Judul: Analisis Kestabilan Protein 1GB1 Menggunakan Simulasi Dinamika Molekul
Abstrak: A mechanism to explain the stability of the protein is still a major problem that is not fully understood. One of the problem is understanding the high thermal stability of 1GB1 protein. The thermal stability of 1GB1 protein can be analyzed using molecular dynamics simulation technique. The aim of this research is to learn molecular dynamics and thermal stability of 1GB1 protein in the range of simulation up to 100 ns. Simulation process consists of the preparation, minimization, heating, equilibration, and production run. The initial coordinate file 1GB1 can be downloaded from Protein Data Bank. The influence of thermal that given by this simulation are 450K and 475K for 100 ns, while 500K is bounded for 2 ns. For 475K simulation, the unfolding process occured at 95 ns indicated by the dissappearance of some secondary structure. For 500K simulation, the unfolding process occured at 745 ps indicated by the dissappearance of most of the secondary structure (collapsing of α-helix and β-hairpin structure).
Keyword: unfolding, thermal stability, 1GB1 protein, 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: Revisi marga Ptychopyxis miquel (Euphorbiaceae) di kawasan Malesia
Abstrak: Ptychopyxis adalah salah satu marga dari 317 marga yang termasuk ke dalam suku Euphorbiaceae. pertama kali dipublikasikan oleh Miquel (1860). Marga ini Marga ini pernah dimasukkan kedalam marga lain, yaitu Podadenia, Mallotus dan Clarorivinia. Fakta tersebut menunjukkan bahwa batasan marga Ptychopyxis belum cukup mantap. Persebaran marga ini menurut Van Welzen (1993) jumpai di Thailand, Indochina dan kawasan Malesia, di seluruhnya ada 23 jenis dan 10 jenis diantaranya terdapat di kawasan Malesia. Marga ini umum berperawakan pohon dan berumah dua, tumbuh di hutan hujan dataran rendah sampai pada ketinggian 1500 m dpl. Penelitian taksonomi yang komprehensif tentang marga ini telah dilakukan oleh Airy Shaw pada tahun 1960; sejak saat itu belum ada penelitian taksonomi yang lebih kompre- hensif, khususnya untuk kawasan Malesia. Kini dengan bertambahnya jumlah spesimen koleksi baru, maka tepatlah kiranya dilakukan revisi marga. Tujuan penelitian ini adalah untuk memberikan batasan marga serta jenis-jenisnya yang termasuk dalam Ptychopyxis selain itu diteliti pula hubungan kekerabatan antar jenis dan keterangan-keterangan..dst
Keyword: Herbarium Bogoriense, Podadenia, Mallotus, Clarorivinia