Indian Institute of Science Bangalore
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Modeling of Lightning Attachment to Aircraft and a Novel Methodology to Quantify Strike Rate
No full textAir transport plays a vital role in global economic growth and long-distance commutation. The aviation industry is found to double its fleet size every fifteen years. According to Air Transport Action Group (ATAG), 45 million aircraft took off worldwide in 2019, which translates to 1.5 lakh per day. Similar numbers are reported for other years under normal circumstances. Therefore, aviation appears to be an indispensable part of modern human civilization. Lightning is known to be one of the serious environmental threats to aircraft. Past incidents show that lightning strikes can lead to structural damage, operational interruption, and loss of lives. Field data suggest that, on average, an aircraft can get struck by lightning once or twice a year. Further, according to NOAA, The lightning strikes typically cost approximately two billion dollars to airline operators annually. Therefore, lightning protective measures are considered a crucial aspect of aircraft design.
Design of suitable lightning protective measures involves Zoning of aircraft’s outer surface. Aircraft Zoning intends to differentiate lightning attachment points, channel slipping regions, and regions that carry just the stroke current. The first step in Zoning is to identify the initial attachment points. For the same, different methods like laboratory experiments, similarity principle, Rolling Sphere Method (RSM), and field-based approach are suggested in the standard, Aerospace Recommended Practice (ARP)-5414. Several aircraft accidents attributed to lightning strikes during the mid-20th century encouraged engineers to investigate the phenomena more closely. Therefore, several in-flight measurement campaigns were carried out in the late 80's, where the aircraft were flown inside the thunderstorm with the intention of getting struck by lightning. Field observation from these campaigns suggests two modes of lightning attachment,
Aircraft-initiated and aircraft-intercepted. In the former one, under the influence of a thundercloud or descending lightning leader, the aircraft initiates bipolar leaders that lead to a strike. These leaders are deemed to propagate hundreds of meters to complete the lightning strike. In aircraft-intercepted strikes, the aircraft intercepts a descending lightning leader and hence gets struck. The methods suggested in the standard for identifying initial attachment points on aircraft are simple and have limitations.
− The laboratory experiments on scaled aircraft models or isolated aircraft parts cannot portray all the aspects of discharges leading to the attachment. Therefore, the laboratory results cannot be directly extended to actual aircraft.
− The similarity principle suggested in the standard is qualitative and can’t be extended to aircraft of any size and shape.
− The field-based approach is not properly described in the standard, and hence, lacks clarity.
− The 25 m Rolling Sphere Method (RSM) is routinely employed to determine the
initial attachment points. Being a striking-distance-based approach, RSM only depicts the last stage of aircraft- intercepted attachment and, thus, doesn’t consider aircraft-initiated leaders. However, it is reported that 90% of the lightning strikes to aircraft are attributed to aircraft-initiated mode, which involves significant connecting leader activities. Therefore, precise assessment of initial attachment points requires considering the aircraft-initiated leader discharges.
From the above discussion, it is evident that modeling bipolar leader discharges from aircraft is imperative in the context of lightning protection design. In literature, it is difficult to find a model for bipolar leader discharges from aircraft. However, works on either negative or positive leader discharge from energized electrodes in laboratory gaps
and their extension to grounded objects are well-regarded in the literature. Knowledge from these works is found to be helpful to the present work. In spite of being responsible for most attachments, a model for bipolar leader discharges
from aircraft is hard to find in the literature. Therefore, this work aims to develop a model for the inception and propagation of bipolar leaders from aircraft.
Electrical discharges being field-driven phenomena, field computation is essential. Identifying the problem in hand as an open-geometry problem, a boundary-based method, Surface Charge Simulation Method (SCSM), is chosen for field computation. SCSM provides the global field distribution around the aircraft. Aircraft extremities are the most probable regions that can initiate discharges and, therefore, requires capturing the field around them in detail. The same is achieved by employing sub-modeling at the extremities. Sub-model charges are calculated using Charge Simulation Method (CSM), while the boundary condition on the sub-model is extracted from the global field solution.
Modeling aircraft-initiated leader discharges involve modeling positive and negative leader discharges. Several models for positive and negative leader discharges in laboratory gaps are available in the literature. The latest model available in the literature for a positive leader discharge was developed by Becerra and Cooray. To reduce the computational burden, a simplified version of the model, which is also suggested by them, is considered in the present work. For negative leader discharge, a simplified physical model proposed by Z.Guo et al. is considered.
Using the constructed model, the mechanism involved in the inception and propagation of the aircraft-initiated leader discharges is investigated and quantified. In contrast with discharges from energized electrodes or objects on the grounds, a few salient aspects of bipolar leader discharge from aircraft are pointed out. It is shown that aircraft potential changes with the development of connecting leaders, which modifies the field around it. As a consequence of the same, unipolar stable leader discharge from an aircraft is not viable. Therefore, the aircraft-initiated positive and negative leader discharges in a mutually supporting form are essential for the stable propagation of connecting leaders.
The minimum ambient fields required for the stable propagation of bipolar leaders from a medium (DC-10) and a small aircraft (SDM) are determined. The values are well within the fields measured during different measurement campaigns. Subsequently, the dependency of this threshold field on permissible pitch and roll angle, aircraft flying altitude, and humidity are quantified. The aircraft-intercepted lightning strikes are also accounted for in this work. It is shown that, being electrically floating, the magnitude of aircraft potential increases, keeping the polarity the same as the descending leader tip potential. However, it is not the case for objects on the ground (i.e., buildings, towers, etc.). Therefore, the striking-distance-based approach, routinely employed for designing lightning protection for grounded objects, cannot be directly extended to aircraft. This also indicates a possible limitation of RSM while applied on aircraft. Further, The critical stroke current below which aircraft-intercepted mode of attachment is most probable is determined for two aircraft models, DC-10 and SDM.
Unlike structures on the ground, the weight and volume of the lightning protection for aircraft should be constrained. Therefore, to provide adequate protection, it is absolutely essential to quantify the probability of lightning strikes to aircraft. Thus, based on the above model for lightning attachment, this work develops a methodology for estimating
the rate of lightning strikes to aircraft. This method takes aircraft dimensions and spatial densities of lightning flashes and thunderstorms along its route as input. The proposed method is employed to estimate the average annual number of strikes to aircraft worldwide.
Subsequently, the dependency of the strike rate on aircraft size and flying altitude are investigated. The entire exercise is carried out for medium-sized (DC-10) and small (SDM) aircraft. The estimated strike rates are well within the range of reported field data. Further, the estimated variation of strike rates with altitudes (below 3 km) correlates well with the
data published by Boeing. The small deviations observed in the estimated strike rates are attributed to the assumption of cloud heights and takeoff/landing trajectory. Therefore, given exact data on thunderstorms, lightning flashes, and the operational behavior of an aircraft, the methodology can reliably estimate the rate of lightning strikes to aircraft.
In summary, this work has developed a model for the inception and propagation of bipolar leaders from aircraft and also correctly picturizes the direct streamer mode of bridging involved in aircraft-intercepted attachment. The role of the air density (hence, altitude) is incorporated in the model, along with selected humidity values. The proposed model provides a discharge-physics-based method of identifying initial attachment points on aircraft. Therefore, the limitations of the methods suggested in the standard are overcome.The work has also developed a methodology for estimating the strike rate as a function of altitude, aircraft size, thunderstorms, and lightning flash density. The estimated strike rates correlate well with the reported data from field observation
Experimental and computational approaches to understand collective behaviors of bacterial pathogen Pseudomonas aeruginosa
No full textPseudomonas aeruginosa is a Gram-negative opportunistic pathogen, estimated to account for 15-20% of hospital-acquired infection-related deaths around the globe in a year. This bacterium exhibits two distinct collective behaviors, biofilm formation and swarming motility. During biofilm formation, the P. aeruginosa population is comprised of sessile cells - covered in a self-produced polysaccharide matrix. Swarming, on the other hand, is group motility facilitated by flagella and bio-surfactant. Such cooperative behaviors help P. aeruginosa to thrive in hostile environmental conditions. However, the triggers that regulate these behaviors remain unknown and form the focus of my Ph.D. thesis.
P. aeruginosa forms biofilms on indwelling medical devices such as endotracheal tubes (ETTs), urinary catheters, vascular access devices, tracheostomies, and feeding tubes, often leading to hospital-acquired infections. Pseudomonas aeruginosa is one of the four frequently encountered bacteria causing pneumonia. In the current work, we have established an in vitro model mimicking the biofilm formation on the endotracheal tube. We have identified two-component system (TCS) genes contributing to this process. The TCS comprises a membrane-associated sensor kinase and an intracellular response regulator. We have found that out of 112 TCS mutants studied, 56 had altered biofilm biomass on ETTs. Some of these are novel ETT-specific TCSs that could serve as targets to prevent biofilm formation on indwelling devices frequently used in clinical settings.
Swarming in P. aeruginosa is a collective movement of the bacterial population over a semisolid surface, but specific signals that trigger this motility are unclear. We hypothesized that specific environmental signals could induce swarming in P. aeruginosa. Our data show that a low ethanol concentration under nutrient-limiting conditions provides a strong ecological motivation for swarming in P. aeruginosa PA14. Ethanol serves as a signal and not a carbon source under these conditions. Moreover, ethanol-driven swarming relies on the ability of the bacteria to metabolize ethanol to acetaldehyde using a periplasmic quinoprotein alcohol dehydrogenase, ExaA. We found that ErdR, an orphan response regulator linked to ethanol oxidation, is necessary for the transcriptional regulation of a cluster of 17 genes, including exaA, during swarm lag. Finally, we show that as a volatile, ethanol could induce swarming in P. aeruginosa at a distance, suggesting long-range spatial effects of ethanol as a signaling molecule.
P. aeruginosa exists in multispecies consortia in the environment and during the infection of various hosts, including humans. The physicochemical properties which mediate interactions between P. aeruginosa and its neighbors remain elusive. We began our study using P. aeruginosa and Cryptococcus neoformans, a pathogenic yeast species, in a surface-based co-culture assay. We found that the P. aeruginosa colony spread more on the lawn of C. neoformans. Upon microscopic investigation, we found that P. aeruginosa shows exploratory behavior in proximity to C. neoformans cells, and this exploratory behavior does not require metabolic active yeast cells. We hypothesize that the fluid accumulation near C. neoformans cells plays an essential role in the microscopic interaction leading to the macroscopic growth of the P. aeruginosa colony. To test this hypothesis, we have developed an individual-based model with experimentally motivated constraints such as microbial division time, fluid accumulation near yeast cells, and the motility of individual P. aeruginosa and scaled the parameters to simulate macroscopic behavior using the cellular automata modeling approach. We found that the presence of yeast lawn allowed P. aeruginosa to cover more area by utilizing the fluid accumulated around yeast cells
Raman Spectroscopy on Few layer graphene
No full textGraphene is a two-dimensional allotrope of carbon exhibiting planer honeycomb lattice
structure.1 A carbon atom in graphene makes three σ-bonds with the neighbouring atoms in the
plane and one π-bond perpendicular to the plane of these carbon atoms. The delocalized electron
due to side overlapping of π-bond in graphene gives high intrinsic carrier mobility. The
maximum carrier mobility of single layer suspended graphene is 200,000 cm2V-1s-1,2 whereas the
maximum carrier mobility of silicon is 1,400 cm2V -1s-1.
3 Hence, graphene is an excellent
substitute for high-frequency FET switch over silicon FET switch. The three σ-bonds (tight
bonds) make graphene the strongest material among all other materials. The free-standing singlelayer graphene shows Young's modulus as high as 1TPa, while that of carbon nanotube is
reported to be around 270-950 GPa.
4 This implies that graphene can be a promising material for
nanoelectromechanical systems (NEMS). The distinct electronic and mechanical properties of
graphene have attracted a lot of attention for developing alternative graphene-based alternative,
which helps address the technical limits of current technologies.
Few layers graphene (FLG) have been studied both theoretical and experimentally.6,7 These
studies show that the number of layers and staking orders of FLG has a strong influence on its
characteristic properties. Hence, identifying the structural differences in FLG is a crucial
requirement in developing FLG-based devices. The characteristic properties of monolayer and
bilayer graphene have been extensively studied. However, there are very few reports on three or
more-layers of graphene. Here, we have focused on identifying and fabricating few layers
graphene (FLG) devices and studying their electrical and optical characteristics. Different
techniques have been reported in the literature for the synthesis of graphene.
Mechanical exfoliation is the method that we have used here. The structural and electronic characteristics of
graphene are studied using Raman spectroscopy.
The thesis is arranged as follows. Chapter 2 explains the fabrication of graphene devices.
Mechanical exfoliation technique used to obtain few layers of graphene flakes and optical
microscopy used to locate graphene flakes is briefly explained. I have described the fabrication
of graphene devices for electrical measurements. The electron-beam lithography method is used
to fabricate these devices. Chapter 3 discusses Raman spectroscopy to identify the number of
layers of graphene flakes. In this section, I have compared peaks up to five layers of graphene
flakes. Also, statistical analysis is performed to obtain the number of layers in the graphene
flakes. Chapter 4 discusses electrical measurements on few layers graphene FET device.
Chapter 5 describes the exfoliation of graphene flakes on flexible substrates and Raman
spectroscopy measurements. Chapter 6 provides the summary of the result
On commuting isometries and commuting isometric semigroups
No full textThis thesis consists of two parts- commuting isometries and commuting isometric semigroups. In the first part, we study the Taylor joint spectrum for a pair of commuting isometries in certain cases. We show that the joint spectrum of two commuting isometries can range from being small (of measure zero or an analytic disc for example) to the
full bidisc. En route, we discover a new model pair in the negative defect case and relate it to the modified bi-shift.
The rest of the thesis focuses on the study of a pair of commuting C_0-semigroups of isometries. An analogue of the Wold decomposition for an isometry is the Cooper’s decomposition for a C_0 -semigroup of isometries. This decomposition provides a comprehensive structure for a C_0 -semigroup of isometries. We discover a structure for a pair of commuting C_0 -semigroups of isometries in generality as well as under certain additional assumptions like double commutativity or dual double commutativity.
Cooper showed that the role of the unilateral shift in the Wold decomposition of an isometry is played by the right-shift-semigroup for a C_0 -semigroup of isometries. The factorizations of the unilateral shift have been explored by Berger, Coburn, and Lebow. We give a complete description of the factorizations of the right-shift-semigroup under
the assumption of the multiplicity space being finite dimensional. We employ novel function theoretic methods and classical convex analysis to arrive at the factorization
Computational study of membrane driven secondary structural changes in proteins
No full textConformational changes in proteins, the most abundant biomolecule found in all living organisms, are ubiquitous and triggered by several factors essential for protein function. Protein conformational changes typically occur on time scales of tens of microseconds to milliseconds, lying well outside the sampling regime of conventional molecular dynamics (MD) simulations. Although MD simulations have been extensively used to study protein folding to obtain free energy landscapes, membrane assisted protein folding, the primary focus of this thesis, has received less attention. In this thesis, we present a finite temperature string method path based approach to obtain the free energy of protein conformational changes utilizing path collective variables. We rigorously test and validate our approach and demonstrate its ability to capture the α-helix to β-sheet transformation in the mini G-protein in a reduced two-dimensional collective variable space. We apply the method to study phospholipid membrane driven protein conformational changes associated with the assembly of bacterial pore forming toxins (PFTs) and antimicrobial peptides (AMPs).
The mammalian cell membrane contains cholesterol, and several proteins of the PFT family require cholesterol recognition for lytic activity. Although cholesterol has been shown to enhance lytic activity, the molecular underpinning of the role of cholesterol for cytolysin A (ClyA) activity, an α-PFT expressed by E. coli, remains elusive. Using the string method, we unravel the critical role played by cholesterol by obtaining the free energy of the β-tongue transformation to the helix-turn-helix motif of the pore state. Cholesterol was found to assist pore formation by stabilizing an unfolded on-pathway intermediate of the membrane inserted β-tongue motif. Specifically, a tyrosine residue located at the phospholipid protein interface was found to be critical in catalyzing unfolding. Using extensive thermal unfolding MD studies on point mutations of the protein, we concluded that inherent flexibility in key membrane binding domains is essential for pore formation. Point mutations that reduced flexibility were detrimental to pore formation, concurring with experimental observations where a point mutation of tyrosine implicated in cholesterol binding completely abrogated lytic activity.
We next applied the string method approach to study the insertion free energy and mechanism of insertion of the AMP ‘CM15’ in the inner bacterial membrane. Our free energy analysis showed that a single membrane-bound peptide unfolded state is more stable than a membrane-inserted folded state, with the insertion mechanism triggered by the N-terminus interactions with the cardiolipin lipid molecules of the bacterial membrane. Cardiolipin has not been considered in the previous studies, and our study points to the vital role of this four tail lipid in AMP-membrane interactions. We also report strong interactions of water molecules with one side of the membrane-inserted amphiphilic peptide, which can potentially be responsible for bacterial cell lysis.
In summary, the string method based approach developed in this thesis can be applied to a wide variety of protein conformational changes and can be used to study complex membrane driven protein unfolding, refolding, and conformational changes
Deciphering the role of host protein HuR in RNA virus life cycle and pathogenesis: Hepatitis C Virus and SARS-CoV-2 as exemplars.
No full textViruses pose a major threat to human health and the ongoing SARS-CoV-2 pandemic proves as the best evidence for that. Historically, RNA viruses have a major potential to cause such pandemics. They utilise RNA binding proteins at several stages of their life cycle. We have worked on one such RBP, ELAVL1 (also known as HuR) to study its role in life cycle and pathogenesis of two kind of RNA viruses, one which causes chronic infection, Hepatitis C Virus and the other that causes lytic infection, SARS-CoV-2. HuR is an RNA-binding protein which binds to AU-rich elements in the RNA and regulates the transport, stability and translation of associated RNAs. The function of HuR is regulated by its cellular localisation, post-translational modifications and binding partners. We have outlined the following objectives to understand the role and regulation of HuR in HCV and SARS-CoV-2 life cycle and pathogenesis.
Objective 1: To study the mechanism and implications of HuR relocalisation from Nucleus to cytoplasm upon HCV infection.
Hepatitis C virus is a positive sense, single-stranded RNA virus which completes its life cycle in the cytoplasm of the host cells, primarily, in hepatocytes. Host protein HuR translocation from nucleus to cytoplasm following infection is crucial for the life cycle of several RNA viruses including hepatitis C virus (HCV), a major causative agent of hepatocellular carcinoma. HuR assists the assembly of replication-complex on the viral-3′UTR, and its depletion hampers viral replication. Although cytoplasmic HuR is crucial for HCV replication, little is known about how the virus orchestrates the mobilization of HuR into the cytoplasm from the nucleus. We show that two viral proteins, NS3 and NS5A, act coordinately to alter the equilibrium of the nucleo-cytoplasmic movement of HuR. NS3 activates protein kinase C (PKC)-δ, which in turn phosphorylates HuR on S318 residue, triggering its export to the cytoplasm. NS5A inactivates AMP-activated kinase (AMPK) resulting in diminished nuclear import of HuR through blockade of AMPK-mediated phosphorylation and acetylation of importin-α1. Cytoplasmic retention or entry of HuR can be reversed by an AMPK activator or a PKC-δ inhibitor. Our findings suggest that efforts should be made to develop inhibitors of PKC-δ and AMPK, either separately or in combination, to inhibit HCV infection.
Objective 2: HuR protein interaction with SARS-CoV-2 RNA and its consequences in viral RNA translation.
SARS-CoV-2, the causative agent of the ongoing COVID-19 pandemic is a positive strand RNA virus belonging to Coronaviridae family and causes mild to severe respiratory illness. The viral genome is 30 Kb long and accumulates various mutations as it spreads. RNA-binding proteins (RBPs) play important roles in the life cycle of RNA viruses. Viral 5’UTR and 3’UTR are more than 99% conserved in the emerging mutants, suggesting the importance of sequence conservation in viral processes. We searched for sequence dependent potential RBP binding sites in the viral 5’UTR. Of the proteins obtained, we focused on HuR which is also known to influence translation and replication of other RNA viruses and has been found to be SARS-CoV-2 interacting RBP in genome-wide screens. Strong binding of HuR with viral 5’UTR was observed in in vitro, and ex vivo assays. The binding sites of HuR in the 5’UTR was mapped, and it was found that the mutations in 5’UTRs of SARS-CoV-2 Variants of Concern (VoC) altered the HuR binding affinity. While deciphering the mechanism of HuR effect on CoV-2 lifecycle, we found that it promotes the binding of another host factor PTB to the 5’UTR, promoting viral RNA translation. Interestingly, the role of HuR was found to be completely opposite on the sub-genomic (sg) RNAs of SARS-CoV-2, which code for the structural proteins. While knockout of HuR inhibited translation from genomic 5’UTR, it enhances sg5’UTR translation resulting higher ratio of structural to non-structural proteins. In conclusion, we show the role of an RNA binding protein in differential translation regulation of SARS-CoV-2 genomic and sub-genomic RNAs which opens up new avenues for the design of antivirals against the virus.
Objective 3: Role of HuR in SARS-CoV-2 virus replication and pathogenesis.
We have shown that HuR binds to SARS-CoV-2 5’UTR. Therefore, we checked its effect on virus life cycle. The knock-down and knock-out of HuR reduced viral RNA levels and viral titres. The alpha variant exhibited lesser and delayed dependence on HuR as compared to the original Wuhan and Delta variant, which could be one of the mechanisms behind the longer generation time and hence lesser transmission of the alpha variant. Interestingly, Anti-sense oligo (ASO) targeting the HuR binding site was found to reduce the viral titre in WT, but not in HuR KO cell line. We further show that the knockout of HuR increased the sensitivity of the cells for Remdesivir treatment by decreasing its IC50 10 folds. Since HuR KO reduced viral RNA levels in the cells, to uncouple it from pathogenesis, we looked for a system harbouring viral proteins, but was replication deficient. For this, a non-infectious Virus like particle (VLP) system was designed. The VLPs from Baculovirus expression system were purified and characterised and its similarity studied with the kinetics of infectious virus infection. VLPs were used as a platform to study the impact of mutations in the variants and the corresponding changes in virus entry, virus pathogenesis and also explored as vaccine candidates. It appears, the knock-down of HuR did not alter the VLP entry in the cells but altered the pathogenesis. IL-8 was used as a marker for pro-inflammatory cytokines, and we found that the VLP-induced IL-8 secretion was hampered in the HuR KO cell line. Results suggest that in addition to virus life cycle, HuR regulates SARS-CoV-2 pathogenesis and could be an attractive target for possible therapeutics, possibly using ASO alone or in combination with remdesivir.
Taken together, we demonstrate important roles of an RNA binding protein HuR, in two RNA viruses, HCV and SARS-CoV-2, and explored different ways to target it for tackling virus infections. The chronic virus, HCV manipulates HuR by post-translational modifications and alteration of subcellular localisation; and the lytic virus, SARS-CoV-2, utilises it to maintain a balanced ratio of structural and non-structural proteins for productive virus infection, while maintaining its subcellular localisation and exploiting it to induce inflammation.CSIR-SP
Exponential Resummation of QCD at Finite Chemical Potential
No full textA comprehensive study of the QCD phase diagram is one of the challenging and open
problems in high energy physics. Having significant astrophysical implications, this is
also important in constructing the chronological evolution of the universe. With this
aim, this thesis describes the behaviour of thermodynamic observables like pressure and
number density with changing chemical potential µ, through the method of an unbiased
exponential resummation of lower order Taylor series of these observables at a finite µ.
We address the problem of biased estimates, which manifest uncontrollably in exponential
resummation and which become severe in the domain of large values, higher orders of µ
and also in observables which are higher µ derivatives of the thermodynamic potential. We
show that our new formalism of unbiased exponential resummation can eliminate these
biased estimates exactly upto a given order of µ, and can capture important contributions
of higher order Taylor series for all our working temperatures starting from hadronic phase
to the plasma phase, including the crossover region. We also demonstrate that this new
formalism is highly efficient in saving appreciable computational time and storage space
for computations
Direct Numerical Simulation of Square Vortex Flows
No full textAtmospheric and oceanic flows are often modeled as two-dimensional due to their large planar extents (∼ 1000 km) and small vertical extent (∼ 10 km). Most phenomena in these systems are governed by the theory of two-dimensional turbulence. Rather than truncating the third dimension, its effect is modeled using additional friction term in the 2D Navier-Stokes equations. These equations are said to be applied to a class of flows called quasi-two-dimensional (Q2D) flows, which are essentially three-dimensional but almost planar flows. The approximation of Q2D-ness is widely applied for shallow fluid layers in laboratory experiments.
We study Q2D flows generated by electromagnetically driving a shallow electrolyte layer. The specific form of forcing mimics that of a chessboard, where the laminar flow is composed of counter rotating square vortices arranged in a chessboard like array. The forcing function is carefully chosen to mimic experimental measurements of a laboratory realization, which is not purely sinusoidal as in the well-known Taylor Green vortex flow. The steadily forced flow leads to a statistically stationary state which is analyzed over a wide Reynolds number range. We analyze how the dynamics and flow structures change with increasing Reynolds number. We illustrate methods to discuss when and how the Q2D model ceases to accurately represent experiments
Ultrastrong coupling in a cavity-electromechanical device
No full textCavity optomechanics is a field that explores the interaction between light and motion of matter via radiation pressure force. Such systems mainly consist of an optical/microwave cavity coupled to a mechanical resonator. Cavity optomechanical systems provide a convenient way to realize a wide range of experiments down to the quantum regime. Various quantum effects, such as cooling to the quantum ground state of the mechanical resonator, coherent state transfer, and quantum entanglement between microwave and mechanical modes, have been demonstrated experimentally. In addition, such systems have shown excellent performance in sensing the smallest of displacements, mass, and forces. The coupling strength between the cavity and the mechanical resonator is a crucial parameter in such systems. A coupling strength that exceeds the dissipations of the system opens the possibility for various interesting experiments mentioned above. Ultra-strong coupling is a regime in which two coupled oscillators (cavity and mechanical resonator) exchange energy in a time shorter than their time periods of oscillations. In this thesis, I will describe our experimental results from microwave optomechanical devices operating in the ultra-strong coupling limit, including the engineering aspects that enable such large coupling rates.
In the first part of the thesis, I present results from a microwave cavity-optomechanical system using a rectangular 3-dimensional (3D) superconducting waveguide cavity to couple mechanical vibrations of a nanomechanical resonator. The mechanical resonator is a thin circular plate of aluminum suspended over another aluminum plate on a substrate via clamps, forming a parallel plate capacitor. The oscillation of the mechanical membrane modulates the capacitance of the parallel plate capacitor, which in turn modulates the dressed resonance frequency of the microwave cavity. It enables the interaction between the microwave photons in the 3D cavity and the motion of the mechanical resonator. The single photon coupling strength is a crucial parameter that determines how strongly the mechanical motion is coupled to the electromagnetic field inside the 3D cavity. To maximize the single photon coupling strength, the device must be engineered to minimize parasitic capacitance. To facilitate it, we perform numerous simulations of various design parameters and analysis strategies to engineer such devices. After the design is optimized, we fabricate our cavity optomechanical device based on the optimized parameters and demonstrate that our experimental results are in line with the simulation results. We also include experimental results showing effects such as optomechanically-induced Absorption (OMIA).
In the second part of the thesis, I demonstrate the highest level of parametric coupling that is possible between the microwave mode and the mechanical resonator. It is achieved with the help of a parametric drive, which brings these two oscillators into resonance. We achieve the ultra-strong coupling where the coupling strength is comparable to the frequency of the mechanical resonator itself, exceeding all the system's dissipation rates. We also perform time-domain measurements of the OMIA effect, from which we can infer the energy swap rate between the microwave mode and the mechanical resonator. We found that the shortest swap time is on par with the time period of the mechanical oscillation. We also demonstrate that by increasing the drive signal strength beyond a certain threshold in the red sideband of the cavity frequency, the system shows parametric instabilities. I discuss various nonlinear phenomena, such as period doubling, tripling, and chaotic mechanical vibrations that lie in the parametric instability phase space
Structural and functional insights into hybrid AT-less megaenzyme synthase (NRPS) and DNA-MsDps2 complexes using single particle cryo-EM
No full textMicroorganisms, mainly bacteria and fungi, are the producers of structurally diverse, complex organic compounds called as secondary metabolites. These metabolites include polyketides (PKs), non-ribosomal peptides (NRPs), and hybrid PKs/NRPs. The final products from these three classes display different characteristics like antibiotics, antiparasitic agents, antifungals, anticancer drugs, and immunosuppressants. As these products have wide range of potential application in pharmaceuticals, a number of biochemical studies have been carried out to elucidate of their biosynthetic pathways. The biosynthesis of these products is catalysed by large, multi-modular proteins including the NRPSs (non-ribosomal peptide synthases), the PKSs (polyketide synthases) and hybrid NRPS/PKS. Knowledge of the quaternary structure of PKS, NRPS and hybrid NRPS/PKS assembly line enzymes have been topic of interest since it helps not only in elucidating the crosstalk between different domains but also useful in modification of products. It has been demonstrated in the literature that FAS and PKS are homodimeric enzyme complexes, whereas the majority of NRPS are monomeric in nature. Whether NRPS is monomeric or homodimeric in the case of hybrid NRPS/PKS of a modular enzymatic manufacturing line has been questioned. To gain structural insights into the hybrid multidomain NRPS, we focused module-2 (Cy1-Cy2-A-PCP-Ox) of hybrid NRPS/PKS of leinamycin biosynthetic pathway. We performed cryo-EM of module 2 (Cy1-Cy2-A-PCP-Ox) which resulted in a low resolution cryo-EM map of this NRPS perhaps as a result of the linkers present in between the domains. However, to elucidate crucial interdomain interfaces and interactions that occur during different steps of the NRPS catalytic cycle, we undertook truncation studies including the domains (Cy1-Cy2) and (A-PCP-Ox) of the module2 of NRPS. We determined the structure of multidomain constructs (PCP-Cy1-Cy2) and (A-PCP-Ox) at overall resolutions of 5.2 Å and 7 Å respectively. The unravelling of architecture, organization, and mechanism of NRPS module 2 of leinamycin biosynthesis by cryo-EM will help design bioengineering approaches to understand the mechanistic insight into this novel pathway (swapping modules and domains).
DNA-binding protein under starvation (Dps), is a miniature ferritin complex, which plays a vital role in protecting bacterial DNA during starvation for maintaining the integrity of bacteria from hostile conditions. Mycobacterium smegmatis is one such bacteria that express MsDps2, which binds DNA to protect it under oxidative and nutritional stress conditions. Several approaches, including cryo-electron tomography (Cryo-ET), were implemented to identify the structure of the Dps protein that is bound to DNA. However, none of the structures of the Dps-DNA complex was resolved to high resolution to be able to identify the DNA binding residues. In this study, we implemented various biochemical and biophysical studies to characterize the DNA protein interactions of Dps protein. We employed single-particle cryo-EM-based structural analysis of MsDps2-DNA and identify that the region close to N-terminal confers the DNA binding property. Based on cryo-EM data, we performed mutations of several arginine residues proximal to the DNA binding region, which dramatically reduced the MsDps2-DNA interaction. In addition, we propose a model for DNA compaction during lattice formation. We performed single-molecule imaging experiments of MsDps2-DNA interactions that corroborate well with our structural studies. Single molecule imaging also deciphers the mechanism of compaction required for DNA protection