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Browsing by Author "Lodge, Timothy P"

Now showing 1 - 12 of 12
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    1D SAXS indexing macro for Igor Pro
    (2021-09-08) Lindsay, Aaron P; Mueller, Andreas J; Mahanthappa, Mahesh K; Lodge, Timothy P; Bates, Frank S; bates001@umn.edu; Bates, Frank S; UMN Polymer Group
    This code was developed for the facile analysis of 1D SAXS data collected from ordered materials in Igor Pro. A robust file loading algorithm is included, allowing for rapid generation of publication quality stack plots. Also included is a straightforward indexing macro, enabling indexing of 1D SAXS data to a variety of phases. New phases can be added with minimal effort and multiple indexing options are included (e.g., ticks, lines, color, etc.), minimizing time spent analyzing data and producing plots for presentations or publications.
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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 Superlattice by charged block copolymer self-assembly
    (2019-04-09) Shim, Jimin; Bates, Frank S; Lodge, Timothy P; lodge@umn.edu; Lodge, Timothy P; Bates Research Group; Lodge Research Group
    These files contain data along with the associated output from instrumentation supporting all results reported in "Superlattice by charged block copolymer self-assembly" by Shim et. al. We report the discovery of an intriguing superlattice morphology from compositionally symmetric charged block copolymers, poly[(oligo(ethylene glycol) methyl ether methacrylate–co–oligo(ethylene glycol) propyl sodium sulfonate methacrylate)]–b–polystyrene (POEGMA–PS). These materials are conveniently prepared by sequential reversible addition–fragmentation chain transfer (RAFT) polymerization, followed by introduction of charged groups, in a manner that allows for systematic variation of the molecular structure in general, and the charge content in particular. POEGMA–PS self-assembles into a superlattice lamellar morphology, a previously unknown class of diblock nanostructures, but strikingly similar to oxygen-deficient perovskite derivatives, when the fraction of charged groups in the POEGMA block is about 5–25%. The charge fraction in the POEGMA block, and the tethering of the ionic groups, both play critical roles in driving the formation of the superlattice. This study highlights the accessibility of novel morphologies by introducing charges in a controlled manner.
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    Role of chain length in the formation of Frank-Kasper phases in diblock copolymers
    (2018) Lewis III, Ronald M; Arora, Akash; Beech, Haley K; Lee, Bongjoon; Lindsay, Aaron P; Lodge, Timothy P; Dorfman, Kevin D; Bates, Frank S
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    Supporting Data for "Development of a PointNet for Detecting Morphologies of Self-Assembled Block Oligomers in Atomistic Simulations"
    (2021-08-30) Shen, Zhengyuan; Sun, Yangzesheng; Lodge, Timothy P; Siepmann, J Ilja; siepmann@umn.edu; Siepmann, J Ilja; University of Minnesota MRSEC
    Molecular simulations with atomistic or coarse-grained force fields are a powerful approach for understanding and predicting the self-assembly phase behavior of complex molecules. Amphiphiles, block oligomers, and block polymers can form mesophases with different ordered morphologies describing the spatial distribution of the blocks, but entirely amorphous nature for local packing and chain conformation. Screening block oligomer chemistry and architecture through molecular simulations to find promising candidates for functional materials is aided by effective and straightforward morphology identification techniques. Capturing 3-dimensional periodic structures, such as ordered network morphologies, is hampered by the requirement that the number of molecules in the simulated system and the shape of the periodic simulation box need to be commensurate with those of the resulting network phase. Common strategies for structure identification include structure factors and order parameters, but these fail to identify imperfect structures in simulations with incorrect system sizes. Building upon pioneering work by DeFever et al. [Chem. Sci.2019, 10, 7503–7515] who implemented a PointNet (i.e., a neural network designed for computer vision applications using point clouds) to detect local structure in simulations of single-bead particles and water molecules, we present a PointNet for detection of nonlocal ordered morphologies of complex block oligomers. Our PointNet was trained using atomic coordinates from molecular dynamics simulation trajectories and synthetic point clouds for ordered network morphologies that were absent from previous simulations. In contrast to prior work on simple molecules, we observe that large point clouds with 1000 or more points are needed for the more complex block oligomers. The trained PointNet model achieves an accuracy as high as 0.99 for globally ordered morphologies formed by linear diblock, linear triblock, and 3-arm and 4-arm star-block oligomers, and it also allows for the discovery of emerging ordered patterns from nonequilibrium systems.
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    Supporting Data for "Effects of Electrolytes on Thermodynamics and Structure of Oligo(ethylene oxide)/Salt Solutions and Liquid–Liquid Equilibria of a Squalane/Tetraethylene Glycol Dimethyl Ether Blend"
    (2021-01-22) Shen, Zhengyuan; Chen, Qile P; Lodge, Timothy P; Siepmann, J Ilja; siepmann@umn.edu; Siepmann, J Ilja
    Data including input/output and restart files for all the systems, analysis codes (python, fortran, cpp), and figures in the paper "Effects of Electrolytes on Thermodynamics and Structure of Oligo(ethylene oxide)/Salt Solutions and Liquid–Liquid Equilibria of a Squalane/Tetraethylene Glycol Dimethyl Ether Blend". Sample movie files of the production trajectory are provided.
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    Supporting Data for "From Order to Disorder: Computational Design of Triblock Amphiphiles with 1 nm Domains"
    (2020-07-06) Shen, Zhengyuan; Chen, Jingyi L; Vernadskaia, Viktoriia; Ertem, S Piril; Mahanthappa, Mahesh K; Hillmyer, Marc A; Reineke, Theresa M; Lodge, Timothy P; Siepmann, J Ilja; siepmann@umn.edu; Siepmann, J Ilja; Materials Research Science & Engineering Center (MRSEC)
    Data including input/output and restart files for all the systems, analysis codes (python, fortran, cpp), and figures in the paper "From Order to Disorder: Computational Design of Triblock Amphiphiles with 1 nm Domains." Sample molecular dynamics trajectories pieces are provided due to the extremely long simulation trajectories.
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    Supporting data for Core−Shell Gyroid in ABC Bottlebrush Block Terpolymers
    (2023-05-25) Cui, Shuquan; Zhang, Bo; Shen, Liyang; Bates, Frank S; Lodge, Timothy P; lodge@umn.edu; Lodge, Timothy P; University of Minnesota Department of Chemistry
    These files contain primary data supporting all results reported in Cui et al. "Core−shell gyroid in ABC bottlebrush block terpolymers." A series of bottlebrush block polymers containing 24 PEP-PS diblock copolymers and 109 PEP-PS-PEO triblock terpolymers were synthesized by ring-opening metathesis polymerization (ROMP) of norbornene-functionalized poly(ethylene-alt-propylene) (PEP), poly(styrene) (PS), and poly(ethylene oxide) (PEO) macromonomers. The molecular weights of the three macromonomers were around 1 kg/mol. The relatively modest total backbone degrees of polymerization ranged from ca. 20 to 40. Morphologies of these bottlebrush block polymers were characterized by small-angle X-ray scattering (SAXS). The PEP-PS diblocks exhibited only cylindrical (HEX) and lamellar (LAM) morphologies; the desired network phases did not appear in these materials, consistent with previous experimental studies. However, adding variable-length bottlebrush PEO blocks to diblocks containing 30% to 50% PS led to a substantial core-shell double gyroid (GYR) phase window in the ternary phase portrait. Encouragingly, the GYR unit cell dimensions increased almost linearly with the backbone degree of polymerization, portending the ability to access larger network dimensions than previously obtained with linear block polymers. This finding demonstrates a periodic network phase in bottlebrush block polymers for the first time and highlights extraordinary opportunities associated with applying facile ROMP chemistry to multiblock bottlebrush polymers.
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    Supporting Data for Internal Structure of Methylcellulose Fibrils
    (2020-08-26) Schmidt, Peter W; Morozova, Svetlana; Ertem, S. Piril; Coughlin, McKenzie L; Davidovich, Irina; Talmon, Yeshayahu; Reineke, Theresa M; Bates, Frank S; Lodge, Timothy P; lodge@umn.edu; Lodge, Timothy P; Materials Research Science & Engineering Center (MRSEC)
    Data files used to generate all figures in the manuscript "Internal Structure of Methylcellulose Fibrils" and its supplementary information.
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    Supporting Data for Salt-Dependent Structure in Methylcellulose Fibrillar Gels
    (2022-06-09) Liberman, Lucy; Schmidt, Peter W; Coughlin, McKenzie L; Matatyaho Ya'akobi, Asia; Davidovich, Irina; Edmund, Jerrick; Ertem, Sedef P; Morozova, Svetlana; Talmon, Yeshayahu; Bates, Frank S; Lodge, Timothy P; lodge@umn.edu; Lodge, Timothy P; Materials Research Science & Engineering Center (MRSEC)
    Data files used to generate all figures in the manuscript "Salt-Dependent Structure in Methylcellulose Fibrillar Gels" and its supplementary information.
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    Supporting Data for Self-Assembly of Unusually Stable Thermotropic Network Phases by Cellobiose-Based Guerbet Glycolipids
    (2024-04-08) Das, Soumi; Zheng, Caini; Calabrese, Michelle A; Reineke, Theresa M; Siepmann, Ilja J; Mahanthappa, Mahesh K; Lodge, Timothy P; treineke@umn.edu; Reineke, Theresa M; University of Minnesota
    These files contain data along with associated output from instrumentation supporting all results reported in the referenced paper. Bicontinuous thermotropic liquid crystal (LC) materials, such as double gyroid (DG) phases, are highly promising for various applications due to their intricate 3D network structures. However, the lack of robust molecular design rules for shape-filling amphiphiles hinders their utility. To address this, we synthesized cellobiose-based glycolipids with Guerbet-type branched alkyl tails and examined their thermotropic LC self-assembly. Through techniques including differential scanning calorimetry (DSC), polarized optical microscopy (POM), and small-angle X-ray scattering (SAXS), we found that Guerbet cellobiosides have a strong propensity to form DG morphology across broad thermotropic phase ranges. The stability of these assemblies depends on the alkyl tail structure and anomeric configuration of the glycolipid in a previously unrecognized manner. Molecular simulations provide further insights, revealing molecular motifs crucial for network phase self-assembly, paving the way for future designs and applications of network LC materials.
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    Wigner-Seitz Cell generation and calculations in MATLAB
    (2021-09-08) Lindsay, Aaron P; Mueller, Andreas J; Mahanthappa, Mahesh K; Lodge, Timothy P; Bates, Frank S; bates001@umn.edu; Bates, Frank S; UMN Polymer Group
    This series of MATLAB codes was developed to generate publication-quality Wigner-Seitz cells for a variety of structures. These are frequently desired for self-assembled micellar systems, wherein the geometry of the Wigner-Seitz cell plays a role in the emergence of several packings. The main algorithm (VoronoiTesselation.m) is generalized, allowing specification of lattice positions and parameters or the upload of these values from a .xtl file exported from Vesta. Added is the ability to determine various cell parameters, including the coordination number, area/volume, and the second-moment volume, which is proportional to the stretching moment for polymer chains stretched from the cell center to the cell edges. A simple algorithm for simulation of 2D diffraction patterns is also included (diffraction.m).