ScholarWorks@UMassAmherst

Recent Submissions

  • PublicationOpen Access
    The Literary Career of Isaiah Thomas, 1749-1831
    (1978-06) Osterholm, John Roger
    The primary purpose of this study is to establish the various contributions that Isaiah Thomas made to early American literature and thought. His extensive participation in newspapers, magazines, and book publishing from 1770 through the first quarter of the nineteenth century makes his career particularly important to a more complete understanding of those times.
  • PublicationOpen Access
    Deep Learning Surrogates for Gas Dynamics: A Physics-Informed Pedagogical Approach
    (2025-12-09) Roohi, Ehsan
    Compressible flow problems are characterized by highly nonlinear, implicit, and often transcendental governing equations. In undergraduate gas dynamics education, solving these equations traditionally relies on iterative numerical methods or extensive look-up tables, which can obscure the physical intuition of the solution space. This paper introduces a comprehensive framework using Deep Learning (DL) to generate high-fidelity surrogate models for five canonical problems: Rayleigh flow, Fanno flow, oblique shocks, convergent-divergent nozzles, and unsteady shock tubes. We detail the specific neural network architectures and physics-informed feature engineering strategies required for each problem, such as using logarithmic inputs for Fanno friction parameters or geometric anchors for oblique shocks. The resulting models achieve high accuracy (< 1% error) and enable instantaneous visualization of complex design spaces, such as thermodynamic T −s diagrams and unsteady x−t wave interactions. This approach demonstrates how modern data-driven techniques can be integrated into the physics curriculum to enhance conceptual understanding.
  • PublicationOpen Access
    Molecular Design of Polymer Combs and Living Gels
    (2025-09) Lorenzana, Adrian
    Thermosetting resins are materials that undergo crosslinking by forming interchain linkages to create robust 3D networks that impart creep, thermomechanical, and solvent resistance. These materials are critical for a number of high-performance applications, such as aerospace and automotives, and biomedical crosslinked hydrogels. Thermosetting materials can be cured chemically or thermally, or by using ultraviolet (UV) light or electron beams. However, these methods are not always possible, accessible, and they can be harsh to embedded cells. Taking inspiration from natural materials such as fibronectin, a protein that contains hidden or cryptic sites that become exposed under tension, this dissertation first presents a new class of synthetic force-responsive materials that exhibit force-responsive behavior by exposing cryptic sites and forming new crosslinks. Long pendant poly(ethylene glycol) (PEG) chains along the polymer backbone create a significant steric barrier and prevent reactive moieties from spontaneously crosslinking, which is overcome by mechanical force. In this dissertation, I extended this approach to densely grafted comb polymers with reactive side chains, which resulted in highly crosslinked comb copolymers with minimal intramolecular crosslinking. Finally, I harnessed xanthogen disulfides to produce telechelic acrylic polymers and hydrogels responsive to visible light. Overall, I successfully designed and produced methods of easily implementing mechanosensitivity in synthetic polymers, strategies for producing high molecular weight crosslinkable resins, and fast techniques for synthesizing biocompatible gels. Importantly, the design principles laid out in this work provide a blueprint for developing next-generation stimuli responsive materials.
  • PublicationEmbargo
    STUDYING FUNCTIONAL AND REGULATORY MECHANISMS OF BIOMOLECULES USING SIMULATIONS
    (2025-09) Huang, Jian
    Elucidating molecular mechanisms of biomolecule functions is crucial for advancing understanding of biological processes, pathology of many hereditary and acquired diseases, as well as developing novel therapeutic strategies or targeting drugs. Recent years have witnessed a huge pike on high resolution structures of biologically critical membrane proteins shedding lights on atomistic level details, meanwhile functional studies have provided us with abundant macroscopic functional measurements upon perturbations, such as mutations and change of experimental conditions. Rationalizing those functional data in the molecular level based on resolved structures has been an important but challenging knowledge gap, which can be bridged by dynamics studies through computational simulations achieving high spatial and temporal resolutions. In Chapter two to four, we focused on studying gating and regulation mechanisms of two membrane channel protein: the TMEM16F lipid scramblase and the TRPV4 ion channel. We performed all-atom simulations on the inner gate charged TMEM16F mutants and observed spontaneous the pore opening and hydration process. The sampled closed-to-open transition detailed in pore-forming helices movements on different specific directions in the atomistic level. The resulting open state was found to be functionally active since a direct lipid scrambling event was sampled. Our study predicted a possible biologically relevant open state eluded from previous cryo-EM studies and revealed the activation transition process as well as the ion and lipid translocation pathways. In the TRPV4 gating study, we aimed at resolving free energy barrier contributions from the classic bundle-crossing gating mechanism and the hydrophobic gating mechanism. We first demonstrated the dewetting transition can readily happen in the bundle-crossing and highly hydrophobic pore. Through thorough free energy calculations, we showed that disruption of the hydrophobicity of the pore can significantly reduce the ion permeation barrier through lowering down the hydration free energies of the lower pore region. In Chapter four, we presented a story of PI(4,5)P2 regulation of the TRPV4 ion channel. We first disapproved previously proposed PI(4,5)P2 binding sites and identified two more plausible binding sites in the inner leaflet-protomer interface. Relative free energy calculations between the two sites showed they almost have similar binding affinities, indicating the possibility of dynamic binding of multiple PI(4,5)P2 for regulation. Careful dynamic coupling network analysis further resolved dynamics implications of binding in those two sites, suggesting PI(4,5)P2 can prime the channel for temperature activation. In Chapter five, we used extensive coarse-grained simulations to examine important domain-domain interaction modes in the chemotaxis protein CheA, the autokinase initiating phosphorylation cascade to regulate downstream flagellar rotation for motile bacteria to swim towards favorable environment. Important P1-P4 trans- productive contacting modes and P1/P1’ dimerization modes were predicted, generating testable measurements and hypotheses for experimental validations. All Chapters together showed how powerful it is to combine functional studies, structural biology and computational simulations for investigating functional and regulatory mechanisms of biomolecules in the biologically relevant environment.
  • PublicationEmbargo
    mRNA Therapeutics for Innate Immune Modulation: Engineering Immunogenicity for Therapeutic Applications in Chronic Inflammation and Cancer
    (2025-09) Forster III, James
    Messenger RNA (mRNA) delivery has revolutionized the therapeutic landscape, allowing for precise, intracellular control of previously undruggable targets through potent therapeutic protein expression. However, the mRNA platform also contains several intrinsic inefficiencies, including low stability, immunogenicity, and delivery challenges. Throughout mRNA’s history, researchers have worked to overcome these limitations by re-engineering the in vitro mRNA transcription (IVT) process, resulting in significant improvements in immunogenicity, stability, and translational efficiency. Furthermore, mRNA delivery platforms like lipid nanoparticles (LNPs) help shield the mRNA from degradation and enable controlled release to target tissues. Despite these advancements, widespread challenges related to immunogenicity and stability remain, limiting broader clinical application in diseases that would otherwise benefit from mRNA’s favorable pharmacokinetics. Innate immunomodulation is a critically underexplored area for mRNA application, stemming from our limited understanding of how mRNA delivery’s intrinsic immunogenicity results in inefficient expression, or worse yet, unexpected off-target exacerbations in disease state. Therefore, the primary objective of this dissertation is to broaden this understanding and enable therapeutic applications in the innate immune system and inflammatory disease. In Aim 1, we investigate how LNP lipid composition influences activation of the NLRP3 inflammasome, a highly dysregulated and disease-relevant innate immune pathway. We demonstrate that mRNA-LNPs activate the NLRP3 inflammasome in a lipid-formulation dependent manner, yielding key insights for future therapeutic and clinical design. In Aim 2, we focus on the mRNA cargo itself, assessing how production method, nucleotide modifications, and purification influence immunogenicity and therapeutic viability. Using novel co-tethered transcription systems, we perform comprehensive in vitro and in vivo screening, and also explore the potential of unmodified IVT RNA, coined immunoagonist non-coding RNA (incRNA), to act as a combination toll-like receptor agonist for cancer immunotherapy. In Aim 3, we integrate all our previous LNP design and mRNA engineering insights to develop the first mRNA therapeutic systems targeting gouty arthritis, a localized inflammatory disease mediated by NLRP3 activation. Together, these findings establish new principles for designing mRNA therapeutics that either evade or harness innate immune signaling and lay considerable groundwork for future clinical applications in chronic inflammatory disease and cancer.