182 research outputs found
Stretched Polymers in a Poor Solvent
Stretched polymers with attractive interaction are studied in two and three
dimensions. They are described by biased self-avoiding random walks with
nearest neighbour attraction. The bias corresponds to opposite forces applied
to the first and last monomers. We show that both in and a phase
transition occurs as this force is increased beyond a critical value, where the
polymer changes from a collapsed globule to a stretched configuration. This
transition is second order in and first order in . For we
predict the transition point quantitatively from properties of the unstretched
polymer. This is not possible in , but even there we can estimate the
transition point precisely, and we can study the scaling at temperatures
slightly below the collapse temperature of the unstretched polymer. We find
very large finite size corrections which would make very difficult the estimate
of the transition point from straightforward simulations.Comment: 10 pages, 16 figure
Different pathways in mechanical unfolding/folding cycle of a single semiflexible polymer
Kinetics of conformational change of a semiflexible polymer under mechanical
external field were investigated with Langevin dynamics simulations. It is
found that a semiflexible polymer exhibits large hysteresis in mechanical
folding/unfolding cycle even with a slow operation, whereas in a flexible
polymer, the hysteresis almost disappears at a sufficiently slow operation.
This suggests that the essential features of the structural transition of a
semiflexible polymer should be interpreted at least on a two-dimensional phase
space. The appearance of such large hysteresis is discussed in relation to
different pathways in the loading and unloading processes. By using a minimal
two-variable model, the hysteresis loop is described in terms of different
pathways on the transition between two stable states.Comment: 19 pages, 5 figure
Early Stages of Homopolymer Collapse
Interest in the protein folding problem has motivated a wide range of
theoretical and experimental studies of the kinetics of the collapse of
flexible homopolymers. In this Paper a phenomenological model is proposed for
the kinetics of the early stages of homopolymer collapse following a quench
from temperatures above to below the theta temperature. In the first stage,
nascent droplets of the dense phase are formed, with little effect on the
configurations of the bridges that join them. The droplets then grow by
accreting monomers from the bridges, thus causing the bridges to stretch.
During these two stages the overall dimensions of the chain decrease only
weakly. Further growth of the droplets is accomplished by the shortening of the
bridges, which causes the shrinking of the overall dimensions of the chain. The
characteristic times of the three stages respectively scale as the zeroth, 1/5
and 6/5 power of the the degree of polymerization of the chain.Comment: 11 pages, 3 figure
clusterMaker: a multi-algorithm clustering plugin for Cytoscape
<p>Abstract</p> <p>Background</p> <p>In the post-genomic era, the rapid increase in high-throughput data calls for computational tools capable of integrating data of diverse types and facilitating recognition of biologically meaningful patterns within them. For example, protein-protein interaction data sets have been clustered to identify stable complexes, but scientists lack easily accessible tools to facilitate combined analyses of multiple data sets from different types of experiments. Here we present <it>clusterMaker</it>, a Cytoscape plugin that implements several clustering algorithms and provides network, dendrogram, and heat map views of the results. The Cytoscape network is linked to all of the other views, so that a selection in one is immediately reflected in the others. <it>clusterMaker </it>is the first Cytoscape plugin to implement such a wide variety of clustering algorithms and visualizations, including the only implementations of hierarchical clustering, dendrogram plus heat map visualization (tree view), k-means, k-medoid, SCPS, AutoSOME, and native (Java) MCL.</p> <p>Results</p> <p>Results are presented in the form of three scenarios of use: analysis of protein expression data using a recently published mouse interactome and a mouse microarray data set of nearly one hundred diverse cell/tissue types; the identification of protein complexes in the yeast <it>Saccharomyces cerevisiae</it>; and the cluster analysis of the vicinal oxygen chelate (VOC) enzyme superfamily. For scenario one, we explore functionally enriched mouse interactomes specific to particular cellular phenotypes and apply fuzzy clustering. For scenario two, we explore the prefoldin complex in detail using both physical and genetic interaction clusters. For scenario three, we explore the possible annotation of a protein as a methylmalonyl-CoA epimerase within the VOC superfamily. Cytoscape session files for all three scenarios are provided in the Additional Files section.</p> <p>Conclusions</p> <p>The Cytoscape plugin <it>clusterMaker </it>provides a number of clustering algorithms and visualizations that can be used independently or in combination for analysis and visualization of biological data sets, and for confirming or generating hypotheses about biological function. Several of these visualizations and algorithms are only available to Cytoscape users through the <it>clusterMaker </it>plugin. <it>clusterMaker </it>is available via the Cytoscape plugin manager.</p
Self- generated disorder and structural glass formation in homopolymer globules
We have investigated the interrelation between the spin glasses and the
structural glasses. Spin glasses in this case are random magnets without
reflection symmetry (e.g. - spin interaction spin glasses and Potts
glasses) which contain quenched disorder, whereas the structural glasses are
here exemplified by the homopolymeric globule, which can be viewed as a liquid
of connected molecules on nano scales. It is argued that the homopolymeric
globule problem can be mapped onto a disorder field theoretical model whose
effective Hamiltonian resembles the corresponding one for the spin glass model.
In this sense the disorder in the globule is self - generated (in contrast to
spin glasses) and can be related with competitive interactions (virial
coefficients of different signs) and the chain connectivity. The work is aimed
at giving a quantitative description of this analogy. We have investigated the
phase diagram of the homopolymeric globule where the transition line from the
liquid to glassy globule is treated in terms of the replica symmetry breaking
paradigm. The configurational entropy temperature dependence is also discussed.Comment: 22 pages, 4 figures, submitted to Phys. Rev.
Multifractal behavior of linear polymers in disordered media
The scaling behavior of linear polymers in disordered media modelled by
self-avoiding random walks (SAWs) on the backbone of two- and three-dimensional
percolation clusters at their critical concentrations p_c is studied. All
possible SAW configurations of N steps on a single backbone configuration are
enumerated exactly. We find that the moments of order q of the total number of
SAWs obtained by averaging over many backbone configurations display
multifractal behavior, i.e. different moments are dominated by different
subsets of the backbone. This leads to generalized coordination numbers \mu_q
and enhancement exponents \gamma_q, which depend on q. Our numerical results
suggest that the relation \mu_1 = p_ c \mu between the first moment \mu_1 and
its regular lattice counterpart \mu is valid.Comment: 11 pages, 12 postscript figures, to be published in Phys. Rev.
Sustained virological response after treatment with direct antiviral agents in individuals with HIV and hepatitis C co-infection.
INTRODUCTION
Randomized trials and observational studies have consistently reported rates of sustained virological response (SVR), equivalent to hepatitis C virus (HCV) cure, as high as 95% following treatment with direct-acting antiviral (DAA) treatment in individuals with HIV and HCV co-infection. However, large studies assessing whether SVR rates differ according to demographic and clinical strata are lacking. Additionally, the SVR rates reported in the literature were typically computed in non-random samples of individuals with available post-DAA HCV-RNA measures. Here, we aimed to estimate the probability of SVR after DAA treatment initiation in persons with HIV and HCV co-infection overall and by demographic and clinical characteristics with and without adjustment for missing HCV-RNA testing.
METHODS
We included adults with HIV-HCV co-infection who received DAA treatment between 2014 and 2020 in HepCAUSAL, an international collaboration of cohorts from Europe and North America. We estimated the proportions of DAA recipients who had documented SVR (defined as an undetectable HCV-RNA at least 12 weeks after the end of DAA treatment) overall and by strata defined by age, sex, presence of cirrhosis, calendar period, mode of HIV acquisition, CD4 cell count and HCV genotype at DAA treatment. We then compared these rates with those obtained using the parametric g-formula to impute SVR status for individuals with no SVR assessment.
RESULTS AND DISCUSSION
A total of 4527 individuals who initiated DAA treatment (88% males, median [IQR] age 56 [50, 62] years) were included. Of the total of 642 (14%) individuals had no HCV-RNA test on or after 12 weeks after the end of treatment. The overall observed and g-formula imputed SVR rates were 93% (95% CI 93, 94) and 94% (95% CI 92, 95), respectively. SVR estimates were similarly high across all strata. A substantial proportion of individuals who received DAA treatment were never assessed for SVR post-DAA and strategies for more systematic routine HCV-RNA testing should be considered.
CONCLUSIONS
Our estimates with and without adjustment for missing HCV-RNA testing indicate SVR rates of approximately 95%, like those reported in clinical trials
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