Browsing by Author "Dorfman, Kevin D"

Now showing 1 - 20 of 77
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    Data and code supporting: Simulations corroborate telegraph model predictions for the extension distributions of nanochannel confined DNA
    (2019-08-12) Bhandari, Aditya Bikram; Dorfman, Kevin D; dorfman@umn.edu; Dorfman, Kevin D; Dorfman
    Hairpins in the conformation of DNA confined in nanochannels close to their persistence length cause the distribution of their fractional extensions to be heavily left skewed. A recent theory rationalizes these skewed distributions using a correlated telegraph process, which can be solved exactly in the asymptotic limit of small but frequent hairpin formation. Pruned-enriched Rosenbluth method simulations of the fractional extension distribution for a channel-confined wormlike chain confirm the predictions of the telegraph model. Remarkably, the asymptotic result of the telegraph model remains robust well outside the asymptotic limit. As a result, the approximations in the theory required to map it to the polymer model and solve it in the asymptotic limit are not the source of discrepancies between the predictions of the telegraph model and experimental distributions of the extensions of DNA during genome mapping. The agreement between theory and simulations motivates future work to determine the source of the remaining discrepancies between the predictions of the telegraph model and experimental distributions of the extensions of DNA in nanochannels used for genome mapping.
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    Data files for Liquid-Like States in Micelle-Forming Diblock Copolymer Melts
    (2023-07-06) Dorfman, Kevin D; Wang, Zhen-Gang; dorfman@umn.edu; Dorfman, Kevin D; Dorfman Research Group
    These are the SCFT output and processed files reported in this paper. Instructions for regenerating all intermediate data files are also included.
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    Data for "3D Printing-Enabled DNA Extraction for Long-Read Genomics" published as ACS Omega 2020, 5, 20817-20824
    (2020-08-31) Agrawal, Paridhi; Reifenberger, Jeffrey G; Dorfman, Kevin D; agraw135@umn.edu; Agrawal, Paridhi; University of Minnesota Dorfman Lab
    The deposited data files have DNA size measurement critical to demonstrating long DNA extraction in the microfluidic device, and DNA concentration measurement to show the yield of the platform.
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    Data for "Identifying a critical micelle temperature in simulations of disordered asymmetric diblock copolymer melts"
    (2021-10-18) Chawla, Anshul; Bates, Frank S; Dorfman, Kevin D; Morse, David C; chawl029@umn.edu; Chawla, Anshul; University of Minnesota
    We have used coarse-grained molecular dynamics simulations to identify a critical micelle temperature in a diblock copolymer melt by analyzing the appearance of micelles. The files contain the data and an example simulation file which can be used with Hoomd-blue version 2.9.0. The data has been published as "Identifying a critical micelle temperature in simulations of disordered asymmetric diblock copolymer melts" in Physical Review Materials.
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    Data for "Stability of Cubic Single Network Phases in Diblock Copolymer Melts"
    (2022-07-25) Chen, Pengyu; Mahanthappa, Mahesh K; Dorfman, Kevin D; dorfman@umn.edu; Dorfman, Kevin D; Dorfman Research Group
    This dataset contains the self-consistent field theory (SCFT) simulation results and data for geometric analysis in "Stability of cubic single networks in diblock copolymer melts" by Chen et. al. (DOI: 10.1002/pol.20220318). SCFT was used to investigate the stability of cubic single and double network phases. Geometric analysis, including the calculations of mean curvatures and interfacial areas per unit volume of the domain interface, was used to understand the metastability of the single network phases. With this dataset, users should be able to regenerate the calculations and figures that appeared in the paper.
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    Data for "Stability of the Double Gyroid Phase in Bottlebrush Diblock Copolymer Melts"
    (2021-10-04) Park, So Jung; Cheong, Guo Kang; Bates, Frank S; Dorfman, Kevin D; dorfman@umn.edu; Dorfman, Kevin D; Dorfman Research Group
    This data set contains the input and output data files used for the self-consistent field theory simulations in "Stability of the double gyroid phase in bottlebrush diblock copolymer melts" by Park et al. Self-consistent field theory was used to study the self-assembly of bottlebrush block copolymers, focusing on the effect of the bottlebrush architecture on the stability of the double gyroid phase.
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    Data for "The disordered micelle regime in a conformationally asymmetric diblock copolymer melt"
    (2021-10-21) Cheong, Guo Kang; Dorfman, Kevin D; dorfman@umn.edu; Dorfman, Kevin D; Dorfman Research Group
    Data appearing in the publication "The disordered micelle regime in a conformationally asymmetric diblock copolymer melt". This paper reports Monte Carlo Field Theoretic Simulation (MC-FTS) results for diblock copolymers in the sphere-forming region of the phase diagram. The archived data are the post-processed trajectories. Owing to their size, the raw trajectories for the fields are not stored.
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    Data for A soft crystalline packing with no metallic analogue
    (2024-04-08) Chen, Pengyu; Dorfman, Kevin D; dorfman@umn.edu; Dorfman, Kevin D; Dorfman Research Group - University of Minnesota Department of Chemical Engineering and Materials Science
    This dataset contains the input and output files for self-consistent field theory (SCFT) simulations in the associate paper.
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    Data for Alternating Gyroid in Block Polymer Blends
    (2022-04-27) Park, Sojung; Bates, Frank S; Dorfman, Kevin D; dorfman@umn.edu; Dorfman, Kevin D; Dorfman Research Group - University of Minnesota Department of Chemical Engineering and Materials Science
    This data set contains the input and output files from the PSCF C++ program used for the self-consistent field theory (SCFT) simulation in "Alternating gyroid in block polymer blends" by Park et al. (doi/10.1021/acsmacrolett.2c00115). Self-consistent field theory was used to investigate the stability of alternating gyroid phase in the ternary AB/BC/ABC block polymer mixture. With this dataset, users should be able to regenerate all the calculations that appeared in the paper, using the open-source C++ SCFT program.
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    Data for Alternating Gyroid Stabilized by Surfactant-like Triblock Terpolymers in IS/SO/ISO Ternary Blends
    (2023-03-22) Chen, Pengyu; Bates, Frank S; Dorfman, Kevin D; dorfman@umn.edu; Dorfman, Kevin, D; Dorfman Research Group - University of Minnesota Department of Chemical Engineering and Materials Science
    This dataset contains the self-consistent field theory (SCFT) simulation results in the associated paper (https://doi.org/10.1021/acs.macromol.2c02485)
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    Data for Boundary Frustration in Double-Gyroid Thin Films
    (2024-02-29) Magruder, Benjamin R; Morse, David C; Ellison, Christopher J; Dorfman, Kevin D; dorfman@umn.edu; Dorfman, Kevin D; Dorfman Group, UMN CEMS
    We have used self-consistent field theory to predict the morphology and preferred orientation of the double-gyroid phase in thin films of AB diblock polymers. A manuscript has been submitted containing this data, and is expected to appear shortly. The data were generated using the C++ version of the open-source software PSCF (https://pscf.cems.umn.edu/). All input and output files from PSCF used to generate the data in the paper are included in this dataset, as well as the code used to process the data and generate the figures.
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    Data for Chain and Structural Dynamics in Melts of Sphere-Forming Diblock Copolymers
    (2024-07-22) Chawla, Anshul; Bates, Frank S; Dorfman, Kevin D; Morse, David C; dorfman@umn.edu; Dorfman, Kevin D; Dorfman Research Group
    Processed simulation data appearing in the related manuscript
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    Data for Deformation and failure of glassy polymer-polymer interfaces compatibilized by linear multiblock copolymers
    (2024-07-08) Collanton, Ryan P; Dorfman, Kevin D; dorfman@umn.edu; Dorfman, Kevin
    Using coarse-grained molecular dynamics simulations, we study the mechanical properties and stress transfer mechanisms of weakly entangled, glassy polymer blends compatibilized by diblock, triblock, or pentablock copolymers. For a given number of copolymer junctions per unit area, copolymer architecture is found to play a minimal role, whereas block degree of polymerization and copolymer loading qualitatively impact the interfacial mechanics. Explicitly, the stress-strain and density-strain curves reveal distinctly different deformation mechanisms at low and high compati- bilizer loading related to cavitation and fibril formation near the A/B interface. Furthermore, the competition between interfacial cavitation and chain pullout from the bulk leads to non-monotonic dependencies of the toughness and strain-at-break on copolymer loading. For sufficiently long copolymers, the simulations predict an optimum loading that produces mechanical properties that nearly match those of the homopolymer glass. These results imply that moderate loading of long block copolymers is ideal for effective compatibilization and stress transfer across the interface.
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    Data for Diffusion of knots in nanochannel-confined DNA molecules
    (2023-05-04) Mao, Runfang; Dorfman, Kevin D; dorfman@umn.edu; Dorfman, Kevin D; Dorfman Research Group - University of Minnesota Department of Chemical Engineering and Materials Science
    This data set contains the input and output files from the simulation in " Diffusion of knots in nanochannel-confined DNA molecules." Langevin dynamics simulations were used to investigate the knot diffusion behavior in the nanochannel confined DNA molecules. With this dataset, users should be able to regenerate all the figures that appeared in the paper.
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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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    Data for Gaming self-consistent field theory: Generative block polymer phase discovery
    (2023-10-18) Chen, Pengyu; Dorfman, Kevin D; dorfman@umn.edu; Dorfman, Kevin D; Dorfman Research Group - University of Minnesota Department of Chemical Engineering and Materials Science
    This dataset contains the input and output files for self-consistent field theory (SCFT) simulations and the training of generative adversarial networks (GANs) in the associated paper.
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    Data for Mechanism of Escape of a Single Chain from a Diblock Copolymer Micelle
    (2022-12-19) Seeger, Sarah C; Lodge, Timothy P; Dorfman, Kevin D; dorfman@umn.edu; Dorfman, Kevin D; Dorfman Research Group
    Simulation input files and processed data appearing in the related manuscript.
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    Data for Order and Disorder in ABCA′ Tetrablock Terpolymers
    (2020-11-16) Radlauer, Madalyn R; Arora, Akash; Matta, Megan E; Bates, Frank S; Hillmyer, Marc A; Dorfman, Kevin D; dorfman@umn.edu; Dorfman, Kevin D; Dorfman Group
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    Data for Simulations of sphere-forming diblock copolymer melts
    (2022-09-15) Chawla, Anshul; Bates, Frank S; Dorfman, Kevin D; Morse, David C; dorfman@umn.edu; Dorfman, Kevin D; Dorfman Research Group
    Processed simulation data appearing in the related manuscript.
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    Data for Single Gyroid in H-shaped Block Copolymers
    (2023-10-05) Park, Sojung; Bates, Frank S; Dorfman, Kevin D; dorfman@umn.edu; Dorfman, Kevin D; Dorfman Research Group - University of Minnesota Department of Chemical Engineering and Materials Science
    This data set contains the input and output files from the PSCF C++ program used for the self-consistent field theory (SCFT) simulation in "Single Gyroid in H-shaped Block Copolymers." Self-consistent field theory was used to investigate the equilibrium phase behavior of H-shaped block copolymers. With this dataset, users should be able to regenerate all the calculations that appeared in the paper, using the open-source C++ SCFT program available on GitHub (https://github.com/dmorse/pscfpp).