4,318 research outputs found
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
Adsorption-like Collapse of Diblock Copolymers
A linear copolymer made of two reciprocally attracting N-monomer blocks
collapses to a compact phase through a novel transition, whose exponents are
determined with extensive MC simulations in two and three dimensions. In the
former case, an identification with the statistical geometry of suitable
percolation paths allows to predict that the number of contacts between the
blocks grows like . In the compact phase the blocks are mixed and, in
two dimensions, also zipped, in such a way to form a spiral, double chain
structure.Comment: 4 pages, 5 Postscript figure
A possible mechanism for cold denaturation of proteins at high pressure
We study cold denaturation of proteins at high pressures. Using
multicanonical Monte Carlo simulations of a model protein in a water bath, we
investigate the effect of water density fluctuations on protein stability. We
find that above the pressure where water freezes to the dense ice phase
( kbar), the mechanism for cold denaturation with decreasing
temperature is the loss of local low-density water structure. We find our
results in agreement with data of bovine pancreatic ribonuclease A.Comment: 4 pages for double column and single space. 3 figures Added
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Preliminary Biomarkers for Identification of Human Ascending Thoracic Aortic Aneurysm
Background: Human ascending thoracic aortic aneurysms (ATAAs) are life threatening and constitute a leading cause of mortality in the United States. Previously, we demonstrated that collagens α2(V) and α1(XI) mRNA and protein expression levels are significantly increased in ATAAs. Methods and Results: In this report, the authors extended these preliminary studies using highâthroughput proteomic analysis to identify additional biomarkers for use in whole blood realâtime RTâPCR analysis to allow for the identification of ATAAs before dissection or rupture. Human ATAA samples were obtained from male and female patients aged 65±14 years. Both bicuspid and tricuspid aortic valve patients were included and compared with nonaneurysmal aortas (mean diameter 2.3 cm). Five biomarkers were identified as being suitable for detection and identification of ATAAs using qRTâPCR analysis of whole blood. Analysis of 41 samples (19 small, 13 mediumâsized, and 9 large ATAAs) demonstrated the overexpression of 3 of these transcript biomarkers correctly identified 79.4% of patients with ATAA of â„4.0 cm (P<0.001, sensitivity 0.79, CI=0.62 to 0.91; specificity 1.00, 95% CI=0.42 to 1.00). Conclusion: A preliminary transcript biomarker panel for the identification of ATAAs using whole blood qRTâPCR analysis in men and women is presented
A high-performance track fitter for use in ultra-fast electronics
This article describes a new charged-particle track fitting algorithm
designed for use in high-speed electronics applications such as hardware-based
triggers in high-energy physics experiments. Following a novel technique
designed for fast electronics, the positions of the hits on the detector are
transformed before being passed to a linearized track parameter fit. This
transformation results in fitted track parameters with a very linear dependence
on the hit positions. The approach is demonstrated in a representative detector
geometry based on the CMS detector at the Large Hadron Collider. The fit is
implemented in FPGA chips and optimized for track fitting throughput and
obtains excellent track parameter performance. Such an algorithm is potentially
useful in any high-speed track-fitting application
Prediction of peptide and protein propensity for amyloid formation
Understanding which peptides and proteins have the potential to undergo amyloid formation and what driving forces are responsible for amyloid-like fiber formation and stabilization remains limited. This is mainly because proteins that can undergo structural changes, which lead to amyloid formation, are quite diverse and share no obvious sequence or structural homology, despite the structural similarity found in the fibrils. To address these issues, a novel approach based on recursive feature selection and feed-forward neural networks was undertaken to identify key features highly correlated with the self-assembly problem. This approach allowed the identification of seven physicochemical and biochemical properties of the amino acids highly associated with the self-assembly of peptides and proteins into amyloid-like fibrils (normalized frequency of ÎČ-sheet, normalized frequency of ÎČ-sheet from LG, weights for ÎČ-sheet at the window position of 1, isoelectric point, atom-based hydrophobic moment, helix termination parameter at position j+1 and ÎGÂș values for peptides extrapolated in 0 M urea). Moreover, these features enabled the development of a new predictor (available at http://cran.r-project.org/web/packages/appnn/index.html) capable of accurately and reliably predicting the amyloidogenic propensity from the polypeptide sequence alone with a prediction accuracy of 84.9 % against an external validation dataset of sequences with experimental in vitro, evidence of amyloid formation
Protein sequence and structure: Is one more fundamental than the other?
We argue that protein native state structures reside in a novel "phase" of
matter which confers on proteins their many amazing characteristics. This phase
arises from the common features of all globular proteins and is characterized
by a sequence-independent free energy landscape with relatively few low energy
minima with funnel-like character. The choice of a sequence that fits well into
one of these predetermined structures facilitates rapid and cooperative
folding. Our model calculations show that this novel phase facilitates the
formation of an efficient route for sequence design starting from random
peptides.Comment: 7 pages, 4 figures, to appear in J. Stat. Phy
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