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Alternative Role of Motif B in Template Dependent Polymerase Inhibition

Chinese Journal of Chemical Physics 2022年第3期35卷 407-412,I0001页

作者： Xueying Luo Tiantian Xu Xin Gao Lu Zhang State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhou 350002China University of Chinese Academy of Sciences Beijing 100049China Computer Science Program ComputerElectrical and Mathematical Sciences and Engineering(CEMSE)DivisionKing Abdullah University of Science and TechnologyThuwal 23955-6900King-dom of Saudi Arabia KAUST Computational Bioscience Research Center(CBRC) King Abdullah University of Science and TechnologyThuwal 23955-6900Kingdom of Saudi Arabia Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry Xiamen 361005China

Severe acute respiratory syndrome coronavirus 2(SARS-Co V-2) relies on the central molecular machine RNA-dependent RNA polymerase(Rd Rp) for the viral replication and transcription. Remdesivir at the template strand has been shown to effectively inhibit the RNA synthesis in SARS-Co V-2 Rd Rp by deactivating not only the complementary UTP incorporation but also the next nucleotide addition. However, the underlying molecular mechanism of the second inhibitory point remains unclear. In this work, we have performed molecular dynamics simulations and demonstrated that such inhibition has not directly acted on the nucleotide addition at the active site. Instead, the translocation of Remdesivir from +1 to-1 site is hindered thermodynamically as the posttranslocation state is less stable than the pre-translocation state due to the motif B residue G683. Moreover, another conserved residue S682 on motif B further hinders the dynamic translocation of Remdesivir due to the steric clash with the 1′-cyano substitution. Overall,our study has unveiled an alternative role of motif B in mediating the translocation when Remdesivir is present in the template strand and complemented our understanding about the inhibitory mechanisms exerted by Remdesivir on the RNA synthesis in SARS-Co V-2 Rd Rp.

关键词： SARS-CoV-2 RNA-dependent RNA polymerase Inhibitory mechanism Nu-cleotide analog Molecular dynamics simulation

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Parameter Estimation for Partially Observed McKean-Vlasov Diffusions

arXiv

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arXiv 2024年

作者： Jasra, Ajay Maama, Mohamed Tempone, Raul School of Data Science The Chinese University of Hong Kong CN Shenzhen China Applied Mathematics and Computational Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Chair of Mathematics for Uncertainty Quantification RWTH Aachen University Aachen52062 Germany

In this article we consider likelihood-based estimation of static parameters for a class of partially observed McKean-Vlasov (POMV) diffusion process with discrete-time observations over a fixed time interval. In particular, using the framework of [5] we develop a new randomized multilevel Monte Carlo method for estimating the parameters, based upon Markovian stochastic approximation methodology. New Markov chain Monte Carlo algorithms for the POMV model are introduced facilitating the application of [5]. We prove, under assumptions, that the expectation of our estimator is biased, but with expected small and controllable bias. Our approach is implemented on several examples. Copyright © 2024, The Authors. All rights reserved.

关键词： Stochastic systems

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Secure analysis over generalized-K channels

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science China(Information sciences) 2020年第4期63卷 242-244页

作者： Luyao ZHANG Hui ZHAO Gaofeng PAN Liang YANG Jiawei CHEN School of Mathematics and Statistics Southwest University Computer Electrical and Mathematical Science and Engineering DivisionKing Abdullah University of Science and Technology School of Information and Electronics Beijing Institute of Technology College of Computer Science and Electronic Engineering Hunan University

Dear editor,The secrecy outage probability (SOP) is used to estimate the secrecy outage performance when the transmitter has no state information about potential wiretap channels [1], i.e., silent eavesdropping. Most previous work, such as [2, 3], has focused on the SOP defined in [1], which we call the conventional SOP in this study, where both un-

关键词： SOP Secure analysis over generalized-K channels

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Classification Of Environmental Micro-Fibres Using Stimulated Raman Microspectroscopy

Classification Of Environmental Micro-Fibres Using Stimulate...

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Conference on Lasers and Electro-Optics Europe (CLEO EUROPE)

作者： S. Laptenok L. Genchi C. Martin F. M. Baalkhuyur C. M. Duarte C. Liberale Biological and Environmental Science and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia Red Sea Research Center and Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal Saudi Arabia SEZ Department of Environmental Sustainability AlRaidah Digital City Red Sea Global Riyadh Saudi Arabia Computer Electrical and Mathematical Sciences and Engineering King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia

ISBN: (纸本)9798350345995

The mass usage of plastic materials in daily life has exponentially increased the amount of plastic waste in the environment. Various environmental factors degrade bigger plastic debris into smaller microplastic particles (less than 5 mm in size). Those particles have been detected in every possible environment, from oceans to fresh bottled water, from deserts to agricultural soils, food and air, and human blood. Due to its long degradation time and high surface-to-value ratio, microplastic can become an efficient vehicle for various pollutants that can accumulate in time. Therefore, accumulation in the human tissue will likely have a negative long-term effect. Microfibers are considered the most abundant microparticle type in the environment - their size (small, often < 15 μm in diameter, and relatively long length) and light weight allow easy and fast distribution even using aerial pathways.

关键词： Glass Materials Microfibers Raman microscopy Raman scattering Stimulated Raman scattering

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A Survey of DDoS Attacks Detection Schemes in SDN Environment

A Survey of DDoS Attacks Detection Schemes in SDN Environmen...

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2023 IEEE International Conference on computer, Information, and Telecommunication Systems, CITS 2023

作者： Rawat, Surabhi Gusain Obaidat, Mohammad S. Pundir, Sumit Wazid, Mohammad Kumar Das, Ashok Singh, Devesh Pratap Hsiao, Kuei-Fang Graphic Era Deemed to Be University Department of Computer Science and Engineering Dehradun248002 India King Abdullah Ii School of Information Technology The University of Jordan Amman11942 Jordan University of Science and Technology Beijing Beijing100083 China Center for Security Theory and Algorithmic Research International Institute of Information Technology Hyderabad500 032 India Computer Science Department University of Texas-Permian Basin 4901 E. University Blvd. OdessaTX79762 United States

ISBN: (纸本)9798350336092

Denial-of-service (DoS) attacks are a major concern in the field of Internet technology, and they pose a difficult security challenge. Among the different types of DoS attacks, distributed denial-of-service (DDoS) attacks are especially concerning because they can quickly drain the resources of a target, disrupting their computational and communication capabilities without warning. In response to the severity of this problem, various defense strategies have been developed to defend against DDoS attacks. In this paper, a survey on the various DDoS attacks detection schemes is presented. An overview of the DDoS attack methodology is given. The information on different types of DDoS detection methods in SDN environment is also provided. Then a comparative study of different DDoS attack detection schemes is given, which contains the comparisons of different schemes in terms of their advantages, limitations, accuracy values, and time complexity. © 2023 IEEE.

关键词： Denial-of-service attack

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Electromagnetic Imaging of Rough Dielectric Surface Profiles using a Single-Frequency Reverse Time Migration Method

Electromagnetic Imaging of Rough Dielectric Surface Profiles...

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Antennas and Propagation Society International Symposium

作者： Ahmet Sefer Ali Yapar Hakan Bagci Division of Computer Electrical and Mathematical Science and Engineering King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia Department of Electrical and Electronics Engineering Işιk University Istanbul Turkey Department of Electronics and Communications Engineering Istanbul Technical University Istanbul Turkey

An electromagnetic imaging scheme, which makes use of a single-frequency reverse time migration (RTM) technique to reconstruct two-dimensional (2D) rough surface profiles from the scattered field data, is formulated and implemented. The unknown surface profile, which is expressed as a one-dimensional height function, is the interface between two dielectric media. It is assumed that the profile is illuminated from one side and the scattered fields are “measured” along a line on this same side. RTM is used to construct a cross-correlation imaging functional that is numerically evaluated to yield an image of the investigation domain. The maxima of this functional yields an accurate reconstruction of the rough dielectric surface profile.

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High-Bandwidth,Low-Power CMOS Transistor Based CAB for Field programmable Analog Array

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computers, Materials & Continua 2023年第3期74卷 5885-5900页

作者： Ameen Bin Obadi Alaa El-Din Hussein Samir Salem Al-Bawri Kabir Hossain abdullah Abdulhameed Muzammil Jusoh Thennarasan Sabapathy Ahmed Jamal abdullah Al-Gburi Mahmoud A.Albreem Advanced Communication Engineering(ACE) Centre of ExcellenceUniversiti Malaysia Perlis(UniMAP)Faculty of Electronic Engineering TechnologyKangar01000Malaysia Electrical Engineering King Fahd University of Petroleum and MineralsDhahranEastern31261Saudi Arabia Space Science Centre Climate Change InstituteUniversiti Kebangsaan MalaysiaBangi43600Malaysia Department of Electronics&Communication Engineering Faculty of Engineering&PetroleumHadhramout UniversityAl-MukallaHadhramout50512Yemen Faculty of Engineering Norwegian University of Science and Technology(NTNU)GjovikN-2815Norway Faculty of Electronic Engineering Technology Universiti Malaysia Perlis(UniMAP)Kampus Alam UniMAP Pauh PutraArau02600Malaysia Department of General Educational Development Faculty of Science and Information Technology(FSIT)Daffodil International UniversityDhaka1207Bangladesh Department of Electronics and Computer Engineering(FKEKK) Center for Telecommunication Research and Innovation(CeTRI)Universiti Teknikal Malaysia Melaka(UTeM)Durian Tungal76100Malaysia Department of Electrical Engineering University of SharjahSharjah27272United Arab Emirates

This article presents an integrated current mode configurable analog block(CAB)system for field-programmable analog array(FPAA).The proposed architecture is based on the complementary metal-oxide semiconductor(CMOS)transistor level design where MOSFET transistors operating in the saturation region are *** proposed CAB architecture is designed to implement six of thewidely used current mode operations in analog processing systems:addition,subtraction,integration,multiplication,division,and pass *** functionality of the proposed CAB is demonstrated through these six operations,where each operation is chosen based on the user’s selection in the CAB interface *** architecture of the CAB system proposes an optimized way of designing and integrating only three functional cells with the interface circuitry to achieve the six ***,optimized programming and digital tuning circuitry are implemented in the architecture to control and interface with the functional ***,these designed programming and tuning circuitries play an essential role in optimizing the performance of the proposed *** of the proposed CMOS Transistor Based CAB system is carried out using Tanner EDA Tools in 0.35μm standard CMOS *** design uses a±1.5 V power supply and results in maximum 3 dB bandwidth of 34.9 MHz and an approximate size of 0.0537 *** demonstrates the advantages of the design over the current state-of-the-art designs presented for comparison in this ***,the proposed design has a clear aspect of simplicity,low power consumption,and high bandwidth operation,which makes it a suitable candidate for mobile telecommunications applications.

关键词： CMOS field programmable analog array configurable analog block current mode circuit

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RIS-Assisted Grant-Free NOMA

RIS-Assisted Grant-Free NOMA

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IEEE International Conference on Communications (ICC)

作者： Recep Akif Tasci Fatih Kilinc Abdulkadir Celik Asmaa Abdallah Ahmed M. Eltawil Ertugrul Basar Department of Electrical and Electronics Engineering Communications Research and Innovation Laboratory (CoreLab) Koç University Istanbul Turkey Computer Electrical and Mathematical Sciences & Engineering (CEMSE) Division King Abdullah University of Science and Technology (KAUST) Thuwal KSA

This paper introduces a reconfigurable intelligent surface (RIS)-assisted grant-free non-orthogonal multiple access (GF-NOMA) scheme. To ensure the power reception disparity required by the power domain NOMA (PD-NOMA), we propose a joint user clustering and RIS assignment/alignment approach that maximizes the network sum rate by judiciously pairing user equipments (UEs) with distinct channel gains, assigning RISs to proper clusters, and aligning RIS phase shifts to the cluster members yielding the highest cluster sum rate. Once UEs are acknowledged with the cluster index, they are allowed to access their resource blocks (RBs) at any time requiring neither further grant acquisitions from the base station (BS) nor power control as all UEs are requested to transmit at the same power. In this way, the proposed approach performs an implicit over-the-air power control with minimal control signaling between the BS and UEs, which has shown to deliver up to 20% higher network sum rate than benchmark GF-NOMA and grant-based optimal (OPT) PD-NOMA schemes depending on the network parameters. The given numerical results also investigate the impact of UE density, RIS deployment, and RIS hardware specifications on the overall performance of the proposed RIS-aided GF-NOMA scheme.

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SLA-SCA: Secure and Lightweight Authentication and Key Agreement Mechanism for Smart City Applications

SLA-SCA: Secure and Lightweight Authentication and Key Agree...

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2023 IEEE International Conference on Communications, Computing, Cybersecurity and Informatics, CCCI 2023

作者： Pant, Bhairvi Obaidat, Mohammad S. Singh, Shreya Pant, Mudita Wazid, Mohammad Das, Ashok Kumar Hsiao, Kuei-Fang Graphic Era Deemed to Be University Department of Computer Science and Engineering Dehradun248002 India King Abdullah Ii School of Information Technology The University of Jordan Amman11942 Jordan University of Science and Technology Beijing Beijing100083 China School of Computing Srm University TN Kattankulathur603203 India Ctr. for Security Theory and Algorithmic Research International Institute of Information Technology Hyderabad 500032 India University of Texas-Permian Basin Computer Science Department OdessaTX 79762 United States

ISBN: (纸本)9798350302561

The notion of a smart city is a modern concept characterized by the widespread integration of the Internet of Things (IoT) across various facets of urban life, including healthcare, traffic management, agriculture, and more. This establishes real-time communication and data exchange between all users, servers and devices through the Internet. As we begin to discuss communication between parties, one must also recognize the imperative need for this exchange to be secure and private, as such exchanges are extremely vulnerable to attacks such as man-in-the-middle and replay attacks and even situations like compromising of anonymity during exchanges. This paper focuses on finding an innovative solution to the same challenge. It proposes a mechanism to establish secure communication between the smart IoT devices and the connected cloud servers through a secure mutual authentication and key establishment process with a short name 'SLA-SCA'. The security analysis of the proposed SLA-SCA is done, which proves its resilience against the various potential attacks of such a communication. The proposed SLA-SCA outperformed the other existing schemes regarding important security and functionality features. © 2023 IEEE.

关键词： Internet of things

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Transportation Mode Recognition based on Cellular Network Data

Transportation Mode Recognition based on Cellular Network Da...

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Smart Mobility (SM), IEEE International Conference on

作者： Kalamkas Zhagyparova Ahmed Bader Nour Kouzayha Hesham ElSawy Tareq Al-Naffouri Computer Electrical and Mathematical Sciences and Engineering Department King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia School of Computing Queen's University Kingston Ontario Canada

A variety of modern technologies leveraging ubiquitous mobile phones have addressed the transportation mode recognition problem, which is the identification of how users move about (walking, cycling, driving a car, taking a bus, etc). It has found applications in areas such as smart city transportation, greenhouse emission calculation, and context-aware mobile assistants. To date, significant work has been devoted to the recognition of mobility modes from the GPS and motion sensor data available on smartphones. However, these approaches often require users to install a special mobile application on their smartphone to collect the sensor data, they are power inefficient and privacy intrusive. Also, bus and car modes are similar in terms of motion due to the same roads, traffic regulations and speed, which makes it challenging to accurately distinguish between the two modes. In this research, we handle these issues by offering a user-independent system that distinguishes three forms of locomotion-walk, bus, and car-solely based on mobile data (3G and 4G) of a smartphone. The system was developed using data collected in Makkah city, kingdom of Saudi Arabia. Using statistical classification and boosting techniques, we successfully achieved an accuracy of 82%, and with post-processing step we achieved an accuracy of 99%.

关键词： Smart cities Roads Transportation 3G mobile communication Regulation Motion detection Mobile applications

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