304 research outputs found
sj-docx-1-pie-10.1177_09544089221142427 - Supplemental material for Statistical analysis and optimization of fuel cells using the design of experiment
No full textSupplemental material, sj-docx-1-pie-10.1177_09544089221142427 for Statistical analysis and optimization of fuel cells using the design of experiment by Sarthak Dwivedi, Lanka Tata Rao, Shashwat Goel, Satish Kumar Dubey, Arshad Javed and Sanket Goel in Proceedings of the Institution of Mechanical Engineers, Part E: Journal of Process Mechanical Engineering</p
Protein characterization using a computational microscope: Nanopore sequencing and biological condensates
No full textSubmission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2025-08-01The student, Kumar Sarthak, accepted the attached license on 2023-07-11 at 14:08.The student, Kumar Sarthak, submitted this Dissertation for approval on 2023-07-11 at 14:34.This Dissertation was approved for publication on 2023-07-13 at 13:55.DSpace SAF Submission Ingestion Package generated from Vireo submission #19625 on 2023-12-04 at 17:33:53Proteins are the workhorses of the cell, forming the basic building block of life. The structure, shape and sequence of the proteins in the human cell modulate the major biological processes in our body. Deciphering the sequence of any protein in a single-molecule measurement and understanding the molecular mechanism of structural rearrangements are the two major roadblocks in our fight against curing several deadly diseases. This thesis focuses on these two major areas of research, with the first part on single-molecule identification and sequencing of proteins and the second part on elucidating the molecular conformations of intrinsically disordered proteins in biomolecular condensates. The first part consists of six chapters describing the following areas of research in protein sequencing. Firstly, we describe a robust and inexpensive computational approach, the steric exclusion model (SEM) to calculate ionic current in nanopore systems that is orders of magnitude more efficient than all-atom molecular dynamics (MD) and yet is sensitive enough to account for the atomic structure of the nanopore and the analyte. Then in collaboration with the Oukhaled Lab at U. Cergy Pontoise France, we show the molecular mechanism underlying nanopore recognition of all twenty proteinogenic amino acids, a critical step toward realization of single-molecule protein sequencing. In collaboration with the Behrends Lab at U. Freiburg Germany, we demonstrate the use of an engineered protein nanopore to differentiate isomeric peptides, derived from human histone H4 protein of identical mass according to the positions of acetylated lysine residues. In collaboration with the Maglia Lab at U. Groningen Netherlands, we uncover the molecular mechanism of nanopore mass spectrometry using a FraC nanopore that can capture peptides of varying charge. We then combined all-atom molecular dynamics simulations and electrophysiology experiments to determine the molecular mechanism of the ionic current modulation and improve resolution of detecting biochemical reactions at single-molecule resolution using engineered nanopores. Lastly, we demonstrate a proof-of-principle proteome characterization system that relies on ionic current signatures produced by complete translocation of natively folded proteins through an array of nanopores. In the second part, we provide the first molecular-level insights into the microscopic structure of a biological condensate. Firstly, we benchmarked the efficacy of nine presently available molecular force fields in describing the structure and dynamics of a fused in sarcoma (FUS) protein. We validated and implemented the most efficient force fields in NAMD simulation package, enabling microscopic simulations of biological condensate systems containing tens of millions of atoms
Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma
No full textScience and Engineering Research Board 10.13039/50110000184
Field Model Identification and Control of a Mobile Electromagnet for Remote Actuation of Soft Robots
No full textThe actuation of miniaturized robots through external magnetic fields has great potential formedical applications. The controllability properties of the miniaturized robots are affected by magnetic field generation modality. In this work, themagnetic field of a mobile electromagnet, notably capable to generate a desired magnetic field in large 3D workspaces, has been identified first. Then, a control model of the field generation system has been developed to produce a desired magnetic field designed to generate a locomotion gait in a legged miniaturized robot. Preliminary experiments prove the viability of the approach
Data Management Plan Examples Database
No full textThis dataset is comprised of a collection of example DMPs from a wide array of fields; obtained from a number of different sources outlined in the README. Data included/extracted from the examples included the discipline and field of study, author, institutional affiliation and funding information, location, date modified, title, research and data-type, description of project, link to the DMP, and where possible external links to related publications, grant pages, or French language versions.
This CSV document serves as the content for a McMaster Data Management Plan (DMP) Database as part of the Research Data Management (RDM) Services website, located at https://u.mcmaster.ca/dmps. Other universities and organizations are encouraged to link to the DMP Database or use this dataset as the content for their own DMP Database.
This dataset will be updated regularly to include new additions and will be versioned as such. We are gathering submissions at https://u.mcmaster.ca/submit-a-dmp to continue to expand the collection
An analysis of intrusion detection classification using supervised machine learning algorithms on NSL-KDD dataset / Sarthak Rastogi ... [et al.]
No full textFrom the past few years, Intrusion Detection Systems (IDS) are employed as a second line of defence and have shown to be a useful tool for enhancing security by detecting suspicious activity. Anomaly based intrusion detection is a type of intrusion detection system that identifies anomalies. Conventional IDS are less accurate in detecting anomalies because of the decision taking based on rules. The IDS with machine learning method improves the detection accuracy of the security attacks. To this end, this paper studies the classification analysis of intrusion detection using various supervised learning algorithms such as SVM, Naive Bayes, KNN, Random Forest, Logistic Regression and Decision tree on the NSL-KDD dataset. The findings reveal which method performed better in terms of accuracy and running time
A Tale of Two Campaigns, The Hindu Centre for Politics and Public Policy
No full textAs Bihar enters the final phases of polling in the Assembly Elections, Sarthak Bagchi reflects on the competitive campaigns launched by the Bharatiya Janata Party led National Democratic Alliance (NDA) and the Grand Alliance of Nitish Kumar and Lalu Yadav, called the Mahagathbandhan. Bagchi’s reports bring out the divergent and distict campaign strategies of the two alliances, with one clearly on a grand scale catering to a richer, upper-caste voter base, designed to razzle and dazzle, while the other targets individuals in villages and hamlets, and is low-key. However, as Bagchi points out, both campaigns have been hard pressed to strike a balance between the rhetoric of caste and development.Asian Studie
Inclusion of the economically backward students: Scope and tenet of Indian school libraries
No full textThe study aims to find out how far a school library can contribute in the issue of inclusion of the economically backward class students. Meanwhile the author has opined three major issues: Economical, Psychological and Societal as the reasons behind the school dropouts in India; while theoretical analyses have unveiled that the school library has enough scope and potential to reduce the dropout rate by offering several innovative approaches. Further, the author has investigated the reality and forwarded ten unique approaches (broadly classified into Library beyond school, Increase the reading habit and Empowerment of the student) which could be fruitful to impede the dropout rates in school education and also framed a flowchart to describe the steps of the process. The study shows that the approaches are well construct and self-explanatory and proper implications of those ideas can uplift the literacy rate. Later, two cases are being cited in the study to understand the applicability of those initiatives. The result shows that through the appropriate application of the ideas the dropout rates have decreased in both the cases
Design of Wide Range Injection Locked Bang-Bang Phase Locked Loop for Dielectric Spectroscopy Applications
No full textThe biological activities inside human bodies are regulated by the electrical andmechanical properties of cells and its constituent molecules. Pathological changes within the cells due to diseases are accompanied by a corresponding change in these physical properties and consequently can be used to differentiate between the healthy and diseased cells. The electrochemical impedance spectroscopy (EIS) is one of the techniques used for characterization of purity of cells. The characterization involves measuring the response of the dielectric constant 휖' with frequency. The dielectric response shows the amount of polarization of the cell volume which is high at low frequencies and almost none at high frequencies. The frequency band during which the response makes this transition is known as 훽 dispersion. By observing the changes in the pattern for 훽 dispersion, the percentage of healthy cells can be estimated. The location of 훽 dispersion frequency band depends on the type of molecules, ranging from 10Hz for tissues till 5GHz for water. In this work, the design of phase locked loop is presented which is used for such EIS system to enable characterizing the materials for a wide range of frequencies.The PLL is designed for frequencies ranging from 0.5GHz to 5.12GHz which willenable the system to characterize purity of molecules from human cells to as small as water. The PLL uses injection locking technique to improve the frequency resolution required for the dielectric measurement. This technique allows power efficient way to reduce the phase noise of the PLL and hence increase the resolution of the frequency measurement. Further, counter assisted tracking is used to enhance the lock-in range of the PLL so that it stays locked during the frequency variation measurements. The required frequency resolution for dielectric measurement of water is found to be 1.2MHz for 1.25% accuracy. The current implementation can achieve worst case frequency error of 350kHz enabling the system to measure the dielectric constant until water.Electrical Engineerin
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