Judul: Identification of Potential Compounds in Red Ginger (Zingiber officinale var. Rubrum) as SARS-CoV-2 3CL Protease Inhibitor with Molecular Docking Method
Abstrak: Virus korona merupakan virus yang menimbulkan kondisi patologis yang disebut sebagai Coronavirus Disease 2019 (COVID-19), dengan patogennya disebut sebagai Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Belum ada pengobatan pasti untuk menyembuhkan COVID-19, sehingga banyak masyarakat Indonesia yang menggunakan pengobatan tradisional untuk menangkal COVID-19, seperti dengan mengkonsumsi jahe merah (Zingiber officinale var. Rubrum). Penelitian ini bertujuan mengidentifikasi senyawa-senyawa yang terkandung dalam jahe merah, yaitu ar-kurkumin, gingerol, geraniol, shogaol, zingiberen, gingerenon, dan zingiberenol yang akan dijadikan ligan yang berpotensi sebagai inhibitor protease 3CL SARS-CoV-2 denganpendekatan penambatan molekuler melalui lima parameter, yaitu perubahan energi bebas Gibbs (∆G), tetapan inhibisi, jumlah ikatan hidrogen, prediksi aturan Lipinski, dan tingkat toksisitas. Hasil penelitian ini menunjukkan bahwa senyawa gingerenon berpotensi sebagai inhibitor protease 3CL SARS-CoV-2 dengan nilai energi bebas Gibbs sebesar -7,5 kkal /mol, tetapan inhibisi sebesar 3,15 M, membentuk 1 ikatan hidrogen, tergolong ke dalam senyawa dengan toksisitas sedang, dan memenuhi semua aturan Lipinski., Coronavirus is a virus that causes a pathological condition known as Coronavirus Disease 2019 (COVID-19), with the pathogen referred to as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). There is no definite treatment to cure COVID-19, so many Indonesians use traditional medicine to ward off COVID-19, such as by consuming red ginger (Zingiber officinale var. Rubrum). This study aims to identify the compounds contained in red ginger, namely ar-curcumene, gingerol, geraniol, shogaol, zingiberene, gingerenone, and zingiberenol which will be used as ligands that have potential as SARS-CoV-2 3CL protease inhibitors with a molecular docking approach through five parameters, namely changes in Gibbs free energy (∆G), inhibition constant, number of hydrogen bonds, prediction of Lipinski rule, and level of toxicity. These results indicate that the compound has potential as protease inhibitors gingerenon 3CL SARS-CoV-2 with Gibbs free energy value of 7.5 kcal / mol, inhibition constants of 3.15 μM, forming hydrogen bonds 1, belonging to the compound with moderate toxicity, and complies with all Lipinski rules
Keyword: gingerenone, molecular docking, protease 3CL SARS-CoV-2, red ginger

Judul: Potential Active Compound Of White Turmeric (Curcuma  Zedoaria) as PLpro SARS-Cov-2’s Inhibitor by In Silico
Abstrak: SARS-CoV-2 yang menjadi penyebab COVID-19 diketahui mengkode dua protease, yaitu 3CL-Pro (protease utama) dan PLpro (Papain Like protease). PLpro berperan dalam proses pematangan replikasi virus dan dapat menghambat respon imun sel inang melalui penghilangan ubiquitin atau deubiquitinasi (DUBs). Hal ini menjadikan PLpro sebagai target obat yang baik. Kunyit putih (Curcuma zedoaria) merupakan tanaman herbal yang diketahui memiliki berbagai jenis bioaktivitas seperti antikanker dan antimikroba. Namun, belum pernah dilakukan penelitian terkait potensinya sebagai antivirus. Penelitian ini bertujuan menguji potensi senyawa tanaman kunyit putih dalam menghambat aktivitas proteolitik PLpro SARS-CoV-2 yang dimulai dengan analisis bioavaibilitas ligan, validasi dan penambatan molekuler terarah menggunakan YASARA Structure, analisis interaksi ligan-reseptor menggunakan Discovery Studio, dan visualisasi binding pose menggunakan PyMol. Seluruh ligan uji merupakan inhibitor kompetitif. Epicurzerenone merupakan ligan dengan potensi inhibisi terbaik berdasarkan energi ikatan sebesar -4.734 kkal/mol, interaksi, dan sisi aktif pengikatan. Kata kunci : kunyit putih, Papain Like Protease (PLpro), penambatan molekuler, SARS CoV-2., SARS-CoV-2, which causes COVID-19, is known to encode two proteases, namely 3CL-Pro (main protease) and PLpro (Papain Like protease). PLpro plays a role in the maturation process of viral replication and can inhibit host cell immune responses through ubiquitin removal or deubiquitination (DUBs). This makes PLpro a good drug target. White turmeric (Curcuma zedoaria) is an herbal plant that is known to have various types of bioactivity such as anticancer and antimicrobial. However, no research has been conducted regarding its potential as an antiviral. This study aimed to examine the potential of white turmeric plant compounds in inhibiting the proteolytic activity of PLpro SARS-CoV-2 starting with analysis of ligand bioavailability, validation and directed molecular anchoring using YASARA Structure, analysis of ligand-receptor interactions using Discovery Studio, and visualization of binding poses using PyMol. All test ligands were competitive inhibitors. Epicurzerenone is the ligand with the best inhibitory potential based on the binding energy of -4.734 kcal/mol, interactions, and the active binding site. Keywords : molecular docking, Papain-like protease (PLpro), SARS CoV-2, white turmeric.
Keyword: kunyit putih, Papain Like Protease (PLpro), penambatan molekuler, SARS-CoV-2, molecular docking, white  turmeric

Judul: Hamiltonian formulation for linear waves motion in two layers fluid
Abstrak: The surface wave could be considered as a wave that separates two fluids, namely water and air. Based on this assumption, it is introduced the interfacial wave, a wave between two layers of fluid with different density. The formulation of interfacial waves motion begins with deriving the base equation of irrotational ideal fluid. Furthermore, according to irrotational fluid assumption, the base equation can be stated in velocity potential. In this derivation, the fluids domain is assumed to be restricted by rigid lid boundary conditions, both at the upper and lower limit. Therefore, the interfacial waves motion can be explained in a hamiltonian formulation. In the hamiltonian formulation, total energy is defined as the sum of kinetic and potential energy. The hamiltonian system is obtained from reduction of kinetic energy by using the Dirichlet Neumann Operator. The resulted kinetic energy equation is nonlinear. Therefore, this form is linearized by first part of the Taylor expansion. This linearization gives a dispersion relation of linear wave. Based on this dispersion relation, the phase speed of the linear wave depends on the density ratio of the two layers fluid.
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