46 research outputs found
ACRMGroup/epitopes v1.0
No full text<p>Code and data for our paper on analysis of epitope discontinuity and conformation:</p>
<p><strong>B-cell Epitopes: Discontinuity and Conformational Analysis</strong></p>
<p>Saba Ferdous<sup>a,b</sup>, Sebastian Kelm<sup>c</sup> Terry S. Baker<sup>c</sup> Jiye Shi<sup>c,d</sup> and Andrew C.R. Martin<sup>a,*</sup></p>
<p><sup>a</sup>Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK;<br>
<sup>b</sup>Present address: Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK10 4TG, UK;<br>
<sup>c</sup>UCB Pharma, 216 Bath Road, Slough SL1 4EN, UK;<br>
<sup>d</sup>Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 201800 Shanghai, China<br>
<sup>*</sup>To whom correspondence should be addressed ([email protected] --or-- [email protected])</p>
<p> </p>
First-principles investigations of transition metal hyperdoped silicon and germanium for intermediate band engineering
No full textSilicon is the dominant material in the semiconductor industry, massively used in transistors, rectifiers, microchips, and other solid-state electronic devices. On top of that, its optoelectronic properties are largely utilized in photovoltaics, photodiodes, and photodetectors. However, in many optoelectronic devices silicon is limited by its band gap of 1.12 eV (_ = 1,110 nm) which precludes absorption of low energy infrared photons. For example, current photovoltaic devices suffer energy loss to a great extent due to non-absorption of a large portion of the incoming solar spectrum. Additionally, if the photoresponse of silicon could be extended to the infrared, silicon could be used to replace more expensive germanium based detectors.
My thesis research focuses on defect engineering of silicon to extend the photoresponse to the infrared regime. Recently, introducing defects at large concentrations several orders of magnitude larger than the equilibrium solubility limit has emerged as an approach to engineering the optical response of silicon. Specifically my thesis research addresses three aspects of hyperdoped semiconductors, which are as follows. (i) Carrying out first-principles investigations of gold hyperdoped silicon to provide detailed insights into recent extensive experimental investigations. This analysis helps to reveal the origins of the sub band gap optical response observed in this system, as well as to provide insights into the metastability and atomic scale mechanism of the loss of optical response upon thermal annealing. (ii) Moving beyond gold to consider alternative suitable transition metal dopants. It is of interest to identify candidate dopants that enhance optical absorption, and have sufficient solubility in silicon to remain dissolved in the semiconductor at high concentration and/or can become kinetically trapped to mitigate metastability. (iii) Using the insights gained from gold (Au) hyperdoped silicon systems, which have been extensively studied, to extend defect analysis towards gold hyperdoped germanium. This work involves carrying out high-accuracy first-principles modeling of candidate dopant defects in silicon, and assessing their promise for sub band gap absorption.
For gold hyperdoped silicon, first-principles density functional theory is used to first establish the origins of sub band gap optical absorption. While the experimentally synthesized systems likely contain a distribution of gold-related defects, experiments and the electronic structure analysis presented here strongly suggest that substitutional gold is responsible for the optical response. Unfortunately, the experimentally realized system optically deactivates upon thermal treatment. To understand the deactivation, I propose a mechanism for the evolution of atomic structure during thermal relaxation using simulations of energy barrier calculations, diffusion, and defect reactions. The dissociative mechanism, in which diffusion occurs by exchange of substitutional and interstitial sites via vacancy formation and annihilation, is identified as the likely path for deactivation. Further, the experimentally observed lattice contraction is explained by the presence of vacancies and gold-vacancy complexes in excess concentrations. The presence of these vacancies is attributed to the minimization of the strain that arises from the large volume of gold incorporated into silicon.
Towards the goal of identifying candidate hyperdoped materials for advanced optoelectronic devices such as intermediate band photovoltaics, I have carried out a systematic study of transition metal dopants in silicon in search for better dopants. To find other possible candidate dopants that could exhibit infrared absorption and, possibly, better solubility in silicon, I have assessed alternative transition metals such as Mn, Fe, Co, Ni, Cu and Ag using the optical design rules learned from prior investigations of chalcogen hyperdoped silicon. As the gold doped silicon study shows that not only the optical absorption but the (meta)stability of the system is also important, I have included an analysis of solubility and diffusion in silicon. This investigation also provided an opportunity to reassess the properties of transition metal defects in silicon, which had been studied extensively several decades ago, now using modern first-principles methods. As part of this analysis I have summarized their magnetic and electronic structure using density of states, orbital hybridization analysis, and band diagrams. Finally, I have extended the analysis of gold hyperdoped silicon to gold hyperdoped germanium. The relationship between measured carrier decay dynamics and some possible defect configurations are proposed in conjunction with recent experimentally achieved high
concentrations of gold and demonstrated optical response in germanium.Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2021-12-01The student, Naheed Ferdous, accepted the attached license on 2019-10-24 at 14:40.The student, Naheed Ferdous, submitted this Dissertation for approval on 2019-10-24 at 15:00.This Dissertation was approved for publication on 2019-10-31 at 15:49.DSpace SAF Submission Ingestion Package generated from Vireo submission #14517 on 2020-02-28 at 17:21:15Made available in DSpace on 2020-03-02T22:12:13Z (GMT). No. of bitstreams: 4
FERDOUS-DISSERTATION-2019.pdf: 28847245 bytes, checksum: 3c4a412f988283fd47f175816a4365bd (MD5)
Thesis_Naheed (1).zip: 132375243 bytes, checksum: c2c9fe00c2abbb8d0d771ced51505328 (MD5)
LICENSE.txt: 4211 bytes, checksum: 6b9eb580539e7990781a94b27e239fb0 (MD5)
RNP_19_OCT_019761.pdf: 47335 bytes, checksum: b344b5007965406b3f74ffe6aecd3b23 (MD5)
Previous issue date: 2019-10-31Embargo set by: Seth Robbins for item 113871
Lift date: 2022-03-02T22:12:26Z
Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemEmbargo set by: Seth Robbins for item 113871
Lift date: 2022-03-02T22:15:21Z
Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemEmbargo set by: Seth Robbins for item 113871
Lift date: 2022-03-02T22:18:25Z
Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemU of I Only Restriction Lifted for Item 113871 on 2022-03-03T10:15:13Z
Structural and Conformational Analysis of B-cell Epitopes − component to guide peptide vaccine design
No full textPeptide vaccines have many potential advantages including low cost, lack of need for cold-chain storage and safety. However, it is well known that approximately 90% of B-cell Epitopes (BCEs) are discontinuous in nature making it difficult to mimic them for creating vaccines. To perform a detailed structural analysis of these epitopes, they needs to be mapped onto antigen structures that are complexed with antibody. In order to obtain a clean dataset of antibody-antigen complex crystal structures, a pipeline was designed to process automatically and clean the antibody related structures from the PDB. To store this processed antibody structural data, a database (AbDb) was built and made available online. The degree of discontinuity in B-cell epitopes and their conformational nature was studied by mapping epitopes in the antibody-antigen dataset. The discontinuity of B-cell epitopes was analysed by defining extended ‘regions’ (R, consisting of at least 3 antibody-contacting residues each separated by ≤ 3 residues) and small fragments (F, antibody-contacting residues that do not satisfy the requirements for a region). Secondly, an algorithm was developed to classify region shape as linear, curved or folded. Molecular dynamics simulations were carried out on isolated epitope regions (wild type and mutant peptides). The mutant peptides have been designed by mutating non-contacting and hydrophobic residues in epitopes. Two types of mutations (hy- drophobic to alanine and hydrophobic to glutamine) have been studied using molec- ular dynamics simulations. Furthermore, the effect of end-capping on wild type and mutant epitope regions has been studied. Simulation studies were carried out on 5 linear and 5 folded shape regions. Out of these, 2 epitopes (one linear and one folded), along with their mutants and derivatives, were tested experimentally for conformational stability by CD spectroscopy and NMR. The binding of isolated epitopes with antibody was also validated by ELISA and SPR
AbDb: Antibody structure database - A database of PDB derived antibody structures
No full textIn order to analyse structures of proteins of a particular class, these need to be extracted from Protein Data Bank (PDB) files. In the case of antibodies, there are a number of special considerations: (i) identifying antibodies in the PDB is not trivial, (ii) they may be crystallized with or without antigen, (iii) for analysis purposes, one is normally only interested in the Fv region of the antibody, (iv) structural analysis of epitopes, in particular, requires individual antibody–antigen complexes from a PDB file which may contain multiple copies of the same, or different, antibodies and (v) standard numbering schemes should be applied. Consequently, there is a need for a specialist resource containing pre-numbered non-redundant antibody Fv structures with their cognate antigens. We have created an automatically updated resource, AbDb, which collects the Fv regions from antibody structures using information from our SACS database which summarizes antibody structures from the PDB. PDB files containing multiple structures are split and numbered and each antibody structure is associated with its antigen where available. Antibody structures with only light or heavy chains have also been processed and sequences of antibodies are compared to identify multiple structures of the same antibody. The data may be queried on the basis of PDB code, or the name or species of the antibody or antigen, and the complete datasets may be downloaded.
Database URL: www.bioinf.org.uk/abs/abdb
Comparison of performance of shell-and-tube heat exchangers with conventional segmental baffles and continuous helical baffle
No full textProject Report on “Financial Performance Evaluation of Commercial Banks in Bangladesh”
No full textThe general objective of this study is to evaluate the financial performance of the commercial banks and the Islamic banks in context of Bangladesh. The author tries to critically compare the pros and cons across the commercial and Islamic banks in the country in this report
Representation Of Women In Parliament Of Bangladesh: Is It Hopeful?
No full textThe poor representation of women in nearly each policy-making facet of life is a universal matter. In the entire world, women are represented in government in poor ratio to their entire populace. A component of representative democracy is that irrespective of gender, all people have equal prospects to partake in the political arena. In elective points, better representation of women of power is a matter of fairness and parity. Yet, representation of women in many parliaments is often limited. Democracy cannot embellish without a rational representation of women in the parliament, which is the most influential organization of democratic states. The analytical structure of this study undertakes that the presence of women in parliament does not inevitably turn into the functional picture rather it is a result of organizational, sociological and institutional facets. This has failed to make an effective impact on the representation of women in Parliament in a particular political situation. Therefore, the issues that impede or enable women’s representation in elective points differ with the issue of socioeconomic progress, culture and the form of political arrangement. The author has taken a modest endeavor to disclose about the significant matters linked to women’s poor representation in Bangladesh Parliament
Roundness and taper of holes during drilling composites of various thickness by HSS drill bit under dry condition
No full text
Enhanced IEEE 802.11 by integrating multiuser dynamic OFDMA
No full textThis thesis was scanned from the print manuscript for digital preservation and is copyright the author.
Researchers can access this thesis by asking their local university, institution or public library to
make a request on their behalf. Monash staff and postgraduate students can use the link in the References field
