706 research outputs found
Metastable Knots in Confined Semiflexible Chains
No full textWe study the size distribution of spontaneous knots on semiflexible chains confined in square cross-section channels using Monte Carlo simulations. The most probable knot size, i.e. the metastable knot size, is found to vary nonmonotonically with the channel size. In the case of weak confinement, the metastable knot size is larger than the knot size in bulk because the segments within the knot feel less channel confinement than the segments outside the knot, and the channel pushes the segments into knot cores to reduce the overall free energy. Conversely, in the case of strong confinement, the metastable knot size is smaller than the one in bulk because the segments within the knot experience more channel confinement, and the channel expels segments from the knot core. We demonstrate that a simple theory can capture this nonmonotonic behavior and quantitatively explain the metastable knot size as a function of the channel size. These results may have implications for tuning the channel size to either generate or screen knots.Singapore. National Research Foundation (Singapore-MIT Alliance for Research and Technology)National Science Foundation (U.S.) (Grant CBET-1335938
Untying Knotted DNA with Elongational Flows
No full textWe 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
No full textKnotted 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
No full textRecent 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
No full textWe 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
Jamming of Knots along a Tensioned Chain
No full textWe examine the motion of a knot along a tensioned chain whose backbone is corrugated due to excluded volume effects. At low applied tensions, the knot traverses the chain diffusively, while at higher tensions the knot makes slow, discrete hops that can be described as a Poisson process. In this “jammed” regime, the knot’s long-time diffusivity decreases exponentially with increasing tension. We quantify how these measurements are altered by chain rigidity and the corrugation of the polymer backbone. We also characterize the energy barrier of the reptation moves that gives rise to the knot’s motion. For the simple knot types examined thus far (3[subscript 1], 4[subscript 1], 5[subscript 1], 5[subscript 2]), the dominant contribution to the energy landscape appears in the first step of reptation—i.e., polymer entering the knotted core. We hope this study gives insight into what physics contributes to the internal friction of highly jammed knots.Singapore-MIT Alliance for Research and Technology (SMART)National Science Foundation (U.S.) (NSF grant CBET-1335938
Public worship and practical theology in the work of Benjamin Keach (1640-1704)
No full textThe late seventeenth century was a critical and fruitful period
for the Particular Baptists of England. Severely persecuted following
the Restoration, toleration in 1689 brought its own perils.
Particular Baptists were fortunate in having several strong leaders,
especially the London trio of Hanserd Knollys, William Kiffin, and
Benjamin Keach. Such a small and severely persecuted group as the
Baptists could afford little time for academic pursuits, thus of
necessity most of their theology was practical in nature.
Benjamin Keach (1640-1704) was the most outstanding practical
theologian among the English Particular Baptists of the late
seventeenth century. This dissertation is a study of Keach, in
particular his writings on public worship and practical theology.
Although Keach was a prolific author, he has been almost completely
neglected by scholars.
After a biographical sketch of Keach, this study considers his
writings on public worship and practical theology. In the area of
worship, Keach made two outstanding contributions: First, he was the
most vocal apologist for Baptist views on Baptism of his period.
Secondly, and more importantly, his hymn writing and defense of hymn
singing broke new ground, not just for Baptists, but for English
Protestantism, in general. In addition to his contributions in these
areas, he also dealt with the laying on of hands and the sabbath day
worship controversy.
Keach's contributions to practical theology fall into two main
groups: his writings that concern religious education and those that
deal with polity. In addition to these, Keach's vigorous advocacy of
a high Calvinist soteriology are also considered under the rubric of
practical theology. Keach's most important (although not his most
positive) contribution in this area were his soteriological writings.
Although well within the bounds of orthodoxy, some of the tendencies
in Keach's soteriology were taken up by the following generation of
Baptist leaders and developed into a stultifying hyper-Calvinism that
handicapped Baptist evangelism and missions.
In the conclusion, Keach's contributions to a theory of practical
theology are considered
Obsession, repression, and the men behind Dracula
No full textThe style, characters and action of Bram Stoker’s 1897 Gothic horror novel, Dracula—including the relationships among male characters—can be attributed to the author’s close relationship and bond with famed Victorian actor, Henry Irving. Irving’s demeanor, personality and acting talent highlighted Stoker’s affinity for Irving, and this essay’s primary objective is to determine how Bram Stoker’s social and professional relationship with Irving, influenced and shaped Dracula. The essay will review the lives of both Irving and Stoker individually and separately, but also delve into their personal relationship, symbolic and representative of male bonding and the role that gender plays in Stoker’s novel. Themes of homoeroticism, whether on the conscious or unconscious level, and gender boundaries will be examined for they both are apparent in Stoker’s life as well as the cast of characters in Dracula. This essay will examine any and all nuances or specific methods that Irving used both as an actor and as a producer. Noteworthy chapters, excerpts and moments from Dracula, such as Jonathan Harker’s stay in Castle Dracula and the excavation of Lucy’s tomb by the four men can be indicators of a continuous desire for male bonding on Stoker’s part. He often struggled with the concept of bachelorhood and marriage. The novel does not praise either, but provides an attractive alternative: a socially intimate and sexually ambiguous cast of males. Ranging from the personal to the public to the professional spheres of Stoker and Irving, this essay intends to provide a comprehensive evaluation of Dracula’s style and characters while simultaneously demonstrating the power of social, professional and personal relations in a literary and theatrical world. Even after Irving overlooked Stoker when he passed on his management rights, Stoker was continually drawn to him. Even after Irving left Stoker nothing after his death, Stoker continued to praise him. It is evident in almost all places that, to Stoker, Henry Irving was not just a man but also a source of pleasure, similar to the way that the males in Dracula perceive each other.M.A.Includes bibliographical referencesby Benjamin A. Kukaini
Supporting Data for “Why So Slow? Mechanistic Insights from Studies of a Poor Catalyst for Polymerization of ε-Caprolactone”
No full textThese files contain data along with associated output from instrumentation supporting all results reported in Stasiw, D. E.; Mandal, M.; Neisen, B. D.; Mitchell, L. A.; Cramer, C. J.; Tolman, W. B. Why so slow? Mechanistic insights from studies of a poor catalyst for polymerization of ε-caprolactone. Inorg. Chem., 2016, 56, 725–728. Polymerization of ε-caprolactone (CL) using an aluminum alkoxide catalyst (1) designed to prevent unproductive trans binding was monitored at 110 °C in toluene-d8 by 1H NMR and the concentration versus time data fit to a first-order rate expression. A comparison of t1/2 for 1 to values for many other aluminum alkyl and alkoxide complexes shows much lower activity of 1 toward polymerization of CL. Density functional theory calculations were used to understand the basis for the slow kinetics. The optimized geometry of the ligand framework of 1 was found indeed to make CL trans binding difficult: no trans-bound intermediate could be identified as a local minimum. Nor were local minima for cis-bound precomplexes found, suggesting a concerted coordination–insertion for polymer initiation and propagation. The sluggish performance of 1 is attributed to a high-framework distortion energy required to deform the “resting” ligand geometry to that providing optimal catalysis in the corresponding transition-state structure geometry, thus suggesting a need to incorporate ligand flexibility in the design of efficient polymerization catalysts..
Corresponding author for experimental data is William B. Tolman ([email protected]).
Corresponding author for computational data is Christopher J. Cramer ([email protected]).Funding for this project was provided by the Center for Sustainable Polymers at the University of Minnesota, a National Science Foundation (NSF)-supported Center for Chemical Innovation (Grant CHE-1413862). The X-ray diffraction experiments were performed using a crystal diffractometer acquired through NSF-MRI Award CHE-1229400. The authors acknowledge the MSI at the University of Minnesota for providing resources that contributed to the research results.Tolman, William, B; Cramer, Christopher, J; Stasiw, Daniel E; Mandal, Mukunda; Neisen, Benjamin D; Mitchell, Lauren A. (2017). Supporting Data for “Why So Slow? Mechanistic Insights from Studies of a Poor Catalyst for Polymerization of ε-Caprolactone”. Retrieved from the University Digital Conservancy, https://doi.org/10.13020/D6F60H
319 - Benjamin Wostoupal
No full textIncludes bibliographical references.More than one-third of the global population lives in parts of the world that lack sufficient freshwater resources to support the needs of local populations. In many of these regions, rapid population growth has led to the reallocation of water from agricultural purposes to meet growing urban demands. Rural economies, dependent on agriculture, have suffered as a result. This study examines how water transfers affects rural economies and investigates strategies to protect such economies. Results are of widespread interest for the future health, security, and livelihood of agricultural communities throughout the world and the populations that depend on their productivity
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