Comment on the dynamic bead size and Kuhn segment length in polymers: Example of polystyrene

2004 ◽  
Vol 42 (18) ◽  
pp. 3505-3511 ◽  
Author(s):  
Y. Ding ◽  
A. P. Sokolov
Keyword(s):  
Segment Length ◽  
Kuhn Segment ◽  
Bead Size ◽  
Kuhn Segment Length

MODELLING OF POLYCOMB-DEPENDENT CHROMOSOMAL INTERACTIONS INVOLVED IN DROSOPHILA GENE SILENCING

2006 ◽  
Vol 17 (05) ◽  
pp. 757-767
Author(s):  
SILKE RITTER ◽  
JENS ODENHEIMER ◽  
DIETER W. HEERMANN ◽  
FREDERIC BANTIGNIES ◽  
CHARLOTTE GRIMAUD ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Drosophila Melanogaster ◽  
Gene Silencing ◽  
Polymer Chains ◽  
Segment Length ◽  
Kuhn Segment ◽  
End Points ◽  
Wall Distance ◽  
Repulsive Forces ◽  
Kuhn Segment Length

The conditions of the chromosomes inside the nucleus in the Rabl configuration have been modelled as self-avoiding polymer chains under restraining conditions. To ensure that the chromosomes remain stretched out and lined up, we fixed their end points to two opposing walls. The numbers of segments N, the distances d1 and d2 between the fixpoints, and the wall-to-wall distance z (as measured in segment lengths) determine an approximate value for the Kuhn segment length kl. We have simulated the movement of the chromosomes using molecular dynamics to obtain the expected distance distribution between the genetic loci in the absence of further attractive or repulsive forces. A comparison to biological experiments on Drosophila Melanogaster yields information on the parameters for our model. With the correct parameters it is possible to draw conclusions on the strength and range of the attraction that leads to pairing.

MODELLING OF POLYCOMB-DEPENDENT CHROMOSOMAL INTERACTIONS INVOLVED IN DROSOPHILA GENE SILENCING

2006 ◽  
Vol 01 (02) ◽  
pp. 141-151
Author(s):  
SILKE RITTER ◽  
JENS ODENHEIMER ◽  
DIETER W. HEERMANN ◽  
FREDERIC BANTIGNIES ◽  
CHARLOTTE GRIMAUD ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Drosophila Melanogaster ◽  
Gene Silencing ◽  
Polymer Chains ◽  
Segment Length ◽  
Kuhn Segment ◽  
End Points ◽  
Wall Distance ◽  
Repulsive Forces ◽  
Kuhn Segment Length

The conditions of the chromosomes inside the nucleus in the Rabl configuration have been modelled as self-avoiding polymer chains under restraining conditions. To ensure that the chromosomes remain stretched out and lined up, we fixed their end points to two opposing walls. The numbers of segments N, the distances d1 and d2 between the fixpoints, and the wall-to-wall distance z (as measured in segment lengths) determine an approximate value for the Kuhn segment length kl. We have simulated the movement of the chromosomes using molecular dynamics to obtain the expected distance distribution between the genetic loci in the absence of further attractive or repulsive forces. A comparison to biological experiments on Drosophila Melanogaster yields information on the parameters for our model. With the correct parameters it is possible to draw conclusions on the strength and range of the attraction that leads to pairing.

scholarly journals Conformational properties of biocompatible poly(2-ethyl-2-oxazoline)s in phosphate buffered saline

2018 ◽  
Vol 9 (17) ◽  
pp. 2232-2237 ◽  
Author(s):  
Alexander S. Gubarev ◽  
Bryn D. Monnery ◽  
Alexey A. Lezov ◽  
Ondrej Sedlacek ◽  
Nikolai V. Tsvetkov ◽  
...  
Keyword(s):  
Segment Length ◽  
Kuhn Segment ◽  
Physiological Conditions ◽  
Conformational Properties ◽  
Phosphate Buffered Saline ◽  
Kuhn Segment Length

The Kuhn segment length of PEtOx as a flexible macromolecule under physiological conditions is undoubtedly decreasing when approaching the LCST.

scholarly journals The Structure of Dipolar Polymer Brushes and Their Interaction in the Melt. Impact of Chain Stiffness

Polymers ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 2887
Author(s):  
Ivan V. Mikhailov ◽  
Victor M. Amoskov ◽  
Anatoly A. Darinskii ◽  
Tatiana M. Birshtein
Keyword(s):  
Polymer Brushes ◽  
Dipole Moments ◽  
Segment Length ◽  
Chain Rigidity ◽  
Chain Stiffness ◽  
Dipole Interactions ◽  
Consistent Field ◽  
Self Consistent Field ◽  
Two Populations ◽  
Kuhn Segment Length

By using the numerical lattice Scheutjens–Fleer self-consistent field (SF-SCF) method we have studied the effect of the restricted flexibility of grafted chains on the structure and mutual interaction of two opposing planar conventional and A-type dipolar brushes. Brushes are immersed in the solvent consisting of chains similar to the grafted ones. The increase of the chain rigidity enhances the segregation of grafted chains in a A-type dipolar brush into two populations: backfolded chains with terminal monomers near the grafting surface and chains with the ends at the brush periphery. The fraction of backfolded chains grows by an increase of the Kuhn segment length. It is shown that two opposite A-type dipolar brushes from semi-rigid chains are attracted to each other at short distances. The attraction becomes more pronounced and begins at larger distances for more rigid chains with the same brush characteristics: polymerization degree, grafting density, and dipole moments of monomer units. This attraction is connected with the dipole-dipole interactions between chains of oncoming brushes with oppositely directed dipoles penetrating deeply into each other upon contact. This effect of the chain rigidity is opposite to that for conventional brushes without dipoles in the chains. For such brushes, an increase in the chain rigidity leads to the enhanced repulsion between them.

Removal of Mn(II) and Fe(II) by Aspergillus Sp. TU-GM14 immobilized on Detarium Microcarpum matrix

2014 ◽  
Vol 16 (4) ◽  
pp. 597-608 ◽  
Keyword(s):  
Sorption Process ◽  
Isotherm Models ◽  
Freundlich Model ◽  
Equilibrium Time ◽  
Bead Size ◽  
Detarium Microcarpum ◽  
Bet Isotherm ◽  
Immobilization Matrix ◽  
Aspergillus Sp ◽  
Spore Load

<div> <p>Removal of Fe(II) and Mn(II) ions from aqueous solution by fungal biosorbent <em>Aspergillus sp. TU-GM14</em>immobilized on <em>Detarium microcarpum</em> matrix was investigated in this study. Effects of biosorption parameters pH, biosorbent concentration, bead size and equilibrium time on Fe(II) and Mn(II) ions sorption were also determined. Equilibrium was attained within in 3 hours while optimum Fe(II) and Mn(II) ions removal was observed at pH 6, 8 mm bead size, 2 g l<sup>-1</sup> spore load respectively. Adsorption capacity was described using Langmuir, Freundlich and BET isotherm models. The experimental data fitted best to the Freundlich model (<em>R</em><sup>2</sup> 0.992 and 0.996 for Mn(II) and Fe(II) respectively). Favourable surface sorption process was described by Langmuir isotherm for both metals (<em>Q</em><sub>max </sub>34 and 14 mg g<sup>-1</sup> for Mn(II) and Fe(II) ions) while the BET isotherm constant, <em>B</em>, described high metals sorption beyond the biosorbent surface in a multi-layer sorption process (4.8 and 9.0 for Mn(II) and Fe(II)&nbsp; respectively). Results of the study showed that <em>Aspergillus sp. TU-GM14 </em>biosorbent can remove large quantities of Fe(II) and Mn(II) ions from solution in both surface and multi-layer sorption process with <em>Detarium microcarpum</em> acting as a cheap immobilization matrix.</p> </div> <p>&nbsp;</p>

Understanding the CoVID-19 pandemic Curve through statistical approach (Preprint)

2020 ◽  
Author(s):  
Ibrar Ul Hassan Akhtar
Keyword(s):  
Probability Density ◽  
Change Point ◽  
Statistical Approach ◽  
Sudden Change ◽  
Global Scale ◽  
Change Point Detection ◽  
Segment Length ◽  
Infected Population ◽  
The Mean ◽  
Point Detection

UNSTRUCTURED Current research is an attempt to understand the CoVID-19 pandemic curve through statistical approach of probability density function with associated skewness and kurtosis measures, change point detection and polynomial fitting to estimate infected population along with 30 days projection. The pandemic curve has been explored for above average affected countries, six regions and global scale during 64 days of 22nd January to 24th March, 2020. The global cases infection as well as recovery rate curves remained in the ranged of 0 ‒ 9.89 and 0 ‒ 8.89%, respectively. The confirmed cases probability density curve is high positive skewed and leptokurtic with mean global infected daily population of 6620. The recovered cases showed bimodal positive skewed curve of leptokurtic type with daily recovery of 1708. The change point detection helped to understand the CoVID-19 curve in term of sudden change in term of mean or mean with variance. This pointed out disease curve is consist of three phases and last segment that varies in term of day lengths. The mean with variance based change detection is better in differentiating phases and associated segment length as compared to mean. Global infected population might rise in the range of 0.750 to 4.680 million by 24th April 2020, depending upon the pandemic curve progress beyond 24th March, 2020. Expected most affected countries will be USA, Italy, China, Spain, Germany, France, Switzerland, Iran and UK with at least infected population of over 0.100 million. Infected population polynomial projection errors remained in the range of -78.8 to 49.0%.

scholarly journals Fast and robust identity-by-descent inference with the templated positional Burrows-Wheeler transform

2020 ◽  
Author(s):  
William A Freyman ◽  
Kimberly F McManus ◽  
Suyash S Shringarpure ◽  
Ethan M Jewett ◽  
Katarzyna Bryc ◽  
...  
Keyword(s):  
Isolation By Distance ◽  
False Negative ◽  
Segment Length ◽  
Data Sets ◽  
Haplotype Sharing ◽  
Binary File ◽  
Inference Algorithms ◽  
Out Of Sample ◽  
Massive Scale ◽  
Burrows Wheeler Transform

Abstract Estimating the genomic location and length of identical-by-descent (IBD) segments among individuals is a crucial step in many genetic analyses. However, the exponential growth in the size of biobank and direct-to-consumer (DTC) genetic data sets makes accurate IBD inference a significant computational challenge. Here we present the templated positional Burrows-Wheeler transform (TPBWT) to make fast IBD estimates robust to genotype and phasing errors. Using haplotype data simulated over pedigrees with realistic genotyping and phasing errors we show that the TPBWT outperforms other state-of-the-art IBD inference algorithms in terms of speed and accuracy. For each phase-aware method, we explore the false positive and false negative rates of inferring IBD by segment length and characterize the types of error commonly found. Our results highlight the fragility of most phased IBD inference methods; the accuracy of IBD estimates can be highly sensitive to the quality of haplotype phasing. Additionally we compare the performance of the TPBWT against a widely used phase-free IBD inference approach that is robust to phasing errors. We introduce both in-sample and out-of-sample TPBWT-based IBD inference algorithms and demonstrate their computational efficiency on massive-scale datasets with millions of samples. Furthermore we describe the binary file format for TPBWT-compressed haplotypes that results in fast and efficient out-of-sample IBD computes against very large cohort panels. Finally, we demonstrate the utility of the TPBWT in a brief empirical analysis exploring geographic patterns of haplotype sharing within Mexico. Hierarchical clustering of IBD shared across regions within Mexico reveals geographically structured haplotype sharing and a strong signal of isolation by distance. Our software implementation of the TPBWT is freely available for non-commercial use in the code repository https://github.com/23andMe/phasedibd.

scholarly journals A Chromosome-Based Model for Estimating the Number of Conserved Segments Between Pairs of Species From Comparative Genetic Maps

Genetics ◽  
2000 ◽  
Vol 154 (1) ◽  
pp. 323-332
Author(s):  
David Waddington ◽  
Anthea J Springbett ◽  
David W Burt
Keyword(s):  
Maximum Likelihood ◽  
Dna Sequences ◽  
Common Ancestor ◽  
Length Distribution ◽  
Genetic Maps ◽  
Segment Length ◽  
Syntenic Block ◽  
Comparative Maps

Abstract Comparative genetic maps of two species allow insights into the rearrangements of their genomes since divergence from a common ancestor. When the map details the positions of genes (or any set of orthologous DNA sequences) on chromosomes, syntenic blocks of one or more genes may be identified and used, with appropriate models, to estimate the number of chromosomal segments with conserved content conserved between species. We propose a model for the distribution of the lengths of unobserved segments on each chromosome that allows for widely differing chromosome lengths. The model uses as data either the counts of genes in a syntenic block or the distance between extreme members of a block, or both. The parameters of the proposed segment length distribution, estimated by maximum likelihood, give predictions of the number of conserved segments per chromosome. The model is applied to data from two comparative maps for the chicken, one with human and one with mouse.

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