418 research outputs found

    Untying Knotted DNA with Elongational Flows

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    We present Brownian dynamics simulations of initially knotted double-stranded DNA molecules untying in elongational flows. We show that the motions of the knots are governed by a diffusion–convection equation by deriving scalings that collapse the simulation data. When being convected, all knots displace nonaffinely, and their rates of translation along the chain are topologically dictated. We discover that torus knots “corkscrew” when driven by flow, whereas nontorus knots do not. We show that a simple mechanism can explain a coupling between this rotation and the translation of a knot, explaining observed differences in knot translation rates. These types of knots are encountered in nanoscale manipulation of DNA, occur in biology at multiple length scales (DNA to umbilical cords), and are ubiquitous in daily life (e.g., hair). These results may have a broad impact on manipulations of such knots via flows, with applications to genomic sequencing and polymer processing.Singapore-MIT Alliance for Research and Technology (SMART)National Science Foundation (U.S.) (Grant CBET-1335938

    Metastable Tight Knots in Semiflexible Chains

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    Knotted structures can spontaneously occur in polymers such as DNA and proteins, and the formation of knots affects biological functions, mechanical strength and rheological properties. In this work, we calculate the equilibrium size distribution of trefoil knots in linear DNA using off-lattice simulations. We observe metastable knots on DNA, as predicted by Grosberg and Rabin. Furthermore, we extend their theory to incorporate the finite width of chains and show an agreement between our simulations and the modified theory for real chains. Our results suggest localized knots spontaneously occur in long DNA and the contour length in the knot ranges from 600 to 1800 nm.National Science Foundation (U.S.) (NSF Grant No. 1335938)Singapore. National Research FoundationSingapore-MIT Alliance for Research and Technology (SMART

    Origin of Metastable Knots in Single Flexible Chains

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    Recent theoretical progress has explained the physics of knotting of semiflexible polymers, yet knotting of flexible polymers is relatively unexplored. We herein develop a new theory for the size distribution of knots on a flexible polymer and the existence of metastable knots. We show the free energy of a flexible molecule in a tube can be mapped to quantitatively reproduce the free energy distribution of a knot on a flexible chain. The size distribution of knots on flexible chains is expected to be universal and might be observed at a macroscopic scale, such as a string of hard balls.Singapore-MIT Alliance for Research and TechnologyNational Science Foundation (U.S.) (Grant 1335938

    Translocation dynamics of knotted polymers under a constant or periodic external field

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    We perform Brownian dynamics simulations to examine how knots alter the dynamics of polymers moving through nanopores under an external field. In the first part of this paper, we study the situation when the field is constant. Here, knots halt translocation above a critical force with jamming occurring at smaller forces for twist topologies compared to non-twist topologies. Slightly below the jamming transition, the polymer's transit times exhibit large fluctuations. This phenomenon is an example of the knot's molecular individualism since the conformation of the knot plays a large role in the chain's subsequent dynamics. In the second part of the paper, we study the motion of the chain when one cycles the field on and off. If the off time is comparable to the knot's relaxation time, one can adjust the swelling of the knot at the pore and hence design strategies to ratchet the polymer in a controllable fashion. We examine how the off time affects the ratcheting dynamics. We also examine how this strategy alters the fluctuations in the polymer's transit time. We find that cycling the force field can reduce fluctuations near the knot's jamming transition, but can enhance the fluctuations at very high forces since knots get trapped in metastable states during the relaxation process. The latter effect appears to be more prominent for non-torus topologies than torus ones. We conclude by discussing the feasibility of this approach to control polymer motion in biotechnology applications such as sequencing.Singapore-MIT Alliance for Research and Technology (SMART)National Science Foundation (U.S.) (Grant CBET-1335938

    Coil-globule transition of a single semiflexible chain in slitlike confinement

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    Single polymer chains undergo a phase transition from coiled conformations to globular conformations as the effective attraction between monomers becomes strong enough. In this work, we investigated the coil-globule transition of a semiflexible chain confined between two parallel plates, i.e. a slit, using the lattice model and Pruned-enriched Rosenbluth method (PERM) algorithm. We find that as the slit height decreases, the critical attraction for the coil-globule transition changes non-monotonically due to the competition of the confinement free energies of the coiled and globular states. In wide (narrow) slits, the coiled state experiences more (less) confinement free energy, and hence the transition becomes easier (more difficult). In addition, we find that the transition becomes less sharp with the decreasing slit height. Here, the sharpness refers to the sensitivity of thermodynamic quantities when varying the attraction around the critical value. The relevant experiments can be performed for DNA condensation in microfluidic devices.Singapore-MIT Alliance for Research and Technology CenterNational Science Foundation (U.S.) (CBET-1335938

    Enhanced electrohydrodynamic collapse of DNA due to dilute polymers

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    We experimentally demonstrate that addition of small, charge-neutral polymers to a buffer solution can promote compression of dilute solutions of single electrophoresing DNA. This phenomenon contrasts with the observed extension of DNA during capillary electrophoresis in dilute solutions of high molecular weight polymers. We propose these discrepancies in micron-scale DNA configurations arise from different nano-scale DNA-polymer collision events, controlled by solute polymer properties. We build upon theories previously proposed for intermolecular DNA aggregation in polymer-free solutions to develop scaling theories that describe trends seen in our data for intramolecular DNA compaction in dilute polymer solutions.National Science Foundation (U.S.) (Grant 1335938)Singapore. National Research Foundation (Singapore-MIT Alliance for Research and Technology

    Marktgärtnereien – Die Zukunft des kleinstrukturierten Gemüseanbaus?

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    Der Traum mit wenig Land, eine große Gemüsevielfalt zu produzieren um davon als Direktvermarkter*in gut leben zu können, birgt für viele mutige Menschen eine besondere Attraktivität. Über 150 Personen besuchten die vom FiBL Österreich organisierte Bionet Gemüsetagung I Fokus: Market Gardening. Es wurde auf der Tagung an alle Teilnehmer*innen ein Fragebogen ausgegeben, um zu überprüfen, wie praktikabel und wirtschaftlich Market Gardening in der Praxis tatsächlich ist. Knapp ein Drittel davon (n = 47 Besucher*innen) haben an der Umfrage teilgenommen. Davon waren 11 Marktgärtner*innen, 10 Gärtner*innen und 26 Noch-Nicht-Gärtner*innen. Marktgärtner*innen produzieren auf kleiner Fläche eine hohe Diversität. Bei den befragten 11 Marktgärtner*innen waren das im Schnitt 3000 m² Freiland- und 400 m² Gewächshausfläche, mit durchschnittlich 49 Gemüsearten pro Betrieb. Die Marktgärtner*innen erwirtschafteten 2019 damit im Durchschnitt Umsätze von 65.000 € je Betrieb. Das entspricht umgerechnet auf die angegebenen Flächen Erlöse von 2,70 € bis 37,20 € pro Quadratmeter. Drei Viertel aller Befragten sind mit dem Begriff Marktgärtner*in sehr zufrieden oder zufrieden. 19 von 26 Noch-Nicht-Gärtner*innen haben vor in den nächsten 2 Jahren eine Marktgärtnerei aufzubauen. Es ist zu erwarten, dass zahlreiche neue Marktgärtnereien in den kommenden Jahren ihre Arbeit aufnehmen werden. Um diese Entwicklungen gut begleiten zu können empfiehlt es sich im engen Austausch mit interessierten Marktgärtner*innen, Institutionen und engagierten Einzelpersonen, begleitende Beratungs-, Bildungs-, Vernetzungs- und Forschungsaktivitäten zu koordinieren und durchzuführen

    Quivers of monoids with basic algebras

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    We compute the quiver of any monoid that has a basic algebra over an algebraically closed field of characteristic zero. More generally, we reduce the computation of the quiver over a splitting field of a class of monoids that we term rectangular monoids (in the semigroup theory literature the class is known as DO\mathbf{DO}) to representation theoretic computations for group algebras of maximal subgroups. Hence in good characteristic for the maximal subgroups, this gives an essentially complete computation. Since groups are examples of rectangular monoids, we cannot hope to do better than this. For the subclass of R\mathscr R-trivial monoids, we also provide a semigroup theoretic description of the projective indecomposables and compute the Cartan matrix.Comment: Minor corrections and improvements to exposition were made. Some theorem statements were simplified. Also we made a language change. Several of our results are more naturally expressed using the language of Karoubi envelopes and irreducible morphisms. There are no substantial changes in actual result

    In-Situ Instructions Exceed Side-by-Side Instructions in Augmented Reality Assisted Assembly

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    Blattgerste J, Renner P, Strenge B, Pfeiffer T. In-Situ Instructions Exceed Side-by-Side Instructions in Augmented Reality Assisted Assembly. In: Proceedings of the 11th ACM International Conference on PErvasive Technologies Related to Assistive Environments (PETRA'18). New York, NY, USA: ACM; 2018: 133-140.Driven by endeavors towards Industry 4.0, there is increasing interest in augmented reality (AR) as an approach for assistance in areas like picking, assembly and maintenance. In this work our focus is on AR-based assistance in manual assembly. The design space for AR instructions in this context includes, e.g., side-by-side, 3D or projected 2D presentations. In previous research, the low quality of the AR devices available at the respective time had a significant impact on performance evaluations. Today, a proper and up-to-date comparison of different presentation approaches is missing. This paper presents an improved 3D in-situ instruction and compares it to previously presented techniques. All instructions are implemented on up-to-date AR hardware, namely the Microsoft HoloLens. To support reproducible research, the comparison is made using a standardized benchmark scenario. The results show, contrary to previous research, that in-situ instructions on state-of-the-art AR glasses outperform side-by-side instructions in terms of errors made, task completion time, and perceived task load

    Scheduling Recurring Distributed Dataflow Jobs Based on Resource Utilization and Interference

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    Resource management systems like YARN or Mesos enable users to share cluster infrastructures by running analytics jobs in temporarily reserved containers. These containers are typically not isolated to achieve high degrees of overall resource utilizations despite the often fluctuating resource usage of single analytic jobs. However, some combinations of jobs utilize the resources better and interfere less with each others when running on the same nodes than others. This paper presents an approach for improving the resource utilization and job throughput when scheduling recurring data analysis jobs in shared cluster environments. Using a reinforcement learning algorithm, the scheduler continuously learns which jobs are best executed simultaneously on the cluster. Our evaluation of an implementation built on Hadoop YARN shows that this approach can increase resource utilization and decrease job runtimes. While interference between jobs can be avoided, co-locations of jobs with complementary resource usage are not yet always fully recognized. However, with a better measure of co-location goodness, our solution can be used to automatically adapt the scheduling to workloads with recurring batch jobs
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