

Despite several loss of heterozygosity studies, a comprehensive genomic survey of pheochromocytomas is still lacking. To identify DNA copy number changes which might be important in tumor development and progression and which may have diagnostic utility, we evaluated genetic aberrations in 29 sporadic adrenal and extra-adrenal pheochromocytomas (19 clinically benign tumors and 10 malignant lesions). Comparative genomic hybridization was performed using directly fluorochrome-conjugated DNA extracted from frozen (16) and paraffin-embedded (13) tumor tissues. The most frequently observed changes were losses of chromosomes 1p11-p32 (86%), 3q (52%), 6q (34%), 3p, 17p (31% each), 11q (28%), and gains of chromosomes 9q (38%) and 17q (31%). No amplification was identified and no difference between adrenal and extra-adrenal tumors was detected. Progression to malignant tumors was strongly associated with deletions of chromosome 6q (60% versus 21% in clinically benign lesions, P = 0.0368) and 17p (50% versus 21%). Fluorescence in situ hybridization confirmed the comparative genomic hybridization data of chromosomes 1p, 3q, and 6q, and revealed aneuploidy in some tumors. Our results suggest that the development of pheochromocytomas is associated with specific genomic aberrations, such as losses of 1p, 3q, and 6q and gains of 9q and 17q. In particular, tumor suppressor genes on chromosomes 1p and 3q may be involved in early tumorigenesis, and deletions of chromosomes 6q and 17p in progression to malignancy

Dynamical model and nonextensive statistical mechanics of a market index on large time windows

The shape and tails of partial distribution functions (PDF) for a financial signal, i.e. the S&P500 and the turbulent nature of the markets are linked through a model encompassing Tsallis nonextensive statistics and leading to evolution equations of the Langevin and Fokker-Planck type. A model originally proposed to describe the intermittent behavior of turbulent flows describes the behavior of normalized log-returns for such a financial market index, for small and large time windows, both for small and large log-returns. These turbulent market volatility (of normalized log-returns) distributions can be sufficiently well fitted with a $\chi^2$-distribution. The transition between the small time scale model of nonextensive, intermittent process and the large scale Gaussian extensive homogeneous fluctuation picture is found to be at $ca.$ a 200 day time lag. The intermittency exponent ($\kappa$) in the framework of the Kolmogorov log-normal model is found to be related to the scaling exponent of the PDF moments, -thereby giving weight to the model. The large value of $\kappa$ points to a large number of cascades in the turbulent process. The first Kramers-Moyal coefficient in the Fokker-Planck equation is almost equal to zero, indicating ''no restoring force''. A comparison is made between normalized log-returns and mere price increments.Comment: 40 pages, 14 figures; accepted for publication in Phys Rev

Why do we need a theory and metrics of technology upgrading?

This paper discusses why we need theory and metrics of technology upgrading. It critically reviews the existing approaches to technology upgrading and motivates build-up of theoretically relevant but empirically grounded middle level conceptual and statistical framework which could illuminate a type of challenges relevant for economies at different income levels. It conceptualizes technology upgrading as three dimensional processes composed of intensity and different types of technology upgrading through various types of innovation and technology activities; broadening of technology upgrading through different forms of technology and knowledge diversification, and interaction with global economy through knowledge import, adoption and exchange. We consider this to be necessary first step towards theory and metrics of technology upgrading and generation of more relevant composite indicator of technology upgrading