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Approaches to Regional Analysis of Hydro-Meteorological Processes and Extremes
No full textRegional analysis of hydrometeorological variables (e.g., evapotranspiration, precipitation), hydrological processes (e.g., runoff), and their extremes (e.g., drought, floods) is essential for various applications. The analysis can be effective when based on homogeneous regions (groups of sites). Conventionally, hard regions are formed using a regionalization approach considering lumped (time-invariant) statistics of different hydrometeorological variables as attributes. The information on the temporal dynamics of attributes and the degree of resemblance between different sites, which could prove useful in delineating effective regions, is often discarded. To address this, a new regionalization methodology referred to as fuzzy dynamic clustering (FDC) is presented in Chapter 2 for the formation of regions in the fuzzy framework. It accounts for temporal dynamics of various attributes influencing the predictand. Application of the methodology to regionalization of potential evapotranspiration (PET) considering predictor climate variables as attributes, yielded eighteen regions in India, which are validated for homogeneity using PET-related statistics. The regions are shown to be statistically more homogenous than existing agro-ecological zones and regions formed using the global fuzzy c-means clustering method.
Various applications of the homogeneous PET regions formed using the proposed FDC approach are demonstrated in Chapter 3. For each region, relevance vector regression (RVR) relationships are developed between FAO-PM estimate of PET and subsets of its predictor climate variables for estimation of PET from fewer variables at data-sparse locations in the regions. The performance of the RVR relationships in arriving at PET estimates at data-sparse locations is shown to be better than multiple linear regression-based relationships and three widely used empirical equations (Hargreaves, Mcguinnes-Bordne, Priestly-Taylor).
Regional trend analysis was carried out on each of the 18 homogeneous PET regions. A significantly decreasing trend in annual PET was evident for nine regions in north India, whereas a contrasting increasing trend in the same was noted for three regions in south India during the period 1951-2013. Furthermore, change points were identified for PET and its predictor climate variables in each of the regions.
The sensitivity of PET and surface runoff to changes in their predictor climate variables was assessed for each region by considering a newly developed third-order Taylor series approximation of their functional relationships. PET and surface runoff from different regions were found to be sensitive to relative humidity, net solar radiation, Tmax, wind speed, and Tmin (in that order). In the regions located in south and northeast India, net solar radiation and relative humidity (RH) were found to be the key climate variables that govern the PET changes. On the other hand, wind speed followed by RH appeared to have the most influence on PET for regions in rest of the India.
The evaporation paradox (i.e., decrease in PET despite an increase in temperature) was evident in four regions. The paradox in two north-east regions could be attributed to global stilling (i.e., decrease in wind speed), global dimming (i.e., decrease in net solar radiation), and an increase in relative humidity, whereas that in two north-west regions could be attributed to global stilling.
Bouchet-Morton's hypothesis on the complementary relationship (CR) between PET and actual evapotranspiration (AET) was found to be valid in eleven of the eighteen homogeneous PET regions that are located in central, west, and north India. Significant divergence in the trend of PET and AET was evident for two regions in north-east India.
In Chapter 4, future regional changes in PET and its effect on freshwater availability (FWA) were assessed for the 18 homogeneous PET regions. For this purpose, climate simulations were considered for the period 2015-2100 from three CMIP-6 GCMs corresponding to four socio-economic pathways (SSPs 126, 245, 370, and 585) and the ensemble average of those GCMs for the four scenarios. The regional trend of annual PET was projected to increase significantly (at a 5% significance level) in all the regions for all four SSPs. An increase in net solar radiation and increasing/decreasing changes in relative humidity were found to be the main factors (in that order) causing future PET changes. Future projections of PET and temperature did not indicate possibility of evaporation paradox in any of the 18 regions, although the paradox was evident in the north-west and north-eastern parts of India in analysis with historical data. Despite projected increase in PET, significant increase in future FWA was projected for all the regions corresponding to higher SSPs (245, 370, and 585) due to a significant increase in projected precipitation. Consequently, future FWA per capita is projected to significantly increase for SSPs 245 and 585, as expected. However, for SSPs 126 and 370, projected trends in future FWA were significantly increasing and decreasing, respectively. It could be attributed to the higher projected population for SSP-370 and a lower projected population for SSP-126 relative to other SSPs.
To account for nonstationarities of climate variables in drought analysis, nonstationary versions of two multivariate drought indices (namely NSPEI, and NSDDI) were proposed in Chapter 5. The indices were quantified by fitting time-varying probability distribution to the drought reference variable considering the distribution’s location parameter as a function of large-scale climate indices. Regional analysis is appropriate for analyzing drought characteristics/phenomena. To facilitate this, the fuzzy dynamic clustering methodology presented in Chapter 2 is extended for use in regionalization for drought analysis. It aids in delineating homogeneous drought regions by accounting for temporal dynamics of the drought reference variable. Further, a multi-site block bootstrap-based modified seasonal Mann-Kendall test was proposed for testing nonstationarity in regional trend of drought reference variable. It is helpful to a modeler in deciding whether the drought analysis for the target region is appropriate to be performed with nonstationary or stationary drought indices.
In addition, for the first time, the performances and agreement of different pairs of stationary and nonstationary versions of three multivariate standardized drought indices, namely SPEI, SDDI, RDI (Reconnaissance Drought Index), were analyzed at at-site and regional scales through study on different climate regions in Karnataka state, India. Drought Severity-Area-Frequency (SAF) curves indicated that estimates of regional drought severity based on nonstationary versions of drought indices are generally lower than those based on their stationary counterparts for 6-12 months accumulation periods. Similarly, drought Intensity-Area-Duration (IAD) curves indicated that estimates of regional drought intensity are lower with nonstationary drought indices than with their stationary counterparts for various chosen durations and areal extents.
In Chapter 6, a partial duration series-based approach was presented for at-site and regional frequency analysis of extreme precipitation events resulting from different mechanisms. Its effectiveness in arriving at extreme precipitation quantile estimates (EPQEs) at ungauged and sparsely gauged locations is illustrated through a study on central India. The monsoon trough passes through this region over which extreme precipitation is known to be affected by severe low pressure systems and other weather systems. Errors in EPQEs obtained for ungauged locations were within ±20% when derived using regional frequency analysis (RFA) considering causal mechanism-based samples and regional transfer of information from surrounding grids and kriging procedures. The errors were relatively higher when RFA was performed, considering ROI-based regions. In analysis with partial duration series, the EPQEs obtained based on a single sample were found to be generally higher than those obtained using causal mechanism-based samples at the majority of grids. Consequently, the peaks of flood hydrographs were considerably lower when EPQEs were based on the proposed approach than those based on the conventional procedure. This was illustrated through a study on the Chiddgaon Ganges catchment in the Narmada basin, India. Overall the results indicated that the use of the proposed approach for estimating EPQEs could lead to economical designs of flood control/conveyance infrastructure
On Hypergeometric solutions of Feynman integrals using Mellin-Barnes Integrals with Applications
No full textExperimental measurements of physical observables in particle colliders rely on high-precision theoretical calculations to validate the predictions of any theoretical model and detect signals of new physics. These theoretical calculations, in the perturbative framework of quantum field theory, require the computation of complicated integrals, commonly known as Feynman integrals. Therefore, the evaluation of Feynman integrals is the backbone of theoretical precision calculations. However, this is a highly non-trivial task as we go to higher order in the perturbative series expansion, where the number of scales and loops of the associated Feynman diagrams become large, and the number of Feynman diagrams grows factorially. Nevertheless, such computations are necessary to match the extraordinary precision level of modern and future colliders, and thus the study of Feynman integrals has become a very active field of research in recent years.
In this thesis, we focus on studying the mathematical aspects of Feynman integrals and devise techniques to compute them. This field of research is at the cutting edge of theoretical physics, mathematics and computer programming, with new efficient tools proposed every year. Some of the well-known techniques to compute Feynman integrals include the method of differential equations, Mellin-Barnes (MB) representation, hypergeometric functions,
Gelfand-Kapranov-Zelevinsky (GKZ) system of equations etc.
Our primary focus in this thesis is the study of the Mellin-Barnes (MB) representation approach to solving Feynman integrals in terms of hypergeometric functions. In one of the projects reported in this thesis, we present the first systematic computational technique to solve N-fold MB integrals commonly appearing in the context of Feynman integrals. This technique is based on a surprising geometrical connection between MB integrals and the theory of conic hulls, and therefore we call this the conic hull method. This method yields the final solution in terms of hypergeometric series, which are useful for further analytic study as well as numerical computation. Along with this project, we also present a computer implementation of the conic hull method in the form of the package MBConicHulls.wl based on Mathematica.
In another project in this thesis, we apply the conic hull method to solve the previously unsolved dual-conformal hexagon and double box Feynman integrals. These integrals remained unsolved as they involve solving a nine-fold MB integral. However, the conic hull method is successful in solving both the above integrals as it is applicable to N-fold MB integrals. The solutions we obtain for the hexagon and double box are cross-checked numerically against direct integration of Feynman parametrization and analytically using the differential equation satisfied by the double box and hexagon integrals.
In another project, we show yet another application of the conic hull method by computing one-loop N-point massive conformal Feynman integrals. Here, we prove two conjectures, first proposed from the Yangian bootstrap approach, stating that any one-loop N-point massive conformal Feynman integral can be written as a single multi-fold hypergeometric series. To prove this, we show that there is always a conic hull, associated with the MB integral of the Feynman integrals, which does not intersect with any other conic hulls, and therefore yields a series solution with a single hypergeometric series.
Finally, in the last project of this thesis, we use the conic hull method to illustrate the limitations of the method of brackets. The latter is a computational technique based on the Ramanujan Master Theorem, and was devised originally to evaluate Feynman integrals but is also useful to evaluate certain definite integrals. However, the method is plagued with divergences whose origin is not from the ultraviolet divergence of the Feynman integral, but from the breakdown of one of the rules of the method of brackets. Studying this method in parallel with the conic hull method helps us show some of the fundamental issues of the method of brackets and point out the domain of validity of the method.Ministry of Human Resource Development (MHRD), Government of Indi
A study of extracellular matrix dynamics in epithelial cancer progression with a special focus on ovarian cancer spheroidogenesis
No full textEpithelial ovarian cancer (EOC) is one of the most debilitating gynecological cancers in women worldwide due to its insidious symptoms. The predominant subtype of ovarian cancer: high-grade serous ovarian carcinoma (HGSOC), is responsible for 75% of all fatalities associated with EOC. 90% of EOC patients have already reached an advanced stage of metastasis when they are diagnosed with the disease. Metastasis is frequently associated with ascites: an abnormal accumulation of fluid in the peritoneal cavity due to the occurrence of spheroids, clusters of disseminated malignant EOC cells. Spheroids contribute significantly to the morbidity and mortality associated with EOC. Despite this, the mechanisms associated with the formation of EOC spheroids are ill-understood.
Investigations indicate intricate connections between these signaling modules with elements of reciprocal and hierarchical connections that underlie spheroidal morphogenesis and may provide insights into the identification of targets for future therapeutic strategies for EOC
Structural and biochemical studies on mycobacterial Uracil-DNA glycosylase (Ung) and MutT1, key proteins involved in maintaining the genomic integrity in Mycobacteria
No full textMaintaining genomic integrity is indispensable for the survival and propagation of an organism. Failure to do so can cause mutations involving structural and functional aberrations, leading to severe diseases. The causative agent of TB, Mycobacterium tuberculosis (Mtb), is considered one of the most successful human pathogens. It is an intracellular pathogen that infects and multiplies within the host macrophages. Inside macrophages, the bacterium is exposed to various DNA-damaging agents. Additionally, endogenous factors such as by-products of many normal physiological processes and the extracellular environment, most commonly ultraviolet radiations, can also damage the DNA. The errors in replication and transcription, resulting in the incorporation of inappropriate bases, can also disrupt genomic integrity. The precursor molecules for DNA synthesis, i.e., the nucleotide pool, can also get altered and incorporated into the DNA. Furthermore, the G+C-rich genome (~ 64%) of Mtb makes it more susceptible to guanine oxidation and cytosine deamination. The pathogen's success lies in its ability to survive all these harsh conditions. Therefore, Mtb has developed various DNA-repair and error-avoidance mechanisms. The enzymes in these pathways recognize and rectify DNA damage and maintain genomic integrity. It is crucial to understand these, which may help design novel therapeutic approaches for controlling this disease.
The research described in this thesis involves the structural and functional characterization of uracil-DNA glycosylase (Ung) from Mtb and MutT1 from Mycobacterium smegmatis. A brief overview of the relevant literature on DNA damage and repair with emphasis on structural and biochemical studies of these two proteins is discussed in the introductory chapter. The first half of this chapter presents a brief account of DNA repair involving base excision, emphasizing uracil removal by uracil-DNA glycosylase. Details on the generation of oxidatively damaged nucleotides, their consequences, and sanitization by MutT proteins are provided in the latter half. Oxidative stress can cause modification of nucleotide bases in both the nucleotide pool and the DNA/RNA. Guanine is most susceptible to oxidation among all the nucleotides because of its low redox potential. Guanine oxidation at the 8th position forms 8-oxo-7,8-dihydroguanine (8-oxo-G), the most frequent among the oxidatively modified bases. 8-oxo-dGTP can be ambiguously incorporated against cytosine (C) and adenine (A) during DNA replication, resulting in G:C to T:A and A:T to C:G transversions, respectively. Additionally, direct oxidation of guanine in DNA forms an 8-oxo-G:C pair that, if not efficiently eliminated or repaired, can induce a G:C to T:A transversion. MutT proteins are a part of a three-component GO repair system that prevents mutations caused by 8-oxo-G. They belong to the Nudix hydrolase superfamily and catalyze the hydrolysis of substrates with a typical structure involving a nucleoside diphosphate linked to a moiety X (NDP-X) to NMP and P-X. Several previous studies have established an antimutator role of MutT proteins, i.e., strains lacking MutT leads to an increase in the frequency of mutations compared to the wild type. Mycobacterial MutT proteins, MutT1 and MutT2, have been shown to have an 8-oxo-Guanosine triphosphatase activity. Mycobacterium smegmatis MutT1 (MsMutT1) is a multifunctional two-domain enzyme. It consists of an N-terminal Nudix hydrolase domain and a C-terminal histidine phosphatase domain. The action of MsMutT1 towards Nudix substrates such as 8-oxo-dGTP, 8-oxo-GTP, and diadenosine polyphosphates has already been established. An exciting aspect of the mode of action of MsMutT1 is its modulation by the nature of the molecular interactions. This enzyme, which hydrolyses 8-oxo derivatives of guanosine triphosphate, does not act on GTP and dGTP under normal conditions. To further explore this aspect and elucidate the structural basis of its differential action on 8-oxo-NTPs and unsubstituted NTPs, the crystal structures of the enzyme complexes with 8-oxo-dGTP, GMPPNP, and GMPPCP were determined. This permitted a detailed comparison of the enzyme interactions with 8-oxo derivatives of guanosine triphosphates and with non-hydrolyzable analogs of GTP. This comparison led to further elucidation of the structural basis for the difference between the action of MsMutT1 on GTP and its 8-oxo derivatives. The work also gave insights into the correlation among intermolecular interactions, plasticity, and the activity of MsMutT1.
Uracil is a nucleotide base that is usually a component of RNA. However, it can erroneously get incorporated into DNA, which, if not corrected, can lead to mutations and interfere with the DNA binding proteins. Uracil can arise in DNA either by deamination of cytosine within DNA or by incorporating dUTP in DNA during replication. Uracil-DNA glycosylase is an important class of DNA repair enzymes that recognizes and catalyzes uracil excision from single-stranded and double-stranded DNA substrates and initiates the base-excision repair (BER) pathway. Molecular genetics studies have shown the importance of Ung in mycobacteria. The mutation rate substantially increases in the absence of this enzyme. Another study showed the importance of Ung in the survival of Mtb inside its host. A proteinaceous inhibitor (Ugi) encoded by Bacillus subtilis bacteriophage PBS1 or PBS2 is well known to inhibit UNG/Ung proteins. The bacteriophage expresses it as a part of the defense mechanism against host Ung. Structural studies showed that Ugi binds at the DNA-binding surface of UNG by mimicking the DNA backbone interactions, preventing UNG-DNA binding. MtUng has been well-characterized biochemically and structurally. The crystal structures of the native enzyme in various forms and in complex with different small molecules, namely, citrate, uracil, and uracil derivatives, are known. These structures comprehensively describe the uracil binding site and the extended binding site. The extended binding pocket involves the region which interacts with the sugars and phosphates of DNA. The element which leads to the enzyme's specificity is primarily its uracil binding pocket, making it an ideal target for drug design. The products formed from the Ung action on uracil-containing DNA are known to act as its inhibitors. The product, uracil, binds to the enzyme's active site and serves as its inhibitor. The enzyme is also inhibited to various extents by uracil analogs. Therefore, uracil-directed ligand tethering is an efficient strategy for inhibitor development of uracil-DNA glycosylase. We developed a molecular beacon-based fluorescence method to analyze the real-time action of MtUng on DNA substrates and its inhibition by small molecules. The method uses a hairpin oligo (5'-5-FAM-CUUUUUGAGCTTTTGCTCAAAAAG-BHQ-1-3') wherein five consecutive uracil residues in the stem region of the hairpin were incorporated. The oligomer was terminally attached with a commonly used fluorophore, 5-carboxyfluorescein (5-FAM), which is quenched by BHQ-1. Upon treatment with Ung, excision of the consecutive uracils results in the unwinding of the stem region of the oligomer to rapidly separate the quencher from the fluorophore yielding an intense fluorescence signal. We demonstrate the sensitivity of this method and its application in determining the efficiency of inhibition of MtUng by uracil derivative. The inhibition analysis by this method endorses high-throughput screening of compounds which can accelerate the process of drug discovery against infectious diseases by targeting their DNA-associated proteins.
To identify novel MtUng inhibitors, we systematically compiled and screened small molecule libraries in silico. The molecular docking and Molecular Mechanics Generalised Born Surface Area (MMGBSA) methodology were adopted for Structure-based virtual screening (SBVS), resulting in the identification of several hits. For experimental validation, 20 molecules were sourced and screened in vitro against MtUng, resulting in six hits with the half maximal inhibitory concentration (IC50) lower or equivalent to uracil. The results suggest that the probability of obtaining high MtUng inhibition increases with the presence of a uracil ring. Several uracil derivatives and compounds similar to uracil were also tested for inhibition. In this study, nineteen crystal structures accounting for twelve unique inhibitor complexes were determined. A network of conserved water molecules at the ligand-binding site was identified. This observation can be further used in the water mimic inhibitor design of MtUng.
MsMutT1 is a versatile multifunctional enzyme. Based on structural data and information available in the literature, we hypothesized that MsMutT1 could hydrolyze diphosphoinositol pentakisphosphate (PP-IP5 or IP7) to inositol hexakisphosphate (IP6), a reaction significant in many signaling processes. However, the individual domains of MsMutT1 do not hydrolyze IP7. In this thesis, we report three independent crystal structures of the complex between MsMutT1 and IP6. We note that the Nudix domain of MsMutT1 is the active site for the hydrolysis of IP7. However, the presence of the C-terminal domain is necessary for either recognition or efficient catalysis of IP7. This work is presented as an appendix in this thesis.Council of Scientific and Industrial Researc
Robustness of Neural Activity Dynamics in the Medial Entorhinal Cortex
No full textBiological systems exhibit considerable heterogeneity in their constitutive components and encounter stochasticity across all scales of analysis. Therefore, central questions that span all biological systems are: (a) How does the system manifest robustness in the face of parametric variability and stochasticity? (b) What are the mechanisms used by disparate biological systems to maintain the robustness of physiological outcomes? In this thesis, we chose the mammalian medial entorhinal cortex (MEC) as the model system to systematically study the principles that govern functional robustness across different scales of analysis.
At the neuronal level, we assessed the impact of heterogeneities in channel properties on the robustness of cellular-scale physiology of MEC stellate cells and cortical interneurons. We demonstrated that the expression of cellular-scale degeneracy, wherein disparate combinations of molecular scale parameters (e.g., ion channels) yielded similar characteristic physiological properties (e.g., firing rate). These analyses and observations underscored the role of degeneracy as a mechanism to achieve functional robustness in cellular-scale activity despite widespread heterogeneities in the underlying molecular scale properties. An important cellular scale signature of MEC stellate cells is their ability to manifest peri-threshold intrinsic oscillations. Although different theoretical frameworks have been proposed to explain these oscillatory patterns, these frameworks do not jointly account for heterogeneities in intrinsic properties of stellate cells and stochasticity in ion-channel and synaptic physiology. In this thesis, using a combination of theoretical, computational, and electrophysiological methods, we argue for heterogeneous stochastic bifurcations as a unifying framework that fully explains peri-threshold activity patterns in MEC stellate cells. We also provide quantitative evidence for stochastic resonance, involving an optimal noise that improves system performance, as a mechanism to enhance robustness of intrinsic peri-threshold oscillations.
At the network level, we chose a well-characterized function of the MEC involving grid-patterned activity generation in a 2D continuous attractor network (CAN) model of the MEC. We quantitatively addressed questions on the impact of distinct forms of biological heterogeneities on the functional stability of grid-patterned activity generation in these models. We showed that increasing degrees of biological heterogeneities progressively disrupted the emergence of grid-patterned activity and resulted in progressively large perturbations in low-frequency neural activity. We postulated that suppressing low-frequency perturbations could ameliorate the disruptive impact of biological heterogeneities on grid-patterned activity. As a physiologically relevant means to suppress low-frequency activity, we introduced intrinsic neuronal resonance either by adding an additional high-pass filter (phenomenological) or by incorporating a slow negative feedback loop (mechanistic) into our model neurons. Strikingly, 2D CAN models with resonating neurons were resilient to the incorporation of heterogeneities and exhibited stable grid-patterned firing. We extended these findings to one-dimensional CAN models built of heterogeneous conductance-based excitatory and inhibitory neuronal models. We found that slow negative feedback loops, introduced by HCN channels that are naturally endowed with slow restorative properties, stabilized activity propagation in heterogeneous 1D CAN models. Together, these findings established slow negative feedback loops as a mechanism to enhance functional robustness in heterogeneous neural networks.
Together, the analyses presented in different parts of this thesis emphasize the need to account for all forms of neural-circuit heterogeneities and stochasticity in assessing robustness of biological function across scales. The findings presented here highlight degeneracy, stochastic resonance, and negative feedback loops as powerful generalized principles and mechanisms that could drive robustness in biological systems across different scales
Mechanobiology of cell-substrate interactions
No full textCell adhesion to substrates is a complex process facilitated by focal adhesion (FA) complexes that help them perform vital cellular functions like migration, growth, and division. Cells probe their surroundings through contractile stresses generated via cross-bridge cycling between actin and myosin. These stresses induce exquisite feedback between the underlying substrate and actomyosin stress fibers, resulting in the remodeling of the cytoskeleton and FA. A repertoire of signaling molecules, including calcium and a mechanosensitive protein, talin, facilitates these interactions in FA. Do cells remodel under dynamic mechanical loads in tissues such as arteries? How do individual components of the FA regulate cell adhesions and tractions? I use numerical methods to address these questions on cell-substrate interaction.
I quantified the cell tractions using micro-pillar array detectors (mPAD) created using soft lithography as a first study. Our study shows that mPAD topography resulted in persistent migration of fibroblasts. I used image analysis to quantify the micropillar deflection and calculated tractions through the neo-Hookean model to report traction variation along the cell length. I next developed a multiscale cell model, incorporating SF, calcium signaling, and FA dynamics. Using the model, I investigated the effects of cyclic stretch and substrate stiffness on cell-substrate interactions.
I used the modified Hill model and reaction-diffusion equations to model SF contractility in the presence of calcium. Furthermore, the Gillespie algorithm was used to simulate the stochastic adaptor protein engagements at FAs. The model shows that cell adhesions and tractions vary along their length under static and cyclic stretch conditions; the maxima occurred behind the cell edge. Cell tractions and adhesion increased initially with substrate stiffness and ligand density but decreased beyond an optimum substrate stiffness. Cyclic stretch enhanced tractions and integrin recruitment on compliant substrates; in contrast, it reduced them on stiff substrates.
Talin orchestrates FA formation and aids in force transfer to cytoskeletal actin in the presence of vinculin. I simulated the force response of talin using a composite worm-like chain model. I show that the talin-vinculin assembly is mechanosensitive to substrate stiffness and extension rate. Talin extension on stiffer substrates resulted in higher tension and vinculin recruitment at a low extension rate. In contrast, a high extension rate lowered vinculin recruitment and abolished talin sensitivity to stiffness. These studies show the importance of adaptor protein mechanics in substrate sensing during cell adhesion
Investigation of Psychrophilic SUMO Proteases: Towards a More Efficient SUMO Protease at Lower Temperature
No full textCovalent attachment of the fusion protein, Small Ubiquitin-like modifier (SUMO), to recalcitrant
target proteins (especially transmembrane proteins) make purification of the target protein much
easier by enhancing its recombinant overexpression, protecting from degradation and improving
protein folding, solubility and stability. After purification of the SUMO-tagged protein, SUMO
protease (Ulp1), which specifically cleaves the SUMO-tag, is required to regenerate the native target
protein. However, the known SUMO protease enzyme from Saccharomyces cerevisiae i.e., S.ce.
Ulp1 enzyme is not very efficient, and the cleavage reaction requires many hours of incubation with
the SUMO-tagged protein at room temperature or above for partial cleavage of the SUMO-tag.
Under such conditions, many target proteins, especially the integral membrane proteins, get
denatured and inactivated. Herein, we aim to provide a solution to this problem by discovering and
producing psychrophilic (cold-active) SUMO proteases, which will deSUMOylate the SUMO-tagged
protein efficiently at low temperature thus keeping the target protein stable and active.
To reach this goal, we have successfully overexpressed and purified two novel psychrophilic SUMO
proteases- C.ps. Ulp1 enzyme and M.an. Ulp1 enzyme from psychrophilic yeasts, identified through
bioinformatics studies. Comparative activity studies performed with different SUMO-tagged proteins
have suggested that M.an. Ulp1 has better activity than the S.ce. Ulp1. Further, bioinformatics tools
have been utilized to explore the probable reasons for better activity observed for M.an. Ulp1
enzyme in certain cases compared to S.ce. Ulp1 enzyme
Resource Allocation for Natural Disasters using a Game-theoretic Framework
No full textThe occurrence of a severe natural disaster causes loss of life and
destruction of properties. The overall criticality of the disaster depends
on the nature of the disaster and the physical characteristics of
the affected locations. In the aftermath of a natural disaster, multiple
emergencies often evolve at different geographical locations with casualties
and infrastructure damage. In post-disaster scenarios, responsible
authorities should initiate relevant disaster management activities
to mitigate the devastating effects of natural disaster. Resource allocation
is an integral part of the post-disaster activities.
In general, resource allocation deals with the issue of distributing necessary
resources to multiple users depending on their demand and the
availability of resources. It aims to achieve efficient and fair assignment
of limited resources. The devastation caused by a natural disaster
enforces the need for various critical resources in disaster-affected
locations to reduce the impact of the disaster. When adequate resources
are available, the problem of allocating resources becomes
trivial, and all the crisis locations can be fully satisfied in terms of
their resource requirements. However, if there is a scarcity of essential
resources after the simultaneous occurrence of multiple emergencies
at distinct geographical locations, providing resources to all those regions
and fulfilling their demands simultaneously becomes challenging.
In such situations, efficient decision-making is necessary to execute a
fair and socially agreeable allocation of resources to the affected locations.
One cannot rely on human-controlled decision-making since
it can have a bias for, or prejudice against, some of the disaster locations.
A fair and impartial approach to the allocation of resources can be implemented by designing an automated decision-making system.
This thesis proposes a game-theoretic framework which can form the
basis for such a system.
In this thesis, we develop a multi-event emergency management system
using a non-cooperative, single-stage, strategic form game model
to facilitate the allocation of resources to the respective disaster locations.
Each emergency event is assumed to occur at different locations
simultaneously, and some amount of resources are demanded by
each location to mitigate the impact of disasters. These locations are
represented as players in the game, which are assumed to play in a
self-interested manner with the other players to get an allocation of
scarce resources available at the resource station. However, it should
be noted that the disaster locations are not actively involved in playing
a game. It is a centralized decision-making executed by the responsible
disaster management authority, which implements the algorithm
designed using the game-theoretic framework to decide reasonable allocations
to the players. The authority assumes different allocations
to be the possible strategies of the players and arrive at a fair solution.
As a game utility, the authority imposes a non-monetary cost on each
player for obtaining a certain amount of resource units. The objective
of the proposed game is to derive socially acceptable strategies for an
effective and fair allocation of resources to the respective players. In
the thesis, it is established that the game model is unique in structure
and always possesses pure strategy Nash equilibria (PSNE). Each
PSNE consists of possible allocations to the players; hence, those can
be implemented by the disaster management authority as potential
allocation vectors.
As the resources needed during disaster management can be both
divisible and indivisible, we investigate the game for both types of resources.
Mathematical analysis shows that the existence of PSNEs is
independent of the nature of resources. The only difference it makes
is that in the case of indivisible resources, the players have a discrete set of strategies, and divisible resources make their strategy sets continuous.
It is also shown that the game-theoretic algorithm can be
used for any number of players or disaster locations at various stages
of resource allocations. The investigation is conducted using twoplayer,
three-player and n-player game models. Different case studies
are presented in the chapters of this thesis to validate the mathematical
results developed in this work and to indicate how this proposed
method can be helpful in practical disaster resource allocations. This
work also includes the statistical analysis of the game-theoretic algorithm
and the study of its computational complexity.
This thesis also includes a study on the preparedness and damage assessment
of a natural disaster using unmanned aerial vehicles (UAV).
Preparedness is a pre-disaster activity which is essential to build resilience
against natural disasters. Damage assessment is one of the
post-disaster activities which estimates the loss of human lives, properties,
and infrastructure. This phase is important to initiate the
response and recovery work after a natural disaster. These activities
become challenging and time-consuming when human effort is the
only option. In our study, we focus on the possible applications of
UAVs to make these activities speedy and effective
Excited State Intramolecular Charge Transfer: Ultrafast Electronic and Vibrational Spectroscopic Study
No full textThis thesis incorporates the understanding of the ultrafast excited state photoinduced intramolecular charge transfer (ICT) process in liquid phase. The molecular systems are studied by employing Ultrafast Raman Loss Spectroscopy (URLS) and transient absorption (TA) spectroscopy. The primary goal of this thesis is to observe structural dynamics immediately after the formation of Franck-Condon state and the effect of slight modifications in the structure and solvent onto the excited state ICT process
Comprehensive Study on Synthesis and Characterization of Nanocellulose Reinforced Green Composites
No full textEnvironmental issues caused by the non-biodegradability of synthetic thermoplastics have
increased interest in more environmentally friendly alternatives that should be derived from
renewable resources. This work focuses on producing green composites and biofilms by
synthesizing nanocellulose (NC) from readily available natural and renewable sources like
cellulose. The term NC refers to cellulose that has been reduced to the nanoscale. NC is used
to describe a variety of cellulose nanostructures, including Micro Crystal Cellulose (MCC),
Cellulose Micro Fibrils (CMF), Cellulose nanocrystals (CNC), and Cellulose nanofibers
(CNF). Because of its versatility, low toxicity, biodegradability, and carbon neutrality,
nanocellulose has attracted considerable attention for generating new materials in several
industrial, technological, and biological applications. Nanocellulose has a sizable global
market and demand because of these numerous applications. One of the challenges for
commercial and industrial production of nanocellulose is finding a source of cellulose that is
economically viable, abundant, and sustainable. Bacteria, plants (including trees, shrubs, and
herbs), algae, and animals (Tunicates) are the primary sources of nanocellulose. In this study,
cellulose nanofibers are synthesized from the bamboo pulp through TEMPO oxidation, high-
pressure homogenization, and ultrasonication treatment.
Characterization of CNF was done using Transmission Electron Microscopy (TEM), Scanning Electron Microscopy (SEM), Fourier-Transform Infrared Spectroscopy (FTIR), X-ray powder Diffraction (XRD), and Dynamic Mechanical Analysis (DMA). After characterization, the synthesized NC was evaluated by turning it into films and using it as reinforcement to prepare composites. Bamboo particles are reinforced with CNF suspension to prepare composites using the hot press (HP) and oven-dried (OD) methods. The mechanical properties of these fabricated composites are investigated, such as modulus of elasticity (MOE), modulus of rupture (MOR), and interfacial strength. The properties of the NC and composites are compared for 1st , and 3rd homogenization passes. The mechanical characteristics of the film have been investigated using uniaxial tensile and nanoindentation experiments.
The morphological characteristics examined using SEM and TEM showed that the cellulose in the bamboo pulp is reduced to the nanoscale, confirming the formation of CNF. The average diameter of nanofibres of bamboo calculated from TEM images was 8 to 10 nm, respectively. The CNF analyzed using FTIR spectroscopy exhibited the presence of functional groups and their vibrational modes. Further, crystal size (CS)andcrystallinity index (CI) of CNF synthesized from different homogenization passes were calculated usingthe XRD technique. Properties like viscosity, storage modulus, and loss modulus were determined from the rheological characterization, which confirmed the non-Newtonian behavior of pure NC suspension. In addition to morphology analysis, mechanical properties of NC films computed from uniaxial tensile test and nanoindentation showed a 58 MPa tensile strength and a 0.2228 GPa hardness, respectively. Also, dynamic mechanical properties like storage modulus, loss modulus, and tanδ were determined to examine the viscoelastic behavior of the film as a function of temperature. However, from the results, no phase transformation was noticed until 75°C. Furthermore, composites reinforced with 1 % weight consistency of CNF showed an increase in interfacial strength, MOE, and MOR as a function of density. The MOE increased 9 times for HP samples compared to the OD samples. MOR nearly increased by a factor of 4, and the energy-absorbing capacity also increased to 182% in the case of HP samples. From these results, it can be inferred that hot-pressing was an effective manufacturing method than oven drying as it removes maximum moisture content and enhances adhesion between bamboo powder and CNF.
Therefore, it can be concluded from the results that nanocellulose derived from bamboo has highly entangled fibers, which can be transformed into a film and used in packaging and biomedical applications. Also, bamboo CNF acts as a binding agent to prepare composites. Hence, the concept of using matrix and reinforcement derived from the same natural sources can be used to make green composites. Consequently, there is a great deal of potential for the TEMPO-oxidized bamboo celluloses to develop into ground-breaking nanotechnology that will connect the domains of biomass and forest refinement with cutting-edge high-tech research