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Development and benchmark of an electrostatic PIC/MCC numerical code for simulation of gas discharge plasmas Arda, İbrahim; Rafatov, İsmail; Department of Physics (2023-1-10) This work deals with the development of the Particle-in-Cell/Monte Carlo Collision (PIC/MCC) numerical code for simulations of gas discharge plasmas. The study of these discharges is stimulated by various scientific and technological applications, which include surface modification, etching, lasers, spacecraft thrusters, plasma displays, and biomedicine. The efficient adoption of these discharges as sources of plasma for these applications depends on the ability to control plasma properties in the relevant ...
HIBIT Proceedings 2022 Aydın Son, Yeşim; Karahan, Arzu; Otlu Sarıtaş, Burçak (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) ABOUT HIBIT The International Symposium on Health Informatics and Bioinformatics (HIBIT), first held in 2005, aims to bring together academics, researchers, and practitioners who work in these popular and fulfilling areas and create the much-needed synergy among the medical, biological, and information technology sectors. The HIBIT Conference Series is an international conference that brings together those working in health informatics, bioinformatics and information technology, academics, and researcher...
A Viral Enzymatic Reaction Prioritization Tool for Development of Viral Biosensors Kıyıkçı , Hüseyin Furkan; Anık , Ülkü; Süzek, Barış Ethem (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) Viruses are small pathogens that are capable of infecting most eukaryotes. Their effect varies from slight to fatal for the infected organism. Viral infections may lead to significant ecological, social, and financial costs. Despite significant advancements in vaccine and virus research, virus viral diseases continue to be a major public health concern. Biosensors, in general, are compact devices that convert bio-recognition processes into measurable signals in a short amount of time. More specifically, vir...
PageRank-flux On Graphlet-Guided-Network(PRO-GGNet): A Method for Pathway Reconstruction and Multi-Omic Data Integration Arıcı, Kaan; Tunçbağ, Nurcan (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) The recent advancement of omic technologies provides snapshots of cells, tissues, or patients identifying prominent genes, proteins, metabolites, and small molecules. However, accumulated big data on various omic data types may inherently make diseases or perturbations incomprehensible. Network inference or reconstruction methods map a set of significantly altered proteins/genes/metabolites to a given reference network that is composed of already known relations or interactions. Followingly, the signals fro...
Evaluation and Ranking of Protein Docking Models by 3D Convolutional Neural Networks Fathi, Amir; Rehman Azhar Khokhar, Moaaz Ur (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) Protein-protein interactions, which occur at protein-protein interfaces, are essential for biological activities. Understanding the mechanics of protein binding and predicting new interactions requires identifying protein-protein interface areas. It’s crucial to be able to determine protein-protein interactions quickly and accurately. Protein-protein complex structure is required to extract a protein interface. Because finding a single protein complex structure experimentally requires time and effort, compu...

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