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"ABSTRACTOne of the processes requiring HPC environments is Molecular Dynamics ( MD ) . In tropical countries, the MD process is very important in the preparation of virtual screening experiments for anti-malaria search. Previous works on the virtual screening project for anti-malaria search conducted by WISDOM project uses grid infrastructure with 1,700 CPUs of various infrastructure provided in 15 countries [13]. In silico anti malaria compounds searching from Indonesian medical plants using virtual screening methods are urgently required. This can reduce the cost and time required compared to the direct searching or examining each compound by in vitro and in vivo which will spend a lot of time and expense . However, the use of thousands of processors is difficult for the researchers with limited resources in developing countries such as Indonesia. Our of previous studies using MD with GROMACS shows the improvement of the simulation time using Cluster. But that is not the case for some of our previous works with AMBER on Cluster where we did not obtain significant speed up. However, our previous works running GROMACS on GPUs provided significant speed up about 12 times faster than that run on Cluster. In this study , we build a GPU -based computing environment and have some MD simulation with AMBER. We used several computing environments such as cluster with 16 cores , GPU Geforce GTX 465 , GTX 470 , GTX 560 , GTX 680 , and GTX 780 . In addition to PfENR ( Plasmodium falciparum Enoyl acyl Carrier Protein Reductase ) enzyme , as benchmark we also conducted MD experiments on Myoglobin protein , Dihydrofolate reductase (DHFR) protein, and Ras - Raf protein . All experimental results showed that the slowest MD processes occurred on Cluster, followed in increasing order by GTX 560, GTX 465, GTX 470, GTX 680 and GTX 780. While the GPU speed up relative to cluster is about 24 , 26 , 32 , 24 , 77 and 101, respectively. "

"Fiksasi biologis yang melibatkan mikroalga adalah proses kompleks yang masih belum sepenuhnya dipahami karena keterbatasan metode eksperimental saat ini yang hanya menyediakan analisis pada skala makroskopik. Dalam penelitian ini, kami menyelidiki mekanisme permeasi molekul CO2 melalui membran sel mikroalga menggunakan simulasi dinamika molekuler. Kami memodelkan membran sel mikroalga sebagai molekul DPPC (Dipalmitoylphosphatidylcholine), sebuah jenis fosfolipid yang dominan dalam membran sel makhluk hidup. Kami menggunakan model atom lengkap dengan gaya medan CHARMM (Chemistry at Harvard Macromolecular Mechanics). Semua simulasi, termasuk minimisasi, ekuilibrasi , dan pengumpulan data, dilakukan menggunakan paket perangkat lunak LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). Hasil penelitian menunjukkan bahwa molekul CO2 dapat menembus membran sel mikroalga, dengan hambatan energi tinggi pada antarmuka antara wilayah lipid dan air. Koefisien difusi molekul CO2 melalui membran sel mikroalga berkisar antara 1.81 hingga 2.69 x 10-5 cm²/s, dan permeabilitasnya berkisar antara 0.17 hingga 0.22. Variasi suhu antara 300 dan 320 K tidak menunjukkan efek signifikan pada karateristik perpindahan molekul CO2.

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Biological fixation involving microalgae is a complex process that remains poorly understood due to the limitations of current experimental methods, which only provide macroscopic analysis. In this research, we investigate the mechanism of CO2 molecule permeation through the microalgae cell membrane using molecular dynamics simulations. We model the microalgae cell membrane as DPPC (Dipalmitoylphosphatidylcholine), a dominant phospholipid in living cell membranes. We use an all-atom model with the CHARMM (Chemistry at Harvard Macromolecular Mechanics) force field. All simulations, including minimization, equilibration, and data collection, are conducted using the LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) software package. The results show that CO2 molecules can permeate through the microalgae cell membrane, encountering a high energy barrier at the interface between the lipid and water regions. The diffusion coefficient of CO2 molecules through the microalgae cell membrane ranges from 1.81 to 2.69 x 10-5 cm²/s, and the permeability ranges from 0.17 to 0.22. The temperature variation between 300 and 320 K shows no significant effect on the transport properties of CO2 molecules."

"Molecular dynamic simulation is one field of science that uses computer as a resource for computational methods to calculate the number of forces acting within a molecular system and analyzing its movement. This simulation is useful for the discovery of drug compounds from an illness. This study uses Gromacs as molecular dynamics application which is running on cluster computing environment. A significant speed up is obtained during the experiments. "

"ABSTRAKHidrogen merupakan salah satu unsur yang melimpah dimuka bumi, hidrogen ditemukan bersenyawa dengan atom lain sehingga banyak terdapat di udara (seperti H2 dan NH2) maupun air (H2O), ketersediannya di kerak bumi sebesar 15,4%. Karena ketersediannya yang melimpah dan kemampuan menghasilkan sumber energi tanpa menghasilkan polusi udara dan air, maka hidrogen diproyeksikan sebagai sumber energi masa depan. Namun pemilihan material untuk alat penyimpanan hidrogen sangat penting karena hidrogen dalam fasa gas merupakan molekul yang reaktif sehingga membutuhkan penyimpanan dengan material yang tepat. Selain dari faktor keamanan, efektivitas adsorpsi hidrogen ke permukaan material juga menjadi fokusan utama. Oleh karena itu dipilihlah Grafena oksida, Grafena oksida adalah lembaran yang terbentuk dari lapisan tunggal Grafit oksida yang mudah untuk disintetis yang memiliki sifat elektoronik dan optik yang baik. Kelebihan menggunakan material Grafena oksida adalah harganya yang lebih murah dibanding Grafena murni dan tersedia dengan jumlah yang banyak. Gas yang dapat diserap material ini antara lain H2, CH4, CO2, N2, NH3, NO2, H2S, dan SO2. Riset yang dilakukan secara simulasi ini memungkinkan untuk menguji efektivitas adsorpsi dengan variasi temperatur dan tekanan yang lebih luas dan menggunakan biaya yang relatif lebih rendah dibandingkan dengan riset eksperimental. Maka riset yang dilakukan penulis menggunakan metode Simulasi Dinamika Molekuler. Variasi temperatur yang digunakan adalah 77 K, 100 K, 200 K, 250 K, 295K dan tekanan memiliki variasi 1 bar, 5 bar, 10 bar, 20 bar, 40 bar dan 80 bar pada sistem yang dibuat konstan. Hasil yang didapat akan dibandingkan dengan literatur hasil riset secara ekperimental.

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ABSTRACT

Hydrogen is one of the abundant elements on earth, hydrogen is found in compound with other atoms so that there are many in the air (such as H2 and NH2) and water (H2O), its availability in the earth's crust is 15.4%. Due to its abundant availability and ability to produce energy sources without producing air and water pollution, hydrogen is projected as a future energy source. But the selection of materials for hydrogen storage devices is very important because hydrogen in the gas phase is a reactive molecule that requires storage with the right material. Aside from safety factors, the effectiveness of hydrogen adsorption onto the surface of the material is also the main focus. Therefore graphene oxide was chosen, graphene oxide is a sheet formed from a single layer of graphite oxide which is easy to synthesize which has good electric and optical properties. The advantage of using graphene oxide material is that the price is cheaper than pure graphene and is available in large quantities. The gases that can be absorbed by this material include H2, CH4, CO2, N2, NH3, NO2, H2S, and SO2. Research conducted in this simulation makes it possible to test the effectiveness of adsorption with a wider variety of temperatures and pressures and uses a relatively lower cost compared to experimental research. Then the research conducted by the author uses the Molecular Dynamics Simulation method. The temperature variations used are 77 K, 100 K, 200 K, 250 K, 295 K, the pressure has a variation of 1 bar, 5 bar, 10 bar, 20 bar, 40 bar and 80 bar in a constant system. The results obtained will be compared with the research results experimentally."

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Gas Hidrogen memiliki potensial yang cukup baik untuk digunakan sebagai sumber energi yang bersih pada masa depan. Gas hidrogen yang digunakan sebagai energi saat ini masih memiliki kendala, dimana dalam sistem penyimpanan gas hirdrogen itu sendiri. Ada salah satu cara untuk mengatasinya dimana dengan menggunakan metode yang dinamakan adsorpsi. Material Grafit merupakan adalah material yang memiliki potensial yang digunakan sebagai material penyimpanan gas hidrogen. Pada riset secara eksperimental memerlukan biaya yang sangat tinggi. Sehingga, dibutuhkan metode riset lain yang melakukan riset tersebut. Pada riset yang dilakukan, penulis menggunakan metode simulasi salah satunya adalah metode Simulasi Dinamika Molekuler. Pada riset simulasi yang dilakukan adanya variasi temperatur adalah 77 K, 100 K, 150 K, 200 K, 273 K, dan 296 K dan variasi tekanan pada temperatur adalah pada 1 atm, 8 atm, 10 atm ,14 atm ,18 atm,  dan 20 atm. Kemudian hasil simulasi dibandingkan dengan hasil riset eksperimental yang telah dilakukan oleh peneliti sebelumnya.

 

 

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Hydrogen gas has good potential to be used as a clean energy source in the future. Hydrogen gas that is used as energy at this time still has an administration, whereas in the hydrogen storage system itself. There is one way to overcome it where by using a method called adsorption. Graphite is a material that has the potential to be used as a hydrogen gas storage material. In this study, the cost of experiments is very high. Required, other research methods are needed that conduct the research. In the research conducted, the author uses simulation methods, one of which is the Molecular Dynamics Simulation method. In the simulation research conducted there are variations in temperature namely 77 K, 100 K, 150 K, 200 K, 273 K, and 296 K and variations in pressure at temperatures are 1 atm, 8 atm, 10 atm, 14 atm, 18 atm, and 20 atm. Then the results of the experiment are compared with the results of experimental studies that have been done by previous researchers.

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"Liposom adalah teknologi pengiriman obat untuk meningkatkan kemanjuran dan keamanan obat. Liposom adalah vesikel amphiphilic yang memiliki bagian kutub dan non-kutub. Ini memungkinkan liposom untuk membawa obat-obatan hidrofilik dan hidrofobik. Kafein adalah zat psikoaktif yang disebut xanthine alkaloid yang memiliki sifat penetrasi kulit yang buruk. Ini karena kafein memiliki sifat hidrofilik. Jadi untuk meningkatkan konsentrasi kafein di lapisan kulit yang lebih dalam, diperlukan vesikel seperti liposom. Proses pembuatan liposom konvensional membutuhkan waktu lama, rumit dan dapat menghasilkan racun dari residu pelarut organik yang digunakan. Simulasi dinamika molekul dapat mengatasi keterbatasan pembuatan liposom konvensional dengan memvisualisasikan ikatan molekul dan menganalisis sifat-sifat liposom berdasarkan interaksi antar ikatan. Molekul kafein akan dikombinasikan dengan molekul kolesterol dan fosfolipid DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine). Simulasi dinamika molekul dilakukan pada Kafein dan liposom dengan komposisi Kolesterol - DPPC (1: 1; 1: 2; 1: 4) yang dipanaskan oleh 323 K dalam kotak virtual 100 Å dan diproduksi pada 125 ns. Sistem akan diproses menggunakan kuning. Visualisasi menghasilkan ikatan antar molekul untuk membentuk koleksi padat, ikatan tidak sempurna antar molekul dalam bentuk bola berlubang. Ini karena keterbatasan komputer dan kebutuhan untuk pelarut yang cocok. Sedangkan hasil analisis yang diperoleh dari ketiga liposom di atas stabil pada 323 K dan Kolesterol-DPPC (1: 4) memiliki ikatan paling padat dan volume terkecil adalah 44,7 Å X 43,4 Å X 58,8 Å (X, Y, Z). Energi potensial dari ketiga liposom akan berkurang yang menunjukkan keseimbangan energi di semua liposom.

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Liposomes are a drug delivery technology to improve the efficacy and safety of drugs. Liposomes are amphiphilic vesicles that have polar and non-polar sections. This allows the liposome to carry hydrophilic and hydrophobic drugs. Caffeine is a psychoactive substance called xanthine alkaloid which has poor skin penetration properties. This is because caffeine has hydrophilic properties. So to increase the concentration of caffeine in the deeper layers of the skin, vesicles such as liposomes are needed. The process of making conventional liposomes takes a long time, is complicated and can produce toxins from the residues of organic solvents used. Molecular dynamics simulations can overcome the limitations of making conventional liposomes by visualizing molecular bonds and analyzing the properties of liposomes based on interactions between bonds. Caffeine molecules will be combined with cholesterol molecules and DPPC phospholipids (1,2-dipalmitoyl-sn-glycero-3-phosphocholine). Molecular dynamics simulations were carried out on Caffeine and liposomes with Cholesterol-DPPC composition (1: 1; 1: 2; 1: 4) heated by 323 K in a 100 Å virtual box and produced at 125 ns. The system will be processed using yellow. Visualization produces bonds between molecules to form solid collections, imperfect bonds between molecules in the shape of a hollow ball. This is due to computer limitations and the need for suitable solvents. While the analysis results obtained from the three liposomes above are stable at 323 K and Cholesterol - DPPC (1: 4) has the densest bond and the smallest volume is 44.7 Å X 43.4 Å X 58.8 Å (X, Y, Z). The potential energy of all three liposomes will decrease which shows the energy balance in all liposomes."