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"Over the past 40 years the field of molecular simulations has evolved from picosecond studies of isolated macromolecules in vacuum to studies of complex, chemically heterogeneous biological systems consisting of millions of atoms, with the simulation time scales spanning up to milliseconds. In Biomolecular Simulations: Methods and Protocols, expert researchers illustrate many of the methods commonly used in molecular modelling of biological systems, including methods for electronic structure calculations, classical molecular dynamics simulations and coarse-grained techniques. A selection of advanced techniques and recent methodological developments, which rarely find coverage in traditional textbooks, is also introduced. Written in the highly successful Methods in Molecular Biology series format, chapters include general introductions to well-established computational methodologies, applications to real-world biological systems, as well as practical tips and general protocols on carrying out biomolecular simulations. Special emphasis is placed on simulations of proteins, lipids, nucleic acids, and carbohydrates. Authoritative and practical, Biomolecular Simulations: Methods and Protocols seeks to aid scientists in further simulation studies of biological systems."

"Energi tidak terbarukan di Indonesia seperti batu bara masih sangat banyak digunakan untuk menghasilkan listrik. Energi tidak terbarukan ini dapat digantikan oleh sumber energi terbarukan. Indonesia sebagai negara kepulauan mempunyai banyak potensi energi terbarukan di laut seperti energi arus pasang surut. Energi ini dapat diubah dari bentuk energi kinetik menjadi energi listrik menggunakan turbin arus. Salah satu daerah yang mempunyai potensi cukup besar untuk pemanfaatan arus laut ini adalah Selat Alas yang memisahkan Pulau Lombok dengan Pulau Sumbawa. Pemilihan Selat Alas ini dikarenakan letaknya yang berada diantara dua pulau yang cukup kecil sehingga dapat bermanfaat bagi kedua pulau tersebut. Studi ini bertujuan untuk mengetahui besaran efisiensi dari turbin arus yang disimulasikan secara numerik menggunakan keadaan yang ada pada Selat Alas. Dalam studi ini dilakukan variasi diameter 18, 20, dan 22 meter. Berdasarkan hasil studi, dapat disimpulkan bahwa diameter turbin terbaik yang diperoleh secara numerikal adalah diameter turbin 22 meter dengan memperoleh efisiensi sebesar 42,58%. 

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Non renewable energy in Indonesia like coal still very widely used to generate electricity. This non renewable energy can be replaced by renewable energy sources. Indonesia as an archipelagic country  has a lot renewable enrgy sources potential in the sea such as tidal power. This energy can converted from kinetic energy to electrical energy using tidal turbine. One of the area with the biggest potential is Alas Strait. Alas Strait separate Lombok Island and Sumbawa Island. The selection of this area is based on because this strait separate two small islands so the electricity that generated by this turbine can be useful for the people of this two islands. This study aims to analize the efficiency of tidal turbine simulated with the condition of the Alas Strait using numerical simulation. In this study, variatios in diameters of the turbines are 18, 20, and 22 meters. Based on all the results of the tidal turbine efficiency study, it can be concluded that the best diameter of the turbine is 22 meters, with the efficiency generated is 42,58%."

"The present book presents a collection of simulation studies of this behaviour. Employing conceptually simple but comprehensive models, the fundamental material properties of shape memory alloys are qualitatively explained from first principles. Using contemporary methods of molecular dynamics simulation experiments, it is shown how microscale dynamics may produce characteristic macroscopic material properties. The work is rooted in the materials sciences of shape memory alloys and covers thermodynamical, micro-mechanical and crystallographical aspects."

"Kanker merupakan penyebab kematian utama di seluruh dunia. Salah satu faktor terjadinya kanker adalah modifikasi epigenetik yang abnormal (hipermetilasi). Hipermetilasi yang terjadi pada gen diyakini bahwa yang berperan besar dalam proses karsinogenesis adalah enzim DNA metiltransferase (DNMT). Penelitian-penelitian yang dilakukan saat ini untuk menemukan senyawa inhibitor DNMT dari bahan alam. Salah satu metode yang mendukung untuk analisis ini adalah metode in silico. Dalam penelitian ini, diteliti beberapa senyawa pilihan dari basis data herbal Indonesia hasil penapisan virtual terhadap aktivitasnya sebagai inhibitor DNMT. Hasil penambatan molekuler senyawa Cassiamin C, Procyanidin B2, Ent-epicatechin-4alpha-8-ent-epicatechin, Epicatechin-4beta-8-epicatechin-3-O-gallate, Neorhusflavanone, 3-O-galloylepigallocatechin-4beta-6-epicatechin-3-O-gallate, Withanolide, 3-O-galloylepigallocatechin-4beta-6-epigallocatechin-3-O-gallate, Cyanidin-3-6''-caffeylsophoroside-5-glucoside, Epifriedelinol, Gallo-catechin-4alpha-8-epicatechin, Scutellarein-7-glucosyl-1-4-rhamnoside, Epigallo-catechin-3-gallate (EGCG) (kontrol positif), dan sinefungin (kokristal) didapatkan nilai ΔG secara berturut-turut, -9.34, -10.95, -7.95, -11.01, -8.78, -8.87, -11.49, -7.98, -5.92, -8.92, -9.17, -8.76, -9.70, dan -9.11 kkal/mol. Senyawa cassiamin C, procyanidin B2, epicatechin-4beta-8-epicatechin-3-O-gallate, withanolide, dan gallocatechin-4alpha-8-epicatechin memiliki ΔG lebih rendah dari senyawa sinefungin (kokristal) dan EGCG (kontrol positif). Sehingga, tahap selanjutnya akan dilakukan simulasi dinamika molekuler terhadap tujuh ligan tersebut. Hasil simulasi dinamika molekuler menunjukkan aktivitas terbaik secara keseluruhan yaitu pada senyawa procyanidin B2, epicatechin-4beta-8-epicatechin-3-O-gallate, dan gallocatechin-4alpha-8-epicatechin. Residu asam amino yang penting bagi aktivitas inhibitor DNMT1 adalah Phe1145, Glu1168, Met1169, Cys1191, Glu1266, Ala1579, dan Val1580.

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Cancer is the leading cause of death worldwide. Factors of cancer is an abnormal epigenetic modifications (hypermethylation). Hypermethylation that occur in genes believed that played a major role in process of carcinogenesis is DNA methyltransferase (DNMT) enzyme. Recent studies is conducted to find DNMT inhibitor compounds from natural materials. Method that support for this analysis is in silico studies. In this study, several selected compounds from herbal database Indonesia results of virtual screening will be studying for the activity as an inhibitor DNMT. Results molecular docking of Cassiamin C, Procyanidin B2, Epicatechin-4alphaent-8-ent-epicatechin, Epicatechin-4beta-8-epicatechin-3-O-gallate, Neorhusflavanone, 3-O-galloylepigallocatechin-4beta-6-epicatechin-3-O-gallate, Withanolide, 3-O-galloylepigallocatechin-4beta-6-epigallocatechin-3-O-gallate, Cyanidin-3-6''-caffeylsophoroside-5-glucoside, Epifriedelinol, Gallocatechin-4alpha-8-epicatechin, Scutellarein-7-glucosyl-1-4-rhamnoside, Epigallocatechin-3-gallate (EGCG) (positive control), and Sinefungin (co-crystal) compounds, ΔG values obtained -9.34, -10.95, -7.95, -11.01, -8.78, -8.87, -11.49, -7.98, -5.92, -8.92, -9.17, -8.76, -9.70, and -9.11 kcal/mol, respectively. Cassiamin C, Procyanidin B2, Epicatechin-4beta-8-epicatechin-3-O-gallate, Withanolide, and Gallocatechin-4alpha-8-epicatechin compounds had lower ΔG than Sinefungin (co-crystal) and EGCG (positive control) compounds. Therefore, molecular dynamic simulation of seven selected compounds will be performed. The results of molecular dynamic simulation shows the best overall activity is Procyanidin B2, Epicatechin-4beta-8-epicatechin-3-O-gallate, and Gallocatechin-4alpha-8-epi-catechin compounds. Amino acid residues which are important for the activity of DNMT1 inhibitor is Phe1145, Glu1168, Met1169, Cys1191, Glu1266, Ala1579, and Val1580."

"Histon Deasetilase 2 (HDAC2) merupakan salah satu enzim dari suatu superfamily 18 enzim zinc-dependent yang kini tengah banyak diteliti sebagai target terapeutik. HDAC2 merupakan bagian dari HDAC kelas 1 yang diketahui memiliki aktivitas kuat sebagai katalis, dan umumnya merupakan target bagi inhibitor HDAC (HDACi). HDAC2 berperan pada gejala komplikasi akhir diabetes seperti nefropati diabetes. Sehingga penelitian lebih lanjut terkait inhibitor enzim-enzim HDAC khususnya HDAC2 perlu dikembangkan.Dalam penelitian ini, diteliti senyawa-senyawa dari basis data herbal Indonesia terhadap aktivitasnya sebagai inhibitor HDAC2, dengan melakukan penapisan virtual, untuk mendapatkan senyawa-senyawa pilihan, kemudian dilakukan simulasi dinamika molekuler untuk mengetahui interaksi senyawa sebagai inhibitor enzim. Didapatkan sepuluh besar peringkat senyawa penapisan virtual, kemudian diambil lima diantaranya dengan kriteria terbaik untuk dilakukan simulasi dinamika molekuler yaitu senyawa Boesenbergin B, Pongachalcone I, 6,8-Diprenylgenistein, Marmin, Mangostin, dengan kristal ligan N-(2-aminophenyl)benzamide sebagai kontrol positif, dengan nilai ΔG secara berturut-turut -8.28; -9.15; -7.05; -9.07; -7.15 dan ΔG kontrol positif -10.27. Dari simulasi dinamika molekuler diketahui aktivitas inhibitor HDAC2 berinteraksi pada residu asam amino penting yaitu His145C, Tyr308C, Zn379C, Leu276C, Phe155C, Phe210C, Leu144C, Met35C.

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Histone Deacetylase 2 (HDAC2) is one of a superfamily of 18 zinc-dependent enzymes, which now being widely investigated as therapeutic targets. HDAC2 is part of class I HDAC enzymes which knownly active as a strong catalys, and generally is the target for HDAC inhibitors (HDACi). HDAC2 play a role in the symptoms of late complications of diabetes such as diabetic nephropathy. So further research related to HDAC inhibitors, particularly HDAC2 need to be developed.In this study, research will be performed using virtual screening method to obtain several herbal compounds against their activities as HDAC2 inhibitors from the Indonesian herbal database, molecular dynamics simulations are then conducted to understand the interaction of compounds as inhibitors of the enzyme. The results of virtual screening process managed to obtained ten compounds with the highest Pharmacophore fit score rating, and would selected five compounds with the best criteria for molecular dynamics simulations, which are Boesenbergin B, Pongachalcone I, 6,8-Diprenylgenistein, Marmin, Mangostin, and active crytal ligand N-(2-aminophenyl)benzamide as a positive control, with respectively ΔG values obtained -8.28; -9.15; -7.05; -9.07; -7.15 and -10.27 as the ΔG value of active crystal ligand. From moleculer dynamics simulation of the activity of HDAC2 inhibitors are known to interact in two important amino acid residue that is His145C, Tyr308C, Zn379C, Leu276C, Phe155C, Phe210C, Leu144C, Met35C."