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All Journal Jurnal Penelitian Fisika dan Aplikasinya (JPFA) Jurnal Ilmu Fisika Molekul: Jurnal Ilmiah Kimia
Ahmad, Faozan
Unknown Affiliation
Astronomy Biochemistry, Genetics & Molecular Biology Chemistry Earth & Planetary Sciences Education Materials Science & Nanotechnology Physics

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Model Kinetik Amyloid-Beta (Aβ) pada Penyakit Alzheimer Menggunakan Metode Euler dan Runge-Kutta Order ke-4 Cindyawati, Cindyawati; Ahmad, Faozan; Hardhienata, Hendradi; Kartono, Agus
Jurnal Ilmu Fisika Vol 17 No 2 (2025): September 2025
Publisher : Jurusan Fisika FMIPA Universitas Andalas

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.25077/jif.17.2.125-134.2025

Abstract

Alzheimer's disease (AD) is a neurological disease that causes decreased brain function. It is known that the accumulation of amyloid-beta (Aβ) plaques in the brain is one of the causes of AD. The accumulation of Aβ plaques in the brain is a dynamic process; it begins with the growth of amyloid-beta monomers (M1). Furthermore, amyloid-beta dimers (M2) and so on, so that this collected into oligomers (O), fibrils (P), and plaques in the brain. This disrupts the communication pathways between nerve cells. In this study, each process of amyloid-beta plaque accumulation is presented with a mathematical model in the form of an ordinary differential equation. Therefore, the coupled ordinary differential equations are given for the entire process of Aβ plaque accumulation. In this study, this coupled model is calculated using numerical methods, such as the Euler and fourth-order Runge-Kutta methods. The Euler methods is simple and efficient, but its accuracy is low and can accumulate errors with larger step sizes. The fourth-order Runge-Kutta methods offers higher accuracy, better numerical stability, and greater control over the accuracy of the solution. These two numerical methods have never been compared for estimating numerical solutions of coupled ordinary differential equations.
A Bibliometric Analysis of Carbon Dots in Sensors Application Putro, Permono Adi; Hardhienata, Hendradi; Isnaeni, Isnaeni; Ahmad, Faozan; Khaerudini, Deni Shidqi; Prasetyo, Andhika Prima; Maddu, Akhiruddin
Jurnal Penelitian Fisika dan Aplikasinya (JPFA) Vol. 12 No. 2 (2022)
Publisher : Universitas Negeri Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26740/jpfa.v12n2.p138-155

Abstract

The exponential increase in carbonaceous-based research has prompted the scientific community to apply it to numerous value-added applications. This paper aimed to systematically analyze the comprehensive contributions clusters of publications per year, country, institution, authors, and keywords-wise by using a quantitative review technique called bibliometric analysis. The data was retrieved from the Scopus database to identify the overall scientific trend results with the keyword "carbon dots as a sensor" from 2010 to 2020. The VOSviewer, WordItOut, and Datawrapper are selected as tools for bibliometric analysis and data visualization. In this work, the total citations from the Scopus Core Set and the total citations in the most recent year have only been used for the assessment of highly cited papers. The results showed that after 2014, the number of publications increased significantly with the work related to “carbon dots as sensors.” Thus, comprehensive journals like the Angewandte Chemie - International Edition were the most popular in publishing articles, contributing to almost 6.39% of the research area. The country-wise analysis revealed that China accounted for more than 67.18% of the articles published, followed by the United States and India, comprising 6.24% and 6.13%, respectively. Lastly, keyword cluster analysis revealed five major research hotspots for future discussion. Thus, this analysis provides an important starting point for further studies on research concerning the direction of "carbon dots as a sensor" for positive development in the research area.
Structural Insights into Mutant and Wild-Type InhA Proteins: Implications for Targeting Tuberculosis and the Role of NAD Cofactors Dwi Iryani, Ryscha; Ahmad, Faozan; Muscifa, Zahra Silmi; Wahyudi, Setyanto Tri
Molekul Vol 20 No 3 (2025)
Publisher : Universitas Jenderal Soedirman

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20884/1.jm.2025.20.3.11655

Abstract

ABSTRACT. The high death rate and prevalence of multidrug-resistant tuberculosis (MDR-TB) pose a significant global health challenge. Enoyl-acyl carrier protein reductase (InhA) from Mycobacterium tuberculosis is one of the main targets for drug development to treat tuberculosis. Wever, mutations in the InhA structure found in Mycobacterium tuberculosis are responsible for MDR-TB. The Protein Data Bank (PDB) 3D structure of InhA was used in this study. The PDB has 102 3D structures, with 77 structures for wild-type proteins and 25 structures for mutant proteins. The structures with the best resolution values and most favorable region statistics in Ramachandran plots were selected, and redocking and cross-docking simulations were performed with Autodock Vina software to study the binding affinity of protein-ligand complexes and to assess the impact of mutations on binding affinity. This research also provides insights into the influence of Nicotinamide Adenine Dinucleotide (NAD) cofactors, which increase ligand binding efficiency. The results show how important the NAD cofactor is for improving ligand binding and how mutations can change the therapeutic potential of the found ligands. They also give suggestions for structures that can be used to make drugs that fight multidrug-resistant tuberculosis. Based on the docking results, with an RMSD value of less than 2.00 Å, the structures recommended for the virtual screening stage are 5COQ, 5CP8, and 5OIF for mutant proteins and 2X23, 4BQP, 4D0S, 4OHU, 4OXK, 4TRJ, and 5MTR for the wild-type protein. Keywords: Autodock Vina, Enoyl-acyl carrier protein reductase (InhA), multidrug-resistant tuberculosis (MDR-TB), NAD, Tubercolosis.
Co-Authors Agus Kartono Akhiruddin Maddu Andhika Prima Prasetyo cindyawati, cindyawati Deni Shidqi Khaerudini Dwi Iryani, Ryscha Hardhienata, Hendradi Isnaeni Isnaeni Muscifa, Zahra Silmi Permono Adi Putro Setyanto Tri Wahyudi