Judul: Paralellization Multiple Sequence Alignment
Abstrak: Sequence alignment (sequence alignment) is one of the problems in molecular biology that can be solved with the help of computer programs. The purpose of an alignment is to identify similarity region of sequence in Deoxyribonucleic acid (DNA), Ribonucleic acid (RNA), or protein. One of sequence alignment methods is Needleman-Wunsch which includes all sequences in its alignment. The Needleman-Wunsch method has high computational complexity with value of O(n2). Similarly, multiple sequence alignment (MSA) that processes k sequences one by one by using Star Alignment method has complexity of O(k2n2). Therefore, the main problem in MSA using Star Alignment method is computational time. However, the Star Alignment method can still obtain high accuracy. The time consuming problem faced by Star Alignment method can be solved by applying parallel computing technique implemented using multiple computers working together as a network system. This research focuses on finding a faster method to process MSA based on Star Alignment method using parallel computing. The proposed method is implemented using Message Passing Interface (MPI). The evaluation is conducted by calculating speed up. The experiment results show that the paralellization of the Star Alignment method can increase speed up 4-6 times faster than that of using single CPU.
Keyword: Needleman-Wunsch, Multiple Sequence Alignment, Star Alignment, Parallel Computing

Judul: Paralelisasi Algoritme Pairwise Alignment dan Neighbor Joining pada Progressive Multiple Sequence Alignment
Abstrak: Multiple sequence alignment (MSA) adalah permasalahan dasar dalam Bioinformatika yang bertujuan menjajarkan lebih dari dua sekuens biologi untuk menemukan kemiripan pada masing-masing sekuens. MSA digunakan dalam analisis phylogenetic, identifikasi motif pada keluarga protein dan pemodelan homologi tiga dimensi. Tantangan yang dihadapi dalam melakukan implementasi MSA adalah kompleksitas algoritme dan ukuran data sekuens yang besar. Progressive MSA ClustalW merupakan metode heuristic yang banyak digunakan untuk menyelesaikan masalah kompleksitas algoritme MSA. Beberapa penelitian membuktikan bahwa paralelisasi progressive MSA dapat meningkatkan kinerja dalam menghadapi ukuran data sekuens yang besar. Penelitian ini bertujuan melakukan paralelisasi algoritme pairwise alignment dan neighbor joining pada progressive MSA ClustalW menggunakan model pemrograman message passing, shared memory, dan gabungan keduanya. Perancangan program paralel dilakukan dengan empat tahap yaitu partitioning, communication, agglomeration dan mapping. Perancangan program paralel tersebut menghasilkan lima skenario implementasi untuk algoritme pairwise alignment dan satu skenario untuk algortime neighbor joining. Skenario tersebut antara lain pureMPI, pureOpenMP, ompInner, mpiOmpInner, dan mpiOmpOuter pada algoritme pairwise alignment serta skenario pureOpenMP pada algoritme neighbor joining. Skenario pureOpenMP menjadi skenario terbaik pada algoritme pairwise alignment dengan speedup hingga 12.20 kali menggunakan 20 prosesor. Skenario pureOpenMP pada algoritme neighbor joining menghasilkan speedup hingga 6.11 kali menggunakan 20 prosesor. Algoritme pairwise alignment dan neighbor joining memperoleh speedup terbaik menggunakan skenario pureOpenMP yang merupakan implementasi model pemrograman shared memory. Penggunaan skenario tersebut pada gabungan kedua algoritme diperoleh speedup hingga 12 kali menggunakan 20 prosesor. Paralelisasi kedua algoritme tersebut menggunakan skenario pureOpenMP berkontribusi untuk menjaga algoritme gabungan tetap kokoh pada data yang memiliki sekuens yang panjang dan jumlah sekuens yang banyak.
Keyword: message passing, multiple sequence alignment, neighbor joining, pairwise alignment, shared memory

Judul: Elektrodeposisi Film Tipis Semikonduktor Cu2ZnSnS4 (CZTS) pada Substrat Kaca ITO
Abstrak: Semiconductor Cu2ZnSnS4 (CZTS) thin film that can be used as absorber layers on solar cell module was made via electrodeposition method. CZTS thin film was electrodeposited on the surface of a silicate glass coated with a thin layer of indium tin oxide (ITO). Deposition process was done using potentiostatic mode at room temperature with a potential of 1.05 V for 30, 45, and 60 minutes, followed with annealing the film at 2 different temperatures, 500 ºC using furnace and 180 ºC using hot plate, both treatments for 45 minutes in N2/H2S atmosphere. The X-ray difractograms were analyzed using Match 2 program and showed that the CZTS thin films had kesterit crystalline structure, with a low percentage of CZTS phase. The thin film also contained secondary phases such as Cu2S, ZnS, and SnS. The obtained CZTS thin films had a thickness between 1.039 and 1.676 μm. Absorption study showed that the band gap energy of CZTS thin films which was annealed using furnace ranged from 1.50 to 1.52 eV, whereas that annealed using the hot plate was not observed. The band gap energy value showed that CZTS thin films can be used as sunlight absorber layers on solar cell. The formation of CZTS crystal film on this investigation was effectively performed using furnace annealing process at a temperature of 500 ºC with deposition time of 45 minutes.
Keyword: Thin film, Electrodeposition, Cu2ZnSnS4