Browsing by Subject "Polymer physics"

Now showing 1 - 5 of 5
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    Data for DNA fragmentation in a steady shear flow
    (2022-09-23) Qiao, Yiming; Ma, Zixue; Onyango, Clive; Cheng, Xiang; Dorfman, Kevin D; qiao0017@umn.edu; Qiao, Yiming; University of Minnesota Dorfman Research Lab
    We have determined the susceptibility of T4 DNA (166 kilobase pairs, kbp) to fragmentation under steady shear in a cone-and-plate rheometer.
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    Dynamics of Knotted DNA Molecules Confined in Nanochannels
    (2022-03) Ma, Zixue
    Knots are intriguing topological objects and ubiquitous in biopolymers such as DNA molecules. The occurrence of knots in DNA confounds the accuracy of genomics technologies, such as nanochannel-based genome mapping and nanopore sequencing, that require uniformly stretching the DNA molecules. Knots existing in vivo also influence biological processes, such as DNA replication, and hence leads to cellular malfunction. The control of DNA knots is, thus, significant for genomics technologies and cell survival, which require first understanding the fundamental properties of knotted DNA in a crowded environment. The aim of this thesis is to address fundamental questions related to knot transport in nanochannel-confined DNA molecules, particularly the knot diffusion mechanism, the effect of knots on DNA diffusion in nanochannels and the interactions between two knots. We first determined the knot diffusive behavior along DNA confined in nanochannels to distinguish between two predicted knot diffusion mechanisms, self-reptation and knot region breathing. With a recently developed nanofluidic "knot factory" device, we generated knots in DNA molecules efficiently. The experimental results of knot motion along DNA chains show that knots undergo subdiffusion, i.e. their mean-squared displacement grows sublinearly with time, which supports the knot diffusion mechanism of self-reptation. We then investigated the effects of knots on DNA center-of-mass diffusion in nanochannels, thus resolving the open question which of these competing effects, the shortening of DNA chains or the increased DNA-wall friction, dominates knotted DNA diffusion in nanochannels. To address this question, we measured the diffusivity of DNA molecules before and after knot formation via a combination of the nanofluidic knot factory device for knot generation and laser-induced fluorescence microscopy for DNA observation. The experimental results show that the presence of knots decreases the diffusivity of DNA chains confined in nanochannels. The reduced diffusivity indicates that the DNA-wall friction, rather than the shortening of the confined chain size, dominates the friction of knotted DNA in nanochannels. Our previous work focused on the dynamical properties of single knots. Long DNA molecules are susceptible to form multiple knots in the chains. In the third research project, we investigated the interactions between two knots in nanochannel-confined DNA by analyzing the motion of the two knots along DNA chains. The free energy profiles of knot-knot interactions show that the separated knot state is more stable than the intertwined knot state, with dynamics in the separated knot state that are consistent with independent diffusion of the two knots. The thesis work provides deep insights into the dynamical properties of DNA knots under nanochannel confinement. We hope such fundamental knowledge gained in this dissertation could prescribe avenues for suppression and removal of knots under nanofluidic systems and crowded environments, thereby improving the genomic technologies and controlling knots in living cells.
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    Equilibrium properties of DNA and other semiflexible polymers confined in nanochannels
    (2016-01) Muralidhar, Abhiram
    Recent developments in next-generation sequencing (NGS) techniques have opened the door for low-cost, high-throughput sequencing of genomes. However, these developments have also exposed the inability of NGS to track large scale genomic information, which are extremely important to understand the relationship between genotype and phenotype. Genome mapping offers a reliable way to obtain information about large-scale structural variations in a given genome. A promising variant of genome mapping involves confining single DNA molecules in nanochannels whose cross-sectional dimensions are approximately 50 nm. Despite the development and commercialization of nanochannel-based genome mapping technology, the polymer physics of DNA in confinement is only beginning to be understood. Apart from its biological relevance, DNA is also used as a model polymer in experiments by polymer physicists. Indeed, the seminal experiments by Reisner et al. (2005) of DNA confined in nanochannels of different widths revealed discrepancies with the classical theories of Odijk and de Gennes for polymer confinement. Picking up from the conclusions of the dissertation of Tree (2014), this dissertation addresses a number of key outstanding problems in the area of nanoconfined DNA. Adopting a Monte Carlo chain growth technique known as the pruned-enriched Rosenbluth method, we examine the equilibrium and near-equilibrium properties of DNA and other semiflexible polymers in nanochannel confinement. We begin by analyzing the dependence of molecular weight on various thermodynamic properties of confined semiflexible polymers. This allows us to point out the finite size effects that can occur when using low molecular weight DNA in experiments. We then analyze the statistics of backfolding and hairpin formation in the context of existing theories and discuss how our results can be used to engineer better conditions for genome mapping. Finally, we elucidate the diffusion behavior of confined semiflexible polymers by comparing and contrasting our results for asymptotically long chains with other similar studies in the literature. We expect our findings to be not only beneficial to the design of better genome mapping devices, but also to the fundamental understanding of semiflexible polymers in confinement.
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    Graft Polymer Physics
    (2010-05) Haugan, Ingrid
    Graft polymers have polymeric side chains grafted onto a common backbone and exhibit extended conformations due to steric repulsion from densely grafted side chains. The ability to modulate conformation, and thus material performance, has made graft polymers a rich area of research in the last decade. This thesis expands the fundamental understanding of the physical properties of graft polymers in order to aid in the design of novel materials and focuses in three areas: rheology, thermodynamics, and mechanical properties. First, the effect of grafting density on the linear viscoelasticity of graft polymers is investigated. We demonstrate that graft polymers experience the same relaxational modes as linear polymers and their viscoelastic behavior can be described by the same Rouse and reptation theories. The experimental data is compared to scaling models to determine the conformation of the graft polymers, and a new model is proposed to better capture the behavior of experimentally relevant graft polymers. Next, the thermodynamics of densely grafted bottlebrush block polymers is explored. Bottlebrush block polymers were prepared with homopolymer side chains added in blocks along the backbone, varying side chain and backbone length. Their order-disorder transition temperatures were measured by temperature controlled small-angle X-ray scattering. The bottlebrush block polymers display a higher segregation strength compared to linear diblock polymers at the order-disorder transition, indicative of the shielding of the segments near the backbone. The segregation strength at the order-disorder transition decreased with increasing side chain and backbone length. Finally, the mechanical properties of graft polymers with diblock side chains are studied in an attempt to produce tough and sustainable polylactide plastics. The addition of a rubber domain initially toughens the polylactide but the polymers still undergo physical aging and become brittle over time; the time to brittle failure is found to be strongly dependent on the rubber content of the graft block polymers. Pre-straining of the polymers is used to produce stronger and tougher plastics that do not embrittle upon aging.
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    Structure and Dynamics of Compositionally Asymmetric Diblock Copolymers
    (2018-09) Lewis, Ronald
    Diblock copolymers are among the simplest amphiphilic molecules, and thus provide a model platform for understanding self-assembly in soft matter. The research presented in this work is broadly focused on the interplay between structure and dynamics in particle-forming diblock copolymer melts, motivated by a recent rise in the number of reports describing complex phase formation in these materials. Analogous complex, low-symmetry structures have been observed in hard materials, such as metals and metal alloys, pointing to the existence of underlying universalities within condensed matter physics. In this work, thermal processing methods commonly employed on hard materials are applied to short, compositionally asymmetric poly(1,4-isoprene)-block-poly(±-lactide) (IL) diblock copolymers. Two disordered IL samples exhibiting characteristic spherical micelle fluctuations above the order-disorder transition (ODT) were quenched in liquid nitrogen and reheated to target temperatures. This processing method lead to the formation of unconventional, low symmetry phases that were not otherwise formed by direct cooling from the disordered state, bearing similarities to metallurgy. However, unlike metals, the ordered states below the ODT imprinted particle densities onto the samples that persisted in the disordered state. This remarkable feature is a manifestation of the fluctuating disordered fluid in self-assembling soft materials. A recent report showed that conformational asymmetry in diblock copolymers, or the difference in space-filling capability between each block, is a key factor in complex phase formation. However, the most important parameter in polymer physics is the length of the polymer chain, which in a diblock copolymer may be represented by the invariant block degree of polymerization N ̅_b. In this work, the role of chain length on complex phase formation is investigated by probing the behavior of asymmetric poly(styrene)-block-poly(1,4-butadiene) (SB; N ̅_b ≈ 80) diblock copolymers. This system was devoid of complex phases, in contrast to previous results for short asymmetric poly(ethylethylene)-block-poly(±-lactide) (EL; N ̅_b ≈ 800) diblock copolymers with approximately the same conformational asymmetry. Differences in phase behavior associated with packing and entanglement theory and resulted in calculation of a universal crossover parameter, N ̅_x ≈ 400. In the case of SB, where N ̅_b > N ̅_x, asymmetry in space-filling capabilities are less important and the system exhibits phase behavior analogous to mean-field predictions. Conversely, the N ̅_b < N ̅_x regime places emphasis on conformational asymmetry and presumably other molecular factors that stabilize complex structures. In a diblock copolymer system, a dynamic constraint is imposed upon complex phase formation as mass (chain) exchange between particles is required to accommodate the multiple discrete particle shapes and sizes comprising these structures. In this work, the dynamics associated with particles below the ODT is investigated using dynamic mechanical spectroscopy (DMS) and X-ray photon correlation spectroscopy (XPCS). In the supercooled liquid prior to ordering, DMS and XPCS measurements conducted on a BCC-forming SB diblock copolymer revealed that particle dynamics are dependent on the ergodicity temperature, above which particle rearrangements are mediated by ergodic chain dynamics and below which non-ergodic ‘frozen’ particle motion becomes dominant. Additionally, a new analytical framework was developed to investigate the time evolution of particle dynamics via XPCS, which uncovered a wealth of dynamic features including time-resolved relaxation time and speed distributions associated with particles in grains.