Faculty Publications
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Publications by NITK Faculty
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Item A Crossbar Interconnection Network in DNA(Institute of Electrical and Electronics Engineers Inc., 2015) Talawar, B.DNA computers provide exciting challenges and opportunities in the fields of computer architecture, neural networks, autonomous micromechanical devices, and chemical reaction networks. The advent of digital abstractions such as the seesaw gates hold many opportunities for computer architects to realize complex digital circuits using DNA strand displacement principles. The paper presents a realization of a single bit, 2×2 crossbar interconnection network built using seesaw gates. The functional correctness of the implemented crossbar was verified using a chemical reaction simulator. © 2015 IEEE.Item Synthesis, chemical characterization of novel 1,3-dimethyl acridones as cytotoxic agents, and their DNA-binding studies(2010) Sathish, N.K.; Gopkumar, P.; Rajendra Prasad, V.V.S.; Shanta Kumar, S.M.; Mayur, Y.C.A series of new 1,3-dimethyl acridone derivatives were synthesized with different alkyl side chain (propyl and butyl) substitution at N 10-position and highly basic amine groups at terminal end of alkyl side chain. All the synthesized molecules were screened for their cytotoxic activity against human breast adenocarcinoma (MCF-7) and human promyelocytic leukemia (HL-60) cell lines. DNA binding constants (Ki) of selected compounds were determined with calf-thymus DNA. Results showed that the molecules 7, 8, 10, 11, 12, 13, 14, and 15 exhibited good cytotoxic activity with IC50 value <10 ?M. Compound 14 having (?- hydroxyethyl) piperazine butyl side chain exhibited potent cytotoxic activity against MCF-7 cell line and DNA-intercalating properties. Examination of the relationship between lipophilicity and acridone derivatives showed poor correlation. © Birkhäuser Boston 2009.Item A novel DNA based password authentication system for global roaming in resource-limited mobile environments(Springer, 2020) Madhusudhan, R.; Shashidhara RMobile environments are highly vulnerable to security threats and pose a great challenge for the wireless and mobile networks being used today. Because the mode of a wireless channel is open, these networks do not carry any inherent security and hence are more prone to attacks. Therefore, designing a secure and robust protocol for authentication in a global mobile network is always a challenging. In these networks, it is crucial to provide authentication to establish a secure communication between the Mobile User (MU), Foreign Agent (FA) and Home Agent (HA). In order to secure communication among these entities, a number of authentication protocols have been proposed. The main security flaw of the existing authentication protocols is that attackers have the ability to impersonate a legal user at any time. Moreover, the existing authentication protocols in the literature are exposed to various kind of cryptographic attacks. Besides, the authentication protocols require larger key length and more computation overhead. To remedy these weaknesses in mobility networks, DNA (Deoxyribo Nucleic Acid) based authentication scheme using Hyper Elliptic Curve Cryptosystem (HECC) is introduced. It offers greater security and allows an MU, FA and HA to establish a secure communication channel, in order to exchange the sensitive information over the radio link. The proposed system derive benefit from HECC, which is smaller in terms of key size, more computational efficiency. In addition, the security strength of this authentication system is validated through widely accepted security verification tool called ProVerif. Further, the performance analysis shows that the DNA based authentication system using HECC is secure and practically implementable in the resource-constrained mobility nodes. © 2019, Springer Science+Business Media, LLC, part of Springer Nature.Item Fluorescent MoS2 Quantum Dot-DNA Nanocomposite Hydrogels for Organic Light-Emitting Diodes(American Chemical Society service@acs.org, 2020) Pandey, P.K.; Ulla, H.; Satyanarayan, M.N.; Rawat, K.; Gaur, A.; Gawali, S.; Hassan, P.A.; Bohidar, H.B.In this study, we report the synthesis of water-soluble MoS2 quantum dots (MoS2, QD) by a hydrothermal one-step method. These QDs were mixed in an aqueous solution of 2 kbp DNA to form fluorescent nanocomposite hydrogels at a very low concentration of the nucleic acid (1.0% (w/v), normal gelation occurs at 2% (w/v)). The melting temperature Tmelt of these gels was 50 ± 2 °C while the hydrogels melt at 40 ± 2 °C, and the low-frequency storage modulus/gel strength G0 was 40 ± 2 Pa (9 ± 2 Pa for hydrogel). This clearly implied that MoS2 acted as a pseudo-cross-linker in the nanocomposite hydrogel formation. The remarkable synergy of interaction between DNA and QDs can be gauged from the fact that the gel strength and melting temperature increased with QD content regardless of the fact that both carried negative charge. Dynamic light scattering studies showed arrested dynamics at the onset of gelation, and the gel transition time or ergodicity breaking time ?EB decreased with the increase in QD concentration. Small-angle X-ray scattering data captured the internal structure of these gels. Thus, we have a unique nanocomposite DNA-based hydrogel that is fluorescent, and in 2-D, this soft matter remarkably exhibits the behavior of an organic light-emitting diode (OLED), which imparts sufficient novelty to this work. © © 2020 American Chemical Society.Item Growth Reaction of Gold Nanorods in the Presence of Mutated Peptides and Amine-Modified Single-Stranded Nucleic Acids(John Wiley and Sons Ltd, 2023) Sahu, J.K.; Singh, O.; Chakraborty, D.; Sadhu, K.K.Conformation of biomolecules like DNA, peptides and amino acids play vital role during nanoparticle growth. Herein, we have experimentally explored the effect of different noncovalent interaction between a 5′-amine modified DNA sequence (NH2−C6H12-5′-ACATCAGT-3′, PMR) and arginine during the seed-mediated growth reaction of gold nanorods (GNRs). Amino acid-mediated growth reaction of GNRs results in a snowflake-like gold nanoarchitecture. However, in case of Arg, prior incubation of GNRs with PMR selectively produces sea urchin-like gold suprastructures, via strong hydrogen bonding and cation-π interaction between PMR and Arg. This distinctive structure formation strategy has been extended to study the structural modulation caused by two structurally close α-helical RRR (Ac-(AAAAR)3A−NH2) peptide and the lysine mutated KKR (Ac−AAAAKAAAAKAAAARA−NH2) peptide with partial helix at the amino terminus. Simulation studies confirm that a greater number of hydrogen bonding and cation-π interaction between the Arg residues and PMR resulted in the gold sea urchin structure for RRR peptide against KKR peptide. © 2023 Wiley-VCH GmbH.Item Plasmonic Biosensor for DNA Hybridization Using Integrated Graphene-Porous Silicon Waveguide(Institute of Electrical and Electronics Engineers Inc., 2023) Vankalkunti, S.; Singh, M.This work uses the full-vectorial finite element method to study a novel 3-D integrated graphene-porous silicon (p-Si) plasmonic waveguide-based nanostructure for deoxyribonucleic acid (DNA) hybridization. In this study, a p-Si waveguide is designed using the Maxwell Garnett model and is sandwiched between two low-indexed silicon dioxide (slot) layers. Next, a single graphene layer is deposited in both slot regions to enhance the sensor's absorption, tuneability, and sensitivity. The extraordinary optical transmission (EOT) through subwavelength nanoaperture reduces the ohmic losses and improves the optical transmission near the infrared region. Moreover, to optimize the sensor's design, a parametric analysis involving variations in the geometric dimensions of the sensor is performed using COMSOL multiphysics software. With 10% porosity of p-Si, the highest sensitivity value of 318.5 nm/RIU, 3.395/RIU figure of merit, 17.36 quality factor, and 0.01/nm detection accuracy with the presence of rectangular nanoaperture is achieved. Due to nanoscale size, the proposed label-free multilayer or hybrid plasmonic slot waveguide (HPSWG) biosensor offers the potential for future lab-on-a-chip (LOC) biological applications. © 2001-2012 IEEE.Item Machine Learning Framework for Classification of COVID-19 Variants Using K-mer Based DNA Sequencing(John Wiley and Sons Inc, 2025) Kumar, S.; Raju, S.; Bhowmik, B.Accurate classification of viral DNA sequences is essential for tracking mutations, understanding viral evolution, and enabling timely public health responses. Traditional alignment-based methods are often computationally intensive and less effective for highly mutating viruses. This article presents a machine learning framework for classifying DNA sequences of COVID-19 variants using K-mer-based tokenization and vectorization techniques inspired by Natural Language Processing (NLP). DNA sequences corresponding to Alpha, Beta, Gamma, and Omicron variants are obtained from the Global Initiative on Sharing All Influenza Data (GISAID) database and encoded into feature vectors. Multiple classifiers, including Extra Trees, Random Forest, Support Vector Classifier (SVC), Decision Tree, Logistic Regression, Naive Bayes, K-Nearest Neighbor (KNN), Ridge Classifier, Stochastic Gradient Descent (SGD), and XGBoost, are evaluated based on accuracy, precision, recall, and F1-score. The Extra Trees model achieved the highest accuracy of 93.10% (Formula presented.) 0.42, followed by Random Forest with 92.60% (Formula presented.) 0.38, both demonstrating robust and balanced performance. Statistical significance tests confirmed the robustness of the results. The results validate the effectiveness of K-mer-based encoding combined with traditional machine learning models in classifying COVID-19 variants, offering a scalable and efficient solution for genomic surveillance. © 2025 Wiley Periodicals LLC.