scholarly journals Entropic Competition between Supercoiled and Torsionally Relaxed Chromatin Fibers Drives Loop Extrusion through Pseudo-Topologically Bound Cohesin

Biology ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 130
Author(s):  
Renáta Rusková ◽  
Dušan Račko
Keyword(s):  
Surrounding Medium ◽  
Energy Difference ◽  
Coarse Grained ◽  
Generic Fiber ◽  
Contact Maps ◽  
Wide Range ◽  
Mathematical Equations ◽  
Chromatin Fibers ◽  
Negative Supercoiling ◽  
The Given

We propose a model for cohesin-mediated loop extrusion, where the loop extrusion is driven entropically by the energy difference between supercoiled and torsionally relaxed chromatin fibers. Different levels of negative supercoiling are controlled by varying imposed friction between the cohesin ring and the chromatin fiber. The speed of generation of negative supercoiling by RNA polymerase associated with TOP1 is kept constant and corresponds to 10 rotations per second. The model was tested by coarse-grained molecular simulations for a wide range of frictions between 2 to 200 folds of that of generic fiber and the surrounding medium. The higher friction allowed for the accumulation of higher levels of supercoiling, while the resulting extrusion rate also increased. The obtained extrusion rates for the given range of investigated frictions were between 1 and 10 kbps, but also a saturation of the rate at high frictions was observed. The calculated contact maps indicate a qualitative improvement obtained at lower levels of supercoiling. The fits of mathematical equations qualitatively reproduce the loop sizes and levels of supercoiling obtained from simulations and support the proposed mechanism of entropically driven extrusion. The cohesin ring is bound on the fibers pseudo-topologically, and the model suggests that the topological binding is not necessary.

Patterns in diversity and composition of the microbenthos of subarctic intertidal beaches with different morphodynamics

2020 ◽  
Vol 648 ◽  
pp. 19-38
Author(s):  
AI Azovsky ◽  
YA Mazei ◽  
MA Saburova ◽  
PV Sapozhnikov
Keyword(s):  
Species Abundance ◽  
Abundance Ratio ◽  
Wave Action ◽  
Coarse Grained ◽  
Sediment Properties ◽  
Β Diversity ◽  
Α Diversity ◽  
Wide Range ◽  
Similar Mode ◽  
Abundance And Diversity

Diversity and composition of benthic diatom algae and ciliates were studied at several beaches along the White and Barents seas: from highly exposed, reflective beaches with coarse-grained sands to sheltered, dissipative silty-sandy flats. For diatoms, the epipelic to epipsammic species abundance ratio was significantly correlated with the beach index and mean particle size, while neither α-diversity measures nor mean cell length were related to beach properties. In contrast, most of the characteristics of ciliate assemblages (diversity, total abundance and biomass, mean individual weight and percentage of karyorelictids) demonstrated a strong correlation to beach properties, remaining low at exposed beaches but increasing sharply in more sheltered conditions. β-diversity did not correlate with beach properties for either diatoms or ciliates. We suggest that wave action and sediment properties are the main drivers controlling the diversity and composition of the intertidal microbenthos. Diatoms and ciliates, however, demonstrated divergent response to these factors. Epipelic and epipsammic diatoms exhibited 2 different strategies to adapt to their environments and therefore were complementarily distributed along the environmental gradient and compensated for each other in diversity. Most ciliates demonstrated a similar mode of habitat selection but differed in their degree of tolerance. Euryporal (including mesoporal) species were relatively tolerant to wave action and therefore occurred under a wide range of beach conditions, though their abundance and diversity were highest in fine, relatively stable sediments on sheltered beaches, whereas the specific interstitial (i.e. genuine microporal) species were mostly restricted to only these habitats.

scholarly journals Predictive modelling of soils’ hydraulic conductivity using artificial neural network and multiple linear regression

2021 ◽  
Vol 3 (2) ◽  
Author(s):  
Charles Gbenga Williams ◽  
Oluwapelumi O. Ojuri
Keyword(s):  
Neural Network ◽  
Artificial Neural Network ◽  
Hydraulic Conductivity ◽  
Linear Regression ◽  
Multiple Linear Regression ◽  
Coarse Grained ◽  
Soil Types ◽  
Wide Range ◽  
Artificial Neural ◽  
Input Variables

AbstractAs a result of heterogeneity nature of soils and variation in its hydraulic conductivity over several orders of magnitude for various soil types from fine-grained to coarse-grained soils, predictive methods to estimate hydraulic conductivity of soils from properties considered more easily obtainable have now been given an appropriate consideration. This study evaluates the performance of artificial neural network (ANN) being one of the popular computational intelligence techniques in predicting hydraulic conductivity of wide range of soil types and compared with the traditional multiple linear regression (MLR). ANN and MLR models were developed using six input variables. Results revealed that only three input variables were statistically significant in MLR model development. Performance evaluations of the developed models using determination coefficient and mean square error show that the prediction capability of ANN is far better than MLR. In addition, comparative study with available existing models shows that the developed ANN and MLR in this study performed relatively better.

scholarly journals Quantum information probes of charge fractionalization in large-N gauge theories

2021 ◽  
Vol 2021 (5) ◽  
Author(s):  
Brandon S. DiNunno ◽  
Niko Jokela ◽  
Juan F. Pedraza ◽  
Arttu Pönni
Keyword(s):  
Degrees Of Freedom ◽  
Gauge Theories ◽  
Entanglement Entropy ◽  
Coarse Grained ◽  
Strongly Coupled ◽  
Information Theoretic ◽  
Large N ◽  
Wide Range ◽  
Charge Fractionalization ◽  
Electric Flux

Abstract We study in detail various information theoretic quantities with the intent of distinguishing between different charged sectors in fractionalized states of large-N gauge theories. For concreteness, we focus on a simple holographic (2 + 1)-dimensional strongly coupled electron fluid whose charged states organize themselves into fractionalized and coherent patterns at sufficiently low temperatures. However, we expect that our results are quite generic and applicable to a wide range of systems, including non-holographic. The probes we consider include the entanglement entropy, mutual information, entanglement of purification and the butterfly velocity. The latter turns out to be particularly useful, given the universal connection between momentum and charge diffusion in the vicinity of a black hole horizon. The RT surfaces used to compute the above quantities, though, are largely insensitive to the electric flux in the bulk. To address this deficiency, we propose a generalized entanglement functional that is motivated through the Iyer-Wald formalism, applied to a gravity theory coupled to a U(1) gauge field. We argue that this functional gives rise to a coarse grained measure of entanglement in the boundary theory which is obtained by tracing over (part) of the fractionalized and cohesive charge degrees of freedom. Based on the above, we construct a candidate for an entropic c-function that accounts for the existence of bulk charges. We explore some of its general properties and their significance, and discuss how it can be used to efficiently account for charged degrees of freedom across different energy scales.

scholarly journals On the formation and stability of fermionic dark matter halos in a cosmological framework

2020 ◽  
Author(s):  
Carlos R Argüelles ◽  
Manuel I Díaz ◽  
Andreas Krut ◽  
Rafael Yunis
Keyword(s):  
Black Hole ◽  
Dark Matter ◽  
Space Distribution ◽  
Coarse Grained ◽  
Dark Matter Halos ◽  
The Core ◽  
The Galaxy ◽  
Gravitating Systems ◽  
The Given ◽  
First Time

Abstract The formation and stability of collisionless self-gravitating systems is a long standing problem, which dates back to the work of D. Lynden-Bell on violent relaxation, and extends to the issue of virialization of dark matter (DM) halos. An important prediction of such a relaxation process is that spherical equilibrium states can be described by a Fermi-Dirac phase-space distribution, when the extremization of a coarse-grained entropy is reached. In the case of DM fermions, the most general solution develops a degenerate compact core surrounded by a diluted halo. As shown recently, the latter is able to explain the galaxy rotation curves while the DM core can mimic the central black hole. A yet open problem is whether this kind of astrophysical core-halo configurations can form at all, and if they remain stable within cosmological timescales. We assess these issues by performing a thermodynamic stability analysis in the microcanonical ensemble for solutions with given particle number at halo virialization in a cosmological framework. For the first time we demonstrate that the above core-halo DM profiles are stable (i.e. maxima of entropy) and extremely long lived. We find the existence of a critical point at the onset of instability of the core-halo solutions, where the fermion-core collapses towards a supermassive black hole. For particle masses in the keV range, the core-collapse can only occur for Mvir ≳ E9M⊙ starting at zvir ≈ 10 in the given cosmological framework. Our results prove that DM halos with a core-halo morphology are a very plausible outcome within nonlinear stages of structure formation.

scholarly journals Optimising the AR Engraved Structure on Light-Guide Facets for a Wide Range of Wavelengths

Optics ◽  
2020 ◽  
Vol 2 (1) ◽  
pp. 25-42
Author(s):  
Ioseph Gurwich ◽  
Yakov Greenberg ◽  
Kobi Harush ◽  
Yarden Tzabari
Keyword(s):  
Theoretical Analysis ◽  
Light Guide ◽  
Spectral Band ◽  
Angular Range ◽  
The Past ◽  
Input And Output ◽  
Wide Range ◽  
The Given ◽  
Theoretical Results ◽  
Shape And Size

The present study is aimed at designing anti-reflective (AR) engraving on the input–output surfaces of a rectangular light-guide. We estimate AR efficiency, by the transmittance level in the angular range, determined by the light-guide. Using nano-engraving, we achieve a uniform high transmission over a wide range of wavelengths. In the past, we used smoothed conical pins or indentations on the faces of light-guide crystal as the engraved structure. Here, we widen the class of pins under consideration, following the physical model developed in the previous paper. We analyze the smoothed pyramidal pins with different base shapes. The possible effect of randomization of the pins parameters is also examined. The results obtained demonstrate optimized engraved structure with parameters depending on the required spectral range and facet format. The predicted level of transmittance is close to 99%, and its flatness (estimated by the standard deviation) in the required wavelengths range is 0.2%. The theoretical analysis and numerical calculations indicate that the obtained results demonstrate the best transmission (reflection) we can expect for a facet with the given shape and size for the required spectral band. The approach is equally useful for any other form and of the facet. We also discuss a simple way of comparing experimental and theoretical results for a light-guide with the designed input and output features. In this study, as well as in our previous work, we restrict ourselves to rectangular facets. We also consider the limitations on maximal transmission produced by the size and shape of the light-guide facets. The theoretical analysis is performed for an infinite structure and serves as an upper bound on the transmittance for smaller-size apertures.

Study of Temperature Effect on Servovalve-Controlled Fuel Metering Unit

2015 ◽  
Vol 137 (6) ◽  
Author(s):  
Bin Wang ◽  
Haocen Zhao ◽  
Ling Yu ◽  
Zhifeng Ye
Keyword(s):  
Steady State ◽  
Temperature Variation ◽  
Dynamic Characteristics ◽  
Numerical Study ◽  
Step Response ◽  
Fuel Temperature ◽  
Wide Range ◽  
Fuel Rate ◽  
Testing Condition ◽  
The Given

It is usual that fuel system of an aero-engine operates within a wide range of temperatures. As a result, this can have effect on both the characteristics and precision of fuel metering unit (FMU), even on the performance and safety of the whole engine. This paper provides theoretical analysis of the effect that fluctuation of fuel temperature has on the controllability of FMU and clarifies the drawbacks of the pure mathematical models considering fuel temperature variation for FMU. Taking the electrohydraulic servovalve-controlled FMU as the numerical study, simulation in AMESim is carried out by thermal hydraulic model under the temperatures ranged from −10 to 60 °C to confirm the effectiveness and precision of the model on the basis of steady-state and dynamic characteristics of FMU. Meanwhile, the FMU testing workbench with temperature adjustment device employing the fuel cooler and heater is established to conduct an experiment of the fuel temperature characteristics. Results show that the experiment matches well with the simulation with a relative error no more than 5% and that 0–50 °C fuel temperature variation produces up to 5.2% decrease in fuel rate. In addition, step response increases with the fuel temperature. Fuel temperature has no virtual impact on the steady-state and dynamic characteristics of FMU under the testing condition in this paper, implying that FMU can operate normally in the given temperature range.

scholarly journals Gelation Impairs Phase Separation and Small Molecule Migration in Polymer Mixtures

Polymers ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 1576
Author(s):  
Biswaroop Mukherjee ◽  
Buddhapriya Chakrabarti
Keyword(s):  
Phase Separation ◽  
Rational Design ◽  
Surface Segregation ◽  
Multiscale Methods ◽  
Coarse Grained ◽  
Polymer Gel ◽  
Polymer Mixtures ◽  
Separation Processes ◽  
Surface Migration ◽  
Wide Range

Surface segregation of the low molecular weight component of a polymeric mixture is a ubiquitous phenomenon that leads to degradation of industrial formulations. We report a simultaneous phase separation and surface migration phenomena in oligomer–polymer ( O P ) and oligomer–gel ( O G ) systems following a temperature quench that induces demixing of components. We compute equilibrium and time varying migrant (oligomer) density profiles and wetting layer thickness in these systems using coarse grained molecular dynamics (CGMD) and mesoscale hydrodynamics (MH) simulations. Such multiscale methods quantitatively describe the phenomena over a wide range of length and time scales. We show that surface migration in gel–oligomer systems is significantly reduced on account of network elasticity. Furthermore, the phase separation processes are significantly slowed in gels leading to the modification of the well known Lifshitz–Slyozov–Wagner (LSW) law ℓ ( τ ) ∼ τ 1 / 3 . Our work allows for rational design of polymer/gel–oligomer mixtures with predictable surface segregation characteristics that can be compared against experiments.

scholarly journals A scaled MP-PIC method for bubbling fluidization

2021 ◽  
Author(s):  
Xing Zhao ◽  
Yong Jiang ◽  
Fei Li ◽  
Wei Wang
Keyword(s):  
Fluidized Beds ◽  
Volume Fraction ◽  
Phase Particle ◽  
Scaling Law ◽  
Coarse Graining ◽  
Coarse Grained ◽  
Particle In Cell ◽  
Wide Range ◽  
Pic Method ◽  
Multi Phase

Coarse-grained methods have been widely used in simulations of gas-solid fluidization. However, as a key parameter, the coarse-graining ratio, and its relevant scaling law is still far from reaching a consensus. In this work, a scaling law is developed based on a similarity analysis, and then it is used to scale the multi-phase particle-in-cell (MP-PIC) method, and validated in the simulation of two bubbling fluidized beds. The simulation result shows this scaled MP-PIC can reduce the errors of solids volume fraction and velocity distributions over a wide range of coarse-graining ratios. In future, we expect that a scaling law with consideration of the heterogeneity inside a parcel or numerical particle will further improve the performance of coarse-grained modeling in simulation of fluidized beds.

scholarly journals Dilute Solution Structure of Bottlebrush Polymers

2019 ◽  
Author(s):  
Sarit Dutta ◽  
Matthew A. Wade ◽  
Dylan J. Walsh ◽  
Damien Guironnet ◽  
Simon A. Rogers ◽  
...  
Keyword(s):  
Brownian Dynamics ◽  
Solution Structure ◽  
Coarse Grained ◽  
Poly Lactic Acid ◽  
Linear Polymers ◽  
Molecular Architecture ◽  
Wide Range ◽  
Conformational Properties ◽  
Atomistic Structure ◽  
Insight Into

<div>Bottlebrush polymers are a class of macromolecules that has recently found use</div><div>in a wide variety of materials, ranging from lubricating brushes and</div><div>nanostructured coatings to elastomeric gels that exhibit structural color. These</div><div>polymers are characterized by dense branches extending from a central backbone,</div><div>and thus have properties distinct from linear polymers. It remains a challenge</div><div>to specifically understand conformational properties of these molecules, due to</div><div>the wide range of architectural parameters that can be present in a system, and</div><div>thus there is a need to accurately characterize and model these molecules. In</div><div>this paper, we use a combination of viscometry, light scattering, and computer</div><div>simulations to gain insight into the conformational properties of dilute</div><div>bottlebrush polymers. We focus on a series of model bottlebrushes consisting of</div><div>a poly(norbornene) (PNB) backbone with poly(lactic acid) (PLA) side chains. We</div><div>demonstrate that intrinsic viscosity and hydrodynamic radius are experimental</div><div>observations \emph{sensitive} to molecular architecture, exhibiting distinct</div><div>differences with different choices of branch and backbone lengths. Informed by</div><div>the atomistic structure of this PNB-PLA system, we rationalize a coarse-grained</div><div>simulation model that we evaluate using a combination of Brownian Dynamics and</div><div>Monte Carlo simulations. We show that this exhibits quantitative matching to</div><div>experimental results, enabling us to characterize the overall shape of the</div><div>bottlebrush via a number of metrics that can be extended to more general</div><div>bottlebrush architectures.</div>

«TRADE LOCAL, BUY LOCAL, BE LOCAL»: AGRICULTURAL EXHIBITIONS AND FAIRS IN HALYCHYNA IN THE 20-30S OF THE 20TH CENTURY

2020 ◽  
Vol 8 ◽  
pp. 19-27
Author(s):  
Oksana Pasitska
Keyword(s):  
Crop Production ◽  
Animal Husbandry ◽  
Folk Art ◽  
Cultural Development ◽  
Agricultural Products ◽  
Educational Institutions ◽  
Local Market ◽  
Agricultural Equipment ◽  
Wide Range ◽  
The Given

The article focuses on the exhibition activities of the Ukrainians, which were reflected upon in periodicals. In particular, it analyzes the organizational aspects and features of fairs and exhibitions of the agricultural products that were held upon the initiative of economic institutions and public organizations such as «Silskyi Hospodar» («The Farmer»), «Maslosoiuz», «Tsentrosoiuz», RSUK («The Auditing Union of Ukrainian Cooperatives»), «Soiuz ukrainok» («The Union of Ukrainian Women»), «The Ukrainian Folk Art» («Ukrainske narodne mystetstvo»), «The Hutsul Art» («Hutsulske mystetstvo»), «The Beekeeping Union» («Pasichnycha spilka»), «Rii» («The Swarm»), «Prosvita» («The Education») county unions, cooperatives, etc. Economic educational institutions also took part in the exhibitions. The first Ukrainian agrotechnical exhibitions were held in Stryi in 1909 and 1907, and later they took place in various Halychyna towns and villages, including Staryi Sambir, Dashava, and Sokal. Cooperative figures, such as D. Sembratovych, E. Olesnytskyi, O. Nyzhankivskyi, O. Lutskyi, A. Zhuk, M. Khronoviat, etc., played an important role in the organization of the given exhibitions. The article outlines the main functions performed by the exhibitions and fairs and the range of goods in demand among the visitors. Each exhibition was divided into separate sections, where the passers-by and the buyers could get acquainted with the results of work of the Ukrainian entrepreneurs and farmers in crop production, horticulture, vegetable growing, animal husbandry, beekeeping, crafts, and agricultural equipment. «Maslosoiuz» products, folk art products, and a wide range of medical products were especially popular at agro-technical exhibitions. Exhibitions and fairs were the manifestation of competitiveness in the local market, a factor of the region's economic and cultural development, as they were accompanied by entertainment and educational activities, including lectures, speeches, and presentations of new economic publications. Keywords: exhibitions, fairs, Halychyna, agricultural exhibitions and fairs

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