357 research outputs found
Structural fluctuations and quantum transport through DNA molecular wires: a combined molecular dynamics and model Hamiltonian approach
Charge transport through a short DNA oligomer (Dickerson dodecamer) in
presence of structural fluctuations is investigated using a hybrid
computational methodology based on a combination of quantum mechanical
electronic structure calculations and classical molecular dynamics simulations
with a model Hamiltonian approach. Based on a fragment orbital description, the
DNA electronic structure can be coarse-grained in a very efficient way. The
influence of dynamical fluctuations arising either from the solvent
fluctuations or from base-pair vibrational modes can be taken into account in a
straightforward way through time series of the effective DNA electronic
parameters, evaluated at snapshots along the MD trajectory. We show that charge
transport can be promoted through the coupling to solvent fluctuations, which
gate the onsite energies along the DNA wire
Dissipative Effects in the Electronic Transport through DNA Molecular Wires
We investigate the influence of a dissipative environment which effectively
comprises the effects of counterions and hydration shells, on the transport
properties of short \DNA wires. Their electronic structure is captured by a
tight-binding model which is embedded in a bath consisting of a collection of
harmonic oscillators. Without coupling to the bath a temperature independent
gap opens in the electronic spectrum. Upon allowing for electron-bath
interaction the gap becomes temperature dependent. It increases with
temperature in the weak-coupling limit to the bath degrees of freedom. In the
strong-coupling regime a bath-induced {\it pseudo-gap} is formed. As a result,
a crossover from tunneling to activated behavior in the low-voltage region of
the - characteristics is observed with increasing temperature. The
temperature dependence of the transmission near the Fermi energy, , manifests an Arrhenius-like behavior in agreement with recent transport
experiments. Moreover, shows a weak exponential dependence on
the wire length, typical of strong incoherent transport. Disorder effects smear
the electronic bands, but do not appreciably affect the pseudo-gap formation
Quantum transport through a DNA wire in a dissipative environment
Electronic transport through DNA wires in the presence of a strong
dissipative environment is investigated. We show that new bath-induced
electronic states are formed within the bandgap. These states show up in the
linear conductance spectrum as a temperature dependent background and lead to a
crossover from tunneling to thermal activated behavior with increasing
temperature. Depending on the strength of the electron-bath coupling, the
conductance at the Fermi level can show a weak exponential or even an algebraic
length dependence. Our results suggest a new environmental-induced transport
mechanism. This might be relevant for the understanding of molecular conduction
experiments in liquid solution, like those recently performed on poly(GC)
oligomers in a water buffer (B. Xu et al., Nano Lett 4, 1105 (2004)).Comment: 5 pages, 3 figure
Electrical transport through single-molecule junctions: from molecular orbitals to conduction channels
We present an atomistic theory of electronic transport through single organic
molecules that reproduces the important features of the current-voltage
characteristics observed in recent experiments. We trace these features to
their origin in the electronic structure of the molecules and their local
atomic environment. We demonstrate how conduction channels arise from the
molecular orbitals and elucidate which specific properties of the individual
orbitals determine their contribution to the current.Comment: Revtex4, 4 pages, 4 figures. Version with color figures in
http://www-tfp.physik.uni-karlsruhe.de/~cuevas/Publications.htm
Theory of Current and Shot Noise Spectroscopy in Single-Molecular Quantum Dots with Phonon Mode
Using the Keldysh nonequilibrium Green function technique, we study the
current and shot noise spectroscopy of a single molecular quantum dot coupled
to a local phonon mode. It is found that in the presence of electron-phonon
coupling, in addition to the resonant peak associated with the single level of
the dot, satellite peaks with the separation set by the frequency of phonon
mode appear in the differential conductance. In the ``single level'' resonant
tunneling region, the differential shot noise power exhibit two split peaks.
However, only single peaks show up in the ``phonon assisted''
resonant-tunneling region. An experimental setup to test these predictions is
also proposed.Comment: 5 pages, 3 eps figures embedde
Green function techniques in the treatment of quantum transport at the molecular scale
The theoretical investigation of charge (and spin) transport at nanometer
length scales requires the use of advanced and powerful techniques able to deal
with the dynamical properties of the relevant physical systems, to explicitly
include out-of-equilibrium situations typical for electrical/heat transport as
well as to take into account interaction effects in a systematic way.
Equilibrium Green function techniques and their extension to non-equilibrium
situations via the Keldysh formalism build one of the pillars of current
state-of-the-art approaches to quantum transport which have been implemented in
both model Hamiltonian formulations and first-principle methodologies. We offer
a tutorial overview of the applications of Green functions to deal with some
fundamental aspects of charge transport at the nanoscale, mainly focusing on
applications to model Hamiltonian formulations.Comment: Tutorial review, LaTeX, 129 pages, 41 figures, 300 references,
submitted to Springer series "Lecture Notes in Physics
A framework for mixing methods in quantitative measurement development, validation, and revision: A case study
A framework for quantitative measurement development, validation, and revision that incorporates both qualitative and quantitative methods is introduced. It extends and adapts Adcock and Collier’s work, and thus, facilitates understanding of quantitative measurement development, validation, and revision as an integrated and cyclical set of procedures best achieved through mixed methods research. It also offers a systematic guide concerning how these procedures may be undertaken through detailing key “stages,” “levels,” and practical “tasks.” A case study illustrates how qualitative and quantitative methods may be mixed through the use of the proposed framework in the cross-cultural content- and construct-related validation and subsequent revision of a quantitative measure.The contribution of this article to mixed methods research literature is briefly discussed
Both telomeric and non-telomeric DNA damage are determinants of mammalian cellular senescence
<p>Abstract</p> <p>Background</p> <p>Cellular senescence is a state reached by normal mammalian cells after a finite number of cell divisions and is characterized by morphological and physiological changes including terminal cell-cycle arrest. The limits on cell division imposed by senescence may play an important role in both organismal aging and in preventing tumorigenesis. Cellular senescence and organismal aging are both accompanied by increased DNA damage, seen as the formation of γ-H2AX foci (γ-foci), which may be found on uncapped telomeres or at non-telomeric sites of DNA damage. However, the relative importance of telomere- and non-telomere-associated DNA damage to inducing senescence has never been demonstrated. Here we present a new approach to determine accurately the chromosomal location of γ-foci and quantify the number of telomeric versus non-telomeric γ-foci associated with senescence in both human and mouse cells. This approach enables researchers to obtain accurate values and to avoid various possible misestimates inherent in earlier methods.</p> <p>Results</p> <p>Using combined immunofluorescence and telomere fluorescence <it>in situ </it>hybridization on metaphase chromosomes, we show that human cellular senescence is not solely determined by telomeric DNA damage. In addition, mouse cellular senescence is not solely determined by non-telomeric DNA damage. By comparing cells from different generations of telomerase-null mice with human cells, we show that cells from late generation telomerase-null mice, which have substantially short telomeres, contain mostly telomeric γ-foci. Most notably, we report that, as human and mouse cells approach senescence, all cells exhibit similar numbers of total γ-foci per cell, irrespective of chromosomal locations.</p> <p>Conclusion</p> <p>Our results suggest that the chromosome location of senescence-related γ-foci is determined by the telomere length rather than species differences <it>per se</it>. In addition, our data indicate that both telomeric and non-telomeric DNA damage responses play equivalent roles in signaling the initiation of cellular senescence and organismal aging. These data have important implications in the study of mechanisms to induce or delay cellular senescence in different species.</p
Epithelial to Mesenchymal Transition Is Mechanistically Linked with Stem Cell Signatures in Prostate Cancer Cells
Current management of patients diagnosed with prostate cancer (PCa) is very effective; however, tumor recurrence with Castrate Resistant Prostate Cancer (CRPC) and subsequent metastasis lead to poor survival outcome, suggesting that there is a dire need for novel mechanistic understanding of tumor recurrence, which would be critical for designing novel therapies. The recurrence and the metastasis of PCa are tightly linked with the biology of prostate cancer stem cells or cancer-initiating cells that is reminiscent of the acquisition of Epithelial to Mesenchymal Transition (EMT) phenotype. Increasing evidence suggests that EMT-type cells share many biological characteristics with cancer stem-like cells.In this study, we found that PCa cells with EMT phenotype displayed stem-like cell features characterized by increased expression of Sox2, Nanog, Oct4, Lin28B and/or Notch1, consistent with enhanced clonogenic and sphere (prostasphere)-forming ability and tumorigenecity in mice, which was associated with decreased expression of miR-200 and/or let-7 family. Reversal of EMT by re-expression of miR-200 inhibited prostasphere-forming ability of EMT-type cells and reduced the expression of Notch1 and Lin28B. Down-regulation of Lin28B increased let-7 expression, which was consistent with repressed self-renewal capability.These results suggest that miR-200 played a pivotal role in linking the characteristics of cancer stem-like cells with EMT-like cell signatures in PCa. Selective elimination of cancer stem-like cells by reversing the EMT phenotype to Mesenchymal-Epithelial Transition (MET) phenotype using novel agents would be useful for the prevention of tumor recurrence especially by eliminating those cells that are the "Root Cause" of tumor development and recurrence
Emotion regulation difficulties in anorexia nervosa: associations with improvements in eating psychopathology
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