Open Access Repository of Indian Theses

KATHAVATE, VAIBHAV SANJAY

xiv 
 
SYNOPSIS 
The technology at the driving seat of the 21st century is, of course, “the nanotechnology”, 
and the design of nanostructured materials with novel microstructural features for micro-
electro-mechanical systems (MEMS) and nano-electro-mechanical systems (NEMS) is going 
to play a decisive role in the progress of this century. Of the several materials used in MEMS 
and NEMS, piezoelectric materials are arguably gaining wide attention in applications such 
as actuators, sensors and energy harvesting due to their inherent polarization and electro-
mechanical coupling characteristics. The word “piezo” in Greek means “to press”, and 
“electric” has a Latin root “electrum” implies the flow of electrons. Therefore, piezoelectric 
materials are a class of materials that exhibit electricity upon external mechanical pressure (or 
vice versa), which further intermingles the electric and elastic fields. This piezoelectric 
behaviour is often seen in 20 non-centrosymmetric crystals (out of 32 crystal classes) whose 
centre of positive and negative charges are spaced apart, thereby creating a dipole effect to 
exhibit piezoelectricity. However, of the 20 piezoelectric crystals, 10 crystals show 
reorientation of dipoles upon an external electric field, known as “ferroelectric 
crystals/materials”, while the orientation of dipoles in the remaining 10 crystals can be 
changed upon an external thermal gradient, often known as “pyroelectric crystals/materials”. 
Therefore, essentially all the ferroelectric and pyroelectric crystals are piezoelectric. 
However, the converse is not true. 
The piezoelectric materials used in actuators mainly contain ceramics of various 
compounds and exhibit ABO3 type perovskite structure, with “A” atoms occupying the 
corners of the unit cell, “O” atoms at the centre of six faces and “B” atoms at the centre of 
the unit cell. These perovskites exhibit rhombohedral, monoclinic, and tetragonal crystal 
structure below the Curie temperature (Tc) based on their stoichiometric composition with 
respect to morphotropic phase boundary (MPB), thereby exhibiting the piezoelectric phase, 
while they possess a cubic symmetry above the Tc indicating the paraelectric behaviour of the 
material, shown in Fig.1. Conventional piezoceramics such as lead zirconate titanate (PZT) 
and barium titanate (BT) have a limited operating temperature range (i.e., 130 to 200 °C). 
Therefore, self-heating during service due to high frequency electrical and mechanical 
stresses may induce microstructural incompatibilities in the materials, which further 
deteriorates the electro-mechanical properties. However, the high-temperature applications of 
these piezoceramics in fuel injection systems, military impact fuzes, and structural health 
monitoring demand thermal and electro-mechanical stability. One way to mitigate this 
xv 
 
problem is to alter the intrinsic microstructural features that span across µm sized grains to 
nm sized ferroelectric domains, presented in Fig. 2. Further, the addition of aliovalent 
acceptor/donor cations are reported to enhance the thermal stability (i.e., increase in Tc) of 
Pb-based and Pb-free piezoceramics.   
Fig. 1 Schematic representation of ABO3 type perovskite unit cell of PZT piezoceramics. 
 
Fig. 2 Representation of microstructural length scales in piezoceramics.  
Keeping this in view, polycrystalline systems of (PbZr0.52Ti0.48O3) (PZT undoped), 
Pb0.98K0.02(Zr0.47Ti0.51Al0.02)O3 (hard-doped PZT, abbreviated as PZT-H) and 
Pb0.98La0.02(Zr0.47Ti0.51Nb0.02)O3 (soft-doped PZT, abbreviated as PZT-S), 
0.90(PbMg0.33Nb0.66O3) − 0.10(PbTiO3) (PMN-PT), and 0.94(NaK0.5Nb0.5O3) −
0.06(NaTaO3) (NKN-NT- Pb-free) have been systematically investigated to understand the 
role of intrinsic microstructural length scales on their mechanical and piezoelectric behaviour. 
xvi 
 
In piezoceramics, the region of directionally aligned dipoles along distinct polarization 
directions is known as “ferroelectric domains”. The previous and recent studies [Mehta and 
Virkar, 1990, Haertling, 1999 and Wang et al., 2021] have indicated that the ferroelastic 
effects such as the orientation of the ferroelectric domains and domain wall (DW) motion 
have a pronounced influence on the piezoelectric and mechanical response of the 
piezoceramics. 
 Domain engineering (DE) is a technique used to enhance the electro-mechanical 
properties of piezoceramics by altering the ferroelectric domain configuration i.e., size, 
orientation, and interdomain spacing. Several ways of implementing DE technique in 
piezoceramics are as follows; (i) modifying the crystal structure via aliovalent cation doping, 
(ii) controlling the grain size, (iii) growing the nano-patterns of semiconductor thin films, (iv) 
altering remnant polarization, (v) imposing mechanical stresses during poling and (vi) 
controlled thermal annealing. Of all these techniques obtaining the different ferroelectric 
domain configurations via thermal annealing is quite economical and less tedious. However, 
one of the downsides of thermal annealing is the temperature-induced depolarization in the 
material. Therefore its use as a DE is limited, despite the applications of piezoceramics at 
elevated temperatures. Several studies have been highlighted the importance of DE, 
particularly on single-crystal piezoceramics, as the use of single-crystals rule out the complex 
interaction between ferroelectric domains and grain boundaries. However, most of the 
practical applications of piezoelectric materials are based on ceramic polycrystals. Therefore, 
one of the objectives of the present thesis is to investigate the effects of below- and above-Tc 
thermal annealing on the ferroelectric domain configurations in polycrystalline 
piezoceramics. The piezoresponse force microscopy (PFM) is used to probe the differences in 
local ferroelectric domain configurations in PZT-H, PZT-S and PMN-PT, while piezoelectric 
charge coefficient, d33 studies are performed to probe the bulk response in other 
piezoceramics. The implementation of DE technique via selective annealing revealed the 
following observations; (i) distinct peak splitting is observed in X-ray diffraction (XRD) 
patterns of annealed samples, indicating the change in the ferroelectric domain structure (ii) 
annealed samples showed a transgranular cracking within the grains, (iii) degree of 
crystalline disorderness of ferroelectric domains increases with respect to annealing 
temperature and (iv) the d33, converse piezoelectric charge coefficient, 𝑑33
∗  and remanent 
strain, 𝜀𝑟 decreases with an increase in annealing temperature. 
xvii 
 
Though there have been several studies on understanding the role of domain 
configurations on electro-mechanical coupling characteristics, limited attention is given to 
investigate their influence on mechanical properties. During service, piezoceramics often 
experience variable mechanical loading conditions, particularly at high frequency, and it is 
important to understand the role of ferroelectric domain configurations on the mechanical 
behaviour of piezoceramics. Of the several mechanical properties, indentation hardness, H, a 
quick estimate of material’s resistance to the plastic deformation, is the widely preferred 
technique due to the following advantages; (i) it requires a small volume of the test specimen 
and (ii) it is non-destructive (at small indentation loads, as the indentation impressions are 
confined to the smaller areas). Recent developments in instrumented indentation techniques 
(IIT) such as nanoindentation allows to obtain indentation load, P vs. displacement, h data 
from which it is possible to determine H and elastic modulus, E. During nanoindentation, the 
fully plastic regime in the material can be achieved even at low P (from several µN to few 
mN). However, there is no comprehensive understanding of role of microstructural features 
on the H of piezoceramics despite the few studies which were focused towards understanding 
the fracture response (R-curve behaviour) [Mehta and Virkar, 1990 and Webber et al., 2009].  
The limited bulk indentation experiments (mostly with the spherical indenters on PZT 
and BT samples) and nanoindentation simulations have observed that indentation response in 
piezoceramics is dependent on nature of the material (i.e., poled vs. unpoled), and type of 
indenter (i.e., electrically conducting vs. insulating) [Ramamurty and co-workers, 1999, 2009 
and Cheng and Venkatesh, 2012]. However, these experiments are mostly used for validating 
the continuum level simulations and ignores the role of microstructural parameters (e.g., 
ferroelectric domain configurations and DW motion) on H. It is difficult to probe the 
mechanical properties with bulk indentation tests as the high indentation loads, often leads to 
cracking of materials. Therefore, it would be interesting to examine the effect of different 
ferroelectric domain configurations on H of the polycrystalline piezoceramics both at micro 
and nanoscale. The ferroelectric domain configurations are systematically varied by 
annealing the as poled (AP) piezoceramics at below and above the Tc, referred to as STD and 
ATD, respectively. The different ferroelectric domain configurations are characterized 
directly using piezoresponse force microscopy (PFM), which is also reflected in their 𝑑33
∗  
values. Following this, nano and micro indentation experiments are performed on AP, STD 
and ATD samples and the nanohardness is determined using Oliver and Pharr method while 
the microhardness is obtained from Meyer’s approach. In PZT (undoped), PZT-H, PZT-S, 
and NKN-NT samples, H follows the following trend, 𝐻𝐴𝑇𝐷 > 𝐻𝑆𝑇𝐷 > 𝐻𝐴𝑃, while in PMN-
xviii 
 
PT, it follows the trend as; 𝐻𝑆𝑇𝐷 > 𝐻𝐴𝑇𝐷 > 𝐻𝐴𝑃. In all the samples, the H decreases with 
increasing P, often known as indentation size effects (ISE). The underlying mechanisms 
responsible for the enhancement and anomalies in H and the occurrence of ISE are discussed 
in detail. 
ISE in crystalline materials is attributed to indenter geometry, presence of high plastic 
strain gradients, nucleation of discrete deformation bands underneath the indenter, the surface 
free energy of the material, and high dislocation nucleation stresses. However, limited 
nanoindentation experiments on piezoceramics [Gharbi et al., 2009] have indicated that the 
presence of ISE in contact stiffness is mainly due to the strain gradient polarization (i.e., 
flexoelectricity). The ISE is analyzed with the help of analytical, empirical or semi-empirical 
models which enables to determine the load (or size) dependent and independent H from the 
indentation data. The critical analysis of nanoindentation data using classical Meyer’s law, 
Hays-Kendall (H-K) approach, elastic recovery (ER) model, proportion specimen resistance 
(PSR) model, and modified PSR (MPSR) model lead to the following observations; (i) ISE in 
H of all the samples are sensitive to the differences in ferroelectric domain configurations, (ii) 
all the models show good agreement with the nanoindentation data, and (iii) true (or load 
independent) H values obtained from the ER, PSR and MPSR models are comparable to 
those obtained from nanoindentation experiments (i.e., machine H values). 
During indentation, the material in the vicinity of the impression undergoes a 
significant amount of deformation, which may alter the ferroelectric domain configurations 
[Schneider et al., 2005, Park et al., 2007 and Wang et al., 2021]. Further, beyond a critical 
load, indentation causes cracking at the imprint corners, altering the texture of ferroelectric 
domains and is expected to influence the crack growth characteristics. To date, there is no 
clear experimental evidence on the ferroelectric domain configurations in the vicinity of the 
indentation imprint and near the advancing crack. In the present thesis, ferroelectric domain 
orientation maps and butterfly curves (remnant strain, 𝜀𝑟 vs. electric field, E) (Fig. 3) are 
generated in the vicinity of the indentation zone and crack front leads to the following 
observations; (i) The ferroelectric domains change their texture in the vicinity of the 
indentation zone, thereby exhibiting indentation-induced domain switching (IIDS), (ii) The 
ferroelectric domains ahead of the crack tip undergo a considerable change in domain 
configurations and some of which, based on the location, re-orient back to the initial 
configurations while some remain inelastic, (iii) The indentation fracture toughness, 𝐾𝐼𝐶
𝑖  
xix 
 
determined from the indentation imprints showed distinct dependence, albeit small, on the 
ferroelectric domain configurations.  
 
Fig. 3 The butterfly loops collected in the vicinity of the indentation zone and crack front. 
In summary, the present thesis essentially centered on two parts; (a) altering the 
intrinsic microstructural features (e.g., ferroelectric domain configurations) of piezoceramics 
via selective annealing and (b) investigating the role of ferroelectric domain configurations 
on the mechanical and piezoelectric properties at micro and nanoscale.  
The organization of the present thesis is as follows; 
Chapter 1  presents the introduction of piezoelectric materials, their crystal 
structure, and related fundamentals responsible for piezoelectric properties. Role of the 
complex interaction between the intrinsic microstructural features, particularly at lower 
length scales in the deformation behaviour of piezoelectric materials is difficult to understand 
and explained as the motivation for the present work. Keeping this in view, all the possible 
prior literature is presented with a focus on the theories that tailor the piezoelectric and 
dielectric properties in general and mechanical properties in particular, while specifically 
emphasizing the mechanical response of the piezoceramics under different structural states. 
Further, a brief overview of the nanoscale characterization techniques such as 
nanoindentation and PFM is presented. Finally, possible gaps in previous literature are 
identified to define the objectives for the present thesis. 
xx 
 
Chapter 2  describes the effect of selective annealing (DE technique) on the 
mechanical properties of PMN-PT and NKN-NT piezoceramics with different ferroelectric 
domain configurations. The underlying mechanisms of enhancement in mechanical properties 
in light of crystal structure and ferroelectric behaviour are discussed in detail. 
Chapter 3 presents the important results regarding the role of different ferroelectric 
domain configurations and aliovalent dopants on the mechanical behaviour of PZT 
(undoped), PZT-H and PZT-S. The toughening mechanisms such as IIDS and domain 
rearrangement in the vicinity of the indentation site are explained with the help of 
ferroelectric domain orientation maps.  Butterfly curves (remnant strain, 𝜀𝑟 vs. electric field, 
E) are used to rationalize the results. 
 Chapter 4  deals with the description of observed ISE in nanoindentation H of 
PMN-PT, PZT-H and PZT-S using the mechanistic models. The outcomes of the mechanistic 
modelling and origins of ISE in H are further explained in light of the differences in 
ferroelectric domain configurations. 
Chapter 5  presents the conclusions from the present work. The last part of this 
chapter gives certain directions for the future work from the mechanisms proposed in this 
study.    
 
 
 


English

ROLE OF FERROELECTRIC DOMAIN CONFIGURATIONS ON THE INDENTATION BEHAVIOUR OF PIEZOCERAMICS

NAG, JOYDEEP

Abstract 

Ab initio Calculations of Optical Properties of Clusters

Atomic and molecular clusters have been a topic of great interest for last few decades, mainly because of their unusual properties, tunability and vast technological applications. In this thesis, we have explored the optical properties of few clusters using first principles calculations.

We have performed systematic large-scale all-electron correlated calculations on boron Bn, aluminum Aln and magnesium Mgn clusters (n=2--5), to study their linear optical absorption spectra. Several possible isomers of each cluster were considered, and their geometries were optimized at the coupled-cluster singles doubles (CCSD) level of theory. Using the optimized ground-state geometries, excited states of different clusters were computed using the multi-reference singles-doubles configuration-interaction (MRSDCI) approach, which includes electron correlation effects at a sophisticated level. These CI wavefunctions were used to compute the transition dipole matrix elements connecting the ground and various excited states of different clusters, eventually leading to their linear absorption spectra. The convergence of our results with respect to the basis sets, and the size of the CI expansion was carefully examined. 

Isomers of a given cluster show a distinct signature spectrum, indicating a strong-structure property relationship. This fact can be used in experiments to distinguish between different isomers of a cluster. Owing to the sophistication of our calculations, our results can be used for benchmarking of the absorption spectra and be used to design superior time-dependent density functional theoretical (TDDFT) approaches. The contribution of configurations to many-body wavefunction of various excited states 
suggests that in most cases optical excitations involved are collective, and plasmonic in nature. 

In addition, we have calculated the optical absorption in various isomers of neutral boron B6 and cationic boron B6+ clusters using  computationally less expensive configuration interaction singles (CIS) approach, and benchmarked these results against more sophisticated equation-of-motion (EOM) CCSD based approach. In all closed shell systems, a complete agreement on the nature of configurations involved is observed in both methods. On the other hand, for open-shell systems, minor contribution from double excitations are observed, which are not captured in the CIS method. 

Optical absorption in planar boron clusters in wheel shape, B7, B8 and B9 computed using EOM-CCSD approach, have been compared to the results obtained from TDDFT approach with a number of functionals. This benchmarking reveals that range-separated functionals such as wB97xD and CAM-B3LYP give qualitatively as well as quantitatively the same results as that of EOM-CCSD.




INTERACTION AND MODULATION OF THE HUMAN COMPLEMENT SYSTEM BY CHIKUNGUNYA VIRUS

PURKAIT, TANIYA

SYNTHESIS AND ENGINEERING OF GRAPHENE BASED ELECTRODES FOR ENERGY STORAGE AND CONVERSION APPLICATIONS

Allam, Vinaykumar

CARBOHYDRATES TO CARBOCYCLES: STEREOSELECTIVE APPROACHES FOR THE SYNTHESIS OF SOME CYCLITOLS

Tiwari, Mohit Kumar

i 
 
Synopsis 
The present thesis describes work undertaken to determine the role of the ArgP 
protein in E. coli physiology. Primarily, the project was initiated because of two previous 
findings from this laboratory, namely (i) the gltBD argP double mutant is 
(osmo)sensitive to hyperosmotic stress induced by high concentrations of NaCl in the 
growth medium (Nandineni et al., 2004); and (ii) ArgP is a transcriptional regulator of 
the arginine (Arg) exporter, argO (Nandineni and Gowrishankar, 2004; Laishram and 
Gowrishankar, 2007). 
Bacteria, when under hyperosmotic stress, accumulate glutamate (Glu) 
intracellularly through increased synthesis; Glu serves as a counter-ion for K
+
, which also 
accumulates under these conditions (Csonka, 1989; Csonka and Epstein, 1996). In E. 
coli, gltBD encodes Glu synthase, which catalyzes one of the two pathways of Glu 
synthesis. The second pathway is catalyzed by Glu dehydrogenase (GDH) encoded by 
gdhA. The osmosensitive gltBD argP strain showed reduced intracellular levels of Glu 
and GDH compared to a gltBD single mutant in both low and high osmolarity conditions 
(Nandineni et al., 2004). Therefore, it was suggested that the osmosensitivity of the 
gltBD argP strain is because of limited Glu and that ArgP has a role in osmoregulation 
through regulation of gdhA (Nandineni et al., 2004). 
ArgO (previously designated as YggA) is one of the few amino acid exporters 
that have been reported in E. coli. It is an Arg exporter and shares highest sequence 
similarity with LysE of Corynebacterium glutamicum which mediates both Arg and 
lysine (Lys) export. LysE is under transcriptional control of LysG, a protein that shares 
sequence similarity with E. coli ArgP. Both Arg and Lys, through LysG, serve as 
inducers of lysE expression (Bellmann et al., 2001). In vivo studies with argO-lac fusions 
have established that argO is also under the transcriptional control of ArgP and that its 
expression is induced by Arg as well as by its toxic analog canavanine (CAN). However, 
unlike the situation with C. glutamicum LysE, argO expression is repressed in the 
presence of Lys. Dominant gain-of-function mutations in argP (argP
d
), that confer 
elevated, Arg independent argO expression and thereby a CAN resistant phenotype 
(CAN
r
) were also identified (Nandineni and Gowrishankar, 2004). In vitro studies 
showed that ArgP in presence of either co-effectors, Arg or Lys, can recruit RNA 
polymerase (RNAP) to the argO promoter. This then presents two different scenarios, 
productive transcription in the former but a trapped RNAP and no transcription in the 
ii 
 
latter (Laishram and Gowrishankar, 2007).   
Additionally, there have been various reports from other laboratories on ArgP 
function in E. coli. Arthur Kornberg’s group previously described ArgP as an inhibitor of 
chromosomal initiation (IciA). IciA was shown to bind the AT-rich, conserved 13-mers 
at oriC preventing opening of this region and thereby blocking chromosomal initiation of 
replication (Hwang and Kornberg, 1990, 1992; Thony et al., 1991). Subsequently, IciA 
was reported to be a transcriptional activator of dnaA and nrdA (Lee et al., 1997; Han et 
al., 1998), genes known to have roles in chromosomal replication and DNA synthesis 
respectively. Interestingly, however, the iciA mutant shows no growth or replication 
related phenotype (Thony et al., 1991). In yet other studies, IciA is reported as a nucleoid 
protein (Azam and Ishihama, 1999) that exhibits affinity for AT-rich and curved DNA 
sequences (Wei and Bernander, 1996; Azam and Ishihama, 1999). Recently ArgP was 
described as a transcriptional activator of the genes dapB (encoding an enzyme of the 
Lys biosynthetic pathway) in E. coli and gdhA in Klebsiella aerogenes. The co-effector 
Arg does not have any effect on expression of these genes; Lys represses expression and 
this is through its prevention of ArgP binding to the operator (Bouvier et al., 2008; Goss 
et al., 2008). Accordingly, this thesis describes studies that were undertaken to 
understand ArgP’s role in E. coli physiology and the mechanism of its function. 
To test the hypothesis that ArgP’s role in osmoregulation is through regulation of 
GDH and hence Glu levels in the cell, the effect of ArgP on gdhA-lac expression in vivo 
and ArgP binding in vitro to the gdhA upstream regulatory region were determined. 
Three lines of evidence were obtained to substantiate the same hypothesis:  (i) activation 
by ArgP of gdhA-lac transcription in vivo in a Lys-sensitive manner which clearly 
correlated with the manner of ArgP binding to the cis regulatory region in vitro; (ii) 
osmosensitive phenotype of two strains namely, gltBD argP+ on supplementation with 
Lys, and gltBD argPd-P274S (harboring the argPd allele that is argP-like w.r.t. gdhA-
lac expression); and (iii) the ability of multicopy gdhA
+
 to relieve the osmosensitive 
phenotype of the gltBD argP double mutant strain. Primer extension analysis and site 
directed mutagenesis also enabled the precise location of the functional and ArgP-
regulated gdhA promoter corresponding to a transcription start site that was mapped at 
63-bp upstream of the initiation codon of gdhA. 
To investigate the role of ArgP as a transcriptional activator, data obtained from a 
whole genome differential gene expression microarray along with genes shortlisted using 
iii 
 
a candidate gene approach (of genes repressed in the presence of Lys), were examined. 
Validation of ArgP regulation of the shortlisted genes was achieved through in vivo 
promoter-lac fusion experiments in argP
+
, argP
d
 and argP strain backgrounds; 
electrophoretic mobility shift assays (EMSAs) of genes showing in vivo ArgP activation 
were also performed. 
The microarray experiment revealed that lysP, the gene encoding a protein with 
the dual functions of a Lys-specific permease and a repressor of the Lys decarboxylase 
system, is a potential regulatory target of ArgP. The argP mutation behaved like lysP 
in conferring thialysine (toxic analog of Lys) resistance. Subsequent experiments showed 
that ArgP activates lysP by about 35-fold in vivo and that there is about 5-fold ArgP-
dependent repression in presence of Lys. In vitro ArgP bound the lysP regulatory region, 
and similar to the findings at gdhA (and dapB), the binding affinity was diminished upon 
Lys addition. Furthermore, sequences of the lysP regulatory region between 114 and 
76 (relative to the start site of transcription) were shown to carry important determinants 
for ArgP binding and regulation. 
The argP mutant did not phenocopy a lysP mutant for expression of the Lys 
decarboxylase system (encoded by the cadBA operon) suggesting that the basal levels of 
LysP in a argP strain is sufficient for the negative regulation of cadBA in absence of 
Lys.  
Compared to the wild-type allele, the argP
d
 mutations showed varying in vivo 
effects on lysP-lac expression. A conspicuous difference was presented by argP
d
-P274S, 
which showed much less activation then argP
+
 and 3-fold Lys repression. 
Concomitantly, EMSAs showed no significant differences in binding affinities. On the 
other hand, differences in mobility of the protein-DNA complexes formed by native 
ArgP and the ArgP
d
 variants were seen, such that the ArgP
d
-DNA complexes migrated 
faster than native ArgP-DNA complex. Such differences in mobility of protein-DNA 
complexes have been reported to be due to differences in DNA bending such that less 
bent DNA migrates faster (Wu and Crothers, 1984). It was thus proposed that the 
differences in ArgP
d
 regulation at lysP might be due to differences in bending of the 
regulatory DNA region.  
Two other genes shortlisted from the microarray data as probable ArgP targets 
were lysC and asd, which encode enzymes of the Lys biosynthetic pathway. Using the 
candidate gene approach, dapD and lysA, also encoding enzymes of the Lys biosynthetic 
iv 
 
pathway were further examined for ArgP regulation. lysC, asd, dapD and lysA were 
shown to be activated by ArgP to varying extents in vivo (2- to 4-fold). This activation 
was independent of the co-effector Arg but was Lys-sensitive. The argP
d 
variants used in 
this study behaved much like the argP
+ 
allele both for activation and Lys repression at 
these four loci. However, allele -P274S was again different from the others in that it 
behaved more like the ΔargP mutation; this effect was therefore strikingly different from 
its effect at argO where it activates by 270-fold. EMSA showed Lys-sensitive binding of 
ArgP to the regulatory regions of lysC, asd, dapD and lysA, suggesting that Lys 
repression is due to inability of the activator to bind to these operators. These results 
emphasized the fact that the mechanism of ArgP regulation at argO is fundamentally 
different from that at the other regulated loci. First, argO is the only gene that requires 
Arg as co-effector for its activation. Second, the -P274S variant of ArgP is by far the 
most effective for constitutive argO expression, whereas it behaves much like ΔargP for 
a majority of other target genes. Finally, ArgP binding to the cis regulatory region is Lys-
insensitive at argO whereas it is Lys-sensitive at all other target regulatory loci. 
Thereafter, the previously reported findings of ArgP activation of dnaA and nrdA 
were reexamined. The results indicated that there are no differences in argP
+
, argP
d 
and 
argP for dnaA-lac or nrdA-lac expression suggesting that ArgP does not regulate their 
transcription in vivo. However, in conformity with reports from other groups, in vitro 
binding of ArgP to the regulatory regions of dnaA and nrdA with moderate affinity was 
observed. This binding was Lys-insensitive. 
The role of ArgP in the expression of the arginine uptake genes (artP, artJ, hisJ 
and argT) was also assessed. Results showed that ArgP does not regulate Arg import in 
E. coli. Similar to findings at dnaA and nrdA, ArgP showed weak affinity, Lys-
insensitive binding to the regulatory regions of genes encoding Arg uptake.  
To examine if ArgP binds DNA non-specifically, an internal (from the coding 
region) lacZ DNA fragment was used in EMSA reactions. Negligible binding was 
noticed, lending support to the conclusion that ArgP does not bind DNA non-specifically. 
These studies permitted the conclusion that with the exception of argO (which showed 
Lys-insensitive, high affinity binding), a distinguishing feature between in vivo ArgP 
regulated and non-regulated genes was Lys-sensitive binding in vitro. 
 As previously mentioned, the protein-gene pairs ArgP-argO of E. coli and LysG-
lysE of C. glutamicum are orthologous. Whereas LysE is an exporter of Arg and Lys 
v 
 
whose expression is induced by Arg, Lys, or histidine (His), ArgO exports Arg alone, 
and its expression is activated by Arg but not Lys or His. In an attempt to understand the 
inter-relationship between these orthologous pairs, transcriptional cross-regulation 
studies were performed. Consequently, reconstitution of activation of lysE by LysG in 
the presence of its co-effectors in E. coli was achieved. It was shown that neither ArgP 
nor LysG can regulate expression of the noncognate orthologous target. Of several ArgP
d
 
variants, some namely ArgP
d 
-P274S, -S94L and to a lesser extent, -P108S activated lysE 
expression in E. coli. However, the individual activating effects of LysG and ArgP
d 
on 
lysE were mutually extinguished when both proteins were coexpressed in Arg- or His-
supplemented cultures. In comparison with native ArgP, the active ArgP
d 
variants 
exhibited higher affinity of binding to the lysE regulatory region and less DNA bending 
at both argO and lysE. These findings led to the conclusions that the transcription factor 
LysG from a Gram-positive bacterium, C. glutamicum, is able to engage appropriately 
with the RNAP from a Gram-negative bacterium, E. coli, for activation of its cognate 
target lysE in vivo and that single-amino-acid-substitution variants of ArgP can also 
activate the distantly orthologous target lysE, but by a subtly different mechanism that 
renders them non-interchangeable with LysG. 
The chapter-wise organization of this thesis describing the studies and findings 
summarized above is as follows: 
Chapter 1 introduces topics related to this thesis and is organized into 4 sections 
describing, physiology of Arg and Lys metabolism in E. coli, ArgP as a transcriptional 
regulator in E. coli, LysG-lysE of C. glutamicum and finally the objectives addressed are 
listed. 
Chapter 2 provides a description of experimental materials and methods used in this 
study. 
Chapter 3 describes experiments performed to examine ArgP’s role in osmoregulation 
through its regulation of gdhA. 
Chapter 4 details results from the microarray experiment and ArgP regulation of the 
Lys-specific permease, lysP. The entire list of genes that showed at least 2-fold activation 
or 2-fold repression by ArgP
(d) 
in the microarray experiment are also listed in Appendix I 
and Appendix II respectively. 
Chapter 5 is an account of ArgP regulation of genes lysC, asd, dapD and lysA each 
encoding enzymes of the Lys biosynthetic pathway. 
Chapter 6 revisits the previous findings of ArgP regulation of genes involved in DNA 
vi 
 
replication or metabolism and Arg uptake. Results as presented in this chapter suggest 
that ArgP is a non-canonical transcriptional regulator that binds upstream regulatory sites 
without a regulatory outcome. 
Chapter 7 details the transcriptional cross-regulation studies between orthologous 
regulator-target gene pairs ArgP-argO of E. coli and LysG-lysE of C. glutamicum. 
Chapter 8 provides a brief statement of the conclusions from this study and the future 
perspectives. 
 


Synthetic Studies on Pharmaceutically Privileged Bioactive Heterocycles: Synthesis, Chemistry and Biological Evaluation

Kumar, Akash

Abstract
Spin Hall effect (SHE), first predicted by Dyakonov and Perel for semiconductors in the year
1971, and later remodeled by Hirsch in 1999 for the heavy metal system with large spin-orbit
coupling has shown the possibility for next-generation memory recording media and nano-
oscillators. The discovery of SHE opened a new field of research known as “Spin-orbitronics.”
In the last decade, researchers have extensively studied the SHE and associated spin-orbit
torques (SOTs) in heavy metals (HM) with sizable spin Hall angle such as Pt, β−Ta, β−W,
etc. to generate high-frequency signals in the GHz range and current-induced magnetization
switching. However, efficient control of magnetization still requires significant advancement
in this field. This thesis deals with some of the developments such as interface modification,
crystalline phase engineering, exploring exchange biased systems and 2D materials for better
understanding and control of current-induced SOTs. For these developments, we have studied
three different ferromagnet/non-magnet (FM/NM) heterostructures.
First, the conventional HMs are chosen as a non-magnet in FM/NM system for the study of their
detailed magnetization behavior. The Co/Pt bilayer is one of the most widely studied FM/HM
systems. We have observed an enhanced Gilbert damping and spin mixing conductance due
to post-growth annealing. These results can be correlated with higher spin memory loss at
the inter-diffused interface in Co/Pt system. This study provides insight into spin pumping
in FM/HM heterostructures and suggests a crucial role of interface modification. We have
systematically studied the effect of the phase purity of the Ta thin films on the spin pumping,
SHE and SOTs. Using FMR and inverse spin Hall effect (ISHE) measurements, it is observed
that the crystalline phase-dependent Ta thin films generate a large spin current from the low
resistive mixed-phase Ta. A detailed study of spin-orbit torque is performed using zero-bias and
DC-tuned spin-torque ferromagnetic resonance (STFMR) measurements. These results show
dominant damping-like torque in low resistive mixed-phase Ta and a dominant field-like torque
in pure β−phase Ta pointing to SHE and Rasbha mechanism of SOT, respectively.
Secondly, the magnetization dynamics in the metallic antiferromagnet (AFM) interfaced with
ferromagnet is studied. The heavy metal-based AFM system (e.g., IrMn, PtMn) not only pro-
vides a large exchange bias field but also works as an efficient spin current source. The spin
pumping and SOTs in NiFe/IrMn system are studied using FMR and STFMR measurements.
v
The magneto-dynamic measurements suggest that the exchange bias produces a unidirection-
ality in Gilbert damping. The SOT studied using angle-resolved STFMR measurements in
polycrystalline IrMn thin films suggests the generation of unconventional SOTs in this system,
which is forbidden in the FM/HM system. These unconventional SOTs which are present only in
exchange biased sample, originates from spin current with spin polarization along the direction
of charge current and perpendicular to the FM/AFM interface.
In the last part of the thesis, the 2D materials for the presence of SOTs and interfacial
Dzyaloshinskii-Moriya interaction (iDMI) are investigated. It is found that the monolayer
Graphene (Gr) due to the Rashba spin-orbit coupling generates unconventional SOTs, specifi-
cally a large out-of-plane damping-like torque, that can be useful for switching in perpendicularly
magnetized systems. On the other hand, using direct detection of iDMI with Brillouin light
scattering experiments, a large defect induced iDMI in few-layer MoS2/NiFe heterostructures
is observed.
In summary, the spin current-induced phenomena and SOTs in various FM/NM heterostruc-
tures are studied in detail. It is found that the interface modification in FM/HM and the
crystalline phase of HM play essential roles in the generation and transfer of spin current.
The generation of unconventional SOTs in exchange biased systems (NiFe/IrMn) and low di-
mensional materials (Gr) provide future scope for further study and device designing. The
observation of a large iDMI in few-layer MoS2/NiFe will be useful for obtaining chiral spin
textures.
vi


SPIN-ORBIT TORQUES IN FERROMAGNET/NON-MAGNET HETEROSTRUCTURES

Nag, Manas Kumar

Computer-assisted detection and analysis of cerebral stroke from neuroimages

SAINI, SHIKHA

DESIGNING CLUSTERS FOR EFFICIENT CATALYTIC ACTIVITY AT A REALISTIC CONDITION FROM FIRST-PRINCIPLES SIMULATION

Kumar, Deepak

 
DEVELOPMENT OF A NOVEL STRATEGY FOR RAPID DETECTION OF HUMAN 
SERUM ALBUMIN PSEUDOESTERASE ACTIVITY: A STEP TOWARDS A NOVEL 
POINT OF CARE SCREENING FOR MICROALBUMINURIA 
Microalbuminuria detection is a commonly performed parameter in a clinical biochemistry 
laboratory. Immunochemical methods are popular for such detection, but such methods lack 
sensitivity. It does not sense the immune unreactive albumin fragments excreted in the urine. 
Further, the dye-based methods of albumin detection are not specific for human serum albumin 
(HSA). It senses other proteins as well that are often excreted in the urine. It is in this context 
it was felt that novel strategies have to be innovated for microalbuminuria detection. It is known 
that HSA has a slow turnover esterase activity. It was hypothesized that exploring this unique 
property of HSA, a novel strategy of microalbuminuria can be developed. The study was 
divided in in-silico, in-vitro and in-clinical phase. It was observed that 2-Naphthyl acetate 
(2NA) behaves as a relevant substrate for HSA activity detection. Further, it was observed that 
neostigmine does not inhibit pseudoesterse activity of HSA. Based on the above inventions, a 
method was innovated for sensing albumin in human urine. We believe that the innovations 
recorded here will pave the path of novel microalbuminuria detection system at the point of 
care in days to come. 
 


DEVELOPMENT OF A NOVEL STRATEGY FOR RAPID DETECTION OF HUMAN SERUM ALBUMIN PSEUDOESTERASE ACTIVITY: A STEP TOWARDS A NOVEL POINT OF CARE SCREENING FOR MICROALBUMINURIA

Nigam, Kuldeep

NANO-CARRIER BASED APPROACH FOR NEUROPATHIC PAIN MANAGEMENT

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