Ring closure dynamics for a chemically active polymer

Soft Matter ◽  
2014 ◽  
Vol 10 (47) ◽  
pp. 9577-9584 ◽  
Author(s):  
Debarati Sarkar ◽  
Snigdha Thakur ◽  
Yu-Guo Tao ◽  
Raymond Kapral
Keyword(s):  
Long Range ◽  
Chemical Reaction ◽  
Polymer Chains ◽  
Ring Closure ◽  
Chemical Concentration ◽  
Loop Formation ◽  
Concentration Gradients

Our studies on ring closure of polymer showed how the long-range nature of the chemical concentration gradients, self-generated by the presence of a catalytic bead on which a chemical reaction occurs, could cause a distant bead to chemotactically move towards to the source of the gradient. Such chemically-active polymers hence undergo ring closure or loop formation more rapidly than inactive polymer chains.

3D-Atom Probe Investigation of Vacancy Induced Interdiffusion during High Pressure Torsion Deformation

2006 ◽  
Vol 503-504 ◽  
pp. 433-438 ◽  
Author(s):  
Xavier Sauvage
Keyword(s):  
Experimental Data ◽  
High Pressure ◽  
Long Range ◽  
High Pressure Torsion ◽  
Pearlitic Steel ◽  
Atom Probe ◽  
Concentration Gradients ◽  
Deformed State ◽  
Torsion Deformation ◽  
Probe Investigation

Concentration gradients resulting from long range diffusion during Severe Plastic Deformation (SPD) have been investigated with the 3D Atom Probe technique (3D-AP). First, in a pearlitic steel where alloying elements (Mn, Si and Cr) are partitioned between the ferrite and carbides in the non-deformed state. After processing by High Pressure Torsion (HPT), they are homogeneously distributed in the nanostructure, indicating that long range diffusion occurred along with the dissolution of carbides. 3D-AP data of a Cu-Fe composite processed by HPT show as well a significant interdiffusion of Cu and Fe, probably promoted by additional vacancies. On the basis of these experimental data, and using the theory described for irradiated materials, vacancy fluxes and vacancy production rates were estimated assuming that new vacancies are continuously produced and eliminated on grain boundaries.

scholarly journals An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation

2018 ◽  
Vol 102 (5) ◽  
pp. 776-793 ◽  
Author(s):  
Xiao-Feng Chen ◽  
Dong-Li Zhu ◽  
Man Yang ◽  
Wei-Xin Hu ◽  
Yuan-Yuan Duan ◽  
...  
Keyword(s):  
Long Range ◽  
Loop Formation ◽  
Allele Specific ◽  
Osteoporosis Risk

scholarly journals Electrolyte Metabolism in HeLa Cells

1963 ◽  
Vol 46 (6) ◽  
pp. 1303-1315 ◽  
Author(s):  
Margaret Wickson-ginzburg ◽  
A. K. Solomon
Keyword(s):  
Transport System ◽  
Hela Cells ◽  
Generation Time ◽  
Chemical Concentration ◽  
Concentration Gradients ◽  
K Uptake ◽  
Initial Value ◽  
Electrolyte Metabolism ◽  
K Cells ◽  
Low K

Methods have been developed to study cellular Na, K, and Cl concentrations in HeLa cells. Cell [Na] and [K] are functions of the age of the culture. As the culture grows [K], expressed in mmols/liter cell H2O, rises from an initial value of 121 to a peak of 206 at about 4 days, and thereafter falls until it has almost returned to the initial value by the 9th day. [Na] falls as [K] rises, but there is no fixed relationship between the cellular concentrations of the two cations. There is, however, a correlation between generation time and cellular [K]. Measurements of net K uptake and net Na extrusion were carried out during 1 hour incubation at 37°C of low K cells. Both net K uptake and net Na extrusion took place against chemical concentration gradients, so that at least one transport system must be active; if the Cl distribution is passive both net K uptake and net Na extrusion are active. Studies with inhibitors of respiration and glycolysis lead to the conclusion that respiration is not required for these net transports, which appear to derive their energy from glycolytic sources.

scholarly journals Mediator facilitates transcriptional activation and dynamic long-range contacts at the IgH locus during class switch recombination

2016 ◽  
Vol 213 (3) ◽  
pp. 303-312 ◽  
Author(s):  
Anne-Sophie Thomas-Claudepierre ◽  
Isabelle Robert ◽  
Pedro P. Rocha ◽  
Ramya Raviram ◽  
Ebe Schiavo ◽  
...  
Keyword(s):  
B Cells ◽  
Long Range ◽  
Transcriptional Activation ◽  
Transcription Initiation ◽  
Structural Changes ◽  
Class Switch Recombination ◽  
Mediator Complex ◽  
Loop Formation ◽  
Class Switch ◽  
Igh Locus

Immunoglobulin (Ig) class switch recombination (CSR) is initiated by the transcription-coupled recruitment of activation-induced cytidine deaminase (AID) to Ig switch regions (S regions). During CSR, the IgH locus undergoes dynamic three-dimensional structural changes in which promoters, enhancers, and S regions are brought to close proximity. Nevertheless, little is known about the underlying mechanisms. In this study, we show that Med1 and Med12, two subunits of the mediator complex implicated in transcription initiation and long-range enhancer/promoter loop formation, are dynamically recruited to the IgH locus enhancers and the acceptor regions during CSR and that their knockdown in CH12 cells results in impaired CSR. Furthermore, we show that conditional inactivation of Med1 in B cells results in defective CSR and reduced acceptor S region transcription. Finally, we show that in B cells undergoing CSR, the dynamic long-range contacts between the IgH enhancers and the acceptor regions correlate with Med1 and Med12 binding and that they happen at a reduced frequency in Med1-deficient B cells. Our results implicate the mediator complex in the mechanism of CSR and are consistent with a model in which mediator facilitates the long-range contacts between S regions and the IgH locus enhancers during CSR and their transcriptional activation.

Effects of chemical reaction and activation energy on a Carreau nanoliquid past a permeable surface under zero mass flux conditions

2019 ◽  
Vol 234 (1-2) ◽  
pp. 47-57
Author(s):  
GK Ramesh ◽  
K Ganesh Kumar ◽  
Ali J Chamkha ◽  
Rama Subba Reddy Gorla
Keyword(s):  
Activation Energy ◽  
Differential Equations ◽  
Ordinary Differential Equations ◽  
Chemical Reaction ◽  
Permeable Surface ◽  
Concentration Gradients ◽  
Zero Mass ◽  
Temperature Impact ◽  
Fifth Order ◽  
Physical Quantities

Arrhenius condition has been broadly utilized as a model of the temperature impact on the rate compound responses and organic procedure. Hence, our aim of this article is to examine the effects of chemical reaction and activation energy on a Carreau nanoliquid in a permeable surface. For thermal and mass transport curiosities, the cumulative upgrade of convective type condition and zero mass transition have been considered. The overseeing sets of partial differential equations are rendered into coupled nonlinear ordinary differential equations. The arrangement of the subsequent ordinary differential equations is acquired with the assistance of the Runge-Kutta-Fehlberg-fourth-fifth order (RKF-45) procedure. The influence of relevant parameters and physical quantities is investigated. The results show that the presence of reaction rate and energy activation term decelerates the temperature and concentration gradients.

scholarly journals Topoisomerases I and II facilitate condensin DC translocation to organize and repress X chromosomes in C. elegans

2021 ◽  
Author(s):  
Ana Karina Morao ◽  
Jun Kim ◽  
Daniel Obaji ◽  
Siyu Sun ◽  
Sevinc Ercan
Keyword(s):  
Long Range ◽  
X Chromosome ◽  
Molecular Motors ◽  
Topoisomerase Ii ◽  
Dna Looping ◽  
Loop Formation ◽  
X Chromosomes ◽  
C Elegans ◽  
And Control

Condensin complexes are evolutionarily conserved molecular motors that translocate along DNA and form loops. While condensin-mediated DNA looping is thought to direct the chain-passing activity of topoisomerase II to separate sister chromatids, it is not known if topological constraints in turn regulate loop formation in vivo. Here we applied auxin inducible degradation of topoisomerases I and II to determine how DNA topology affects the translocation of an X chromosome specific condensin that represses transcription for dosage compensation in C. elegans (condensin DC). We found that both topoisomerases colocalize with condensin DC and control its movement at different genomic scales. TOP-2 depletion hindered condensin DC translocation over long distances, resulting in accumulation around its X-specific recruitment sites and shorter Hi-C interactions. In contrast, TOP-1 depletion did not affect long-range spreading but resulted in accumulation of condensin DC within expressed gene bodies. Both TOP-1 and TOP-2 depletions resulted in X chromosome transcriptional upregulation indicating that condensin DC translocation at both scales is required for its function in gene repression. Together the distinct effects of TOP-1 and TOP-2 on condensin DC distribution revealed two distinct modes of condensin DC association with chromatin: long-range translocation that requires decatenation/unknotting of DNA and short-range translocation across genes that requires resolution of transcription-induced supercoiling.

Effect of nonlinear temperature and concentration profiles on the stability of a layer of fluid with chemical reaction

2020 ◽  
Author(s):  
Amit Mahajan ◽  
Vinit Kumar Tripathi
Keyword(s):  
Chemical Reaction ◽  
Piecewise Linear ◽  
Finite Amplitude ◽  
Step Function ◽  
Thermosolutal Convection ◽  
Concentration Gradients ◽  
Non Linear ◽  
Nonlinear Temperature ◽  
Basic Temperature ◽  
The Stability

Investigation of the onset of thermosolutal convection with chemical reaction is carried out for different types of basic temperature and concentration gradients using linear theory and energy method. An unconditional non-linear stability with exponential decay of finite amplitude perturbations is achieved and the Galerkin technique is utilized to solve the resulting Eigen-value problem obtained from linear and non-linear analysis. The numerical scheme is validated with existing results and the results are obtained for linear, parabolic, inverted parabolic, piecewise linear, oscillatory and step-function profiles of temperature and concentration gradients. The linear and non-linear results show the existence of subcritical instability.

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