Chemical Engineering (CE)https://etd.iisc.ac.in/handle/2005/392024-03-29T12:21:53Z2024-03-29T12:21:53ZAccurate Prediction of Enhancement Factors for Water Flow Through Boron Nitride NanotubesKumar, Shivhttps://etd.iisc.ac.in/handle/2005/62742023-10-31T21:32:58ZAccurate 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.
Advancements in Nucleic Acid Lateral Flow AssayAgarwal, Priyankahttps://etd.iisc.ac.in/handle/2005/64522024-03-22T09:10:23ZAdvancements 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
Alternative Mechanisms for Size Control in Synthesis of Nanoparticles - Population Balance Modelling and Experimental StudiesPerala, Siva Rama Krishnahttps://etd.iisc.ac.in/handle/2005/33612019-09-13T11:11:36Z2018-04-06T00:00:00ZAlternative 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.
2018-04-06T00:00:00ZAnalysis Of Dense Sheared Granular FlowsReddy, Katha Ankihttps://etd.iisc.ac.in/handle/2005/10352020-09-28T05:13:41Z2011-01-27T00:00:00ZAnalysis Of Dense Sheared Granular Flows
Reddy, Katha Anki
A granular material is a collection of discrete, solid particles of macroscopic size dispersed in an interstitial fluid, in which the fluid has an insignificant effect on the particle dynamics. Because they exhibit fascinating properties because of dissipative interactions, due to their importance in geophysical and industrial processes, flows of granular materials have been the focus of large amount of research involving physicists and engineers. A good understanding of the physics of granular materials is desired in order to design efficient processing and handling systems. Granular materials can be heaped like a solid, and can flow like a fluid. Though the two distinct regimes of granular flows are well described by kinetic theory (rapid flows) and plasticity theories (quasi-static), the intermediate dense flow regime, where collisional and frictional interactions are important, is not yet described successfully. In this thesis, we examine the applicability of kinetic theory for dense granular flows, the structure and dynamics in sheared inelastic hard disks systems and dynamics of sheared non-spherical particles.
Two complementary simulation techniques, the discrete element (DE) technique for soft particles and the event driven (ED) simulation technique for hard particles, are used to examine the extent to which the dynamics of an unconfined dense granular flow can be well described by a hard particle model when the particle stiffness becomes large. First, we examine the average co-ordination number for the particles in the flow down an inclined plane using the DE technique using both linear and Hertzian contact models. The simulations show that the average co-ordination number decreases below 1 for values of the spring stiffness corresponding to real materials such as sand and glass, even when the angle of inclination is only 1olarger than the angle of repose. The results of the two simulation techniques for the Bagnold coefficients (ratio of stress and square of the strain rate) and the granular temperature (mean square of the fluctuating velocity) are found to be in quantitative agreement. In addition, we also conduct the comparison of the pre-collisional relative velocities of particles in contact. Since momentum is transported primarily by particle contacts in a dense flow, the relative velocity distribution is a sensitive comparison of the dynamics in the two simulation techniques. It is found that the relative velocity distribution in both simulation techniques are well approximated by an exponential distribution for small coefficients of restitution, indicating that the dynamics of a dense granular flow can be adequately described by a hard particle model.
The structure and dynamics of the two-dimensional linear shear flow of inelastic disks at high area fractions are analysed. The event-driven simulation technique is used in the hard-particle limit, where the particles interact through instantaneous collisions. The structure (relative arrangement of particles) is analysed using the bond-orientational order parameter. It is found that the shear flow reduces the order in the system, and the order parameter in a shear flow is lower than that in a collection of elastic hard disks at equilibrium. The distribution of relative velocities between colliding particles is analysed. The relative velocity distribution undergoes a transition from a Gaussian distribution for nearly elastic particles, to an exponential distribution at low coefficients of restitution. However, the single-particle distribution function is close to a Gaussian in the dense limit, indicating that correlations between colliding particles have a strong influence on the relative velocity distribution. This results in a much lower dissipation rate than that predicted using the molecular chaos assumption, where the velocities of colliding particles are considered to be uncorrelated.
The orientational ordering and dynamical properties of the shear flow of inelastic dumbbells in two dimensions are studied, as a first step towards examining the effect of shape on the properties of flowing granular materials. The dumbbells are smooth fused disks characterised by the ratio of the distance between centers (L) and the disk diameter (D), and the ratio (L/D)varies between 0 and 1 in our simulations. Area fractions studied are in the range 0.1 to 0.7, while coefficients of normal restitution from 0.99 to 0.6 are considered. The simulations are similar to the event driven simulations for circular disks, but the procedure for predicting collisions is much more complicated due to the non-circular shape of the particles and due to particle rotation. The average orientation is measured using an orientational order parameter S, which varies between 0 (for a perfectly disordered fluid) and 1 (for a fluid with the axis of all dumbbells in the same direction). It is found that there is a gradual increase in ordering as the area fraction is increased, as the aspect ratio is increased or as the coefficient of restitution is decreased, and the order parameter has a maximum value of about 0.5 for the highest area fraction and lowest coefficient of restitution considered here. However, there is no discontinuous nematic transition for all the parameters studied here. The axis of the dumbbells are preferentially oriented along the extensional axis (at an angle of 45ofrom the flow direction) at low area fraction, but the orientation is closer to the flow direction as the area fraction is increased. The orientation distribution is calculated, and it is found that the orientation distribution is well described by a function of the form P(θ) =(1/π)+ (2S/π)cos(2(θ−θp)), where θis the angle from the flow direction and θpis the principal orientation direction. The mean energy of the velocity fluctuations in the flow direction is found to be higher than that in the gradient direction and the rotational energy, though the difference decreases as the area fraction increases, due to the efficient collisional transfer of energy between the three directions. The distributions of the translational and rotational velocity are found to be Gaussian distributions to a very good approximation. The equation of state for the pressure is calculated, and it is found to be remarkably independent of the coefficient of restitution. The pressure and dissipation rate show relatively little variation when scaled by the collision frequency for all the area fractions studied here, indicating that the collision frequency determines the momentum transport and energy dissipation even at the lowest area fractions studied here. The mean angular velocity of the particles is examined in some detail. It is found that the mean angular velocity is equal to half the vorticity at low area fractions, but the magnitude of the mean angular velocity systematically decreases to less than half the vorticity as the area fraction is increased, even though the stress tensor is symmetric.
2011-01-27T00:00:00Z