https://etd.iisc.ac.in/handle/2005/39 2026-04-23T19:44:50Z https://etd.iisc.ac.in/handle/2005/6274 Accurate Prediction of Enhancement Factors for Water Flow Through Boron Nitride Nanotubes Kumar, Shiv Water in nanoconfined spaces, such as nanotubes, exhibit anomalous yet intriguing behaviour compared to bulk water, a better understanding of which can enable us to realize a sustainable future. Nanotubes are atomically thin sheets (e.g., graphene or hexagonal boron nitride) that have been rolled into tubes. Boron nitride nanotubes (BNNTs) have been explored for a wide variety of applications ranging from water desalination to osmotic power harvesting since their prediction and experimental discovery in 1994 and 1995, respectively. However, even after three decades of research, water flow through BNNTs is not fully understood at a fundamental level. In this thesis, we considered several aspects that were not given enough attention in previous studies of nanoconfined flow through BNNTs. For instance, no simulation work has modelled the changes in the partial charge distribution when a flat sheet is rolled into a tube, up to this point. To address this knowledge gap, we employed electronic density functional theory (DFT) calculations to accurately estimate quantum-mechanically derived partial charges on boron (B) and nitrogen (N) atoms in BNNTs of varying lengths and diameters. We observed a spatially varying charge distribution inside both armchair and zigzag nanotubes of finite length. Performing DFT calculations for longer BNNTs is computationally intractable even using state of the art resources. To solve this issue, we performed DFT calculations for shorter BNNTs and devised a charge assignment scheme to predict partial charges for longer BNNTs, thus overcoming the need to perform expensive DFT calculations. Subsequently, we performed molecular dynamics (MD) simulations to calculate enhancement factors (EFs), that quantify the extent to which the Hagen-Poiseuille equation is disobeyed at the nanoscale, for BNNTs of varying lengths and diameters. To elucidate the effects of electrostatic interactions, we used three different kinds of partial charge distributions on B and N atoms in a BNNT: (i) bulk partial charges from pristine hBN sheets (±0.907e, where e is the magnitude of charge on an electron), (ii) accurate partial charges obtained from DFT calculations, and (iii) the typical partial charge on carbon atoms in carbon nanotubes (0.0e). BNNTs with the bulk and zero partial charges exhibited the lowest and the highest flow enhancements, respectively, whereas those with accurate partial charges had intermediate EFs. We also incorporated atomic vibrations into our study and discovered, surprisingly, that these vibrations lead to a reduction in the water flow through BNNTs. Finally, we also investigated the effect of vacancy defects in a BNNT on water flow and observed that a single boron and diboron vacancy defects do not affect water flow if atomic vibrations are considered. Our results demonstrate the combined role of atomic vibrations, electrostatic interactions, and defects in modulating water flow through BNNTs and unravel partially the reasons for ultra-low flow EFs in BNNTs. Overall, we believe that the insights developed in this thesis can aid in the fabrication of tailor-made nanofluidic devices which can be employed for sustainability applications in the upcoming decades. https://etd.iisc.ac.in/handle/2005/6452 Advancements in Nucleic Acid Lateral Flow Assay Agarwal, Priyanka In recent decades, the demand for rapid and precise nucleic acid amplification tests (NAATs) has grown significantly, driven by the need to address pandemics like COVID-19 and diagnose infectious diseases such as tuberculosis and malaria. Paper-based devices offer a practical solution for disease diagnosis, particularly in regions with limited resources or where advanced laboratories are scarce. Lateral flow assays (LFAs), resembling pregnancy test strips, emerge as a feasible detection method due to their rapidity and user-friendliness. While most LFAs are designed to conduct immunoassays, they have also been adapted to detect nucleic acids; such LFAs are referred to as nucleic acid lateral flow assays (NALFAs). NALFAs have proven to be a robust tool for detecting amplified NAAT products using minimal instrumentation. Nonetheless, despite their utility, NALFAs have not gained the same popularity as lateral flow immunoassays, and consequently, their commercial adoption has been limited. This work aims to overcome this gap. To improve mechanistic understanding of NALFA, we developed a mathematical model of NALFA that incorporates its key transport phenomena and chemical reactions. Subsequently, we introduce two key advancements: firstly, a novel strategy that provides very high sensitivity and specificity for nucleic acid detection, and secondly, Hot- NALFA, a method that enables the detection of point mutations. To date, the design of NALFAs has primarily employed a black box approach; most researchers have adopted a few published protocols without knowledge of the factors that affect its perfor- mance. In this work, we recognize multiple factors that affect the performance of NALFAs and provide a mechanistic explanation for them by utilizing a mathematical model. An impor- tant outcome of this work is the understanding that unreacted PCR primers inhibit the signal in NALFA, which necessitates that PCR be run till the end point before utilizing NALFA as a readout method. We also highlight the hook effect that reduces the NALFA signal and prove that this effect necessitates the dilution of amplicons prior to NALFA, as is commonly reported in NALFA protocols. This result has important implications in designing integrated devices that aim to directly couple a PCR reaction to a NALFA, where dilution of amplicons may not be feasible. In practical applications, it is frequently observed that the amplified nucleic acid product must be diluted to produce a detectable signal in NALFA. Two approaches were developed to obvi- ate the requirement for dilution of amplified products before their introduction onto NALFA. This advancement facilitates the direct connection of an amplification reaction with a NALFA. The first approach involves the modification of the sample pad with different chemicals such as EDC-NHS and TEMPO to immobilize streptavidin. The modified sample pad captures the excess of amplicons and unreacted primers. A proof-of-concept is established that TEMPO- EDC-NHS has the potential to immobilize streptavidin covalently on the sample and help elim- inate the need for dilution step. The second approach is centered on diminishing the production of bi-labeled products from PCR, which was achieved by introducing only a fraction of labeled primers, in contrast to the conventional practice of using all labeled primers. Reduction of biotin-labels improve the signal at the test and control line significantly. These findings mark substantial advancement in removing the dilution step in NALFA, enhancing its accessibility and robustness for diverse applications, such as disease diagnostics and beyond. In nucleic acid detection through NALFA, prior amplification of target DNA is necessary, commonly achieved using the polymerase chain reaction (PCR) method. However, coupling PCR products with the prevalent ’Universal NALFA’ designed for the detection of biotin and FITC bi-labelled molecules is problematic due to the inevitable formation of bi-labeled primer dimers. These bi-labeled primer dimers lead to false positive signals, compromising the relia- bility of PCR-NALFA. We introduce a novel approach integrating Linear-After-The-Exponential PCR (LATE-PCR) with Universal NALFA. LATE-PCR, an advanced form of asymmetric PCR, yields high amounts of single-stranded DNA (ssDNA). The process involves generating biotin- labeled ssDNA through LATE-PCR and hybridizing it with a complementary FITC-labelled probe. The resultant bi-labeled product can be accurately detected on a universal NALFA. This novel method effectively mitigates false signals stemming from bi-labeled primer dimers. Unlike traditional approaches, the primer dimers formed in this context are not bi-labeled, con- sequently evading detection on the assay. We compared our method with a CRISPR-based NALFA format. Furthermore, we conduct a comprehensive comparative analysis between our proposed strategy and dCas9-based CRISPR-NALFA system. The objective is to assess the efficacy and performance of our approach in comparison to the CRISPR-NALFA method. This strategy performs equivalent to the CRISPR-dCas9 method. Additionally, we present a stoi- chiometric model of asymmetric PCR, which aids in determining the optimal concentration of primers to be utilized during the amplification process. Point mutations refer to single nucleotide changes in nucleic acid sequences and their detec- tion is crucial for genotypic antimicrobial resistance (AMR) and accurate disease diagnosis. Molecular beacons are widely embraced tools for point mutation detection in PCR-based meth- ods, uniquely capable of differentiating between wild-type and mutant DNA within a specific temperature range. We substituted molecular beacons for linear probes to differentiate wild and mutant DNA on NALFA. However, the molecular beacon exhibited binding affinity to both wild-type and mutant targets at room temperature. Consequently, the test line appeared for both DNA sequences, impairing the accuracy of point mutation detection. We elevated NALFA’s temperature using a custom heating device to overcome this, ensuring precise point mutation detection with molecular beacon specificity. We demonstrated that point mutation can be detected on a universal NALFA without requiring additional enzymes/proteins and with fewer steps than the other existing methods. An additional study involved the manipulation of fluid velocity across the nitrocellulose mem- brane within a NALFA, achieved by altering the geometry of the wicking pad. Generally, it was observed that wider wicking pads (in the case of rectangular shapes) or divergent geometries exhibited higher fluid velocities compared to the conventional size. This thesis showcases technological advancements in NALFAs, enhancing their capabilities, providing deeper insights into their mechanism, and introducing innovative approaches for integrating amplified products and detecting point mutations https://etd.iisc.ac.in/handle/2005/3361 Alternative Mechanisms for Size Control in Synthesis of Nanoparticles - Population Balance Modelling and Experimental Studies Perala, Siva Rama Krishna The extensive growth of nanotechnology has necessitated the development of economical and robust methods for large scale production of nanomaterials. It requires detailed quantitative understanding of lab-scale processes to enable effective scale-up and development of new contacting strategies for their controlled synthesis. In this thesis, attempts are made in both the directions using experimental and modelling approaches for synthesis of different nanoparticles. The two-phase Brust--Schiffrin protocol for the synthesis of gold nanoparticles was investigated first. The mechanism of transfer of reactants from aqueous to organic phase using phase transfer catalyst (PTC) was investigated using the measurement of interfacial tension, viscosity, SLS, SAXS, 1H NMR, DOSY-NMR, and Karl-Fischer titration. The study shows that the reactants are transferred to organic phase through the formation of hydrated complexes between reactants and PTC rather than through the solubilization of reactants in water core of inverse micelles of PTC, proposed recently in the literature. The particle synthesis reactions thus occur in the bulk organic phase. The extensive body of seemingly disparate experimental findings on Brust--Schiffrin protocol were put together next. The emerging picture ruled out both thermodynamic considerations and kinetics based arguments as exemplified by the classical LaMer's mechanism with sequential nucleation growth capping for size control in Brust--Schiffrin protocol. A new model for particle synthesis was developed. The model brought out continued nucleation--growth--capping based size control, an hitherto unknown mechanistic route for the synthesis of monodisperse particles, as the main mechanism. The model not only captured the reported features of the synthesis but also helped to improve the uniformity of the synthesized particles, validated experimentally. The two-step mechanism of Finke--Watzky---first order nucleation from precursor and autocatalytic growth of particles---proposed as an alternative to LaMer model to explain an induction period followed by a sigmoidal decrease in precursor concentration for the synthesis of iridium nanoparticles was investigated next. The mechanism is tested using an equivalent population balance model for its ability to explain the experimentally observed near constant breadth of the evolving size distribution as well. The predictions show that while it captures precursor conversion well, it fails to explain particle synthesis on account of its inability to suppress nucleation. A minimal four-step mechanism with additional steps for nucleation from reduced iridium atoms and their scavenging using particle surface is proposed. The new mechanism when combined with the first or second order nucleation, or classical nucleation with no scavenging of reduced atoms also fails to suppress nucleation. A burst like onset of nuclei formation with homogeneous nucleation and the scavenging of reduced atoms by particles are simultaneously required to explain all the reported features of the synthesis of iridium nanoparticles. A new reactor is proposed for continuous production of CaCO3 nanoparticles in gas-liquid reaction route. The key feature of the new reactor is the control of flow pattern to ensure efficient mixing of reactants. A liquidliquid reaction route for production of CaCO3 nanoparticles is also optimized to produce nanoparticles at high loading. Optimum supersaturation combined with efficient breakup of initial gel-like structure by mechanical agitation and charge control played a crucial role in producing nano sized CaCO3 particles. 2018-04-06T00:00:00Z https://etd.iisc.ac.in/handle/2005/8538 Analysis of breakage and coalescence of drops in agitated liquid-liquid dispersions Das, Parichay Kumar Abstract not available