DSpace@RPI (Rensselaer Polytechnic Institute)
Not a member yet
6809 research outputs found
Sort by
Optical spectroscopy and photocurrent measurements of 2d materials
No full textAugust 2024School of EngineeringLight-matter interactions in two-dimensional (2D) layered materials have attracted immense interest in the last few years, especially after the discovery of Graphene. These novel class of materials find their application in various optoelectronic devices which were earlier dominated by Silicon as an active material. However, to harness the full potential of these materials, it is necessary to be able to manipulate light- matter interactions so that these materials could be tailored or optimized for different applications and develop metrology tools and knowledge base to rationally design operating device conditions. In this work, I am going to talk about tuning light-matter interactions using these approaches and a Raman spectroscopy based thermometry tool for probing local temperature.This work is divided into four sections. In the first and second part, I am going to discuss electrostatic gating and electrochemical intercalation based modulation of Indium Selenide (InSe), a group iii-vi 2D layered VdW material and in situ observations of intercalation induced changes. In the third part, I am going to discuss Raman spectroscopy based metrology tool to probe heat related effects in graphene based structures. Finally, a chiral perovskite material is demonstrated for spin injection medium in Tungsten Diselenide (WSe2), a well known 2D material largely known for its spin-valley locking effects.Ph
Enzyme driven bacterial detection and decontamination on surfaces
No full textAugust 2024School of EngineeringBacteria are ubiquitous in our everyday lives and are often transmitted through surfaces. The most common places for bacterial transmission are crowded places, such as public transportation, classrooms, healthcare facilities, and food production establishments. The transmission of bacteria on these surfaces often lead to infections and sicknesses, especially in hospitals. Additionally, bacteria have been shown to remain on surfaces after several hours making transmission an even greater concern. The most common method of disinfection is through the use of chemicals. However, these chemicals are often toxic and corrosive to surfaces. As a result, enzymatic decontamination methods have been developed to provide a safe alternative to harsh chemicals. In the first part of this thesis, a surface coating was fabricated to contain an embedded enzyme using a one-step reaction. We analyzed the thermostability, reusability, and activity of these coatings. Additionally, we showed that these coatings contained a broad antibacterial and antiviral spectrum that efficiently kill pathogens in a short period of time. The other part of this thesis will be to deepen our understanding of pathogens on surfaces, where bacterial detection systems utilizing the cell binding domain (CBD) of cell lytic enzymes, which are capable of targeting bacteria with high specificity, were established. We first identified and characterized various CBDs for targeting Gram-positive bacteria. We then applied these CBDs for bacterial detection by coupling them with enzymes such as horseradish peroxidase (HRP) for signal amplification giving a limit of detection (LOD) of 105-106 cells/mL. We also coupled these CBDs with copolymeric dyes for enhanced fluorescent on the surface of the cell compared to monomeric dyes.
Furthermore, we utilized CBDs and a split fluorescent protein (FP) system for multimerization of CBD on the surface of cells for bacterial detection. Here, we designed a self-complementing FP complex where a multimeric FP chain fused with specific CBDs ((FP-CBD)n) is assembled inside the cell resulting in a daisy chained fusion protein with 1, 3, or 7 CBDs linked together. We demonstrated the functionality of these ((FP-CBD)n) for bacterial detection through complexing with HRP and saw a degree of amplification increasing as a function of FP length, reaching a limit of detection (LOD) of 103 cells/droplet within 15 min on a polystyrene surface.
Lastly, we expanded the use of ((FP-CBD)n) proteins by combining with a zymogen-based cascade for signal amplification. These ((FP-CBD)n) proteins were conjugated with an initiator enzyme, enteropeptidase, which activates a cascade consisting of trypsinogen and chymotrypsinogen. With this combined CBD-zymogen based system, a LOD of 105 cells/mL could be achieved. Overall, experiments in this thesis provided us with valuable methods for the detection and disinfection of pathogens on surfaces.Ph
Low-power time-to-digital converters for high-precision measurement
No full textDecember 2023Time-to-digital converters (TDCs), which converts time delays into digital signals, have garnered significant interest for their diverse applications in fields such as high-energy nuclear physics, time-of-flight (ToF) sensors, time-domain analog-to-digital converters (TD-ADCs), and all-digital phase-locked loops (ADPLLs). The performance of a TDC is primarily measured by its resolution, range, sampling rate, and power consumption. To simultaneously achieve a fine resolution and a long range, or a high dynamic range, in an area and power efficient manner, hierarchical architectures with the potential to combine the advantages of several different approaches has been studied. This thesis investigated three different hierarchical designs implemented in technologies ranging from 350nm CMOS to 45nm SOI, each suitable for its specific applications. This work first presents a hierarchical ADC-assisted TDC with reconfigurable resolution. The reconfigurable resolution and range are achieved by adjusting reference currents in the time-to-voltage converter (TVC) and the reference voltages in the ADC. The proposed resolution-reconfigurable approach combined with a two-step hierarchical architecture can be employed in a wide range of applications with different spatial range and resolution requirements. Fabricated using a 350nm CMOS process with a core area of 0.15mm², prototype chips yielded a resolution of 39ps with a 100MHz reference clock or 78ps with a 50MHz reference clock. In both cases, the measurement rate is 384kS/s while consuming less than 6.7mW from a 3.3V supply. Secondly, a multi-channel 4-tier TDC design combining gated-ring oscillators (GRO) coarse measurement stage, time amplifier, and 2D vernier fine measurement stage designed an simulated in 90nm SOI SiPh process. A dual-counter correction scheme is proposed to address the parallel-output-misalignment (POM) error in multi-phase clock based TDCs. The finer two tiers employ time amplifiers and 2D vernier lines to measure the residual signal, achieving a sub-gate-delay resolution while keeping a high conversion rate. Post-layout extracted simulation on the proposed TDC design shows a 2ps LSB size, while consuming 5.11-mW per additional channel from a 1.2V supply when operating at the maximum sampling rate of 500MS/s. Compared to state-of-the-art TDC designs, the proposed architecture shows an improvement in quantization step, conversion time, and dynamic range. The idea of multiphase-clock-based multichannel coarse measurement is further explored in a DLL-based TDC implemented in 45nm SOI technology. Lastly, a hierarchical pipeline TDC in 45nm SOI technology, optimized for high-speed and high-precision applications, is introduced. A novel analytical model for the cross-coupled time amplifier (TA) in the pipeline TDC is formulated. Based on this model, a gain calibration scheme is proposed. To validate the time amplifier analysis, a hierarchical TDC with pipeline fine measurement is designed and fabricated in 45nm SOI technology. With look-up table correction, measurement results of the TDC demonstrate a resolution of 0.95ps, a range of 0.8ns, and a DNL/INL range of 2.14 LSB and 2.13 LSB, respectively. The device operates on 8.851mW from a 1.0V supply at a sampling rate of 120MHz, and it achieves a maximum sampling rate of at least 250MHz, highlighting its capability to simultaneously deliver high speed and fine resolution.Ph
From grief to healing: interweaving sensory experiences in 'and then there was quiet'
No full textMay 2024School of Humanities, Arts, and Social SciencesABSTRACTThis dissertation provides an in-depth exploration and theoretical analysis of the multimedia installation And Then There Was Quiet created in collaboration with choreographer Carson Reiners and videographer Marek Vesely during the 2020 pandemic. This immersive work, featuring multi-projection video and multi-channel sound, embodies an intricate interplay of sound design, visual narratives, and spatial organization to facilitate a transformative audience experience.
Central to this dissertation lies the engagement with diverse theoretical frameworks, employed to scrutinize the unique characteristics of the multimedia installation. These theories showcase how sound design can transcend its conventional role to become a vital element in the narrative, intertwining the soundtrack and sound design into an expressive dialogue with the visual narratives. Furthermore, drawing from the theories Thierry of De Mey and others, the influence of choreographed movement visuals in articulating the story is explored, adding layers of meaning and depth to the audience's experience. The dissertation delves into the nuanced interplay of sound, visuals, and space in the multimedia installation, proposing this convergence as a medium for a transformative experience of healing through grief. Conclusively, guided by the insights of theorists like Tito Rivas and Tim Ingold, the potential variations in perception awareness facilitated by the spatial organization of the work are explicated. This analysis underscores the multimedia installation's innovative use of space, which influences the viewer's perception and experience. The implications of these findings extend beyond the individual work, demonstrating how the interactions between media and collaboration inform and enrich creative practice, and offering insights into art creation under unique circumstances such as a global pandemic.Ph
Intergranular attack of low carbon steel in molten aluminum chloride
No full textMay 2024School of EngineeringAISI 1018 carbon steel exhibits intergranular attack in molten aluminum chloride in actual engineering applications. To elucidate a corrosion mechanism explaining such a phenomenon,
corrosion exposure tests have been conducted to investigate the effects of materials processing,
chemical composition, and molten salt cations on the severity of corrosion. To that end, pure iron,
A106, and AISI 1018 carbon steel have been exposed to pure AlCl3 and AlCl3-FeCl3 melts in
normalized and as-received conditions. Additional tests have been done with longer corrosion
durations and with molten AlCl3-FeCl2 salt. A novel corrosion quantification methodology is
employed. Intergranular corrosion is observed in both 1018 and A106 carbon steels in all the salts
whereas pure iron only shows pitting. Normalization and cold work in the as-received condition
have varying effects on the corrosion depths of pure iron, 1018 and A106 carbon steels. In 1018,
relative to exposure to pure AlCl3, addition of FeCl3 significantly accelerates the corrosion rate
whereas addition of FeCl2 substantially modifies the corrosion morphology. The grain boundary
microchemistry of 1018 carbon steel is examined with in-situ fracture Auger spectroscopy where
molybdenum and carbon segregation are found, and a mechanism is proposed to explain the
present corrosion phenomenon.DEn
Kinetic simulations of relativistic vlasov systems
No full textAugust 2024School of ScienceThis thesis presents high-order discretization techniques for the relativistic continuum kineticVlasov equation in up to 6D phase space. These algorithms have been implemented in the
highly parallel code LOKI. The details of its discretization and implementation are described,
and vigorous verification is carried out using the method of manufactured solutions. The
topic then moves to Landau damping and the dispersion relation of Langmuir waves. A new
technique is introduced to evaluate and solve the dispersion relation which allows for any
equilibrium function and the inclusion of relativistic effects. These results are then compared
to results from LOKI simulations. LOKI is a highly parallel code used to approximate the continuum kinetic Vlasovequation and the associated electrostatic Vlasov-Poisson system and electromagnetic Vlasov-Maxwell system. It is made high order accurate by utilizing up to sixth-order accurate
explicit Runge Kutta (RK) schemes for time integration, and the minimally dissipative
upwinding scheme BWENO to approximate the phase space derivatives. In previous literature, the details of LOKI’s initial implementation in 2+2D (two spatial and two velocity
dimensions) without dissipation and no Maxwell were outlined. In the course of this thesis,
LOKI has been extended to include a variety of dimensional configurations, up to 3+3D,
and the ability to simulate relativistic effects were included. The implementation of such in
3+3D with sixth order accuracy is described in detail for both Vlasov-Poisson and Vlasov-Maxwell. Each physical system is then verified thoroughly for all dimensional configurations
(1+1D, 1+2D, 1+3D, 2+2D, 2+3D, and 3+3D) with and without relativistic effects using
the method of manufactured solutions. These checks show the code is achieving both fourth- and sixth-order convergence in numerical errors for all configurations. Although manufactured solutions are useful for catching coding errors, verification ofnumerical models using theoretical results is required for thorough confidence in simulation
accuracy. An analytical method which evaluates the Langmuir wave dispersion relation to
machine precision is introduced, which suggests integrating directly over the Landau contour, with the inclusion of a residue around the pole in the complex plane when necessary.
This method allows for more general equilibrium functions, and the easy introduction of
relativistic effects into the formulation. The standard one dimensional non-relativistic dispersion relation found with this new method using a Maxwell-Boltzmann distribution function is compared to the exact solution, as well as previous analytical solutions for the same,
and shows excellent agreement to machine precision (approximately 16 digits of accuracy).
Results are then computed in 1D, 2D, and 3D for both the relativistic and non-relativistic
Maxwell-Boltzmann equilibrium function, as well as for the relativistic Maxwell-Juttner equilibrium, and verified through comparison with Landau damping results of the electric field
of kinetic simulations from LOKI. Using these analytical results, observations are made of
Landau damping in highly relativistic plasmas with the Vlasov-Poisson model.Ph
Elucidation of signaling pathways involving magnetic field-driven remote cellular control
No full textDecember 2023School of EngineeringExternal and remote control of signal transduction pathways can provide both on-demand and spatial control over cell function. This control can be used to address diseases where aberrant signaling occurs, including cancer, cardiovascular disorders, and neurodegeneration. Several methods to control signaling pathways have been developed, including chemogenetics, optogenetics, and more recently, magnetogenetics, that when coupled with recent advances in gene delivery offer potentially new therapeutic routes to address these diseases. Each of which aims to control cellular function by applying a different external stimuli, drugs, light, and magnetic fields, respectively. Chemogenetics uses designer small molecule drugs specifically to target genetically engineered cell receptors that regulate cellular pathways when activated, such as neuronal firing and inhibition. However, because chemogenetics requires a pharmacologic intervention, it is strongly dependent on drug pharmacokinetics and pharmacodynamics in vivo. Optogenetics uses specific wavelengths of light to activate light-sensitive ion channels. Unfortunately, invasive probes are required in vivo due to the poor penetration depth of light.
Magnetogenetics was developed to circumvent these issues, providing spatial and temporal control over cell function while being truly remote due to the ability of magnetic fields to freely permeate through tissue. This was accomplished by tethering iron nanoparticles from endogenous ferritin to cation transmembrane channels (TRPV1 in particular). The ferritin acts as the target for the magnetic fields, resulting in channel gating, ion flux, and downstream effects.
The work presented here aims to expand upon the magnetogenetics field by offering insights into the mechanism governing magnetogenetics. Initial hypotheses on how ferritin transduces magnetic fields into channel gating included thermal and mechanical effects, however, these theories have largely been disproven. Recent results have hypothesized a chemical mechanism involving production of reactive oxygen species (ROS) around ferritin. Here, the mechanism is further explored and elucidated. Magnetogenetic response was found to be highly dependent on field properties such as field strength and frequency. Use of several inhibitors explored the complex network of cellular pathways involved in magnetogenetics activation. Furthermore, a bioengineering approach was used to confirm the crucial role of ROS in platform stimulation and the necessity for TRPV1-ferritin tethering. Together, these results provide an important step in evolving the field of magnetogenetics to a level on par with predecessor field.Ph
Moss and air: biofiltration and moss as a fresh air generator
No full textAugust 2024School of ArchitectureThis thesis addresses both indoor air quality (IAQ), the top environmental risk to human health, and building energy consumption, a principal driver of climate change. Plants can enhance both IAQ and building energy efficiency. Botanical biofilters host microbial populations that remediate a diversity of contaminants while plant photosynthesis may provide CO2-O2 balance of occupant respiration, enabling continuous clean air recirculation and HVAC energy savings – by reducing the supply and conditioning of outdoor air. In other words, beyond hosting microbial biofiltration, plants may be complete fresh air generators. Vascular botanical biofilters (state of the art) are a promising nascent technology; facing challenges regarding system size, grow light energy, CO2 assimilation, airflow, and root-zone drying, which can inhibit microbial bioremediation. Vascular biofilters show high VOC removal but insufficient evidence for photosynthetic CO2 assimilation of occupant respiration. Thus, current systems effectively remove VOCs but do not fully regenerate fresh air. This dissertation argues that moss biofiltration is a feasible alternative avenue towards complete indoor fresh air generation. We posit that moss – with its fractal structure, high surface area, porosity, water content, robust microbiotic consortia, mat-like morphology, and high chloroplast efficiency – can facilitate uniform air flux, rapid contaminant mass transfer, and high photosynthetic carbon assimilation in a compact and energy-efficient package. In addition to its (known) filtration efficacy, we hypothesize that moss photosynthesis occurs rapidly under high air flux and CO2 concentrations, potentially allowing for complete indoor air recirculation and resolution of energy-IAQ tradeoffs. We deploy three distinct methodologies. (1) A mini meta-analysis synthesizes botanical biofiltration studies into normalized metrics, such as filtration efficiency and clean air delivery rate, enabling quantitative comparisons with state-of-the-art systems. (2) Empirical experiments on moss biofilter prototypes investigate carbon assimilation at high air flux and CO2 concentrations, VOC and PM filter efficiencies, and evapotranspiration (moss’s cooling effect). Additionally, in vitro tests characterize dose-response inhibition of fungal and microbial activity by moss metabolites. (3) We present a parametric modeling framework that co-simulates air mass balance and building energy for arbitrary biofilter and building systems, enabling estimation of air quality and total energy consumption. We run a suite of modeling studies (over 30,000 individual variants) investigating the impact of climate, occupancy, metabolic rate, HVAC system types, biofiltration systems, future weather, and other parameters. (1) The statistical review of botanical biofiltration research highlights the field's incipient nature. Besides important parameters like airflow rate, the study itself significantly predicts biofilter efficiency, indicating varied experimental parameters and biofilter systems can yield diverse results. (2) Although typically observed to be low-light slow-growers, we observed that under high airflow (approx. > 3 m/s), light (PPFD > 250 µmol/m2/s) and CO2 (approx. > 1000 ppm), moss biofilter photosynthesis outperforms vascular systems (CADRCO2 > 0.5 m3air/m2moss/hr), in a package about ten times smaller (per person) and using a third of the light energy. Thus, moss photosynthesis may typically be limited by environmental parameters, not intrinsic physiology. (3) Our simulations reveal that biofiltration in general surpasses conventional methods for improving IAQ such as (abiotic) filtration and outdoor air dilution; and, in some cases, can resolve energy-IAQ tradeoffs. The indoor-to-outdoor temperature differential is the best predictor of energy savings, with extreme climates benefiting most from indoor air recirculation. Overall and in a detailed multizone energy-air-quality model, moss systems outperform vascular biofilters on net energy use intensity, air quality, and return on investment metrics. We thus provide some evidence that moss is an attractive platform for achieving complete and regenerative indoor air recirculation.Ph
Kinetic stability of 11s globulin storage protein in tree nuts: implications for allergenicity
No full textMay 2024School of ScienceKinetically stable proteins (KSPs) are proteins that display a high activation energy for unfolding that traps them in a specific conformation, which allows them to resist degradation. Kinetic stability (KS) allows proteins to play important biological roles, as it helps them resist harsh in vivo conditions, allows them to persist in high abundance for long periods of time, it protects them from aggregation, and may regulate the timing of physiological events. Because KSPs are known to be more resistant to proteolytic degradation they have been linked to food intolerance and allergy. One of the essential non-animal protein sources present in most human diets involves legumes and nuts, and among them the main proteins are seed storage proteins (SSPs). One of the most abundant SSPs is the 11S globulin, an important nutrient storage protein involved in plant growth and germination, that is a major allergen. Since it is well-known that many allergenic proteins are hyperstable and degradation-resistant, this novel study probes the KS of the 11S globulin SSPs from the nine most common tree nuts (TN), one of the main allergenic food groups in the world. Furthermore, the study explores a possible correlation between KS and allergenicity within this important protein family. This study involved the grinding and preparation of whole-nut, crude protein extracts followed by analysis through various gel electrophoresis methods that allow the assessment of KS without the need for protein purification. We used polyacrylamide gel electrophoresis (PAGE) to assess the target 11S globulins’ resistance to denaturation by the strong detergent sodium dodecyl sulfate (SDS) and the weak detergent sodium lauroyl sarcosinate (SAR) as a proxy for different levels of KS. These two detergents are combined at different ratios in a method known as SDS-SAR-PAGE co-mixing to visualize the denaturation transition of proteins of interest as they unfold due to the increasing SDS:SAR ratio. The resulting KS assessments were then used to categorize each TN 11S globulin into groups of high, medium, or low KS. Finally, the experimental data was correlated with allergy prevalence statistics found in the scientific literature for each TN. Specifically, we used studies which analyzed individuals allergic to each individual TN, and determined which of them recognized the 11S globulin allergen. These studies made it possible to determine the intrinsic and relevant importance of the 11S globulin in eliciting allergic reactions across patients allergic to each TN, when compared to other SSPs. By correlating the extent of experimentally determined KS with allergy prevalence statistics for the different TN, we observed an encouraging correlation between the two factors, suggesting KS may have a significant role in developing TN allergy. The results from this study suggest that within the protein inherent factors that are known to determine the allergenic potential in food, the stability of a protein, specifically its KS, is an important factor that could contribute towards their allergenicity. Hence, further quantifying the KS of 11S globulins in different species could help probe the broader relevance of the results from this study. Furthermore, expanding research efforts focused on KS and its role in allergy across other proteins beyond SSPs could be an important step forward in advancing protein allergy research at the molecular level.
Finally, the implications of these results not only encompass the possible role of protein KS in allergenicity and protein digestibility, but also its possible role in seed germination, survival, and vigor. 11S globulins are known to perform a variety of germination and biodefense roles that may ensure survival. Our results suggest that 11S globulins may have developed varied levels of KS to maintain these non-storage roles. A promising future research direction stemming from the efforts and results of this study include exploring the link between protein KS and different plant biodefense and survival roles.Ph
Cell chirality based mathematical models for left-right asymmetric morphogenesis
No full textMay 2024School of EngineeringLeft-Right (LR) asymmetry is ubiquitous in all bilateral animals, including humans. Proper LR asymmetric morphogenesis is crucial for the structure and function of several internal organs. Disruption of proper LR asymmetry is associated with sever, and often fatal, congenital defects of major asymmetric organs such as the heart. Several hypotheses for the origin of LR asymmetric development are being actively investigated – ranging from cytoskeletal asymmetries to global LR asymmetries in morphogen patterning. Recent evidence suggests that inherent asymmetries in the dynamics of actin polymerization leads to the generation of torque and rotation at the cellular level – termed cell chirality. Cell chirality has also been observed in the biased migration, and alignment of cells both in vitro and in vivo. However, how actin driven chiral rotation mechanically leads to the asymmetric migration of multicellular collectives, and subsequently to the asymmetric morphogenesis of organs, such as heart-looping, is poorly understood. This is due to the inherent difficulties of measuring forces generated by individual rotating cells and measuring the contributions of such to asymmetric morphogenesis. This dissertation attempts to fill this gap by using a cell vertex based biomechanical computational model (CVM).We propose a model of chiral tissues wherein polygonal cells within a gapless array rotate about their area centroid – and show that such a model accurately recapitulates the biased cell migrations observed within micropatterns, as well as the biased elongation and alignment of these cells relative to the micropattern boundaries. This chiral morphogenesis is shown to be regulated by geometric properties of the model which modulates the rigidity of the tissue – such that more fluid-like tissues undergo more drastic chiral morphogenesis. We reveal a novel potential role of chirality in tissue segregation using models of micropatterned tissues that contain clockwise (CW) and counterclockwise (CCW) cells in randomly distributed 50:50 racemic mixture – such that CW
xiv
and CCW cells separate. This process is also shown to be regulated by tissue fluidity, with more fluid tissues demonstrating stronger segregation behavior. The segregation is shown to be driven by the instability of heterogenous edges shared between CW and CCW cells. Finally, we show that CW rotating cells, within the ventral surface of a 2.5D cylindrical CVM of the embryonic heart-tube drives chiral heart-looping. This looping only requires chirality in the right-ventral myocardium, as observed in vivo. The looping direction is dependent on the direction of chiral rotations of the cells, and the strength of looping is dependent on the strength of the torque forces, and the ratio of CW:CCW cells within the ventral myocardium. The CVM also recapitulates the biased alignment of cardiac cells within the model myocardium, in the same direction as in vivo chick cardiomyocytes. This alignment is also mimicked by the colonies made up of a cell’s immediate neighbors.
Overall, our efforts show for the first time that chiral rotation of individual cells, derived from chiral actin dynamics, is sufficient to recapitulate the chiral morphogenesis of tissues on micropatterns, and the chiral looping of the heart-tube. Additionally, we reveal a novel potential role of chiral rotation in the segregation of heterogenous racemic tissues. This work should inspire several theoretical and experimental investigations to reveal further mechanical and biological mechanisms of LR asymmetry breaking.Ph