Judul: Variations of Water Molecule Models in Molecular Dynamics  Simulations: A Murine Double Minute 2 (MDM2) Case Study
Abstrak: Dalam simulasi dinamika molekuler diperlukan molekul air sebagai pelarut agar sistem sesuai dengan kondisi yang sebenarnya. Adanya keterbatasan daya komputasi dan tidak ada satu pun model yang mereproduksi semua nilai eksperimen dengan akurat sehingga perlu dilakukan perbandingan efisiensi komputasi dan akurasi model molekul air yang umum digunakan. Penelitian ini bertujuan mengetahui pengaruh variasi dari model molekul air pada kestabilan protein MDM2, serta menentukan model dengan ketepatan dan kecepatan simulasi yang optimal. Metode yang digunakan berupa simulasi dinamika molekuler selama 100 ns pada suhu 300 K dan 340 K dengan parameter yang dianalisis terdiri dari waktu simulasi, RMSD, radius girasi, jarak protein-ligan, RMSF, ikatan hidrogen, serta energi. Hasil simulasi menunjukkan bahwa meningkatnya suhu sistem dapat menurunkan kestabilan protein dan sebaliknya, serta variasi model molekul air menghasilkan fluktuasi grafik yang berbeda meskipun tidak signifikan. Berdasarkan hasil analisis, diperoleh bahwa simulasi yang menggunakan model SPC/E dan TIP3P lebih cepat daripada yang menggunakan model TIP4P-Ew dan OPC. Selain itu, analisis RMSD model SPC/E lebih sesuai dibandingkan TIP3P., In molecular dynamics simulations, water molecules are required as a solvent so that the system conforms to the real conditions. Due to limited computing power and no single model reproduced all experimental values exactly, it was necessary to compare the computational efficiency and accuracy of the widely used water molecule models. This research aimed to identify the effect of the variations for water molecule models on the stability of the MDM2 protein and determine a model with optimal accuracy and simulation quickness. The method utilised was molecular dynamics simulations for 100 ns at temperatures of 300 K and 340 K, with the parameters analysed consisting of time simulation, RMSD, radius of gyration, protein-ligand distance, RMSF, hydrogen bonds, and energy. Simulation results showed that increasing system temperature could decrease protein stability and vice versa, as well as that variations of water molecule models produced different, albeit insignificant, graph fluctuations. Based on the analysis results, it was obtained that the simulations using SPC/E and TIP3P models were quicker than those using TIP4P-Ew and OPC models. In addition, the RMSD analysis of the SPC/E model was more appropriate than TIP3P.
Keyword: Kestabilan protein, MDM2, model molekul air, simulasi dinamika  molekuler, Protein stability, MDM2, water molecule model, molecular dynamics simulation

Judul: Simulasi Dinamika Molekul Protein 1GB1 Menggunakan Not Just Another Molecular Dynamcs Program (NAMD)
Abstrak: Protein 1GB1 helps Streptomyces griseus to avoid host defense by immunoglobulin binding site properties. The aim of this study are to learn the mechanism of unfolding and molecular dynamics of protein 1GB1 by temperature variance based on some parameters. Coordinate file of 1GB1 that given by NMR (Nuclear Magnetic Resonance) can be downloaded from Protein Data Bank, then it was processed by some steps such as minimization, heating, equilibration and production run using PBC (Periodic Boundary Condition) and PME (Particle Mesh Ewald) methods. Simulation running at 325K, 350K, 375K, 400K, 450K dan 500K. Except simulation 1 ns at 500K, all simulations running for 10 ns. Some parameters shown unfolding process of 1GB1 at 900 ps in 500 K simulation. Secondary structures that broke for the first time is alpha-helix that converted to turn and coil.
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Judul: Etno-ornitologi Burung Kancilan Flores (Pachycephala nudigula nudigula Hartert 1897) pada Masyarakat Lio di Taman Nasional Kelimutu
Abstrak: Bare-throathed whistler is one of several wild birds in Kelimutu National Park (TNKL) that is believed to have correlation with Lio Community‟s belief. The estimation of Bare-throated whistler‟s population in Kelimutu National Park was about 186.41-1668.07 individual by the density about 0.0389-0.3481 ind/ha with the sex ratio 6.2:1 that spreaded on area with height of 1100 – 1600 masl. The characteristic of Bare-throated whistler‟s habitat is a natural forest with various canopy level, high plant species diversity and high density. The habitat characteristics related to the availability of food in the form of insects, cover, safety and a nesting site. Generally the most of Lio community knew the existence of Bare-throated whistler directly or from their parents‟ stories. The perceptions of Lio Community to the Bare-throated whistler‟s existence is generally support the conservation efforts. The perceptions construct the Lio Community‟s atitude that tend to be conservative to the existence of Bare-throated whistler. The attitude shown by their behavior that not cathing the Bare-throated whistler from the TNKL‟s area or the outside. The attitude have an important role to the existence of Bare-throated whistler in Kelimutu National Park‟s area.
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