88 research outputs found
New method for generating low to medium resolution atomic models of protein structures using a structural alphabet in absence of close structural homologues
No full textModelling of protein structures in the absence of known homology is termed as templatefree modelling (TFM), free-modelling (FM) or ab initio modelling. To date this remains the biggest challenge in the field. In the current work, we have made a methodological contribution to address this challenge by exploring the use of a structural alphabet known as protein blocks (PBs). With the help of PBs it is now possible to predict the PB sequence of any protein sequence using tools like PB-kPRED. Our work was motivated by the need to find a method to move forward from predicted PB sequence to 3D structure. We hence developed a strategy that starts from a predicted query PB sequences and searches into a non-homologous structural database for similar PB stretches or fragments. Our strategy then tries to assemble selected fragments to generate meaningful 3D models. For that, we attempted to exploit the inherent property of Modeller by constraining it to use PB fragments along with secondary structures and contact predictions as additional restraints to predict protein models. We validated the results of our strategy on a subset of small proteins from CASP13 target list on the basis of the commonly used scores (GDT_TS and TM-score) for free modelling protocols. We were able to show that good quality models can be generated for small proteins using a combination of PB based fragments and Modeller. This work opened a new explorative path for protein blocks down the lane of solving the ever so perplexing protein folding dogma.La modélisation des structures protéiques en l'absence d'homologie est appelée modélisation sans matrice, modélisation libre ou modélisation ab initio. À ce jour, ce type de modélisation reste le plus grand défi du domaine. Durant cette thèse, nous avons apporté une contribution méthodologique pour relever ce défi en explorant l'utilisation d'un alphabet structurel connu sous le nom de blocs protéiques (BP). Il est maintenant possible de prédire le squelette carbonné d’une protéine sous forme de séquence de BPs de n'importe quelle protéine en utilisant des outils comme PB-kPRED. Notre travail a consisté à trouver une méthode pour passer de la séquence de BPs prédite à la structure 3D. Nous avons donc développé une stratégie qui part d'une requête sous forme de séquences de BP prédites et recherche dans une base de données de structures non homologues des fragments de BPs similaires. Notre stratégie tente ensuite d'assembler des fragments sélectionnés pour générer des modèles 3D. Pour cela, nous avons tenté d'exploiter les propriétés inhérentes de Modeller en la contraignant à utiliser des fragments de BPs et à utiliser des prédictions de structures secondaires et de contact comme contraintes externes supplémentaires. Nous avons validé les résultats de cette stratégie sur un sous-ensemble de petites protéines cibles issues de CASP13 sur la base des scores couramment utilisés (GDT_TS et TM-score) pour les protocoles de modélisation gratuits. Nous avons pu montrer que des modèles de bonne qualité peuvent être générés pour de petites protéines en utilisant une combinaison de fragments à base de PB et de Modeller. Ce travail ouvre de nouvelles perspectives d’application des blocs protéiques pour solutionner l’épineux problème du repliement des protéines
New method for generating low to medium resolution atomic models of protein structures using a structural alphabet in absence of close structural homologues
No full textModelling of protein structures in the absence of known homology is termed as templatefree modelling (TFM), free-modelling (FM) or ab initio modelling. To date this remains the biggest challenge in the field. In the current work, we have made a methodological contribution to address this challenge by exploring the use of a structural alphabet known as protein blocks (PBs). With the help of PBs it is now possible to predict the PB sequence of any protein sequence using tools like PB-kPRED. Our work was motivated by the need to find a method to move forward from predicted PB sequence to 3D structure. We hence developed a strategy that starts from a predicted query PB sequences and searches into a non-homologous structural database for similar PB stretches or fragments. Our strategy then tries to assemble selected fragments to generate meaningful 3D models. For that, we attempted to exploit the inherent property of Modeller by constraining it to use PB fragments along with secondary structures and contact predictions as additional restraints to predict protein models. We validated the results of our strategy on a subset of small proteins from CASP13 target list on the basis of the commonly used scores (GDT_TS and TM-score) for free modelling protocols. We were able to show that good quality models can be generated for small proteins using a combination of PB based fragments and Modeller. This work opened a new explorative path for protein blocks down the lane of solving the ever so perplexing protein folding dogma.La modélisation des structures protéiques en l'absence d'homologie est appelée modélisation sans matrice, modélisation libre ou modélisation ab initio. À ce jour, ce type de modélisation reste le plus grand défi du domaine. Durant cette thèse, nous avons apporté une contribution méthodologique pour relever ce défi en explorant l'utilisation d'un alphabet structurel connu sous le nom de blocs protéiques (BP). Il est maintenant possible de prédire le squelette carbonné d’une protéine sous forme de séquence de BPs de n'importe quelle protéine en utilisant des outils comme PB-kPRED. Notre travail a consisté à trouver une méthode pour passer de la séquence de BPs prédite à la structure 3D. Nous avons donc développé une stratégie qui part d'une requête sous forme de séquences de BP prédites et recherche dans une base de données de structures non homologues des fragments de BPs similaires. Notre stratégie tente ensuite d'assembler des fragments sélectionnés pour générer des modèles 3D. Pour cela, nous avons tenté d'exploiter les propriétés inhérentes de Modeller en la contraignant à utiliser des fragments de BPs et à utiliser des prédictions de structures secondaires et de contact comme contraintes externes supplémentaires. Nous avons validé les résultats de cette stratégie sur un sous-ensemble de petites protéines cibles issues de CASP13 sur la base des scores couramment utilisés (GDT_TS et TM-score) pour les protocoles de modélisation gratuits. Nous avons pu montrer que des modèles de bonne qualité peuvent être générés pour de petites protéines en utilisant une combinaison de fragments à base de PB et de Modeller. Ce travail ouvre de nouvelles perspectives d’application des blocs protéiques pour solutionner l’épineux problème du repliement des protéines
Nouvelles approches pour générer des modèles de moyennes résolutions à l'échelle atomique de structures de protéines à l'aide d'un alphabet structural en absence d'homologues proches
No full textLa modélisation des structures protéiques en l'absence d'homologie est appelée modélisation sans matrice, modélisation libre ou modélisation ab initio. À ce jour, ce type de modélisation reste le plus grand défi du domaine. Durant cette thèse, nous avons apporté une contribution méthodologique pour relever ce défi en explorant l'utilisation d'un alphabet structurel connu sous le nom de blocs protéiques (BP). Il est maintenant possible de prédire le squelette carbonné d’une protéine sous forme de séquence de BPs de n'importe quelle protéine en utilisant des outils comme PB-kPRED. Notre travail a consisté à trouver une méthode pour passer de la séquence de BPs prédite à la structure 3D. Nous avons donc développé une stratégie qui part d'une requête sous forme de séquences de BP prédites et recherche dans une base de données de structures non homologues des fragments de BPs similaires. Notre stratégie tente ensuite d'assembler des fragments sélectionnés pour générer des modèles 3D. Pour cela, nous avons tenté d'exploiter les propriétés inhérentes de Modeller en la contraignant à utiliser des fragments de BPs et à utiliser des prédictions de structures secondaires et de contact comme contraintes externes supplémentaires. Nous avons validé les résultats de cette stratégie sur un sous-ensemble de petites protéines cibles issues de CASP13 sur la base des scores couramment utilisés (GDT_TS et TM-score) pour les protocoles de modélisation gratuits. Nous avons pu montrer que des modèles de bonne qualité peuvent être générés pour de petites protéines en utilisant une combinaison de fragments à base de PB et de Modeller. Ce travail ouvre de nouvelles perspectives d’application des blocs protéiques pour solutionner l’épineux problème du repliement des protéines.Modelling of protein structures in the absence of known homology is termed as templatefree modelling (TFM), free-modelling (FM) or ab initio modelling. To date this remains the biggest challenge in the field. In the current work, we have made a methodological contribution to address this challenge by exploring the use of a structural alphabet known as protein blocks (PBs). With the help of PBs it is now possible to predict the PB sequence of any protein sequence using tools like PB-kPRED. Our work was motivated by the need to find a method to move forward from predicted PB sequence to 3D structure. We hence developed a strategy that starts from a predicted query PB sequences and searches into a non-homologous structural database for similar PB stretches or fragments. Our strategy then tries to assemble selected fragments to generate meaningful 3D models. For that, we attempted to exploit the inherent property of Modeller by constraining it to use PB fragments along with secondary structures and contact predictions as additional restraints to predict protein models. We validated the results of our strategy on a subset of small proteins from CASP13 target list on the basis of the commonly used scores (GDT_TS and TM-score) for free modelling protocols. We were able to show that good quality models can be generated for small proteins using a combination of PB based fragments and Modeller. This work opened a new explorative path for protein blocks down the lane of solving the ever so perplexing protein folding dogma
Implementing the global approaches in local context: Case of ‘Conservation Works’ at nineteenth century ‘Epiphany Church’, Gurugram, India
No full textHeritage conservation ideologies have been under constant change; from ‘antiquity to modernity’, from material based to value-based, and finally turning its course towards sustainability-oriented approaches since the turn of the millennium. Through Convention for the Safeguarding the Intangible Cultural Heritage (2003) followed by the Convention on the Protection and Promotion of the Diversity of Cultural Expressions (2005) and finally, the ‘historic urban landscapes’ (HUL) approach adopted worldwide in 2011, the paradigm shift can be seen. These discourses, on one hand, enabled the inclusion of long-left communal value not only in the heritage conservation domain but also in the urban development domain, thus paving the way for the notion of “heritage as a tool for sustainable development”. In reference to the above, this research adopts an evidence-based methodology in examining the case of ‘Conservation of Epiphany Church’ in Gurugram, India in the year 2021. The church which was once the symbol of association for its parish was in the early stage of decay until November 2020. The church has now been conserved through the efforts of the Epiphany Church Committee, community, and other concerned stakeholders under the supervision of Delhi based conservation team ‘adapt’. The second author has been instrumental in leading the initiative as project manager whereas the first author was the faculty mentor from the Jindal School of Art and Architecture who led the group of students to critically analyze the ongoing conservation works and formulate a conceptual revitalization program for the church complex. The conclusions drawn from this research are recorded, considering the detailed step-by-step process undertaken for conservation, the negotiations involved, and if these methods can work as a model for revitalization of the local heritage in peri-urban areas of Northern Indi
Self-assembled strained nanostructures for light emission grown using molecular beam epitaxy
Get PDFIII-V nanostructures are widely researched for applications in dislocation-resistant light emitters for photonic integrated circuits, quantum computing and single photon emitters. The 0D nanostructures include quantum dots (QDs), dot in a well (DWELLs), sub-monolayer QDs and droplet epitaxy QDs, while 1D elongated structures include quantum dashes and nanowires (NWs). The optical properties of nanostructures can be controlled through size, composition, strain and band-offsets during epitaxial growth and can be tailored precisely to emit light with photon energies suited to the application, spanning 0.2-2.0 eV. This thesis explores two novel QD based light emitters in the visible and near-infrared wavelength regime. In the first part of the thesis, we demonstrate the growth and characterization of tensile strained Ge QDs and Ge NWs phase segregated in the III-V matrix via Volmer-Weber growth mode emitting at 1200 nm. The second part of the thesis demonstrates the dislocation tolerance of compressively strained InP QDs grown on lattice-matched GaAs and lattice-mismatched Si substrate via Stranski-Krastanov growth mode emitting at 713 nm.
The first part of the thesis explores the growth of tensile strained Ge QDs and NWs phase segregated in the III-V matrix. Epitaxial growth of phase segregated Ge nanostructures embedded within III-V compound semiconductors is a promising way to achieve a high biaxial tensile strain along with precise control of nanostructure density, size and morphology. Here we demonstrate growth of phase-segregated Ge quantum dots (QDs) and compare them to our previously reported Ge nanowires (NWs); both are strained to an In0.52Al0.48As matrix with a high biaxial tensile strain of 3.6%. Despite the similar growth conditions, there exist pronounced differences in the lateral size and planar density of Ge QDs and Ge NWs, with Ge QDs showing significantly larger size, lower density and structural anisotropy along the in-plane [1-10] direction. In addition to the difference in morphology, Ge QDs are shown to be more prone to plastic relaxation by formation of dislocations and stacking faults, which we attribute to their larger in-plane size. Finally, tensile Ge QDs are shown to exhibit strong room-temperature photoluminescence at 1176 nm, which is blueshifted from the case of Ge NWs.
In the second part of the thesis, we demonstrate epitaxial InP QDs on GaAs on Si virtual substrates with room-temperature photoluminescence (PL) intensity nearly identical to those grown on GaAs substrates. The similarity in PL characteristics is remarkable considering that the active region on the GaAs/Si virtual substrate has a threading dislocation density (TDD) of ~3×10^7 cm-2, as compared to the bulk GaAs substrate with TDD 50× improvement in the luminescence intensity of InP QDs annealed at ~700⁰C for 100 minutes without observable structural degradation or blue-shift in the PL spectrum.Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2021-05-01The student, Pankul Dhingra, accepted the attached license on 2019-04-25 at 12:06.The student, Pankul Dhingra, submitted this Thesis for approval on 2019-04-25 at 12:16.This Thesis was approved for publication on 2019-04-25 at 14:10.DSpace SAF Submission Ingestion Package generated from Vireo submission #13914 on 2019-08-22 at 16:23:56Made available in DSpace on 2019-08-23T20:48:26Z (GMT). No. of bitstreams: 2
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Previous issue date: 2019-04-25Embargo set by: Seth Robbins for item 112387
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Accelerating (Compressed) SENSE Scans in MRI
No full textMagnetic Resonance Imaging is a painless procedure to produce high-resolution diagnostic images. Today, it is one of the essential clinical imaging modalities. One of the major challenges involved with this imaging modality is its long scanning time. Parallel imaging in combination with compressed sensing has overcome this challenge to a great extent. As a quid pro quo for this reduced scan time is the increase in image reconstruction time. An extensive research is focused to develop algorithms to make the image reconstruction faster. Fast Iterative Shrinkage Threshold algorithm is one of these algorithms (which is clinically viable) that speeds up the image reconstruction process. The present project focuses to speed up the particular algorithm, fast iterative shrinkage threshold algorithm, by preconditioning the convex optimization problem. This work proposes two new preconditioners, specifically in the context of the given algorithm, but otherwise can be used with different frameworks solving similar problems. The first preconditioner is a degree one polynomial of the system matrix and the second preconditioner is a block diagonal matrix where each block is a circulant matrix. The preconditioners are evaluated using two stopping criteria: residual error and relative error. The computation complexity of both the preconditioners are evaluated by measuring the floating point operations and total time consumption. Additionally, the simulations are performed by undersampling the data at two factors r=2 and r=4. The results indicate that the polynomial preconditioner reduces the overall time by a factor of 0.25 however is computationally expensive to construct. On the other side, block diagonal circulant preconditioner is extremely cheap to construct and evaluate on a vector but does not provide the desired results within the current framework. The study concludes that a suitable preconditioner for FISTA is the one that without affecting the largest eigenvalue of the system matrix improves the condition number and simultaneously is cheap to construct and evaluate.Electrical Engineerin
Understanding Non-Photochemical Laser Induced Nucleation
No full textNucleation is the initial step for the creation of new crystalline phase. A precise control over nucleation and its kinetics is important for both research and industries. Thus, alternative methods are sought after to extend the toolbox for controlling nucleation. In the 1990's, Non-Photochemical Laser Induced Nucleation (NPLIN) was suggested as a promising method to alter the nucleation kinetics. Since then, several reports have demonstrated that NPLIN dramatically reduces the nucleation induction time and controls polymorphism of various fine chemicals relevant for industrial practice. Although different hypotheses have been proposed in literature to explain the experimental observations, the mechanism behind NPLIN is still unknown.The objective of this work is to extend the mechanistic understanding of NPLIN. This has been approached by qualitatively studying the effect of different factors on the nucleation efficiency of the non-photochemical process using unfocused pulsed laser in aqueous supersaturated solution of KCl. The factors investigated include wavelength, peak intensity, supersaturation, mixing, and impurity level of the solution. Each of these parameters are studied using high number of samples (80-100) to generate a robust set of results and to avoid the stochastic nature of nucleation.In a separate series of experiments, an acoustic wave was detected in the solution due to the non-linear interaction of the unfocused laser with the system by measuring the pressure signal with a piezo-electric transducer placed just below the air-liquid interface. Further experiments were executed to understand the nature of the acoustic wave and its influence on NPLIN. The results show that laser could induce nucleation at significantly low peak intensities, much below the previously reported intensity threshold in literature. It is also observed that NPLIN shows a strong dependence on peak intensity, supersaturation, impurity level, and mixing of the solution while the dependence on wavelength was found to be weak. Furthermore, the acoustic wave experiments show that the laser induced pressure fluctuations do not affect the nucleation efficiency of the process. Overall, the results suggest that several mechanisms play a role during laser induced nucleation. To summarize, the research provides a robust analysis of different factors that can influence NPLIN. The results can be further utilized to enhance the understanding and applicability of the process
Influence of protein's molecular weight and polymer's PEG content on protein release from polymeric implants
No full textDe begeleider en/of auteur heeft geen toestemming gegeven tot het openbaar maken van de scriptie.
The supervisor and/or the author did not authorize public publication of the thesis.
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