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: Lejeuneaceae Subfamily Ptychanthoideae (Hepaticae) in  West Java
Abstrak: Subfamily Ptychanthoideae of the family Lejeuneaceae (Hepaticae) in West Java is still poorly known. Publications on this subfamily are out of dated and written in the 19th or early of 20th century. The last taxonomic treatment of Ptychanthoideae of West Java was in 1933, many species names have changed since then. Studies on Ptychanthoideae of West Java are urgently needed. Studies on the Ptychanthoideae were based on the specimens collected from West Java. A total number of 361 of specimens deposited in the Herbarium Bogoriense (BO), Herbarium Biotrop (BIOT), Gottingen Herbarium (GOET) and Bangi Herbarium (UKMB) were examined, those are old and several recent specimens collected in West Java. Recent collections were made from Telaga Warna, Ciater, Gunung Halimun Salak National Park, Cibodas Botanical Garden, Bodogol Education Center and Conservation (Gunung Gede Pangrango National Park), University of Indonesia Campus Depok, including several collections from Banten Province. Twenty four species of Lejeuneaceae subfamily Ptychanthoideae are known from West Java, belonging to 8 genera namely Acrolejeunea (Spruce) Schiffn. (2 species), Archilejeunea (Spruce) Schiffn. (1 species), Lopholejeunea (Spruce) Schiffn. (10 species), Mastigolejeunea (Spruce) Schiffn. (3 species), Ptychanthus Nees (1 species), Schiffneriolejeunea Verd. (1 species), Spruceanthus Verd. (2 species) and Thysananthus Lindenb. (4 species). Two new records of Ptychanthoideae: Mastigolejeunea indica Steph. and Thysananthus minor Verdoorn are reported for Java. A determination key to the species is presented including their descriptions and illustrations.
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