A. James Clark School of Engineering
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The collections in this community comprise faculty research works, as well as graduate theses and dissertations.
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Item MOLECULAR-SCALE EXPLORATION OF INTERACTIONS BETWEEN DROPS AND PARTICLES WITH A POLYMERIC LAYER(2023) Etha, Sai Ankit; Das, Siddhartha; Mechanical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Surface-grafted polymer molecules have been extensively employed for surface modifications as they ensure changes to the inherent physical/chemical properties of surface. Bottom-up surface processing with well-defined polymeric structures becomes increasingly important in many current technologies. Polymer brushes, which are polymer molecules grafted to a substrate by its one end at close enough proximity (thereby ensuring that they stretch out like the “bristles” of a toothbrush), provide an exemplary system of materials capable of achieving such a goal. In particular, producing functional polymer brushes with well-defined chemical configurations, densities, architectures, and thicknesses on a material surface has become increasingly important in many fields. In my dissertation, I employ Molecular Dynamics (MD) simulations to study the interplay of interactions between nanoparticles (NPs), solvent drops and polymer grafted surfaces under various system conditions. This study will help us to understand (1) the wetting dynamics of brush grafted surfaces and the associated brush conformational changes, (2) polymer-insoluble solvophilic NP assembly in brush grafted surfaces and the steric interactions driven establishment of direct contacts between a NP and a polymer layer (highly phobic to the NP), and (3) microphase separation and distillation-like behavior of grafted polymer bilayers interacting with a binary liquid mixture, and the resulting nanofluidic valving behavior of swollen polymer bilayers in a weak interpenetration regime. In Chapter 1, I provide the background and motivation of the research presented in this thesis. In Chapter 2, I study the spreading and imbibition of a liquid drop on a porous, soft, solvophilic, and responsive surface represented by a layer of polymer molecules grafted on a solvophilic solid. These polymer molecules are in a crumpled and collapsed globule-like state before the interaction with the drop, but transition to a “brush”-like state as they get wetted by the liquid drop. We hypothesize that for a wide range of densities of polymer grafting (σg), the drop spreading is dictated by the balance of the driving inertial pressure and balancing viscoelastic dissipation, associated with the spreading of the liquid drop on the polymer layer that undergoes globule-to-brush transition and serves as the viscoelastic solid. Finally, I argue that these simulations raise the possibility of designing soft and “responsive” and widely deployable liquid-infused surfaces where the polymer grafted solid, with the polymer undergoing a globule-to-brush transition, serving as the responsive “surface”. In Chapter 3, I employ coarse-grained molecular dynamics (MD) simulations and establish that under appropriate conditions, it is possible to develop numerous stable direct contacts between a polymer-insoluble NP and a solvated polymer layer (the polymer layer is phobic to the NP, while the solvent/liquid is philic to both the NP and the polymer). The NP is driven inside a layer of collapsed and phobic (to the NP) polymer molecules by a drop of this liquid (which is philic to both the NP and the polymer layer). The liquid molecules imbibe and diffuse inside the polymer layer, but the NP remains localized within the polymer layer, due to large Steric effects, ensuring the establishment of highly stable numerous direct contacts between the NP and the highly phobic polymer molecules. Finally, I argue that our finding will open up avenues for leveraging NP-polymer interactions for a myriad of applications even for cases where the polymer molecules are phobic to the NPs. In Chapter 4, I study the interaction of a binary mixture drop, containing two-miscible-liquids, with a polymer functionalized nanochannel that is philic to one of the liquids and phobic to the other. Liquid-liquid phase separation is achieved due to the asymmetry of interaction of the liquid species and we observe distillation like behavior wherein the drop becomes progressively concentrated with the phobic liquid with each ‘“pass” with the polymer bilayer absorbing an increasing fraction of the philic liquid molecules and transitioning into the polymer brush regime. Depending on the nanochannel height, the number of allowed passes varies, as the polymer chains stretch out until the oppositely grafted layers overlap and create a dense region of liquid infused polymer layers that act as a valve. Any further passage of drops through this nano-confined interpenetrating brush bilayer requires a much greater magnitude of applied force on the drop. I finally propose a design of nanovalves based on this mechanism of creating partially porous interpenetrating polymer brush layers.Item WATER, ION, AND GRAPHENE: AN ODYSSEY THROUGH THE MOLECULAR SIMULATIONS(2019) Wang, Yanbin; Das, Siddhartha; Mechanical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Water is known as the most common and complicated liquid on earth. Meanwhile, graphene, defined as single/few layer graphite, is the first member in the 2-dimensional materials family and has emerged as a magic material. Interactions between water and graphene generate many interesting phenomena and applications. This thesis focuses on applying molecular dynamics (MD), a powerful computational tool, for investigating the graphene-water interactions associated with various energetic and environmental applications, ranging from the wettability modification, species adsorption, and nanofluidic transport to seawater desalination. A key component of one domain of applications involves a third component, namely salt ions. This thesis attempts that and discovers a fundamentally new way in which the behavior of ions with the air-water interfaces should be probed. In Chapter 1, we introduce the motivation and methods and the overall structure of this thesis. Chapter 2 focuses on how MD simulations connect the statistical mechanics theory with the experimental observations. Chapter 3 discusses the simulation results revealing that the spreading of a droplet on a nanopillared graphene surface is driven by a pinned contact line and bending liquid-surface dynamics. Chapter 4 probes the interactions between a water drop and a holey graphene membrane, which is prepared by removing carbon atoms in a circular shape and which can serve as catalyst carriers. Accordingly, chapter 5 studies the effects of various terminations on water-holey graphene interactions, showing that water flows faster and more thoroughly through the membrane with hydrophobic terminations, compared to that with hydrophilic terminations. In chapter 6, simulations describe the generation of enhanced water-graphene surface area during the water-holey-graphene interactions in presence of an applied time-varying force on the water drop. In chapter 7, we focus on the ion-water interaction at the water-air interface to fully understand the fluidic dynamics during any seawater desalination. Our research revisits the energetic change while ion approaches water-air interface and shows that the presence of ion at the interface enhances capillary-wave fluctuation. Finally, in chapter 8 we summarize the main findings of the thesis and provide the scope of future research.Item Examining the role of water and hydrophobicity in folding, aggregation, and allostery(2018) Custer, Gregory Scott; Matysiak, Silvina; Bioengineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Solvation and hydrophobicity drive many critical processes in nature, playing an important role in the folding of proteins, aggregation of surfactants into micelles, and in the disorder to order transitions that occur in some allosteric proteins upon ligand binding. Understanding how solvation and hydrophobicity affect these processes at a molecular level is important to finding new ways to use these processes, but it can be difficult to characterize these molecular details using experimental methods. Molecular dynamics (MD) simulations have proven useful in exploring details and thermodynamic conditions inaccessible in experiment, as MD captures the time evolution of the system at a molecular level. The phenomena which can be studied with an MD simulation depend on the mathematical model employed. Atomistic models provide the most detail for a simulation, but due to the computational costs required are not typically used to study phenomena which require large systems and time scales greater than several μs. Coarse-grained (CG) models reduce the complexity of the system being studied, enabling the exploration of phenomena that occur at longer time scales. We have developed CG models to study protein folding and surfactant aggregation. Our CG surfactant model uses a three-body potential to account for hydrogen bonding without an explicit electrostatic potential, reducing the computational cost of the model. With our surfactant model we studied the stability of non-ionic micelles at extremes of temperature, capturing a window of thermal stability with destabilization of the micelles at both high and low temperatures. We observed changes in structure and solvation of the micelle at low temperatures, with a shift in enthalpy of solvation water providing the driving force for destabilization. Solvation and hydrophobicity are also critical in the folding and stability of proteins. With a modified version of our surfactant model we characterized the folding landscape of a designed sequence which folds to a helical bundle in water. We found two competing folded states which differ by rotation of a helix and trade between hydrophobic packing and solvation of protein's core. Changes in hydrophobic packing can also be involved in the disorder to order transitions that occur upon liganding binding in an allosteric protein, such as the E. Coli biotin ligase/repressor (BirA), in which ligand binding promotes dimerization. We have used atomistic simulations of BirA mutants in collaboration with an experimental group to identify structural changes, accompanied by changes in solvation, at both the dimer interface and ligand binding regions for distal mutations which impact the functionality of BirA.Item Feasibility of in vivo SAXS imaging for detection of Alzheimer's disease(2017) Choi, Mina; Chen, Yu; Badano, Aldo; Bioengineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Small-angle x-ray scattering (SAXS) imaging has been proposed as a technique to characterize and selectively image structures based on electron density structure which allows for discriminating materials based on their scatter cross sections. This dissertation explores the feasibility of SAXS imaging for the detection of Alzheimer's disease (AD) amyloid plaques. The inherent scatter cross sections of amyloid plaque serve as biomarkers in vivo without the need of injected molecular tags. SAXS imaging can also assist in a better understanding of how these biomarkers play a role in Alzheimer’s disease which in turn can lead to the development of more effective disease-modifying therapies. I implement simulations of x-ray transport using Monte Carlo methods for SAXS imaging enabling accurate calculation of radiation dose and image quality in SAXS-computed tomography (CT). I describe SAXS imaging phantoms with tissue-mimicking material and embedded scatter targets as a way of demonstrating the characteristics of SAXS imaging. I also performed a comprehensive study of scattering cross sections of brain tissue from measurements of ex-vivo sections of a wild-type mouse brain and reported generalized cross sections of gray matter, white matter, and corpus callosum obtained and registered by planar SAXS imaging. Finally, I demonstrate the ability of SAXS imaging to locate an amyloid fibril pellet within a brain section. This work contributes to novel application of SAXS imaging for Alzheimer's disease detection and studies its feasibility as an imaging tool for AD biomarkers.Item MODELING LIQUID EVAPORATION AND USING MOLECULAR DYNAMICS SIMULATION TO ESTIMATE DIFFUSION COEFFICIENTS AND RELATIVE SOLVENT DRYING TIMES(2017) Choudhary, Rehan; Klauda, Jeffery B; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In this thesis, the Simultaneous Mass and Energy Evaporation (SM2E) model is presented. This model is based on theoretical expressions for mass and energy transfer and can be used to estimate evaporation rates for pure liquids as well as liquid mixtures at laminar, transition, and turbulent flow conditions. However, due to limited availability of evaporation data, the model has so far only been tested against data for pure liquids and binary mixtures. The model can take evaporative cooling into account. For the case of isothermal evaporation, the model becomes a mass transfer-only model. Also in this thesis, molecular dynamics (MD) simulation is used to estimate gas phase diffusion coefficients based on mean-square displacement methods and results are compared with Chapman-Enksog theory. MD simulation is also used to model evaporation of solvents into air and relative solvent drying times based on simulation are compared with measured values.Item HIGH FIELD OPTICAL NONLINEARITIES IN GASES(2013) Cheng, Yu-Hsiang; MILCHBERG, HOWARD M; Electrical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Optical femtosecond self-channeling in gases, also called femtosecond filamentation, has become an important area of research in high field nonlinear optics. Filamentation occurs when laser light self-focuses in a gas owing to self-induced nonlinearity, and then defocuses in the plasma generated by the self-focused beam. The result of this process repeating itself multiple times is an extended region of plasma formation. Filamentation studies have been motivated by the extremely broad range of applications, especially in air, including pulse compression, supercontinuum generation, broadband high power terahertz pulse generation, discharge triggering and guiding, and remote sensing. Despite the worldwide work in filamentation, the fundamental gas nonlinearities governing self-focusing had never been directly measured in the range of laser intensity up to and including the ionization threshold. This dissertation presents the first such measurements. We absolutely measured the temporal refractive index change of O2, N2, Ar, H2, D2 and N2O caused by highfield ultrashort optical pulses with single-shot supercontinuum spectral interferometry, cleanly separating for the first time the instantaneous electronic and delayed rotational nonlinear response in diatomic gases. We conclusively showed that a recent claim by several European groups that the optical bound electron nonlinearity saturates and goes negative is not correct. Such a phenomenon would preclude the need for plasma to provide the defocusing contribution for filamentation. Our results show that the `standard model of filamentation', where the defocusing is provided by plasma, is correct. Finally, we demonstrated that high repetition rate femtosecond laser pulses filamenting in gases can generate long-lived gas density `holes' which persist on millisecond timescales, long after the plasma has recombined. Gas density decrements up to ~20% have been measured. The density hole refilling is dominated by thermal diffusion. These density holes will affect all other experiments involving nonlinear high repetition-rate laser pulse energy absorption by gases.Item Computational Study of the Structure and Mechanical Properties of the Molecular Crystal RDX(2011) Munday, Lynn Brendan; Solares, Santiago D; Mechanical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Molecular crystals constitute a class of materials commonly used as active pharmaceutical ingredients, energetic and high explosive materials. Like simpler crystalline materials, they possess a repeating lattice structure. However, the complexity of the structure - due to having several entire molecules instead of atoms at each lattice site - significantly complicates the relationship between the crystal structure and mechanical properties. Of particular interest to molecular crystals are the mechanically activated processes initiated by large deformations. These include polymorph transitions, slip deformation, cleavage fracture, or the transition to disordered states. Activation of slip systems is generally the preferred mode of deformation in molecular crystals because the long range order of the crystal and its associated properties are maintained. These processes change the crystal structure and affect the physiological absorption of advanced pharmaceutical ingredients and the decomposition of high explosives. This work used molecular dynamics to study the energetic molecule RDX, C3H6N6O6, as a model molecular crystal that is a commonly used military high explosive. Molecular dynamics is used to determine the crystal response to deformation by determination of elastic constants, polymorph transitions, cleavage properties, and energy barriers to slip. The cleavage and the free surface energy are determined through interface decohesion simulations and the attachment energy method. The energy barriers to slip are determined through the generalized stacking fault (GSF) procedure. To account for the steric contributions and elastic shearing due to the presence of flexible molecules, a modified calculation procedure for the GSF energy is proposed that enables the distinction of elastic shear energy from the energy associated with the interfacial displacement discontinuity at the slip plane. The unstable stacking fault energy from the GSF simulations is compared to the free surface energy to differentiate cleavage and slip planes. The results are found to be largely in agreement with available experimental data.