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 Ab initio molecular dynamics study of AlCl4− adsorption on PEDOT conducting polymer chains

2021 ◽  
Vol 7 ◽  
pp. 111-119
Author(s):  
Ben Craig ◽  
Chris-Kriton Skylaris ◽  
Carlos Ponce de Leon ◽  
Denis Kramer
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Conducting Polymer ◽  
Polymer Chains ◽  
Ab Initio Molecular Dynamics

scholarly journals DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations

2021 ◽  
Author(s):  
Stefanos S Nomidis ◽  
Enrico Carlon ◽  
Stephan Gruber ◽  
John F Marko
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Protein Complexes ◽  
Power Stroke ◽  
End Points ◽  
Domains Of Life ◽  
Dynamics Simulations ◽  
Fixed End ◽  
Atp Binding And Hydrolysis ◽  
Low Tension

Structural Maintenance of Chromosomes (SMC) protein complexes play essential roles in genome folding and organization across all domains of life. In order to determine how the activities of these large (about 50 nm) complexes are controlled by ATP binding and hydrolysis, we have developed a molecular dynamics (MD) model that realistically accounts for thermal conformational motions of SMC and DNA. The model SMCs make use of DNA flexibility and looping, together with an ATP-induced "power stroke", to capture and transport DNA segments, so as to robustly translocate along DNA. This process is sensitive to DNA tension: at low tension (about 0.1 pN), the model performs steps of roughly 60 nm size, while, at higher tension, a distinct inchworm-like translocation mode appears, with steps that depend on SMC arm flexibility. By permanently tethering DNA to an experimentally-observed additional binding site ("safety belt"), the same model performs loop extrusion. We find that the dependence of loop extrusion on DNA tension is remarkably different when DNA tension is fixed vs when DNA end points are fixed: Loop extrusion reversal occurs above 0.5 pN for fixed tension, while loop extrusion stalling without reversal occurs at about 2 pN for fixed end points. Our model quantitatively matches recent experimental results on condensin and cohesin, and makes a number of clear predictions. Finally we investigate how specific structural changes affect the SMC function, which is testable in experiments on varied or mutant SMCs.

scholarly journals THE GENETICS OF A SMALL AUTOSOMAL REGION OF DROSOPHILA MELANOGASTER, INCLUDING THE STRUCTURAL GENE FOR ALCOHOL DEHYDROGENASE. V. CHARACTERIZATION OF X-RAY-INDUCED Adh NULL MUTATIONS

Genetics ◽  
1982 ◽  
Vol 102 (3) ◽  
pp. 421-435
Author(s):  
M Ashburner ◽  
C S Aaron ◽  
S Tsubota
Keyword(s):  
Drosophila Melanogaster ◽  
Alcohol Dehydrogenase ◽  
Structural Gene ◽  
End Points ◽  
X Ray ◽  
Autosomal Region ◽  
Nonrandom Distribution ◽  
Chromosome Arm ◽  
Break Points

ABSTRACT Of 31 X-ray-induced and 2 spontaneous Adh null mutations selected for resistance to pentenol (Aaron 1979), 21 are deletions, including Adh and one or more neighboring loci. By contrast, none of 13 EMS-induced Adhn mutations are deletions. On average, the size of these X-ray-induced deletions is shorter than that of 12 formaldehyde-induced Adhn deletions (O'Donnell, Mandell, Krauss and Sofer 1977). Both the X-ray- and formaldehyde-induced deletions show a nonrandom distribution of break points in region 34D to 35D of chromosome arm 2L. Some of the deletions display particular genetic properties associated with one of their end points.

scholarly journals Effect of Chitin Whiskers on the Molecular Dynamics of Carrageenan-Based Nanocomposites

Polymers ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 1083 ◽  
Author(s):  
Marta Carsi ◽  
Maria J. Sanchis ◽  
Clara M. Gómez ◽  
Sol Rodriguez ◽  
Fernando G. Torres
Keyword(s):  
Molecular Dynamics ◽  
Casting Process ◽  
Polymer Chains ◽  
Dielectric Relaxation Spectroscopy ◽  
Solution Casting ◽  
Fragility Index ◽  
Relaxation Dynamics ◽  
Dynamic Mobility ◽  
Chitin Nanowhiskers ◽  
Chitin Whiskers

Films of carrageenan (KC) and glycerol (g) with different contents of chitin nanowhiskers (CHW) were prepared by a solution casting process. The molecular dynamics of pure carrageenan (KC), carrageenan/glycerol (KCg) and KCg with different quantities of CHWs as a filler was studied using dielectric relaxation spectroscopy. The analysis of the CHW effect on the molecular mobility at the glass transition, Tg, indicates that non-attractive intermolecular interactions between KCg and CHW occur. The fragility index increased upon CHW incorporation, due to a reduction in the polymer chains mobility produced by the CHW confinement of the KCg network. The apparent activation energy associated with the relaxation dynamics of the chains at Tg slightly increased with the CHW content. The filler nature effect, CHW or montmorillonite (MMT), on the dynamic mobility of the composites was analyzed by comparing the dynamic behavior of both carrageenan-based composites (KCg/xCHW, KCg/xMMT).

scholarly journals Interface Characteristics of Neat Melts and Binary Mixtures of Polyethylenes from Atomistic Molecular Dynamics Simulations

Polymers ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 1059
Author(s):  
Sanghun Lee ◽  
Curtis W. Frank ◽  
Do Y. Yoon
Keyword(s):  
Molecular Dynamics ◽  
Surface Tension ◽  
Molecular Dynamics Simulations ◽  
Binary Mixtures ◽  
Surface Segregation ◽  
Surface Region ◽  
Polymer Chains ◽  
Methyl Groups ◽  
Free Standing ◽  
Dynamics Simulations

Molecular dynamics simulations of free-standing thin films of neat melts of polyethylene (PE) chains up to C150H302 and their binary mixtures with n-C13H28 are performed employing a united atom model. We estimate the surface tension values of PE melts from the atomic virial tensor over a range of temperatures, which are in good agreement with experimental results. Compared with short n-alkane systems, there is an enhanced surface segregation of methyl chain ends in longer PE chains. Moreover, the methyl groups become more segregated in the surface region with decreasing temperature, leading to the conclusion that the surface-segregation of methyl chain ends mainly arises from the enthalpic origin attributed to the lower cohesive energy density of terminal methyl groups. In the mixtures of two different chain lengths, the shorter chains are more likely to be found in the surface region, and this molecular segregation in moderately asymmetric mixtures in the chain length (C13H28 + C44H90) is dominated by the enthalpic effect of methyl chain ends. Such molecular segregation is further enhanced and dominated by the entropic effect of conformational constraints in the surface for the highly asymmetric mixtures containing long polymer chains (C13H28 + C150H3020). The estimated surface tension values of the mixtures are consistent with the observed molecular segregation characteristics. Despite this molecular segregation, the normalized density of methyl chain ends of the longer chain is more strongly enhanced, as compared with the all-segment density of the longer chain itself, in the surface region of melt mixtures. In addition, the molecular segregation results in higher order parameter of the shorter-chain segments at the surface and deeper persistence of surface-induced segmental order into the film for the longer chains, as compared with those in neat melt films.

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