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Computation, Volume 11, Issue 2

2023 February - 28 articles

Cover Story: Coarse-grained (CG) modeling is an established approach of simulating simplified systems to reach greater space and time scales than expensive all-atomic (AA) molecular dynamics (MD) simulations. The development of CG models requires deriving CG interactions that match AA or experimental properties. We proposed a physics-informed machine learning (PIML) framework for CG modeling, applied it to model the SARS-CoV-2 spike glycoprotein, and determined the force-field parameters using a force-matching scheme. With our framework, CGMD validation simulations reach microsecond time scales and are 40,000 times faster than conventional AAMD. The framework achieves improved accuracy compared to traditional iterative approaches, opening avenues in illuminating protein mechanisms and complex interactions. View this paper
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Articles (28)

  • Article
  • Open Access
9 Citations
3,850 Views
30 Pages

Low-Voltage Photovoltaic System Based on a Continuous Input/Output Current Converter

  • Carlos Andres Ramos-Paja,
  • Juan David Bastidas-Rodriguez and
  • Andres Julian Saavedra-Montes

Low-voltage photovoltaic systems are being widely used around the world, including their introduction into the power grid. The development of these systems requires the adaptation of several power converters, their static and dynamic modeling, the de...

  • Article
  • Open Access
5 Citations
3,903 Views
16 Pages

Composite Mould Design with Multiphysics FEM Computations Guidance

  • Iñaki Garmendia,
  • Haritz Vallejo and
  • Usue Osés

Composite moulds constitute an attractive alternative to classical metallic moulds when used for components fabricated by processes such as Resin Transfer Moulding (RTM). However, there are many factors that have to be accounted for if a correct desi...

(This article belongs to the Special Issue Application of Finite Element Methods)
  • Article
  • Open Access
4 Citations
3,873 Views
14 Pages

First-Principles Investigation of Electronic and Related Properties of Cubic Magnesium Silicide (Mg2Si)

  • Allé Dioum,
  • Yacouba I. Diakité,
  • Yuiry Malozovsky,
  • Blaise Awola Ayirizia,
  • Aboubaker Chedikh Beye and
  • Diola Bagayoko

We present results from ab initio, self-consistent calculations of electronic, transport, and bulk properties of cubic magnesium silicide (Mg2Si). We employed a local density approximation (LDA) potential to perform the computation, following the Bag...

(This article belongs to the Section Computational Chemistry)
  • Article
  • Open Access
12 Citations
3,953 Views
13 Pages

Rapid industrialization and population growth cause severe water pollution and increased water demand. The use of FeCu nanoparticles (nanoFeCu) in treating sewage has been proven to be a space-efficient method. The objective of this work is to develo...

(This article belongs to the Special Issue Intelligent Computing, Modeling and its Applications)
  • Article
  • Open Access
6 Citations
6,031 Views
13 Pages

Impact of Social Media on Knowledge of the COVID-19 Pandemic on Bangladeshi University Students

  • Shanjida Chowdhury,
  • Mahfujur Rahman,
  • Indrajit Ajit Doddanavar,
  • Nurul Mohammad Zayed,
  • Vitalii Nitsenko,
  • Olena Melnykovych and
  • Oksana Holik

This study aimed to examine the role and impact of social media on the knowledge of the COVID-19 pandemic in Bangladesh through disseminating actual changes in health safety, trust and belief of social media’s coverage statistics, isolation, an...

(This article belongs to the Special Issue Computation to Fight SARS-CoV-2 (CoVid-19))
  • Article
  • Open Access
5 Citations
3,779 Views
17 Pages

Benders Decomposition Method on Adjustable Robust Counterpart Optimization Model for Internet Shopping Online Problem

  • Diah Chaerani,
  • Shenya Saksmilena,
  • Athaya Zahrani Irmansyah,
  • Elis Hertini,
  • Endang Rusyaman and
  • Erick Paulus

In this paper, the implementation of the Benders decomposition method to solve the Adjustable Robust Counterpart for Internet Shopping Online Problem (ARC-ISOP) is discussed. Since the ARC-ISOP is a mixed-integer linear programming (MILP) model, the...

  • Article
  • Open Access
17 Citations
4,820 Views
26 Pages

Over the course of the COVID-19 pandemic millions of deaths and hospitalizations have been reported. Different SARS-CoV-2 variants of concern have been recognized during this pandemic and some of these variants of concern have caused uncertainty and...

(This article belongs to the Special Issue Computation to Fight SARS-CoV-2 (CoVid-19))
  • Article
  • Open Access
1 Citations
3,388 Views
16 Pages

Algorithm for Determining Three Components of the Velocity Vector of Highly Maneuverable Aircraft

  • Volodymyr Pavlikov,
  • Eduard Tserne,
  • Oleksii Odokiienko,
  • Nataliia Sydorenko,
  • Maksym Peretiatko,
  • Olha Kosolapova,
  • Ihor Prokofiiev,
  • Andrii Humennyi and
  • Konstantin Belousov

We developed a signal processing algorithm to determine three components of the velocity vector of a highly maneuverable aircraft. We developed an equation of the distance from an aircraft to an underlying surface. This equation describes a general c...

(This article belongs to the Special Issue Integrated Computer Technologies in Mechanical Engineering – Synergetic Engineering Ⅱ)
  • Article
  • Open Access
2 Citations
3,634 Views
11 Pages

Performance Analysis of SiGe-Cladded Silicon MMI Coupler in Presence of Stress

  • Sneha Kumari,
  • Akhilesh Kumar Pathak,
  • Rahul Kumar Gangwar and
  • Sumanta Gupta

In this study, we demonstrate the influence of operating temperature variation and stress-induced effects on a silicon-on-insulator (SOI)-based multi-mode interference coupler (MMI). Here, SiGe is introduced as the cladding layer to analyze its effec...

(This article belongs to the Special Issue Application of Finite Element Methods)
  • Article
  • Open Access
7 Citations
2,981 Views
15 Pages

To reduce traffic congestion and pollution, urban rail transit in China has been in a stage of rapid development in recent years. As a result, rail transit service interruption events are becoming more common, seriously affecting the resilience of th...

(This article belongs to the Section Computational Engineering)
  • Article
  • Open Access
7 Citations
6,583 Views
15 Pages

Multilabel data share important features, including label imbalance, which has a significant influence on the performance of classifiers. Because of this problem, a widely used multilabel classification algorithm, the multilabel k-nearest neighbor (M...

(This article belongs to the Special Issue Intelligent Computing, Modeling and its Applications)
  • Article
  • Open Access
10 Citations
4,188 Views
20 Pages

The paper is written to demonstrate the applicability of the notion of triangulation typically used in social sciences research to computationally enhance the mathematics education of future K-12 teachers. The paper starts with the so-called Brain Te...

(This article belongs to the Special Issue Computational Social Science and Complex Systems)
  • Article
  • Open Access
3 Citations
4,332 Views
20 Pages

Pricing and Hedging Index Options under Mean-Variance Criteria in Incomplete Markets

  • Pornnapat Yamphram,
  • Phiraphat Sutthimat and
  • Udomsak Rakwongwan

This paper studies the portfolio selection problem where tradable assets are a bank account, and standard put and call options are written on the S&P 500 index in incomplete markets in which there exist bid–ask spreads and finite liquidity....

(This article belongs to the Special Issue Quantitative Finance and Risk Management Research)
  • Article
  • Open Access
4 Citations
6,409 Views
17 Pages

Measuring the Recovery Performance of a Portfolio of NPLs

  • Alessandra Carleo,
  • Roberto Rocci and
  • Maria Sole Staffa

The objective of the present paper is to propose a new method to measure the recovery performance of a portfolio of non-performing loans (NPLs) in terms of recovery rate and time to liquidate. The fundamental idea is to draw a curve representing the...

(This article belongs to the Special Issue Computational Issues in Insurance and Finance)
  • Article
  • Open Access
6 Citations
4,724 Views
13 Pages

Nonparametric Estimation of Range Value at Risk

  • Suparna Biswas and
  • Rituparna Sen

Range value at risk (RVaR) is a quantile-based risk measure with two parameters. As special examples, the value at risk (VaR) and the expected shortfall (ES), two well-known but competing regulatory risk measures, are both members of the RVaR family....

(This article belongs to the Special Issue Computational Issues in Insurance and Finance)
  • Article
  • Open Access
16 Citations
5,451 Views
23 Pages

Operation of Gate-Controlled Irrigation System Using HEC-RAS 2D for Spring Flood Hazard Reduction

  • Farida Akiyanova,
  • Nurlan Ongdas,
  • Nurlybek Zinabdin,
  • Yergali Karakulov,
  • Adlet Nazhbiyev,
  • Zhanbota Mussagaliyeva and
  • Aksholpan Atalikhova

Flooding events have been negatively affecting the Republic of Kazakhstan, with higher occurrence in flat parts of the country during spring snowmelt in snow-fed rivers. The current project aims to assess the flood hazard reduction capacity of Alva i...

  • Article
  • Open Access
15 Citations
4,542 Views
26 Pages

A New Extension of the Kumaraswamy Generated Family of Distributions with Applications to Real Data

  • Salma Abbas,
  • Mustapha Muhammad,
  • Farrukh Jamal,
  • Christophe Chesneau,
  • Isyaku Muhammad and
  • Mouna Bouchane

In this paper, we develop the new extended Kumaraswamy generated (NEKwG) family of distributions. It aims to improve the modeling capability of the standard Kumaraswamy family by using a one-parameter exponential-logarithmic transformation. Mathemati...

(This article belongs to the Special Issue Applications of Computational Mathematics to Simulation and Data Analysis)
  • Article
  • Open Access
13 Citations
10,822 Views
8 Pages

Several studies estimate the volatility spillover effects between gold and silver returns, but none of them used the implied volatility to evaluate the long-term relationship between these two metal markets. Our paper aims to fill this gap in the exi...

(This article belongs to the Special Issue Quantitative Finance and Risk Management Research)
  • Article
  • Open Access
4 Citations
4,473 Views
18 Pages

Coarse-Grained Modeling of the SARS-CoV-2 Spike Glycoprotein by Physics-Informed Machine Learning

  • David Liang,
  • Ziji Zhang,
  • Miriam Rafailovich,
  • Marcia Simon,
  • Yuefan Deng and
  • Peng Zhang

Coarse-grained (CG) modeling has defined a well-established approach to accessing greater space and time scales inaccessible to the computationally expensive all-atomic (AA) molecular dynamics (MD) simulations. Popular methods of CG follow a bottom-u...

(This article belongs to the Special Issue Computation to Fight SARS-CoV-2 (CoVid-19))
  • Article
  • Open Access
19 Citations
4,660 Views
13 Pages

A Novel Computational Model for Traction Performance Characterization of Footwear Outsoles with Horizontal Tread Channels

  • Shubham Gupta,
  • Subhodip Chatterjee,
  • Ayush Malviya,
  • Gurpreet Singh and
  • Arnab Chanda

Slips and falls are among the most serious public safety hazards. Adequate friction at the shoe–floor contact is necessary to reduce these risks. In the presence of slippery fluids such as water or oil, the footwear outsole is crucial for ensur...

(This article belongs to the Special Issue Application of Finite Element Methods)
  • Article
  • Open Access
12 Citations
2,999 Views
13 Pages

Optimized Packing Titanium Alloy Powder Particles

  • Zoia Duriagina,
  • Alexander Pankratov,
  • Tetyana Romanova,
  • Igor Litvinchev,
  • Julia Bennell,
  • Igor Lemishka and
  • Sergiy Maximov

To obtain high-quality and durable parts by 3D printing, specific characteristics (porosity and proportion of various sizes of particles) in the mixture used for printing or sintering must be assured. To predict these characteristics, a mathematical...

(This article belongs to the Special Issue Intelligent Computing, Modeling and its Applications)
  • Article
  • Open Access
5 Citations
10,496 Views
9 Pages

Fast-growing technology and the development of IT services have yielded the idea of founding a new application of stochastic processes and their properties. We give a new connection between electronic process management and a relatively new stochasti...

(This article belongs to the Special Issue Applications of Statistics and Machine Learning in Electronics)
  • Article
  • Open Access
32 Citations
7,755 Views
15 Pages

In Indonesia, tomato is one of the horticultural products with the highest economic value. To maintain enhanced tomato plant production, it is necessary to monitor the growth of tomato plants, particularly the leaves. The quality and quantity of toma...

(This article belongs to the Topic Artificial Intelligence and Computational Methods: Modeling, Simulations and Optimization of Complex Systems)
  • Article
  • Open Access
12 Citations
2,506 Views
15 Pages

This study aims to reconstruct hazardous zones after the hydrogen explosion at a fueling station and to assess an influence of terrain landscape on harmful consequences for personnel with the use of numerical methods. These consequences are measured...

(This article belongs to the Special Issue Integrated Computer Technologies in Mechanical Engineering – Synergetic Engineering Ⅱ)
  • Review
  • Open Access
32 Citations
13,404 Views
22 Pages

Dental Age Estimation Using Deep Learning: A Comparative Survey

  • Essraa Gamal Mohamed,
  • Rebeca P. Díaz Redondo,
  • Abdelrahim Koura,
  • Mohamed Sherif EL-Mofty and
  • Mohammed Kayed

The significance of age estimation arises from its applications in various fields, such as forensics, criminal investigation, and illegal immigration. Due to the increased importance of age estimation, this area of study requires more investigation a...

(This article belongs to the Topic Interactive Artificial Intelligence and Man-Machine Communication)
  • Article
  • Open Access
77 Citations
8,958 Views
14 Pages

Water is a valuable, necessary and unfortunately rare commodity in both developing and developed countries all over the world. It is undoubtedly the most important natural resource on the planet and constitutes an essential nutrient for human health....

(This article belongs to the Section Computational Engineering)
  • Article
  • Open Access
1 Citations
2,284 Views
19 Pages

On the Influence of Initial Stresses on the Velocity of Elastic Waves in Composites

  • Alexander G. Kolpakov,
  • Igor V. Andrianov and
  • Sergey I. Rakin

The paper is devoted to the problem of propagation of elastic waves in composites with initial stresses. We suppose initial stresses are well within the elastic regime. We deal with the long-wave case and use the asymptotic homogenization technique b...

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Computation - ISSN 2079-3197