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Simulasi Numerik Osilasi Bioluminesensi Kunang-Kunang Syarif, Nirwan
Jurnal Penelitian Sains No 9 (2001)
Publisher : Faculty of Mathtmatics and Natural Sciences

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Abstract

Penelitian mengenai pola osilasi yang terjadi pada proses bioluminesensi dilakukan dengan menggunakan teknik simulasi numerik. Simulasi numerik diterapkan pada suatu model matematis yang merupakan satu set persamaan differensial kecepatan reaksi spesi kimia yang terlibat dalam reaksi dan merupakan hasil elusidasi dari mekanisme reaksi yang telah diusulkan oleh peneliti lain sebelumnya. Beberapa langkah operasi matematis diterapkan terhadap persamaan diferensial hingga dihasilkan diagram fase parameter. Diagram tersebut merupakan informasi mengenai berbagai kondisi dinamis sistem termasuk pola osilasi dan kestabilan sistem. Hasil pengamatan dari simulasi numerik model matematis yang ditemukan menunjukkan bahwa terdapat empat keadaan dinamis dengan dua pola osilasi yang terjadi pada proses ini, yaitu: osilasi teredam (damped oscillations), dan osilasi berkelanjutan (sustained oscillations) atau osilasi dengan siklus batas. 
Analyses of Non-bonding Length, Partial Atomics Charge and Electrostatic Energy from Molecular Dynamics Simulation of Phospholipase A2 – Substrate Syarif, Nirwan; Rohendi, Dedi
Indonesian Journal of Fundamental and Applied Chemistry Vol 1, No 3 (2016): October 2016
Publisher : Indonesian Journal of Fundamental and Applied Chemistry

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24845/ijfac.v1.i3.72

Abstract

Abstract: This paper reports molecular dynamics simulation of phospholipase A2 (PLA2)– substrate that has been done. Non-bonding length, partial atomic charge and electrostatic energy were used to evaluation the interaction between PLA2 and substrate. The research was subjected for three types of PLA2 of different sources, i.e, homo sapien, bovinus and porcinus, by using computer files of their molecular structures. The files with code 3elo, 1bp2, dan 1y6o were downloaded from protein data bank.  Substrate structure can be found in 1y60 and was separated from its enzyme structure and docked into two other PLA2 structures for simulation purpose. Molecular dynamics simulations were done for 30000 steps with constant in number of molecules, volume and temperature (NVT). The results showed the existing of flip-flop mechanism as basic feature of PLA2 – substrate reactions. Interaction length analysis results indicated the presence of water molecules on the structures of 1bp2 and 3elo at the time of the simulation was completed. The existence of aspagine at the reaction site confirmed the theory that this amino acid is responsible for the survival of the reaction. the electrostatic energy increased substantially in the interaction after homo sapien PLA2 (3elo) and Bovinus (1bp2) with the substrate. Inverse effect took place in the PLA porcinus (1y6o).Keywords: flip flop, inflammation, in-silico, simulation Abstrak (Indonesian): Telah dilakukan penelitian tentang simulasi dinamika molekuler pada Situs Reaksi Phospholipase A2 (PLA2) dengan substratnya. Analisis panjang non-ikatan, muatan atom parsial dan energi elektrostatis digunakan untuk menilai interaksi antara PLA2 dan substratnya. Penelitian dilakukan pada tiga jenis sumber PLA2, yaitu homo sapien, bovinus dan porcinus dengan menggunakan file komputer untuk struktur molekul dengan kode 3elo, 1bp2, dan 1y6o. Pada file 1y60 terdapat struktur substrat yang dapat ditemukan secara alamiah. Kedua file lainnya tidak mengandung struktur molekul substrat. Simulasi dinamika molekul dilakukan untuk 30.000 langkah dengan konstan dalam jumlah molekul, volume dan suhu (NVT). Hasil penelitian menunjukkan keberadaan mekanisme flip-flop sebagai fitur dasar reaksi PLA2 - substrat. Hasil analisis panjang interaksi menunjukkan bahwa kehadiran molekul air pada struktur 1bp2 dan 3elo pada saat simulasi dilakukan. Keberadaan aspagine di lokasi reaksi menegaskan teori bahwa asam amino ini bertanggung jawab untuk kelangsungan hidup reaksi. energi elektrostatik meningkat secara substansial dalam interaksi setelah homo sapien PLA2 (3elo) dan Bovinus (1bp2) dengan substrat. efek terbalik terjadi di porcinus PLA (1y6o).Kata kunci: flip flop, inflamasi, peradangan, in-silico, simulasi
THE DYNAMICS MOLECULER OF WATER MOLECULE ABSORPTION IN SILICATE ZEOLITE Syarif, Nirwan
Jurnal Zeolit Indonesia Vol 6, No 2 (2007)
Publisher : Jurnal Zeolit Indonesia

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Abstract

The water molecule dynamics absorbed at silicalite zeolite was studied with molecule dynamics technique using the computer. This paper reports the effect of temperature on behavior of dynamic system. The result showed the improvement of diffusion coefficient and diffusion activation energy along with the improvement of temperature. Improvement of temperature cause the change of the contact distance of the water molecule in zeolite molecule.
Hubungan Kuantitatif Antara Struktur dan Aktivitas Antioksidan dan Senyawa Flavonoid Dengan Menggunakan Metode Semiempiris AM1 Syarif, Nirwan; Rahmawati, Rully
Jurnal Penelitian Sains No 17 (2005)
Publisher : Faculty of Mathtmatics and Natural Sciences

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Abstract

Telah dilakukan penelitian terhadap hubungan antara struktur dan aktivitas (HKSA) antioksidan senyawa flavonoid dengan menggunakan metode komputasi kimia. Untuk mempelajari HKSA dilakukan proses optimasi geometri dan perhitungan momen dipol dan perubahan energi antara energi HOMO dengan energi LUMO sebagai sifat struktur senyawa flavonoid. Dalam hal ini digunakan metode semiempiris AMI dengan perangkap lunak Hyperchem for windows versi 5.0. aktivitas senyawa sebagai log (1/IC50) diperoleh dari literatur. HKSA diperoleh dari hasil perhitungan dengan menggunakan program analisis regresi multilinier dalam perangkat lunak SPSS for windows versi 11.5. persamaan HKSA terbaik pada senyawa flavonoid yang dihasilkan pada penelitian ini yaitu log 1/IC50 = 0,213 PE + 0,083 μ + 0,104. Senyawa flavonoid yang digunakan dalam penentuan HKSA terbaik terdiri dari sembilan senyawa yang mempunyai kemiripan struktur dan nilai selisih antara IC50 prediksi dengan eksperimen yang kecil. Analisis hubungan interaksi antara prediksi dengan eksperimen yang menggunakan persamaan HKSA terbaik menghasilkan nilai koefisien korelasi (r) sebesar 0,925; dimana nilai tersebut menunjukkan adanya hubungan interaksi antara keduanya.
Electrochemical Impedance Spectroscopy of Polyvinylalcohol Based Gel Electrolyte Syarif, Nirwan; Hidayanti, Nurlisa; Majlan, Edy Herianto; Jayanti, Monica Sari
Indonesian Journal of Fundamental and Applied Chemistry Vol 2, No 1 (2017): February 2017
Publisher : Indonesian Journal of Fundamental and Applied Chemistry

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24845/ijfac.v2.i1.16

Abstract

Research on the effect of electrolyte ammonium salt, concentration electrolyte with plasticizer to ionic and electronic conductivity of polymer gel electrolyte has been conducted with the variations of two electrolyte NH4Cl-PVA and NH4SCN-PVA at a concentration of 10, 30, 40 (wt%). The measurement of using ionic conductivity by using  impedance spectroscopy method showed that the highest value was 0.0156 Scm-1 i.e. in the  54.6% propilen carbonate with 40%  NH4Cl and PVA. The lowest value was 0.009 Scm-1 i.e. in the NH4SCN based electrolyte without propilene carbonate and electronic conductivity showed that the highest value was 0.0156 Scm-1 i.e. 40% NH4Cl-PVA and NH4SCN-PVA and the lowest value was 0.009 Scm-1, i.e. in the NH4SCN based electrolyte without propilene carbonate. Factorial analyses showed that the concentrations of electrolyte and the plasticizer affect conductivity value. FTIR (Fourier Transform Infrared) measurement showed that the  addition of propilene carbonate did not show new bond formation between electrolyte and PVA. It can be shown in absence of characteristic wave number for propilene carbonate and NH4+ ion.Keywords: DOE, plasticizer,  propylenecarbonate, ionic, electronic, conductivity
Colony Morphology of Yeast Isolates from Tuak and Its Application in Producing Ethanol From Sugarcane Bagasse Hermansyah, Hermansyah; Arini, Feggy; Syarif, Nirwan; Yohandini, Heni
Sriwijaya Journal of Environment Vol 1, No 3 (2016): Biodiversity
Publisher : Program Pascasarjana Universitas Sriwijaya

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Abstract

Abstract: Colony morphology yeast isolates from tuak and its application in producing ethanol from sugarcane bagasse has been conducted. Yeast isolates used in this work were HT4, HT5, and HT20 obtained from Tuak. These isolates have cream to yellow in color, spherical to oval in shape, and grow as budding cells. Our goal is to find yeast isolates used as microbial agent in fermentation process producing ethanol from lignocellulosic biomass as raw material.  Based upon morphology showed that these isolates were Candida species.  Isolate HT5 then used to see its potent  as  agent in bioethanol production.  Fermentation of 5 g sugarcane bagasse substrate resulted 0.0008% ethanol.  This results indicated that isolate has a potent as microbial agent for fermentation, however the optimum condition of process is needed to furthermore study.    Keywords: Candida species, bioethanol, TuakAbstrak (Indonesian): Telah dilakukan penelitian terhadap morfologi koloni dari isolat khamir dari tuak dan aplikasinya dalam produksi etanol dari ampas tebu.  Isolat khamir yang digunakan adalah koloni HT4, HT5, dan HT20  yang telah didapat dari tuak.  Isolat-isolat ini memiliki bentuk warna krem hingga kuning dengan bentuk bulat hingga oval dan pertumbuhannya dengan membentuk tunas.  Tujuannya adalah untuk mendapatkan isolat ini akan digunakan sebagai agen mikroba pada proses fermentasi menghasilkan etanol dari biomasa lignoselulosa sebagai bahan bakunya.   Berdasarkan morfologi menunjukan bahwa isolat-isolat ini adalah spesies Candida.  Isolat HT5 selanjutnya digunakan untuk melihat potensinya sebagai agen dalam produksi bioetanol.  Fermentasi menggunakan 5 g subtrat ampas tebu menghasilkan etanol  sebesar 0.0008%.  Hasil ini mengindikasikan bahwa isolat memiliki potensi sebagai agen fermentasi menghasilkan etanol akan tetapi masih perlu diteliti lebih lanjut untuk kondisi optimum prosesnya.Kata kunci: spesies Candida, bioetanol. tuak
Performance Test of Membrane Electrode Assembly in DAFC using Mixed Methanol and Ethanol Fuel with Various Volume Comparison Yulianti, Dwi Hawa; Rohendi, Dedi; Syarif, Nirwan; Rachmat, Addy
IJFAC (Indonesian Journal of Fundamental and Applied Chemistry) Vol 4, No 3 (2019): October 2019
Publisher : IJFAC (Indonesian Journal of Fundamental and Applied Chemistry)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24845/ijfac.v4.i3.139

Abstract

Direct Alcohol Fuel Cell (DAFC) performance is influenced by electrocatalysis reactions that occur in Membrane Electrode Assembly (MEA). In this study, MEA was made with Pt-Ru/C (anode) and Pt/C (cathode) catalysts. The results of the electrode characterization with XRD showed a carbon peak at 26.63° and Ru at 40.58°. Based on the results of Cyclic Voltammetry (CV) measurements, the Electrochemical Surface Area (ECSA) electrode value is known to be 373.601 cm2/mg. Meanwhile, the impedance value is 4.315 ? and the electrical conductivity value is 6.61x10-4 S/cm. MEA testing using MeOH 3 M fuel produces Open Circuit Voltage (OCV) of 0.650 V. Meanwhile, MEA performance testing uses a mixture of methanol and ethanol 2 M in loading conditions obtained the best mixture of fuel composition is methanol: ethanol = 90:10 with a maximum power density of 4.34 mW/cm2 and is able to maintain the voltage at 0.649 V under conditions of 6.875 mA/cm2. The results also showed that the volume of ethanol which was too high resulted in a decrease in cell performance in the fuel mixture caused by the competition of adsorption between competing methanol and ethanol occupying the active site of the catalyst.Keywords: DAFC, fuel cell, Pt-Ru/C, ethanol, methanol, Open Circuit Voltage
The Light Transmittance and Electrical Conductivity Properties of Gelam Wood Carbon Nanosheet and Its Derivatives Syabaniah, Nyimas Febrika; Syarif, Nirwan; Rohendi, Dedi; Wandasari, Mellysa; Rengga, Wara Dyahpita
IJFAC (Indonesian Journal of Fundamental and Applied Chemistry) Vol 4, No 3 (2019): October 2019
Publisher : IJFAC (Indonesian Journal of Fundamental and Applied Chemistry)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24845/ijfac.v4.i3.126

Abstract

The research on the preparation and characterization of transparent electrode carbon nanosheet based gelam woods bark doped with SnO2-SbO2. XRD analysis showed peaks at 2? = 26.87°; 26.38° for carbon crystal and at 2? = 28.59°; 34.35° for SnO; at 2? = 51.99°; 62.20° for SbO2. SEM analysis show that the carbons have self-curling sheets that indicated defection in their surface. The carbons have self-curling sheets, which indicated that their surfaces have many defects. It assumed when exfoliation process is undergone, the layers was significantly decreased as sonication process and formed rCNSO. Diffractogram XRD of CNS, CNSO and rCNSO showed diffraction peak at 2?= 24.3°. Oxygen functional group in CNSO might cause an increasing of interlayers distance between hexagonal networks of carbon layer. It also affect electrical resistant or the conductivity. FTIR spectrum indicate that CNSO has several  absorption peaks at for ?OH stretch for free water and alcohol. At 2337 cm-1 was showed a carboxylic acid peaks and C=C stretch at 1627 cm-1. There is a skeletal vibration rCNSO structure occurred at each graphene layers. The ratio of the integrated intensities (IG/ID = 0.89 for CNS, 0.85 for CNS-O, and 0.93 for rCNSO of Raman spectroscopy is significantly high. Electrical conductivity of transparent electrode ranges from 1.26 x 10-7 Scm-1 ? 5.03 x 10-7Scm -1. The highest conductivity value on transparent electrode contained rCNSO.This result inferred that the usage of rCNSO can increase electrical conductivity. Therefore, the higher value of electrical conductivity can be related to the value of La. The average maximum absorption wavelength is observed at 350-530 nm which means that the transition of the electronic transition ???* occurs in the conjugated carbons system. Electrical conductivity of transparent electrode ranges from 1.26 x 10-7 Scm-1 ? 5.03 x 10-7 Scm -1. The highest conductivity value on transparent electrode contained rCNSO. The band gap values in the transparent electrode range from 2 eV - 3 eV which means they have conductor ? semiconductor characters.Keywords: Nanosheet, Carbon, Electrical, Conductivity, Derivate.