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: Tree sorrel (Averrhoa bilimbi L) Potential in Inhibiting RBD SARS-CoV-2 Interaction with ACE2 through Molecular Docking
Abstrak: Sejak akhir tahun 2019, dunia digemparkan dengan keberadaan strain baru dari virus corona yang diberi nama SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2). Angka infeksi yang terus meningkat menunjukkan bahwa virus SARS-CoV-2 harus ditangani secara serius agar wabah virus ini segera berakhir. Salah satu tindakan yang dapat dilakukan ialah mencari obat herbal yang berpotensi menghambat infeksi virus SARS-CoV–2. Penelitian ini bertujuan menguji potensi senyawa aktif buah belimbing wuluh dalam menghalangi pengikatan virus SARS-CoV-2 dengan reseptor ACE2 pada manusia. Metode yang digunakan dalam penelitian ini ialah penapisan virtual, analisis farmakokinetik dan toksisitas, penambatan molekuler menggunakan Autodock Vina serta visualisasi 2D. Hasil penambatan molekuler menunjukkan bahwa Hydrazinecarboxamide, 2-(2-methylcyclohexylidene) merupakan ligan uji yang memiliki potensi terbaik berdasarkan energi afinitas, interaksi pengikatan, farmakokinetik, dan toksisitas., Since the end of 2019, the world has been shaken by the presence of a new strain of the coronavirus which is named the SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2). Increase infections of SARS-CoV-2 shows that virus must be taken seriously so that this virus outbreak will end soon. One action that can be taken is to look for herbal remedies that have the potential to inhibit infection with the SARS-CoV-2 virus. This study aims to examine the potential of the active compounds of tree sorrel in blocking the binding of the SARS-CoV-2 virus with the ACE2 receptor in humans. The methods used in this study were virtual screening, pharmacokinetic and toxicity analysis, molecular docking used Autodock Vina and 2D visualization. The molecular docking results showed that Hydrazinecarboxamide, 2-(2-methylcyclohexylidene) had the best potential based on its afinity energy, binding interactions, and toxicity.
Keyword: ACE2, COVID-19, In silico, tree sorrel

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.
Keyword: