488 research outputs found
Novel AQM algorithm employing observer-based SMC for efficient internet congestion prevention
No full textDimirovski, Georgi M. (Dogus Author) -- Conference full title: 2010 IEEE International Conference on Systems, Man and Cybernetics, SMC 2010; Istanbul; Turkey; 10 October 2010 through 13 October 2010.An active queue management (AQM) scheme employing state observer and sliding mode control (SMO-SMC) is designed in this paper in order to overcome congestion problem in TCP communication networks. First, sliding mode observer is designed for input delay network system; a sufficient condition is given for the existence of such an observer in terms of linear matrix inequality. Then, on the grounds of estimated system state vector, a controller is synthesized by using the sliding-mode control theory combined with the reaching law technique. The reachability condition in such a SMO-SMC AQM scheme is also discussed. The stability and robustness of the proposed control scheme are then validated for different network scenarios using Matlab/Simulink. Simulation results for the single-bottleneck benchmark network confirmed the proposed scheme achieves high-quality performance as well as outperforms the previous observer-based sliding-mode and traditional controllers
Looping the Genome with SMC Complexes
No full textSMC (structural maintenance of chromosomes) protein complexes are an evolutionarily conserved family of motor proteins that hold sister chromatids together and fold genomes throughout the cell cycle by DNA loop extrusion. These complexes play a key role in a variety of functions in the packaging and regulation of chromosomes, and they have been intensely studied in recent years. Despite their importance, the detailed molecular mechanism for DNA loop extrusion by SMC complexes remains unresolved. Here, we describe the roles of SMCs in chromosome biology and particularly review in vitro single-molecule studies that have recently advanced our understanding of SMC proteins. We describe the mechanistic biophysical aspects of loop extrusion that govern genome organization and its consequences
Single-molecule approaches to unravel the mechanism of SMC proteins
No full textEvery cell deals with the challenge of organising its DNA. First, the DNA needs to be compacted in size by several orders of magnitude. For example, in each human cell, 2 meters of DNA need to fit inside a micron-sized cell nucleus. Second, the DNA needs to stay accessible for cellular processes such as transcription and replication. To achieve these goals, cells are assisted by proteins that organise the DNA by locally bending the DNA, wrapping DNA around them, or by making DNA loops. A prime example are the Structural Maintenance of Chromosomes (SMC) family of proteins,which is known to be essential for DNA organisation. In eukaryotes, the SMC complex cohesin is responsible for keeping sister-chromatids together until the cell is ready to divide. Without cohesin, division might occur prematurely, leading to unevenly divided DNA. The SMC complex condensin is responsible for compacting the DNA into mitotic chromosomes. Indeed, without condensin, the DNA does not formproperly organised chromosomes. This thesis describes a series of experiments that aim to understand the molecular mechanism of these SMC proteins.Casimir PhD Series, Delft-Leiden 2017-36BN/Cees Dekker La
Bridging-induced phase separation induced by cohesin SMC protein complexes
No full textStructural maintenance of chromosome (SMC) protein complexes are able to extrude DNA loops. While loop extrusion constitutes a fundamental building block of chromosomes, other factors may be equally important. Here, we show that yeast cohesin exhibits pronounced clustering on DNA, with all the hallmarks of biomolecular condensation. DNA-cohesin clusters exhibit liquid-like behavior, showing fusion of clusters, rapid fluorescence recovery after photobleaching and exchange of cohesin with the environment. Strikingly, the in vitro clustering is DNA length dependent, as cohesin forms clusters only on DNA exceeding 3 kilo–base pairs. We discuss how bridging-induced phase separation, a previously unobserved type of biological condensation, can explain the DNA-cohesin clustering through DNA-cohesin-DNA bridges. We confirm that, in yeast cells in vivo, a fraction of cohesin associates with chromatin in a manner consistent with bridging-induced phase separation. Biomolecular condensation by SMC proteins constitutes a new basic principle by which SMC complexes direct genome organization
Testing pseudotopological and nontopological models for SMC-driven DNA loop extrusion against roadblock-traversal experiments
No full textDNA loop extrusion by structural-maintenance-of-chromosome (SMC) complexes has emerged as a primary organizing principle for chromosomes. The mechanism by which SMC motor proteins extrude DNA loops is still unresolved and much debated. The ring-like structure of SMC complexes prompted multiple models where the extruded DNA is topologically or pseudotopologically entrapped within the ring during loop extrusion. However, recent experiments showed the passage of roadblocks much bigger than the SMC ring size, suggesting a nontopological mechanism. Recently, attempts were made to reconcile the observed passage of large roadblocks with a pseudotopological mechanism. Here we examine the predictions of these pseudotopological models and find that they are not consistent with new experimental data on SMC roadblock encounters. Particularly, these models predict the formation of two loops and that roadblocks will reside near the stem of the loop upon encounter—both in contrast to experimental observations. Overall, the experimental data reinforce the notion of a nontopological mechanism for extrusion of DNA.</p
SMC complexes can traverse physical roadblocks bigger than their ring size
No full textRing-shaped structural maintenance of chromosomes (SMC) complexes like condensin and cohesin extrude loops of DNA. It remains, however, unclear how they can extrude DNA loops in chromatin that is bound with proteins. Here, we use in vitro single-molecule visualization to show that nucleosomes, RNA polymerase, and dCas9 pose virtually no barrier to loop extrusion by yeast condensin. We find that even DNA-bound nanoparticles as large as 200 nm, much bigger than the SMC ring size, also translocate into DNA loops during extrusion by condensin and cohesin. This even occurs for a single-chain version of cohesin in which the ring-forming subunits are covalently linked and cannot open to entrap DNA. The data show that SMC-driven loop extrusion has surprisingly little difficulty in accommodating large roadblocks into the loop. The findings also show that the extruded DNA does not pass through the SMC ring (pseudo)topologically, hence pointing to a nontopological mechanism for DNA loop extrusion.BN/Cees Dekker LabBN/BionanoscienceBN/Nynke Dekker La
Catching DNA with hoops-biophysical approaches to clarify the mechanism of SMC proteins
No full textStructural maintenance of chromosome (SMC) complexes are central regulators of chromosome architecture that are essential in all domains of life. For decades, the structural biology field has been debating how these conserved protein complexes use their intricate ring-like structures to structurally organize DNA. Here, we review the contributions of single-molecule biophysical approaches to resolving the molecular mechanism of SMC protein function.BN/Cees Dekker La
Author Correction: Testing pseudotopological and nontopological models for SMC-driven DNA loop extrusion against roadblock-traversal experiments (Scientific Reports, (2023), 13, 1, (8100), 10.1038/s41598-023-35359-2)
No full textCorrection to: Scientific Reports, published online 19 May 2023 The original version of this Article contained an error in Figure 1b-1, where the fore- and background order of the strands “DNA” (in black) and “Brn1 Kleisin” (in green), were switched. The original Figure 1 and accompanying legend appear below. (Figure presented.) Description of the mechanism postulated by Shaltiel et al. for roadblock passage into an extruded loop on the DNA and a potential nontopological model. (a) The steps through the proposed DNA loop extrusion cycle are commented in more detail in steps 1–6 within the figure. Adapted from Ref.11. (b) Potential nontopological model which is closely analogous to the pseudotopological model, but with a slight variation in the DNA-SMC topology which allows particle bypass. The original Article has been corrected.author correction DOI 10.1038/s41598-023-35359-2BN/Cees Dekker La
Robust sliding mode control for discrete stochastic systems with mixed time delays, randomly occurring uncertainties, and randomly occurring nonlinearities
No full textThis is the post-print version of the paper. The official published version can be accessed from the link below - Copyright @ 2012 IEEEThis paper investigates the robust sliding mode control (SMC) problem for a class of uncertain nonlinear stochastic systems with mixed time delays. Both the sectorlike nonlinearities and the norm-bounded uncertainties enter into the system in random ways, and such randomly occurring uncertainties and randomly occurring nonlinearities obey certain mutually uncorrelated Bernoulli distributed white noise sequences. The mixed time delays consist of both the discrete and the distributed delays. The time-varying delays are allowed in state. By employing the idea of delay fractioning and constructing a new Lyapunov–Krasovskii functional, sufficient conditions are established to ensure the stability of the system dynamics in the specified sliding surface by solving a certain semidefinite programming problem. A full-state feedback SMC law is designed to guarantee the reaching condition. A simulation example is given to demonstrate the effectiveness of the proposed SMC scheme.This work was supported in part by the National Natural Science Foundation of China under Grants 61028008, 60825303 and 60834003, National 973 Project under Grant 2009CB320600, the Fok Ying Tung Education Fund under Grant 111064, the Special Fund for the Author of National Excellent Doctoral Dissertation of China under Grant 2007B4, the Key Laboratory of Integrated Automation for the Process Industry Northeastern University) from the Ministry of Education of China, the Engineering and Physical Sciences Research Council (EPSRC) of the U.K. under Grant GR/S27658/01, the Royal Society of the U.K., and the Alexander von Humboldt Foundation of Germany
The VISCACHA survey-IV. the SMC West Halo in 8D
No full textIndexación: Scopus.The structure of the Small Magellanic Cloud (SMC) is very complex, in particular in the periphery that suffers more from the interactions with the Large Magellanic Cloud (LMC). A wealth of observational evidence has been accumulated revealing tidal tails and bridges made up of gas, stars, and star clusters. Nevertheless, a full picture of the SMC outskirts is only recently starting to emerge with a 6D phase-space map plus age and metallicity using star clusters as tracers. In this work, we continue our analysis of another outer region of the SMC, the so-called West Halo, and combined it with the previously analysed Northern Bridge. We use both structures to define the Bridge and Counter-bridge trailing and leading tidal tails. These two structures are moving away from each other, roughly in the SMC-LMC direction. The West Halo form a ring around the SMC inner regions that goes up to the background of the Northern Bridge shaping an extended layer of the Counter-bridge. Four old Bridge clusters were identified at distances larger than 8 kpc from the SMC centre moving towards the LMC, which is consistent with the SMC-LMC closest distance of 7.5 kpc when the Magellanic Bridge was formed about 150Myr ago; this shows that the Magellanic Bridge was not formed only by pulled gas, but it also removed older stars from the SMC during its formation. We also found age and metallicity radial gradients using projected distances on sky, which are vanished when we use the real 3D distances. © 2022 The Author(s) Published by Oxford University Press on behalf of Royal Astronomical Society.https://academic-oup-com.recursosbiblioteca.unab.cl/mnras/article/512/3/4334/652837
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