5,147 research outputs found
Phase diagram of force-induced DNA unzipping in exactly solvable models
The mechanical separation of the double helical DNA structure induced by
forces pulling apart the two DNA strands (``unzipping'') has been the subject
of recent experiments. Analytical results are obtained within various models of
interacting pairs of directed walks in the (1,1,...,1) direction on the
hypercubic lattice, and the phase diagram in the force-temperature plane is
studied for a variety of cases. The scaling behaviour is determined at both the
unzipping and the melting transition. We confirm the existence of a cold
denaturation transition recently observed in numerical simulations: for a
finite range of forces the system gets unzipped by {\it decreasing} the
temperature. The existence of this transition is rigorously established for
generic lattice and continuum space models.Comment: 19 pages, 5 eps figures; revised version with minor changes,
presentation simplified in the text with details in appendix. Accepted for
publication in Phys. Rev.
Geometry of compact tubes and protein structures
Proteins form a very important class of polymers. In spite of major advances
in the understanding of polymer science, the protein problem has remained
largely unsolved. Here, we show that a polymer chain viewed as a tube not only
captures the well-known characteristics of polymers and their phases but also
provides a natural explanation for many of the key features of protein
behavior. There are two natural length scales associated with a tube subject to
compaction -- the thickness of the tube and the range of the attractive
interactions. For short tubes, when these length scales become comparable, one
obtains marginally compact structures, which are relatively few in number
compared to those in the generic compact phase of polymers. The motifs
associated with the structures in this new phase include helices, hairpins and
sheets. We suggest that Nature has selected this phase for the structures of
proteins because of its many advantages including the few candidate strucures,
the ability to squeeze the water out from the hydrophobic core and the
flexibility and versatility associated with being marginally compact. Our
results provide a framework for understanding the common features of all
proteins.Comment: 15 pages, 3 eps figure
Re: "Relation of the Traditional Mediterranean Diet to Cerebrovascular Disease in a Mediterranean Population"
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Challenges of liver cancer: Future emerging tools in imaging and urinary biomarkers.
© The Author(s) 2015. Published by Baishideng Publishing Group Inc. All rights reserved.Chronic liver disease has become a global health problem as a result of the increasing incidence of viral hepatitis, obesity and alcohol misuse. Over the past three decades, in the United Kingdom alone, deaths from chronic liver disease have increased both in men and in women. Currently, 2.5% of deaths worldwide are attributed to liver disease and projected figures suggest a doubling in hospitalisation and associated mortality by 2020. Chronic liver diseases vary for clinical manifestations and natural history, with some individuals having relatively indolent disease and others with a rapidly progressive course. About 30% of patients affected by hepatitis C has a progressive disease and develop cirrhosis over a 20 years period from the infection, usually 5-10 years after initial medical presentation. The aim of the current therapeutic strategies is preventing the progression from hepatitis to fibrosis and subsequently, cirrhosis. Hepatic steatosis is a risk factor for chronic liver disease and is affecting about the half of patients who abuse alcohol. Moreover non-alcoholic fatty liver disease is part of the metabolic syndrome, associated with obesity, hypertension, type ? diabetes mellitus and dyslipidaemia, and a subgroup of patients develops non-alcoholic steatohepatitis and fibrosis with subsequent cirrhosis. The strengths and pitfalls of liver biopsy are discussed and a variety of new techniques to assess liver damage from transient elastography to experimental techniques, such as in vitro urinary nuclear magnetic resonance spectroscopy. Some of the techniques and tests described are already suitable for more widespread clinical application, as is the case with ultrasound-based liver diagnostics, but others, such as urinary metabonomics, requires a period of critical evaluation or development to take them from the research arena to clinical practice
Continuum model for polymers with finite thickness
We consider the continuum limit of a recently-introduced model for
discretized thick polymers, or tubes. We address both analytically and
numerically how the polymer thickness influences the decay of tangent-tangent
correlations and find how the persistence length scales with the thickness and
the torsional rigidity of the tube centerline. At variance with the worm-like
chain model, the phase diagram that we obtain for a continuous tube is richer;
in particular, for a given polymer thickness there exists a threshold value for
the centerline torsional rigidity separating a simple exponential decay of the
tangent-tangent correlation from an oscillatory one.Comment: 8 pages, 4 figures. Accepted for publication in J. Phys.
MIRU-VNTR genotyping of Mycobacterium tuberculosis strains using QIAxcel technology: a multicentre evaluation study
Molecular genotyping of M.tuberculosis is an important laboratory tool in the context of emerging drug resistant TB. The standard 24-loci MIRU-VNTR typing includes PCR amplification followed by the detection and sizing of PCR fragments using capillary electrophoresis on automated sequencers or using agarose gels. The QIAxcel Advanced system might offer a cost-effective medium-throughput alternative.Performance characteristics of the QIAxcel Advanced platform for the standard 24 VNTR loci panel was evaluated at two centres on a total of 140 DNA specimens using automated capillary electrophoresis as a reference method. Additionally 4 hypervariable MIRU-VNTR loci were evaluated on 53 crude DNA extracts. The sizing accuracy, interlaboratory reproducibility and overall instrument's performance were assessed during the study.An overall concordance with the reference method was high reaching 98.5% and 97.6% for diluted genomic and crude DNA extracts respectively. 91.4% of all discrepancies were observed in fragments longer than 700bp. The concordance for hypervariable loci was lower except for locus 4120 (96.2%). The interlaboratory reproducibility agreement rates were 98.9% and 91.3% for standard and hypervariable loci, respectively. Overall performance of the QIAxcel platform for M.tuberculosis genotyping using a panel of standard loci is comparable to that of established methods for PCR fragments up to 700bp. Inaccuracies in sizing of longer fragments could be resolved through using in-house size markers or introduction of offset values. To conclude, the QiaXcel system could be considered an effective alternative to existing methods in smaller reference and regional laboratories offering good performance and shorter turnaround times
Lattice model for cold and warm swelling of polymers in water
We define a lattice model for the interaction of a polymer with water. We
solve the model in a suitable approximation. In the case of a non-polar
homopolymer, for reasonable values of the parameters, the polymer is found in a
non-compact conformation at low temperature; as the temperature grows, there is
a sharp transition towards a compact state, then, at higher temperatures, the
polymer swells again. This behaviour closely reminds that of proteins, that are
unfolded at both low and high temperatures.Comment: REVTeX, 5 pages, 2 EPS figure
A numerical approach to copolymers at selective interfaces
We consider a model of a random copolymer at a selective interface which
undergoes a localization/delocalization transition. In spite of the several
rigorous results available for this model, the theoretical characterization of
the phase transition has remained elusive and there is still no agreement about
several important issues, for example the behavior of the polymer near the
phase transition line. From a rigorous viewpoint non coinciding upper and lower
bounds on the critical line are known.
In this paper we combine numerical computations with rigorous arguments to
get to a better understanding of the phase diagram. Our main results include:
- Various numerical observations that suggest that the critical line lies
strictly in between the two bounds.
- A rigorous statistical test based on concentration inequalities and
super-additivity, for determining whether a given point of the phase diagram is
in the localized phase. This is applied in particular to show that, with a very
low level of error, the lower bound does not coincide with the critical line.
- An analysis of the precise asymptotic behavior of the partition function in
the delocalized phase, with particular attention to the effect of rare atypical
stretches in the disorder sequence and on whether or not in the delocalized
regime the polymer path has a Brownian scaling.
- A new proof of the lower bound on the critical line. This proof relies on a
characterization of the localized regime which is more appealing for
interpreting the numerical data.Comment: accepted for publication on J. Stat. Phy
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