scholarly journals Theory and simulations of condensin mediated loop extrusion in DNA

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ryota Takaki ◽  
Atreya Dey ◽  
Guang Shi ◽  
D. Thirumalai

AbstractCondensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular biological phenomenon. This process is driven by the formation of chromosome loops. The ATP consuming motor, condensin, interacts with chromatin segments to actively extrude loops. Motivated by real-time imaging of loop extrusion (LE), we created an analytically solvable model, predicting the LE velocity and step size distribution as a function of external load. The theory fits the available experimental data quantitatively, and suggests that condensin must undergo a large conformational change, induced by ATP binding, bringing distant parts of the motor to proximity. Simulations using a simple model confirm that the motor transitions between an open and a closed state in order to extrude loops by a scrunching mechanism, similar to that proposed in DNA bubble formation during bacterial transcription. Changes in the orientation of the motor domains are transmitted over ~50 nm, connecting the motor head and the hinge, thus providing an allosteric basis for LE.

2020 ◽  
Author(s):  
Ryota Takaki ◽  
Atreya Dey ◽  
Guang Shi ◽  
D. Thirumalai

The condensation of several mega base pair human chromosomes in a small cell volume is a spectacular phenomenon in biology. This process, involving the formation of loops in chromosomes, is facilitated by ATP consuming motors (condensin and cohesin), that interact with chromatin segments thereby actively extruding loops. Motivated by real time videos of loop extrusion (LE), we created an analytically solvable model, which yields the LE velocity as a function of external load acting on condensin. The theory fits the experimental data quantitatively, and suggests that condensin must undergo a large conformational change, triggered by ATP binding and hydrolysis, that brings distant parts of the motor to proximity. Simulations using a simple model confirm that a transition between an open and closed states is necessary for LE. Changes in the orientation of the motor domain are transmitted over ~ 50 nm, connecting the motor head and the hinge, thus providing a plausible mechanism for LE. The theory and simulations are applicable to loop extrusion in other structural maintenance complexes.


Author(s):  
Ethan Corle ◽  
Matthew Floros ◽  
Sven Schmitz

The methods of using the viscous vortex particle method, dynamic inflow, and uniform inflow to conduct whirl-flutter stability analysis are evaluated on a four-bladed, soft-inplane tiltrotor model using the Rotorcraft Comprehensive Analysis System. For the first time, coupled transient simulations between comprehensive analysis and a vortex particle method inflow model are used to predict whirl-flutter stability. Resolution studies are performed for both spatial and temporal resolution in the transient solution. Stability in transient analysis is noted to be influenced by both. As the particle resolution is refined, a reduction in simulation time-step size must also be performed. An azimuthal time step size of 0.3 deg is used to consider a range of particle resolutions to understand the influence on whirl-flutter stability predictions. Comparisons are made between uniform inflow, dynamic inflow, and the vortex particle method with respect to prediction capabilities when compared to wing beam-bending frequency and damping experimental data. Challenges in assessing the most accurate inflow model are noted due to uncertainty in experimental data; however, a consistent trend of increasing damping with additional levels of fidelity in the inflow model is observed. Excellent correlation is observed between the dynamic inflow predictions and the vortex particle method predictions in which the wing is not part of the inflow model, indicating that the dynamic inflow model is adequate for capturing damping due to the induced velocity on the rotor disk. Additional damping is noted in the full vortex particle method model, with the wing included, which is attributed to either an interactional aerodynamic effect between the rotor and the wing or a more accurate representation of the unsteady loading on the wing due to induced velocities.


Author(s):  
Marius C. Banica ◽  
Peter Limacher ◽  
Heinz-Jürgen Feld

In large modern turbochargers, compressors often constitute the main source of noise, with a frequency spectrum typically dominated by tonal noise at the blade passing frequency (BPF) and its harmonics. In transonic operation, inflow BPF noise is mainly generated by rotor locked shock fronts. These and the resulting acoustic fields can be predicted numerically with reasonable accuracy. Outflow noise, while also dominated by BPF tones, is linked to more complex source mechanisms. Its modal structure and the relationships between sources and modal sound pressure levels (SPL) are less well understood. Perhaps this is linked to the intrinsically non-axisymmetric geometries, which results in the need for full stage simulations if high accuracy is of paramount importance. In order to shed some light on outflow noise generation, a transient simulation of a 360° model of a radial compressor stage, including a vaned diffuser and a volute, was carried out using state-of-the-art CFD. Additionally, experimental data was gathered at a multitude of data points downstream of the volute exit for post processing and modal analysis. The sources and the propagation were calculated directly. Optimized values for tempo-spatial acoustic wave resolution and buffer layer design were chosen, based on extensive studies on simplified models. Two grid refinement levels were used to check grid convergence and time step size independence of the results was ensured. Numerical and experimental data match within 1% for total pressure ratio, volume flow and exit total temperature for the studied operating point. Both show the same modal content at the 1st BPF and indicate the presence of the same single dominating mode. The numerical results underpredict overall sound power levels (PWL) at the 1st BPF by 6.6dB. This difference is expected to decrease with further grid refinement and improved accounting for numerical damping. At the 2nd BPF, the experimental data show a significant broadening of the modal content with homogeneous modal PWL distributions. The multitude of modes leads to the generation of complex interference patterns, which shows that single-point acoustic measurements are often inadequate for component noise qualification and should be substituted by modal techniques. The dominating dipole sound sources are found in narrow areas around the vane leading edges and the rotor blade trailing edges. Because of the non-axisymmetric geometry, vane dipole source strengths become a function of circumferential position. The unsteady shedding of vortices from the vane suction surfaces is identified as a further possible source mechanism. However, the contributions of structural vibrations and mode scattering due to small manufacturing imperfections remain unclear.


2014 ◽  
Vol 664 ◽  
pp. 104-110
Author(s):  
Mansour Abtahi ◽  
Gholamreza Vossoughi ◽  
Ali Meghdari

In this paper, a comprehensive model is used to describe dynamic behavior of SDA and its components during stepwise motion. In this model, Hamilton’s principle and Newton's method are used to extract dynamic equations of the SDA plate and dynamic equation for the linear motion of SDA. Comparison between the modeling results and available experimental data shows that this model is very effective in predicting some design objectives such as step size and output force for this type of actuators.


2012 ◽  
Vol 594-597 ◽  
pp. 2680-2683
Author(s):  
Wei Ju ◽  
Yi Liu ◽  
Jue Ding

Underwater explosion is very important for underwater weapons-design technology and research on the damage effect of target structure. In this paper, the flow-out boundary and variable step-size multi-material Euler algorithm were utilized to analyze numerically the whole process of shock wave generation and propagation, as well as bubble formation and impulse of underwater explosion. The computed results reveal the energy output characteristics of underwater explosion by TNT charge, which provide an important scientific basis for formulation design of charge and improvement of damage effects for underwater target.


Author(s):  
Jessica R. Bronson ◽  
James J. Allen ◽  
Gloria J. Wiens

This paper presents the characterization of scratch drive actuators (SDAs) built using Sandia National Laboratories (SNL) SUMMiTTM V micromachining process. Experimental data is used to characterize the output step size as a function of input voltage. This data is correlated to an analytical model in an effort to better understand and predict the stepping motion of these devices. The experimental results match well with the predictions from the model. Experimental data shows that the step sizes are on the order of 10 nm, and force estimates show that one SDA is capable of producing forces in excess of 100 μN for each step.


2018 ◽  
Author(s):  
Lorenz Gönner ◽  
Julien Vitay ◽  
Fred Hamker

AbstractThe sequential activity of hippocampal place cells observed during sleep and awake resting is widely viewed as a neural correlate of memory processes. While recent work has advanced our understanding of the content represented during rest-related place-cell sequences, the nature of hippocampal population dynamics during sequential activity remains poorly understood. A recent experimental study has reported that place-cell sequences show a pattern of step-like movement, reminiscent of transitions between discrete attractor states (Pfeiffer and Foster, 2015). By contrast, previous theoretical models predict that the spatiotemporal structure of place-cell sequences should reflect the disribution of place fields, typically observed to be spatially smooth.Motivated by this discrepancy between models and experimental data, we performed a quantitative comparison between these results and the spike trains generated by a network model for the generation of place-cell sequences (Gönner et al., 2017). Although the model is based on continuous attractor network dynamics, we observed that the movement of sequential place representations was phase-locked to the population oscillation, highly similar to the experimental data interpreted as evidence for discrete attractor dynamics. To resolve this potential contradiction, we performed a detailed analysis of the methodology used to identify discrete attractor dynamics. Our results show that a previous approach to step size decoding is prone to a decoding artefact. We propose a modified approach to estimate step sizes which may help to characterize the underlying circuit dynamics in vivo.


Author(s):  
Hanna Samar

In this paper, we consider ETP using a precisely solvable model of an electron in a crystal. The main characteristics of the transition are given by analytical functions that contain only the parameters of the potential. The results of calculations are compared with experimental data on the Lifshitz phase transition (genus transition) in normal metals. The practical significance of the work is to increase the accuracy of quantitative predictions of the physical properties of alloys of various transition metals.


Author(s):  
J. F. DeNatale ◽  
D. G. Howitt

The electron irradiation of silicate glasses containing metal cations produces various types of phase separation and decomposition which includes oxygen bubble formation at intermediate temperatures figure I. The kinetics of bubble formation are too rapid to be accounted for by oxygen diffusion but the behavior is consistent with a cation diffusion mechanism if the amount of oxygen in the bubble is not significantly different from that in the same volume of silicate glass. The formation of oxygen bubbles is often accompanied by precipitation of crystalline phases and/or amorphous phase decomposition in the regions between the bubbles and the detection of differences in oxygen concentration between the bubble and matrix by electron energy loss spectroscopy cannot be discerned (figure 2) even when the bubble occupies the majority of the foil depth.The oxygen bubbles are stable, even in the thin foils, months after irradiation and if van der Waals behavior of the interior gas is assumed an oxygen pressure of about 4000 atmospheres must be sustained for a 100 bubble if the surface tension with the glass matrix is to balance against it at intermediate temperatures.


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