85 research outputs found
The Essential Interactions in Oxides and Spectral Weight Transfer in Doped Manganites
We calculate the value of the Fr\"ohlich electron-phonon interaction in
manganites, cuprates, and some other charge-transfer insulators and show that
this interaction is much stronger than any relevant magnetic interaction. A
polaron shift due to the Fr\"ohlich interaction, which is about 1 eV, suggests
that carriers in those systems are small (bi)polarons at all temperatures and
doping levels, in agreement with the oxygen isotope effect and other data. An
opposite conclusion, recently suggested in the literature, is shown to be
incorrect. The frequency and temperature dependence of the optical conductivity
of ferromagnetic manganites is explained within the framework of the bipolaron
theory.Comment: 6 pages, REVTeX 3.1 with 3 eps-figures. Journal versio
Is Barbero's Hamiltonian formulation a Gauge Theory of Lorentzian Gravity?
This letter is a critique of Barbero's constrained Hamiltonian formulation of
General Relativity on which current work in Loop Quantum Gravity is based.
While we do not dispute the correctness of Barbero's formulation of general
relativity, we offer some criticisms of an aesthetic nature. We point out that
unlike Ashtekar's complex SU(2) connection, Barbero's real SO(3) connection
does not admit an interpretation as a space-time gauge field. We show that if
one tries to interpret Barbero's real SO(3) connection as a space-time gauge
field, the theory is not diffeomorphism invariant. We conclude that Barbero's
formulation is not a gauge theory of gravity in the sense that Ashtekar's
Hamiltonian formulation is. The advantages of Barbero's real connection
formulation have been bought at the price of giving up the description of
gravity as a gauge field.Comment: 12 pages, no figures, revised in the light of referee's comments,
accepted for publication in Classical and Quantum Gravit
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score
©2008 Pandit and Skolnick; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This article is available from: http://www.biomedcentral.com/1471-2105/9/531doi:10.1186/1471-2105-9-531Background: Protein tertiary structure comparisons are employed in various fields of
contemporary structural biology. Most structure comparison methods involve generation of an
initial seed alignment, which is extended and/or refined to provide the best structural superposition
between a pair of protein structures as assessed by a structure comparison metric. One such
metric, the TM-score, was recently introduced to provide a combined structure quality measure
of the coordinate root mean square deviation between a pair of structures and coverage. Using the
TM-score, the TM-align structure alignment algorithm was developed that was often found to have
better accuracy and coverage than the most commonly used structural alignment programs;
however, there were a number of situations when this was not true.
Results: To further improve structure alignment quality, the Fr-TM-align algorithm has been
developed where aligned fragment pairs are used to generate the initial seed alignments that are
then refined using dynamic programming to maximize the TM-score. For the assessment of the
structural alignment quality from Fr-TM-align in comparison to other programs such as CE and TMalign,
we examined various alignment quality assessment scores such as PSI and TM-score. The
assessment showed that the structural alignment quality from Fr-TM-align is better in comparison
to both CE and TM-align. On average, the structural alignments generated using Fr-TM-align have
a higher TM-score (~9%) and coverage (~7%) in comparison to those generated by TM-align. Fr-
TM-align uses an exhaustive procedure to generate initial seed alignments. Hence, the algorithm is
computationally more expensive than TM-align.
Conclusion: Fr-TM-align, a new algorithm that employs fragment alignment and assembly provides
better structural alignments in comparison to TM-align. The source code and executables of Fr-
TM-align are freely downloadable at: http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/
Causal Set Dynamics: A Toy Model
We construct a quantum measure on the power set of non-cyclic oriented graphs
of N points, drawing inspiration from 1-dimensional directed percolation.
Quantum interference patterns lead to properties which do not appear to have
any analogue in classical percolation. Most notably, instead of the single
phase transition of classical percolation, the quantum model displays two
distinct crossover points. Between these two points, spacetime questions such
as "does the network percolate" have no definite or probabilistic answer.Comment: 28 pages incl. 5 figure
Probing the fuzzy sphere regularisation in simulations of the 3d \lambda \phi^4 model
We regularise the 3d \lambda \phi^4 model by discretising the Euclidean time
and representing the spatial part on a fuzzy sphere. The latter involves a
truncated expansion of the field in spherical harmonics. This yields a
numerically tractable formulation, which constitutes an unconventional
alternative to the lattice. In contrast to the 2d version, the radius R plays
an independent r\^{o}le. We explore the phase diagram in terms of R and the
cutoff, as well as the parameters m^2 and \lambda. Thus we identify the phases
of disorder, uniform order and non-uniform order. We compare the result to the
phase diagrams of the 3d model on a non-commutative torus, and of the 2d model
on a fuzzy sphere. Our data at strong coupling reproduce accurately the
behaviour of a matrix chain, which corresponds to the c=1-model in string
theory. This observation enables a conjecture about the thermodynamic limit.Comment: 31 pages, 15 figure
The Poisson sigma model on closed surfaces
Using methods of formal geometry, the Poisson sigma model on a closed surface
is studied in perturbation theory. The effective action, as a function on
vacua, is shown to have no quantum corrections if the surface is a torus or if
the Poisson structure is regular and unimodular (e.g., symplectic). In the case
of a Kahler structure or of a trivial Poisson structure, the partition function
on the torus is shown to be the Euler characteristic of the target; some
evidence is given for this to happen more generally. The methods of formal
geometry introduced in this paper might be applicable to other sigma models, at
least of the AKSZ type.Comment: 32 pages; references adde
BGWM as Second Constituent of Complex Matrix Model
Earlier we explained that partition functions of various matrix models can be
constructed from that of the cubic Kontsevich model, which, therefore, becomes
a basic elementary building block in "M-theory" of matrix models. However, the
less topical complex matrix model appeared to be an exception: its
decomposition involved not only the Kontsevich tau-function but also another
constituent, which we now identify as the Brezin-Gross-Witten (BGW) partition
function. The BGW tau-function can be represented either as a generating
function of all unitary-matrix integrals or as a Kontsevich-Penner model with
potential 1/X (instead of X^3 in the cubic Kontsevich model).Comment: 42 page
Can pulsed ultrasound increase tissue damage during ischemia? A study of the effects of ultrasound on infarcted and non-infarcted myocardium in anesthetized pigs
BACKGROUND: The same mechanisms by which ultrasound enhances thrombolysis are described in connection with non-beneficial effects of ultrasound. The present safety study was therefore designed to explore effects of beneficial ultrasound characteristics on the infarcted and non-infarcted myocardium. METHODS: In an open chest porcine model (n = 17), myocardial infarction was induced by ligating a coronary diagonal branch. Pulsed ultrasound of frequency 1 MHz and intensity 0.1 W/cm(2 )(I(SATA)) was applied during one hour to both infarcted and non-infarcted myocardial tissue. These ultrasound characteristics are similar to those used in studies of ultrasound enhanced thrombolysis. Using blinded assessment technique, myocardial damage was rated according to histopathological criteria. RESULTS: Infarcted myocardium exhibited a significant increase in damage score compared to non-infarcted myocardium: 6.2 ± 2.0 vs. 4.3 ± 1.5 (mean ± standard deviation), (p = 0.004). In the infarcted myocardium, ultrasound exposure yielded a further significant increase of damage scores: 8.1 ± 1.7 vs. 6.2 ± 2.0 (p = 0.027). CONCLUSION: Our results suggest an instantaneous additive effect on the ischemic damage in myocardial tissue when exposed to ultrasound of stated characteristics. The ultimate damage degree remains to be clarified
Challenges in QCD matter physics - The Compressed Baryonic Matter experiment at FAIR
Substantial experimental and theoretical efforts worldwide are devoted to
explore the phase diagram of strongly interacting matter. At LHC and top RHIC
energies, QCD matter is studied at very high temperatures and nearly vanishing
net-baryon densities. There is evidence that a Quark-Gluon-Plasma (QGP) was
created at experiments at RHIC and LHC. The transition from the QGP back to the
hadron gas is found to be a smooth cross over. For larger net-baryon densities
and lower temperatures, it is expected that the QCD phase diagram exhibits a
rich structure, such as a first-order phase transition between hadronic and
partonic matter which terminates in a critical point, or exotic phases like
quarkyonic matter. The discovery of these landmarks would be a breakthrough in
our understanding of the strong interaction and is therefore in the focus of
various high-energy heavy-ion research programs. The Compressed Baryonic Matter
(CBM) experiment at FAIR will play a unique role in the exploration of the QCD
phase diagram in the region of high net-baryon densities, because it is
designed to run at unprecedented interaction rates. High-rate operation is the
key prerequisite for high-precision measurements of multi-differential
observables and of rare diagnostic probes which are sensitive to the dense
phase of the nuclear fireball. The goal of the CBM experiment at SIS100
(sqrt(s_NN) = 2.7 - 4.9 GeV) is to discover fundamental properties of QCD
matter: the phase structure at large baryon-chemical potentials (mu_B > 500
MeV), effects of chiral symmetry, and the equation-of-state at high density as
it is expected to occur in the core of neutron stars. In this article, we
review the motivation for and the physics programme of CBM, including
activities before the start of data taking in 2022, in the context of the
worldwide efforts to explore high-density QCD matter.Comment: 15 pages, 11 figures. Published in European Physical Journal
Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family
<p>Abstract</p> <p>Background</p> <p>Gram-negative bacteria use periplasmic-binding proteins (bPBP) to transport nutrients through the periplasm. Despite immense diversity within the recognized substrates, all members of the family share a common fold that includes two domains that are separated by a conserved hinge. The hinge allows the protein to cycle between open (apo) and closed (ligated) conformations. Conformational changes within the proteins depend on a complex interplay of mechanical and thermodynamic response, which is manifested as an increase in thermal stability and decrease of flexibility upon ligand binding.</p> <p>Results</p> <p>We use a distance constraint model (DCM) to quantify the give and take between thermodynamic stability and mechanical flexibility across the bPBP family. Quantitative stability/flexibility relationships (QSFR) are readily evaluated because the DCM links mechanical and thermodynamic properties. We have previously demonstrated that QSFR is moderately conserved across a mesophilic/thermophilic RNase H pair, whereas the observed variance indicated that different enthalpy-entropy mechanisms allow similar mechanical response at their respective melting temperatures. Our predictions of heat capacity and free energy show marked diversity across the bPBP family. While backbone flexibility metrics are mostly conserved, cooperativity correlation (long-range couplings) also demonstrate considerable amount of variation. Upon ligand removal, heat capacity, melting point, and mechanical rigidity are, as expected, lowered. Nevertheless, significant differences are found in molecular cooperativity correlations that can be explained by the detailed nature of the hydrogen bond network.</p> <p>Conclusion</p> <p>Non-trivial mechanical and thermodynamic variation across the family is explained by differences within the underlying H-bond networks. The mechanism is simple; variation within the H-bond networks result in altered mechanical linkage properties that directly affect intrinsic flexibility. Moreover, varying numbers of H-bonds and their strengths control the likelihood for energetic fluctuations as H-bonds break and reform, thus directly affecting thermodynamic properties. Consequently, these results demonstrate how unexpected large differences, especially within cooperativity correlation, emerge from subtle differences within the underlying H-bond network. This inference is consistent with well-known results that show allosteric response within a family generally varies significantly. Identifying the hydrogen bond network as a critical determining factor for these large variances may lead to new methods that can predict such effects.</p
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