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Exciton Dynamics Studies from First-Principles Calculations: Radiative Recombination, Exciton-Phonon Interactions, and Ultrafast Exciton Relaxation
Get PDFExcitons are bound electron-hole pairs that dominate the optical response of semi-conductors and insulators, especially in nanoscale and wide bandgap materials where the Coulomb interaction is weakly screened. Excitons can enhance light-matter coupling at certain wavelengths, thus making their host materials candidates for optoelectronic, photovoltaic, and quantum technology devices. For instance, two-dimensional transition metal dichalcogenides have a large and tunable optical response and hold promise for next-generation ultrathin light-emitting diodes. It is remarkable that exciton properties such as the binding energy and radiative lifetime can vary by orders of magnitude in different materials and can be further tuned by material properties like defects and lattice vibrations. Therefore, quantitative studies of exciton interactions and dynamics can advance understanding of the optical response of complex materials and play a role in the design of future devices. Among theoretical studies, numerical approaches based on density functional theory (DFT) can quantitatively address the electronic structure in real materials and their response to external perturbations, enabling accurate calculations of the conductivity and dielectric properties. These first-principle methods, which employ numerical quantum mechanics and use only the atomic structure of the material as input (making no use of empirical parameters) have revolutionized studies of materials and condensed matter physics. Over the last few years, first-principles methods for studies of excitons have focused on the GW-Bathe-Salpeter equation (GW-BSE) method to compute exciton energies and optical absorption spectra. However, going beyond calculations of exciton energetics to address the exciton dynamical processes remains challenging and is an exciting new frontier of first-principles studies.
This thesis develops theory and novel numerical approaches to study exciton radiative and nonradiative interactions from first-principles. For the radiative processes, we demonstrate a systematic derivation of exciton radiative lifetimes in materials ranging from bulk to nanostructures and molecules. The results correctly reproduce the observed power-law temperature dependence of the radiative lifetimes. To benchmark our calculations, we study exciton radiative lifetimes in gas-phase molecules, obtaining excellent agreement between theory and experiment. Our framework is then applied in three different studies. First, we extend the radiative lifetime formula to account for the dependence on light polarization and valley occupation and investigate exciton recombination in two-dimensional transition metal dichalcogenides (2D-TMDs). We show that excitons emit light anisotropically upon recombination when they are in any quantum superposition state of the K and K' inequivalent valleys. When averaged over the emission angle and exciton momentum, our new treatment recovers the temperature-dependent radiative lifetimes derived in early literature. Second, we use the exciton energy and radiative lifetimes to identify the atomic structure of the defects in monolayer hexagonal boron nitride (h-BN). In the study, we narrow down the potential structures to nine candidates and identify the highest-likelihood structure as the VNNB defect, consisting of a nitrogen vacancy plus a carbon replacing boron in h-BN. Finally, we generalize the discussion of isotropic bulk system to accurately compute the exciton radiative lifetimes in bulk uniaxial crystals, focusing on wurtzite GaN. Our computed radiative lifetimes are in very good agreement with experiments at low temperature. We show that taking into account excitonic effect and spin-orbit coupling (to include the exciton fine structure) is essential for computing accurate radiative lifetimes. A model for exciton dissociation into free carriers allows us to compute the radiative lifetimes up to room temperature.
In the study of exciton non-radiative process, we focus on the exciton-phonon (ex-ph)interaction, which plays an important role to understand the dynamics of excitons in materials. We establish and implement a first-principle formalism to compute the ex-ph coupling constants by combining the electron-phonon couplings and the exciton wavefunctions from the GW-BSE approach. Using the computed ex-ph coupling matrix elements, we calculate the ex-ph relaxation times as a function of exciton energy, momentum, temperature, and phonon mode in bulk h-BN. Our calculations reveal the dominant ex-ph coupling with the longitudinal optical (LO) mode and identify the threshold for LO phonon emission with an associated ∼15 fs LO emission characteristic time. In addition, we derive the phonon-assisted photoluminescence(PL) from the ex-ph interaction and correctly reproduce the PL spectrum observed in h-BN at both 8 K and 100 K. Based on our successful study of ex-ph interactions in bulk h-BN, we extend the discussion to materials with strong spin-orbit coupling. We investigate the bright exciton linewidth broadening and PL in monolayer WSe2. The numerical results show an increase of linewidth by 20 meV from 0 K to 250 K as observed in early experiments and identify the main PL peak as a consequence of LA phonon emission while the side band is due to optical phonons. Lastly, we present results from a joint theory-experiment study of the ultrafast exciton dynamics in WSe2. We develop a Boltzmann equation for excitons and employ it to model ultrafast exciton relaxation due to ex-ph processes. The simulation and experiment both show a ~70 fs time delay for the electron intervalley scattering from the K- to the Q-valley due to exciton dynamical effects. We also develop accurate simulations of time-domain angle-resolved photoemission (ARPES) experiments, which are becoming a powerful experimental probe of exciton dynamics in condensed matter. In summary, this thesis work paves the way to quantitative studies of exciton radiative and non-radiative processes, as well as exciton ultrafast dynamics, and quantitative modeling of pump-probe experiments in materials with strongly bound excitons.</p
Streamwise Homogeneous Turbulent Boundary Layers
Get PDFBoundary layers are everywhere and computing direct numerical simulations (DNS) of them is crucial for drag reduction. However, traditional DNS of flat-plate boundary layers are prohibitively expensive. Due to the streamwise inhomogeneity of the boundary layer, simulations of spatially growing boundary layer simulations require long domains and long convergence times. Current methods to overcome streamwise inhomogeneity (and allow for shorter streamwise domains) either suffer from a lack of stationarity or have difficult numerical implementation. The goal of this thesis is to develop and validate a more efficient method for simulating boundary layers that will be both statistically stationary and streamwise homogeneous.
The current methodology is developed and validated for the flat plate, zero pressure gradient, incompressible boundary layer. The Navier-Stokes equations are rescaled by a boundary layer thickness to produce a new set of governing equations that resemble the original Navier-Stokes equations with additional source terms. Streamwise homogeneity and statistical stationarity are verified through non-periodic and periodic simulations, respectively. To test the accuracy of the methodology, a sweep of Reynolds number simulations is conducted in streamwise periodic domains for Reδ*=1460-5650. The global quantities show excellent agreement with established empirical values: the computed shape factor and skin friction coefficient for all cases are within 3% and 1% of empirical values, respectively. Furthermore, to obtain accurate two-point correlations, it is sufficient to have a computational domain of length 14δ99 and width 5δ99, thus, leading to large computational savings by one-to-two orders of magnitude. This translates into increasing the largest possible Reynolds number one could simulate by about a factor of 3.
Thanks to the streamwise homogeneous nature of the simulation results, it is now possible to apply cost-efficient data-driven techniques like spectral proper orthogonal decomposition (SPOD; Towne et al. 2018) to extract turbulent structures. Particular emphasis is place on identifying structures for waves in the inner and outer layers. To interpret these structures, 1D resolvent analysis (McKeon and Sharma 2010) is leveraged. The peak location for the extracted inner wave is captured by traditional resolvent analysis, assuming a parallel flow. However, the peak location for the extracted outer wave differs from that predicted by the classic 1D resolvent analysis by 20%. Recovering the peak location requires including in the resolvent operator the mean wall-normal velocity profile and the streamwise growth of the boundary layer.
This methodology has natural extensions to slowly growing boundary layer flows, including thermal boundary layers, rough wall boundary layers and mild pressure gradient flows.</p
Liquid-Induced Discharge of Polypropylene Microfiber Electret Filters
Get PDFPolymer microfiber electret filters are the technology behind N95 and equivalent type respirators. Understanding how liquids interact with and discharge these filters would allow for the development of non-damaging liquid decontamination protocols. Previous work on liquid/filter interactions has been largely empirical with articles reporting the effect a specific liquid has on the filtration efficiency of a particular filter. This thesis proposes a theoretical model of liquid induced discharge of polymer microfiber electret filters via the ideas of surface wetting and electrical conductivity. This model was tested, and validated, on commercially available polypropylene microfiber electret filters through wetting, thermally stimulated discharge (TSD), and filtration experiments.</p
Eddy Current Damping Stroke Sensor
Get PDFExisting paradigms for stroke diagnosis typically involve computed tomography (CT) or magnetic resonance (MR) imaging to classify ischemic versus hemorrhagic stroke variants, as treatment for these subtypes varies widely. Delays in diagnosis and issues related to transport of unstable patients may worsen neurological status. As such, translational medical devices that accelerate time to treatment in the field or hospital setting have the potential to lower morbidity and mortality in stroke patients. We demonstrated feasibility of rapid and accurate bedside stroke detection using a novel, handheld portable eddy current damping imaging device in laboratory benchtop as well as live human clinical ischemic and hemorrhagic stroke settings. We show that diagnosis of stroke may potentially be reduced from several hours to minutes, with additional spatial localization of intracranial hemorrhage, thereby rapidly guiding time-sensitive medical decisions for clinical intervention such as tissue plasminogen activator (tPA). The sensor additionally detects ischemic and hemorrhagic lesions located deep inside the brain, and its range can be selectively tuned during sensor design and fabrication.</p
Molecular Technologies for Antigen-Based Immunity
Get PDFThe presence and proliferation antigen-specific T cells is a defining characteristic of an adaptive immune response against various disease types (autoimmune, cancer, and infectious). The use of Class I and Class II peptide-major histocompatibility complex (pMHC) reagents to identify such cells, however, is technically difficult and expensive, and it has been challenging to refine synthesis protocols for higher yield and more efficient assembly to accommodate large-scale applications. This achievement would enable high-throughput capture of corresponding T cell receptors (TCR), which may be further used in clinical applications such as adoptive cell transfer therapies. Overcoming this hurdle requires the development and integration of various molecular technologies and analytical methods.
Toward this end, the bulk of my thesis work, covered in Chapter 2, introduces these developments in the context of pMHCs, where the three subunits of each reagent are covalent linked together and expressed as a single protein. These single-chain trimer (SCT) technologies primarily consist of traditional DNA cloning and protein production techniques which have been streamlined for applications requiring output on the scale of 102-103 of reagents. This chapter serves as the foundation for much of the methodology discussed throughout the rest of my thesis, and thus should serve as a reference point. The generated constructs are also functionally validated here, and potential future research directions are outlined.
In Chapter 3, I explore the use of this technology in the context of COVID-19 to enumerate antigen specificity of the CD8+ T cell immune response. Class I SCTs were constructed to present peptides across several SARS-CoV-2 protein domains, using various HLA alleles to match haplotyped participant blood samples. These reagents were then used to capture SARS-CoV-2-specific T cells through flow and nanoparticle cytometry to demonstrate HLA-dependent, domain-dependent immune responses. Identified TCRs were cloned into T cells for confirmation of antigen specificity and functional cytotoxicity.
In Chapters 4 and 5, I explore potential pMHC applications in cancer antigen contexts, covering both tumor-associated and tumor-specific antigens. Through various collaborations across the west coast (UCLA, Parker Institute, Fred Hutchinson Cancer Research Center), I make use of the SCT platform to showcase new assays to discover and rank key tumor targets (Chapter 4). Finally, Chapter 5 is a reproduction of our lab’s published work concerning identification of antigen-specific CD8+ T cells from melanoma cancer patients.
In summary, the adaptation of SCTs in a high-throughput format allows for the rapid enumeration of antigen-specific T-cell receptor sequences. As demonstrated in the contexts of COVID-19 and cancer, this SCT platform enables subsequent downstream applications, such as single-cell, antigen-specific immunophenotypic mapping/analysis and target discovery for personalized immunotherapies.</p
3D Architected Battery Electrodes for Exploring Battery Kinetics from Nano to Millimeter
Get PDFThe ability to design a particular geometry of porous electrodes at multiple length scales in a lithium-ion battery can significantly and positively influence battery performance because it enables control over kinetics and trajectories of ion and electron transport. None of the existing methods of engineering electrode structure is capable of creating 3D architected electrodes designed with independent and flexible form-factors at multiscale that are also resilient against cell packaging pressure. In addition, battery kinetics coupled at multiscale from ion transport in an electrolyte to solid electrolyte interphase (SEI) growth has only been studied by numerical simulations, but has never been experimentally explored.
In this thesis, we demonstrate an additive manufacturing technique to engineer porous electrode structure in 3D and explore battery kinetics at multiscale. First, we develop 3D architected carbon electrodes, whose structural factors are independently controlled and whose dimensions span microns to centimeters, using digital light processing and pyrolysis.
These free-standing lattice electrodes are disordered graphitic carbon composed of several stacked graphitic layers that are mechanically robust. Galvanostatic cycling using these architected carbon electrodes showed sloping capacity, typically observed in pyrolyzed carbon electrodes. We discuss the modified rate performance of the 3D architected carbon electrodes in the framework of ion transport kinetics in the electrode vs. electrolyte and overpotential, enabled by controlling structural factors of battery electrodes, including porosity, surface morphology, electrode thickness, and beam diameter, whose length scales range from nano to millimeter.
We then explore battery kinetics associated with SEI using deterministic, mechanically resilient, and thick 3D architected carbon electrodes, which allow us to study the formation, structure-resistance relationship, and position-dependent growth of SEI by combining the newly developed in operando DC-based technique and post-characterization using secondary ion mass spectroscopy. The amount of Li in SEI agrees with capacity losses, and the amount of F in SEI showed a strong linear correlation with SEI resistance evolutions. The position-dependent SEI growth was experimentally explored; the Li amount in SEI along the electrode thickness agrees with the simulation results in prior work, but the F amount in SEI showed the opposite tendency, suggesting modeling of multilayer SEI is necessary to predict precisely battery aging especially for thick electrodes. Our work demonstrates the use of 3D architected electrodes as a model system to explore multiscale kinetics in Li-ion batteries.</p
CDRxAb: Antibody Small-Molecule Conjugates with Computationally Designed Target-Binding Synergy
Get PDFAntibody-drug conjugates (ADCs), or chimeric modalities in general, combine the advantages and offset the flaws of their constituent parts to achieve a broader target space than traditional approaches of pharmaceutical development. My project combines the concept of ADCs with the full atomic simulation capability of computational protein design to define a new class of molecular recognition agents: CDR-extended antibodies, abbreviated as CDRxAbs. A CDRxAb incorporates a small-molecule binding event into de novo designed antibody/target interactions, creating antibody small-molecule conjugates that bind tighter against the target of the small molecule than the small molecule itself. In a proof-of-concept study using monomeric streptavidin/biotin pairs at either a nanomolar or micromolar-level affinity, nanobody-biotin conjugates were efficiently designed to exhibit >20-fold affinity improvement against the model protein targets, with stepwise optimization of binding kinetics and the overall stability. A yeast display-based workflow was subsequently developed to further improve the off rate of the best designed conjugate by another 6 folds. By fully incorporating the chemical space of immunoglobulins into the optimization of small molecule binding events, the workflow explored in this work could be potentially used as a generalizable new method to optimize small molecule-based therapeutics, by exploring a previously uncharted chemical space and the related target space. Chapter 1 reviews background information to justify the proposed CDRxAb molecular construct. Chapter 2 documents the detailed computational design process that generated the 10 conjugates, of which the characterization and discussion are elaborated in Chapter 3. Appendix I documents a slightly related ongoing work that uses computational design to improve existing antibody therapeutics.</p
Black Holes and Entanglement Entropy
Get PDFWe study the deformation of the thermofield-double (TFD) under evolution by a double-traced operator by computing its entanglement entropy. After saturation, the entanglement change leads to the temperature change. In Jackiw-Teitelboim gravity, the new temperature can be computed independently from two-point function by considering the Schwarzian modes. We will also derive the entanglement entropy from the Casimir associated with the SL(2,R) symmetry. From AdS/CFT correspondence, where TFD is dual to a two-sided black hole, such deformations correspond to the coherent shrinking or expansion of the black hole.
Next, we compute the entanglement entropy after coupling a system to the bath perturbatively as a function of κ, the system-bath coupling. At very early times where the entanglement entropy is a logarithmic function of time, the leading contribution is due to the terms of order 2s in the coupling where s is the number of replicas. In the middle time, the entanglement goes linear as a function of time. Assuming saturation at a later time, we will study the effect of an external perturbation to the entropy at an early time where it is related to the OTOCs. A major simplification appears when the system saturates the chaos bound.</p
Magmatic Differentiation in Arc and Mid Ocean Ridge Settings
Get PDFThe compositional variation of igneous rocks and construction of Earth's crust is the result of magmatic differentiation -- crystallization, melting, and assimilation mechanisms that
cause the composition of magmas to change over time. This thesis investigates magma generation and evolution at both convergent and divergent plate boundaries. The resulting magmatic arcs and mid-ocean ridges create the vast majority of Earth's crust, though the details of crustal construction and the specific processes that generate the observed magmatic and volcanic products are complex. Accordingly, this work uses the geochemical signatures encoded in rocks and minerals to explain magmatic differentiation histories in multiple tectonic settings.
Here, I present five main studies that utilize field and textural observations, geochemical analyses, and computational modeling to investigate the compositional structure of the crust beneath magmatic arcs and mid-ocean ridges. In addition, this work explores the pyroclastic and sedimentary products dispersed by magmatically heated hydrothermal fluids in submarine environments. Chapters 2 and 3 investigate the crystallization histories of mafic intrusions in the eastern-central Sierra Nevada batholith paleo-continental arc, California. This work has implications for the compositional and temporal generation of both mafic and evolved magmas throughout the batholith and in other continental arcs. Chapters 4 and 5 explore records of submarine volcanic ash deposits associated with explosive mid-ocean ridge eruptions from the East Pacific Rise and Pacific-Antarctic Ridge, as well as the effects that sea level change has on melting of the mantle, eruption styles, and the compositional evolution of mid-ocean ridge magmas. Chapter 6 examines the mineral hosting of rare earth elements (REEs) in the Wadi Karim banded iron formation, and the implications of element mobility on interpretations based on REE abundances.</p
Hunting for Fast Radio Transients in the Local Universe and Pulsars Toward the Center of the Milky Way Galaxy
Get PDFThe dynamic radio sky is full of fast radio transients that produce emission on timescales ranging from nanoseconds to seconds. The two classes of fast radio transients studied in this thesis are pulsars and fast radio bursts (FRBs). Pulsars are highly magnetized, rotating neutron stars that produce pulses of electromagnetic radiation as a result of charged particles being accelerated along magnetic field lines. FRBs are short-duration, transient radio pulses with extragalactic origins, but the nature of their progenitors still remains a mystery. The extremely high brightness temperatures of pulsars and FRBs indicate that their emission is produced by coherent radiation mechanisms.
Although the focus of this thesis is centered around pulsars and FRBs, I cover a broad range of topics, including (1) the emission behavior of radio magnetars, rotation-powered radio pulsars, and repeating FRBs, (2) the development of novel, state-of-the-art algorithms for pulsar searching, (3) a new, sensitive search for pulsars toward the Galactic Center (GC), and (4) the X-ray behavior of wind-accreting high-mass X-ray binaries (HMXBs) displaying superorbital modulation. In this thesis, I explore the emission properties of several radio magnetars in the radio and X-ray bands using the NASA Deep Space Network (DSN) radio telescopes and the NICER X-ray telescope. I also study the emission behavior of two repeating FRBs, FRB 121102 and FRB 180916.J0158+65 (also referred to as FRB 20121102A and FRB 20180916B, respectively), at high radio frequencies using the DSN's 70 m radio telescopes. In particular, I show that there is a phenomenological link between the radio pulses observed from radio magnetars and repeating FRB sources. I also describe two novel pulsar search algorithms that have been developed to coherently search for accelerated pulsars in Keplerian orbits. In addition, I describe a new, ongoing survey of the GC region that is being carried out at high radio frequencies to search for GC pulsars using the 70 m DSN radio telescope (DSS-43) in Tidbinbilla, Australia. Lastly, I present the results of a pulsar timing analysis of the wind-accreting HMXB, IGR J16493-4348, which displays a 20.06 day superorbital period of unknown origin.</p