Analyses of Non-bonding Length, Partial Atomics Charge and Electrostatic Energy from Molecular Dynamics Simulation of Phospholipase A2 – Substrate

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, simulas

Connected Mathematics Project (CMP) Model Based on Presentation Media to the Mathematical Connection Ability of Junior High School Student

Connection mathematics ability will be greatly needed by students, especially to solve the problems that need the relation between mathematical concepts with other concepts in mathematics and other disciplines or in everyday life. To get that mathematics ability in this research used Connected Mathematics Project (CMP) model based on Presentation Media. CMP model based on presentation media was a student-centered learning model that involved student more; student not only did the problem but also sought the solution actively that enabled student to explore the relation of mathematical concept in real life. This research was a quasi experiment research with the student of 7th grade of Junior High School of Ujungjaya 2 of Sumedang district, Indonesia as the research sample. After the learning in the experiment class was conducted, the data description by using instrument of pre-test and post-test were collected to find out the student’s ability of mathematical connection, as well as observation sheet to find out the activity and condition of student during mathematical learning. The result of the research showed that the student’s mathematical connection ability by using Connected Mathematics Project (CMP) model based on presentation media was better than the conventional one. Besides, student’s activity in the learning process by using Connected Mathematics Project (CMP) based on presentation media was really positive and they became very active. Keywords: connected mathematics project model, presentation media, mathematical connection ability

Aplikasi Infusum Daun Durian (Durio zibethinus) pada Proses Transportasi Benih Ikan Patin (Pangasius sp.) dengan Sistem Tertutup

Penggunaan anestesi pada proses transportasi merupakan upaya dalam menjaga benih ikan sehat sampai tempat tujuan. Daun durian adalah salah satu bahan alami untuk anestesi karena mengandung senyawa metabolit sekunder. Tujuan penelitian ini mengetahui konsentrasi efektif infusum daun durian sebagai dasar perlakuan pada proses transportasi dan perbandingan pengenceran infusum dengan media air terhadap tingkat kelangsungan hidup, respon tingkah laku, dan kadar glukosa darah pada proses transportasi benih ikan patin dengan sistem tertutup. Rancangan acak lengkap lima perlakuan perbandingan pengenceran infusum daun durian dengan media air pengangkutan (kontrol (P1), 500:1500mL (P2), 1000:1000mL (P3), 1500:500mL(P4) dan (P5) infusum 2000mL) dengan tiga pengulangan. Konsentrasi efektif infusum daun durian yaitu 10% (100g daun durian dalam 1L air rebusan) dengan waktu induktif berbeda nyata dengan konsentrasi 20%, namun tidak berbeda nyata dengan konsentrasi 30% dan 40%. Sedangkan, waktu sedatif berbeda nyata dengan konsentrasi 40%, namun tidak berbeda nyata dengan konsentrasi 20% dan 30%. Kelangsungan hidup pada konsentrasi 10% mencapai 100%. Pasca transportasi diperoleh tingkat kelangsungan hidup tertinggi sebesar 83,33%, kenaikan kadar glukosa darah 54,67-80mg/dL dan respon tingkah laku dipengaruhi perbandingan pengenceran antara infusum daun durian dengan media air. Pada proses transportasi tertutup selama 16 jam, pengenceran infusum daun durian dengan media air 1000:1000mL sebagai perlakuan terbaik

Pembuatan Elektroda Fuel Cell dengan Metode Elektrodeposisi Menggunakan Katalis Pt-Cr/C dan Pt/C dan Karakterisasinya

Telah dilakukan penelitian Pembuatan Elektroda Fuel Cell dengan Metode Elektrodeposisi Menggunakan Katalis Pt-Cr/C dan Pt/C yang dilanjutkan dengan karakterisasi konduktivitas dan massa terdeposisi. Penelitian diawali dengan membuat backing layer dari substrat karbon dengan pengikat teflon emulsion dengan perbandingan karbon dan teflon emulsion 1 : 1, kemudian dikarakterisasi konduktivitasnya. Elektroda Fuel Cell dibuat dengan melakukan elektrodeposisi larutan platina (H2PtCl6.6H2O) dan larutan krom (CrCl6.6H2O) pada backing layer dengan konsentrasi bervariasi pada beda potensial 7,5 Volt dan waktu 10 menit. Hasil pengamatan konduktivitas backing layer menunjukkan bahwa backing layer yang dibuat sudah memenuhi syarat sebagai backing layer fuel cell dengan konduktivitas rata-rata sebesar 1,8133.10−1 mhos untuk permukaan dan 2,397.10−2 mhos untuk konduktivitas penampangnya. Hasil elektrodeposisi Pt dan Cr pada backing layer untuk membuat elektroda Pt-Cr/C dan Pt pada backing layer untuk membuat elektroda Pt/C menunjukkan konduktivitas elektrik permukaan mengalami kenaikan, sementara konduktivitas penampangnya tidak mengalami kenaikan secara signifikan. Hasil elektrodeposisi juga menunjukkan bahwa massa katalis Pt dan Cr terdeposisi paling banyak dalam elektroda Pt-Cr/C diperoleh pada komposisi massa Pt : Cr = 40 : 60 dan massa katalis Pt terdeposisi paling banyak dalam elektroda Pt/C diperoleh pada massa Pt = 0,6 mg/cm2

Ammonia Liquid Waste Processing using Electrolysis Method

AbstractThis study uses an ammonia wastewater treatment system using 6 lanes and uses a batch-continuous system with electrolysis. Ammonia liquid waste content before and after electrolysis was analyzed using the Nessler method and analyzed using the Spectrophotometry method at a wavelength of 460 nm. Ammonia liquid waste with ammonia content can be used between 18,000-22,000 ppm used as a test sample. The results of this study indicate that the decrease in ammonia concentration every time is directly proportional to the amount of strong current and the number of electrode cells applied. The difference in number, by using 1 pair of cells can reduce 49.19%, 3 pairs of cells by 67.89%, and 5 pairs of cells by 85.08%. In the variation of electric current, 1; 5; 10; and 15 amperes produce 34.03%, respectively; 55.99%; 67.68% and 83.28%. On variations in the influence of the flow rate of 250; 500; 750; 1,000; and 1,250 mL/min resulting from a decrease in the concentration of ammonia is relatively the same, ie concentrations between 82% to 84%. The rate of decrease in ammonia concentration at the liquid level reaches 85.08% by using a variation of 5 pairs of electrode cells with a strong current of 15 amperes. The flow rate used is 250 mL/minute, the electrolysis process is carried out for 8 hours. The modification of the wastewater treatment system by using this electrolysis method is feasible for ammonia liquid waste treatment.  Keywords: Electrolysis, modification, batch-continuous, Nessler, Spectrophotometry, ammonia liquid waste, electrode cells, current strength, flow rate, stainless steel

Synthesis and Characterization of Amorphous TiO2 Anode Prepared by Anodizing Method for Na-ion Batteries

Sodium ion battery (SIB) has engage sustainable alternative on replacing lithium ion batteries. The lower potential and larger ionic value has demanded on seeking a potential anode materials. Amorphous TiO2 prepared by electrochemical anodisation technique has provide a suitablility as anode SIB materials, which approved by conducting XRD, FTIR, and SEM-EDX measurements. Electrochemical performance was tested with variations in the concentration of NaOCl4 electrolyte in propylene carbonate (PC) solvent. Diffractogram of TiO2 showed the only peaks of Ti was observed at 2θ = 40.34. The TiO2 IR spectrogram shows that the absorption band at 507 cm-1 is the peak of the vibration characteristics of the Ti-O bond and the peak of 975 cm-1 corresponds to Ti-O-Ti bond. SEM-EDX image analysis showed the morphology of TiO2 was smooth without pore with a ratio of Ti: O elemental composition of 1: 2. Voltammogram showed the anodes in 0.5 M NaOCl4 electrolyte in PC solvent has a good stability potential windows with the high current density 1.2 mA and the capacity of 0.037 F/

Analysis of Greenhouse Gas Mitigation in Energy Sector/Electricity Sub-Sector on Street Lighting (Case Study: Palembang City)

The greatest source of GHG emission from energy sector comes from fossil fuel combustion. Accordingto PLN, 63.75% of electricity distribution in South Sumatra is derived from coal combustion. Coal is a non-renewableenergy source and will deplete in a few decades. The research objective is solving problems related to energyefficiency and GHG emission reduction by reducing electricity consumption in street lighting sector. The researchmethod was carried out through SPSS statistical analysis and LEAP analysis which had been justified based onobservation on the survey results of 1,619 street lighting unit at four distribution areas of Palembang. Theimplementation of electrical energy efficiency is carried out by replacing Son T 250 W lamps into LED lamps withdifferent power. The SPSS statistical analysis determines that 1,000-unit street lightstreet lighting require lightintensity quality of 1,570 lux with correlation coefficient of 0.214. GHG mitigation was conducted in accordancewith convenience and safety standards for road users in which energy efficiency from the replacement of 3,741-unitenergy-saving lamps can reduce GHG emissions by 1,650.9138 tons of CO2e with benefit economic 2,911,481,740rupiahs. In addition, based on LEAP analysis, if 8000 units of LED lamps replace Son T lamps, the electricityconsumption of Street Lighting in 2030 will decrease with a projected efficiency of 17.48%

Hydrogen Adsorption/desorption on lithium Alanat Catalyzed by Ni/C for Sustainable Hydrogen Storage

 LiAlH4 alloy has been believed to have the potential to become one of the hydrogen storages with high storage capacity. In this research, the formation of LiAlH4 alloys with dope and undope Ni/C catalysts and characterization and testing of hydrogen adsorption/desorption capacities using these alloys have been carried out. The alloy was made by the milling method and the resulting alloy was characterized using XRD analysis. The adsorption capacity test of the alloy was carried out by the gravimetric method at various pressures. The adsorption capacity of the LiAlH4 alloy by adding additives in the form of Ni/C as much as 5%w/w was proven to increase the hydrogen adsorption capacity compared to undope a catalyst with the highest storage capacity at a pressure of 3 bar of 13.06%w/w compared to undope a catalyst of 9.84%w/w at the same pressure. Meanwhile, the highest hydrogen desorption capacity was 53.56% w/w (dope catalyst) and 41.75% w/w (undope catalyst)

Influence Durian Leaves (Durio zibethinus) Infusion as Natural Anesthesia of Striped Catfish Juvenile (Pangasius sp.)

The use of anesthesia in the process of living fish transportation is an effort in keeping the physiology of fish alive and healthy to the destination. Durian leaves are one of the natural ingredients that can be used as fish anesthesia. The purpose of this research is to know the effective concentration of infusum durian leaves as anesthetic seeds of patin fish based on inductive time, sedative time and survival rate. Experimental studies use complete randomized designs, four treatments and threefold. The treatment of infusum concentrations of durian leaves 10%, 20%, 30%, and 40%. The time when fish begins to faint when inserted into the anesthesia solution is recorded as inductive time, whereas the time the fish began to recover back or knowingly recorded as a sedative time. The survival calculation is done on the number of fish surviving post-anesthesia with maintenance for 3 days. The results of this study showed that the effective concentration gained was 10%, with the inductive time (71.67 minutes) distinct from the apparent 20% concentration, but no apparent difference with the concentration of 30% and 40%. Meanwhile, the sedative time (0.25 minutes) differs from the concentration of 40%, but does not differ with concentrations of 20% and 30%. The survival rate of the fish seed Patin at a concentration of 10% showed real distinct results and reached 100%. Infusum concentration of durian leaves by 10% is an effective concentration in the anesthetic process of patin fish seeds