Chemistry & Biochemistry Theses and Dissertations
Permanent URI for this collectionhttp://hdl.handle.net/1903/2752
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Item TOWARDS FULLY AUTOMATED ENHANCED SAMPLING OF NUCLEATION WITH MACHINE-LEARNING METHODS(2024) Zou, Ziyue; Tiwary, Pratyush; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Molecular dynamics (MD) simulation has become a powerful tool to model complex molecular dynamics in physics, materials science, biology, and many other fields of study as it is advantageous in providing temporal and spatial resolutions. However, phenomena of common research interest are often considered rare events, such as nucleation, protein conformational changes, and ligand binding, which occur on timescales far beyond what brute-force all-atom MD simulations can achieve within practical computer time. This makes MD simulation difficult for studying the thermodynamics and kinetics of rare events. Therefore, it is a common practice to employ enhanced sampling techniques to accelerate the sampling of rare events. Many of these methods require performing dimensionality reduction from atomic coordinates to a low-dimensional representation that captures the key information needed to describe such transitions. To better understand the current challenges in studying crystal nucleation with computer simulations, the goal is to first apply developed dimensionality reduction methods to such systems. Here, I will present two studies on applying different machine learning (ML) methods to the study of crystal nucleation under different conditions, i.e., in vacuum and in solution. I investigated how such meaningful low-dimensional representations, termed reaction coordinates (RCs), were constructed as linear or non-linear combinations of features. Using these representations along with enhanced sampling methods, I achieved robust state-to-state back-and-forth transitions. In particular, I focused on the case of urea molecules, a small molecule composed of 8 atoms, which can be easily sampled and is commonly used in daily practice as fertilizer in agriculture and as a nitrogen source in organic synthesis. I then analyzed my samples and benchmarked them against other experimental and computational studies. Given the challenges in studying crystal nucleation using molecular dynamics simulations, I aim to introduce new methods to facilitate research in this field. In the second half of the dissertation, I focused on presenting novel methods to learn low-dimensional representations directly from atomic coordinates without the aid of a priori known features, utilizing advanced machine learning techniques. To test my methods, I applied them to several representative model systems, including Lennard Jones 7 clusters, alanine dipeptide, and alanine tetrapeptide. The first system is known for its well-documented dynamics in colloidal rearrangements relevant to materials science studies, while the latter two systems represent problems related to conformational changes in biophysical studies. Beyond model systems, I also applied my methods to more complex physical systems in the field of materials science, specifically iron atoms and glycine molecules. Notably, the enhanced sampling method integrated with my approaches successfully sampled robust state-to-state transitions between allotropes of iron and polymorphs of glycine.Item A NON-INVASIVE ELECTROSTATIC GATING METHOD FOR PROBING TWO-DIMENSIONAL ELECTRON SYSTEMS ON PRISTINE, CHEMICALLY-TERMINATED, INTRINSIC SI SURFACES(2021) Robertson, Luke Daniel; Kane, Bruce E; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)We have demonstrated a new and effective method for the non-invasive electrostatic gating of pristine, chemically-terminated, intrinsic Si surfaces. This was achieved using a silicon-on-insulator (SOI) device design in which two chips, an SOI gate chip and a pristine, Si chip, are Van der Waals bonded to one another. In this architecture, all harsh device processing is relegated to a single SOI chip which is host to all of the electrical components, including the ohmic contacts and the electrostatic gates. The pristine Si chip is bonded to the ohmic contacts on the SOI chip, while the electrostatic gates on the SOI chip are separated from the Si surface by vacuum. This novel design allows for the Si chip to remain free of dopants or metals that are traditionally fabricated directly onto the surface, thus enabling the Si chip to retain its native properties and remain compatible with a wide variety of existing surface preparation techniques, including wet chemical processing and dry ultra-high vacuum processing. Using our non-invasive architecture, we were able to electrostatically gate a hydrogen-terminated Si(111) (H-Si(111)) surface. Transport measurements were performed on a global-gate induced two-dimensional electron system (2DES) on the H-Si(111) surface via electrical access through the ohmic contacts, while the depletion gates confined the 2DES to a Van der Pauw geometry. We also extended the reach of our devices to probe -- for the first time -- 2D electron transport on a pristine, intrinsic iodine-terminated Si(111) (I-Si(111)) surface. To date, no other 2D magnetotransport measurements have been realized on I-Si(111) surfaces due in large part to the difficulties surrounding the electrostatic gating of these fragile surfaces. This novel architecture is not without its own set of challenges. In particular, the series contact resistance that arises at the SOI-Si bond edge, especially at low temperatures, is significant. The current injection across a Van der Waals bond is an inherent feature in our architecture due to the placement of the ohmic contacts on the SOI piece. I developed a mathematical framework for understanding this current injection in our devices, and presented device modifications for decreasing the contact resistance.Item Magnetism and superconductivity in topotactically modified transition metal chalcogenides(2020) Wilfong, Brandon Cody; Rodriguez, Efrain E; Paglione, Johnpierre; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Inspired by the structure of the simplest iron-based chalcogenide superconductor, FeSe, the class of tetrahedral transition metal chalcogenides (TTMCs) exhibit interesting chemical and physical properties due to its structure. This structure consists of tetrahedrally coordinated transition metal chalcogenides stacked to form two dimensional layers held together by van der Waals forces. This structure and its associated tetrahedral coordination of transition metal to chalcogenide, square transition metal sublattice, van der Waals layered structure, and d-electron filling at the Fermi level yields interesting properties from superconductivity to frustrated itinerant magnetism. In this dissertation work, we demonstrate that the anti-PbO type FeCh (Ch = S, Se, Te) structure offers a perfect platform for the study of superconductivity in the iron-based system as well as new physics as the class is expanded to different transition metals. Prior to this work, the binaries of the TTMC family was limited to iron, but has been expanded to cobalt. In the cobalt compound, CoSe, superconductivity in the FeSe binary is suppressed and a frustrated spin glass like magnetic state emerges. Beyond the binaries, we have shown that topotactic hydrothermal synthetic routes on the iron chalcogenide system can lead to novel intercalated phases where long range magnetic order can co-exist with superconductivity in the (LiOH)FeSe system. This synthetic scheme also allows the intercalation of organic molecules, specifically ethylenediamine, to form organic-inorganic hybrids which can offer a new avenue for designing heterolayer compounds with complex interlayer interactions and bonding.Item ATOMICALLY PRECISE FABRICATION AND CHARACTERIZATION OF DONOR-BASED QUANTUM DEVICES IN SILICON(2019) Wang, Xiqiao; Silver, Richard M; Appelbaum, Ian; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Atomically precise donor-based quantum devices in silicon are a promising candidate for scalable solid-state quantum computing and analog quantum simulation. This thesis demonstrates success in fabricating state-of-the-art silicon-phosphorus (Si:P) quantum devices with atomic precision. We present critical advances towards fabricating high-fidelity qubit circuitry for scalable quantum information processing that demands unprecedented precision and reproducibility to control and characterize precisely placed donors, electrodes, and the quantum interactions between them. We present an optimized atomically precise fabrication scheme with improved process control strategies to encapsulate scanning tunneling microscope (STM)-patterned devices and technological advancements in device registration and electrical contact formation that drastically increase the yield of atomic-precision fabrication. We present an atomic-scale characterization of monolayer step edges on Si (100) surfaces using spatially resolved scanning tunneling spectroscopy and quantitatively determine the impact of step edge density of states on the local electrostatic environment. Utilizing local band bending corrections, we report a significant band gap narrowing behavior along rebonded SB step edges on a degenerately boron-doped Si substrate. We quantify and control atomic-scale dopant movement and electrical activation in silicon phosphorus (Si:P) monolayers using room-temperature grown locking layers (LL), sputter profiling simulation, and magnetotransport measurements. We explore the impact of LL growth conditions on dopant confinement and show that the dopant segregation length can be suppressed below one Si lattice constant while maintaining good epitaxy. We demonstrate weak-localization measurement as a high-resolution, high-throughput, and non-destructive method in determining the conducting layer thickness in the sub-nanometer thickness regime. Finally, we present atomic-scale control of tunnel coupling using STM-patterned Si:P single electron transistors (SET). We demonstrate the exponential scaling of tunnel coupling down to the atomic limit by utilizing the Si (100) 2×1 surface reconstruction lattice as a natural ruler with atomic-accuracy and varying the number of lattices counts in the tunnel gaps. We analyze resonant tunneling spectroscopy through atomically precise tunnel gaps as we scale the SET islands down to the few-donor quantum dot regime. Finally, by combining single/few-donor quantum dots with atomically defined single electron transistors as charge sensors, we demonstrate single electron charge sensing in few-donor quantum dots and characterize the tunnel coupling between few-donor quantum dots and precision-aligned single electron charge sensors.Item Pressure Tuning the Topology of Quantum Materials(2019) Liu, I-Lin; Paglione, Johnpierre; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Topological materials have attracted great interest in condensed matter physics because of their potential applications for topological quantum computing. Transition metal dichalcogenides are very promising topological materials due to their novel topological properties. T$_d$-MoTe$_2$ has been highlighted as potential topological superconductor and type-II Weyl semimetal with Fermi arcs and Weyl nodes through density functional theory and angle-resolved photoemission spectroscopy studies. Recently, T'-MoTe$_2$ was proposed to support a higher-order topology via first principle calculations. Pressure plays a significant role in fine tuning the ground state between noncentrosymmetric T$_d$-MoTe$_2$ and T'-MoTe$_2$ preserved lattice inversion symmetry. The corresponding topology of their Fermi surfaces are thus associated with the structural transition, superconducting, and the band structure between T'-MoTe$_2$ and T$_d$-MoTe$_2$ under pressure. This dissertation presents an experimental study of Shubnikov-de Haas oscillations, neutron scattering and first-principles calculations, demonstrating how pressure tunes the band structure, superconducting transition temperature and the first-order structural transition in MoTe$_2$. Although results from angle-resolved photoemission spectroscopy and density functional theory have previously caused controversy, this work confirms the presence of nontrivial topology of higher-order topology in T'-MoTe$_2$ via the experimental determination of a nontrivial Berry's phase. Moreover, we discover a novel phase of topological matter, deemed a Topological Interface Network (TIN) that forms from a natural heterostructure of mixed T$_d$ and T' structural phases. This new electron structure exists at the interfaces between the domains of two topological structures. Such a novel state with superconductivity and its transition between breaking and conservation of lattice inversion symmetry raises the possibility of quantum phase transitions between different types of topological superconductors. This natural microstructure can be potentially useful in topological quantum computing.Item Frustrated Magnetism and Electronic Properties of Hollandite Oxide Materials(2017) Larson, Amber M.; Rodriguez, Efrain E; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Microporous transition metal oxides with the hollandite structure type have been prepared by standard solid-state techniques with varying compositions. With a nominal formula of AxM8O16 and a framework of edge and corner-sharing MO6 octahedra, hollandites feature a pseudo-one dimensional tunnel occupied loosely by cation A. The metastability of these open-framework materials, combined with the ability of accommodating a variety of redox-active transition metals leads to unique and indispensable properties. Inherent to the triangular connectivity of the M cations in the hollandite framework, these materials frequently exhibit frustrated magnetic behavior. This thesis demonstrates that it is possible to significantly affect the magnetic and transport properties of these microporous materials through tuning of their chemical compositions. We have shown that it is possible to synthesize polycrystalline and single crystal hollandite materials under ambient conditions utilizing salt flux techniques. Our efforts to characterize the structure-property relationships provide some of the first magnetic structure determinations of these complex frameworks. The interesting behavior of these materials is a result of the interplay between charge, orbital, and spin degrees of freedom. This work shows that the hollandite framework is quite versatile, leading to the real possibility of tuning the material properties to achieve desired effects and opening up many potential applications for these microporous oxides.Item Investigation of Iron-Based and Topological Superconductors via Point-Contact Spectroscopy(2015) Ziemak, Steven Joseph; Paglione, Johnpierre; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)I report results of point-contact spectroscopy (PCS) measurements preformed on a variety of superconductors which are predicted to exhibit unconventional Cooper pairing mechanisms. Point-contact spectra of the iron pnictide BaFe_{1-x}$Pt$_x$As$_2$ are consistent with a two-gap isotropic s-wave model. This conclusion is supported by previously published results from thermal conductivity, angle-resolved photoemission spectroscopy (ARPES), and Raman spectroscopy, which confirm a lack of nodes in the order parameter and the presence of a gap of magnitude 3 meV. Conductivity spectra were also measured for the half-Heusler materials YPtBi and LuPdBi using the soft point contact method. I argue that the repeated observation of a single peak in $dI/dV$ at zero bias is not consistent with a conventional $s$-wave model. Based on attempts to fit my data to the Blonder-Tinkham-Klapwijk theory and comparison to previous experimental and theoretical work, I conclude that my results are most consistent with a model of triplet Cooper pairs and an order parameter with an odd-parity component.Item Structural Changes and the Nature of Superconductivity in Rare-earth Doped CaFe2As2(2014) Drye, Tyler Brunson; Paglione, Johnpierre; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Chemical substitution into iron-pnictide parent compounds (e.g. AFe2<\sub>As2<\sub> where A=Ba, Sr, or Ca) has proven to be an effective means to induce bulk high-temperature superconductivity in these systems. By doping CaFe2<\sub>As2<\sub> with rare-earth lanthanides (La, Ce, Pr, and Nd), we have observed a 47 K superconducting phase coexisting with a lattice distorting “collapse” transition. Both of these effects have important ramifications: the collapse transition occurs when interlayer As atoms form a bond, shrinking the c-axis<\italic> lattice constant and simultaneously quenching the iron magnetic moment. This transition is further explored in context of a similar system, Sr-doped BaNi2<\sub>As2<\sub>. The superconducting phase, given the right combination of conditions, appears with a critical temperature as high as 49 K, but always in a very small volume of the sample (as determined by shielding effects). This has led to interesting theories about the nature of this superconductivity. A recently posited idea of “interfacial superconductivity” has been ruled out by our tests. Additionally, increasing the concentration of rare-earth atoms does not increase the superconducting volume fraction, but, in fact lowers the transition temperature, excluding the hypothesis that rare-earth defects are responsible for the minority superconducting phase. New pressure measurements have shown that the superconducting phase is stabilized when antiferromagnetic order is fully suppressed.Item TAILORING PROPERTIES AND FUNCTIONALITIES OF NANOSTRUCTURES THROUGH COMPOSITIONS, COMPONENTS AND MORPHOLOGIES(2013) WENG, LIN; Ouyang, Min; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The field of nanoscience and nanotechnology has made significant progresses over the last thirty years. Sophisticated nanostructures with tunable properties for novel physics and applications have been successfully fabricated, characterized and underwent practical test. In this thesis, I will focus on our recent efforts to develop new strategies to manipulate the properties of nanostructures. Particularly, three questions have been answered from our perspective, based on the nanomaterials synthesized: (1) How does the composition affect a novel nanostructure? We started from single-molecule precursors to reach nanostructures whose bulk counterparts only exist under extreme conditions. Fe3S and Fe3S2 are used as examples to demonstrate this synthetic strategy. Their potential magnetic properties have been measured, which may lead to interesting findings in astronomy and materials science. (2) How to achieve modularity control at nanoscale by a general bottom-up approach? Starting with reviewing the current status of this field, our recent experimental progresses towards delicate modularity control are presented by abundant novel heteronanostructures. An interesting catalytic mechanism of these nanostructures has also been verified, which involves the interaction between phonons, photons, plasmons, and excitons. (3) What can the morphology difference tell us about the inside of nanostructures? By comparing a series of data from three types of CdSe/CdS core-shell structures, a conclusion has been reached on the CdS growth mechanism on CdSe under different conditions, which also may lead to a solution to the asymmetry problem in the synthesis of CdSe/CdS nanorods. Finally this thesis is concluded by a summary and future outlook.