Jawab soalan mengikut arahan yang diberikan dalam setiap bahagian. Questions should be answered according to the instructions given in each section.

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1 UNIVERSITI MALAYA UNIVERSITY OF MALAYA PEPERIKSAAN IJAZAH SARJANA MUDA SAINS EXAMINATION FOR THE DEGREE OF BACHELOR OF SCIENCE PEPERIKSAAN IJAZAH SARJANA MUDA SAINS DENGAN PENDIDIKAN EXAMINATION FOR THE DEGREE OF BACHELOR OF SCIENCE WITH EDUCATION SESI AKADEMIK 2016/2017 : SEMESTER 1 ACADEMIC SESSION 2016/2017 : SEMESTER 1 SCES2437 : KIMIA PENGKOMPUTAN I COMPUTATIONAL CHEMISTRY I Dis 2016/Jan 2017 Dec 2016/Jan 2017 MASA : 2 jam TIME : 2 hours ARAHAN KEPADA CALON : INSTRUCTIONS TO CANDIDATES : Kertas soalan ini mengandungi Bahagian A dan B. This paper consists of Sections A and B. Jawab soalan mengikut arahan yang diberikan dalam setiap bahagian. Questions should be answered according to the instructions given in each section. (Kertas soalan ini mengandungi 8 soalan dalam 6 halaman yang dicetak) (This question paper consists of 8 questions on 6 printed pages)

2 Jawab SEMUA soalan dalam bahagian ini. Answer ALL questions in this section. BAHAGIAN A (30 MARKAH) SECTION A (30 MARKS) 1. Kod di bawah adalah sebahagian kecil dari program permainan Black Jack yang dibincangkan di dalam makmal The code below is a small part of the Black Jack game program that was discussed in the lab 1 from random import choice 2 d=[] 3 def Pakau(): 4 global d 5 cd=["*king","*queen","*jack","ace","*10"] 6 smb=["diamond","heart","spade","club"] 7 val=[10,10,10,1,10] 8 for a in cd: 9 for b in smb: 10 dk=a+"_"+b 11 id=dk,val[cd.index(a)] 12 d.append(id) (a) Huraikan perjalanan fungsi python di atas. Describe the workings python function above. (b) Apakah kegunaan pembolehubah senarai val? What do you think is the use of the list variable val? (2 markah/marks) (c) Apakah kepentingan pembolehubah d di dalam permainan ini? What is the importance of the variable d in this game? (4 markah/marks) 2/6

3 (d) Tulis nilai terakhir d dalam bentuknya yang sebenar. Sepuluh elemen pertama sudah mencukupi. Write the final value of d in its proper form. First 10 elements are sufficient. (4 markah/marks) (e) Mengapakah d mesti dideklarasi sebagai global? Why must d be declared global? (3 markah/marks) (f) Baris-baris program yang mana satukah akan memberikan syntax error? Which program lines will cause syntax errors? (4 markah/marks) (g) Adakah baris 1 perlu di dalam fungsi python ini? Is line 1 necessary for this python function? (1 markah/marks) (h) Mengapakah baris 1 perlu ada dalam permainan ini? Why would line 1 be necessary in this game? (2 markah/marks) 3/6

4 Jawab SEMUA soalan dalam bahagian ini. Answer ALL questions in this section. BAHAGIAN B (70 MARKAH) SECTION B (70 MARKS) 2. Andaikan seseorang mahu membuat model molekul untuk mencari ubat untuk denggi. Bagaimana seseorang itu perlu meneruskannya? Berikan dua contoh pangkalan data struktur yang anda telah pelajari di dalam kelas. Apakah jenis maklumat yang boleh didapati di setiap pangkalan data? Apakah kaedah pengiraan yang akan anda gunakan untuk mengira tenaga semua molekul yang terlibat? Assume someone wants to make a molecular model to find the drug for dengue. How must one proceed? Give two examples of structural databases that you have learned in the class. What kind of information that can be found in each database? Which computational method will you use to calculate the energy of all the molecules involved? 3. Berikan 3 teknik yang membolehkan ahli kimia mengkaji struktur tiga dimensi molekul. Give 3 techniques that allows chemists to work on the three dimensional structures of molecules. 4. Terangkan jenis fungsi tenaga keupayaan di bawah. Tuliskan persamaan, terangkan pembolehubah dan nyatakan interaksi terikat dan tak terikat dalam setiap kes. Describe the types of a potential energy functions below. Write down the equation, explain the variables and state a bonded or nonbonded interaction in each case. 4/6

5 5. Berapa banyakkah mod normal yang ada untuk molekul H 2 S? Pada pandangan anda, adakah frekuensi getaran mod normal ini adalah lebih besar atau lebih kecil daripada mod yang sama dalam molekul H 2 O? Mengapa? How many normal modes are attributed to the H 2 S molecule? Do you think the vibrational frequencies of these normal modes are larger or smaller than the corresponding modes in H 2 O molecule? Why? 6. Terangkan dua teknik yang digunakan untuk mengurangkan masa pengiraan untuk simulasi dinamik molekul. Describe two techniques used to reduce computational time for molecular dynamics simulations. 5/6

6 7. Model pelarut membolehkan simulasi dan pengiraan termodinamik digunakan dalam tindak balas dan proses yang berlaku dalam larutan. Terangkan dua model pelarut yang kita telah bincangkan dalam kelas. Solvent models enable simulations and thermodynamic calculations to be applied to reactions and processes which take place in solution. Explain two solvent models that we have discussed in class. 8. Daripada siasatan eksperimen, penyerapan optik UV DNA single stranded yang terikat pada nanotube karbon tunggal berdinding (DNA/SWNT) telah diperhatikan. From experimental investigation, the UV optical absorption of single-stranded DNA bound to single-walled carbon nanotubes (DNA/SWNT) has been observed. (a) Terangkan secara terperinci semua langkah yang terlibat dalam menyediakan simulasi dinamik molekul DNA / SWNT dalam air. Anda boleh menganggap bahawa terdapat struktur kristal DNA / SWNT. Describe in detail all steps involved in setting up a molecular dynamics simulation of DNA/SWNT in water. You can assume that there is a crystal structure of DNA/SWNT. (b) Terangkan bagaimana anda akan mengira nilai jangkaan tenaga jika anda mempunyai fail output yang mengandungi sejuta gambar dari simulasi dinamik molekul pada 298 K. Explain how you would compute the expectation value of the energy if you have an output file containing one million snapshots from a 298 K molecular dynamics simulation. (c) Terangkan bagaimana anda akan mencari tenaga konformer terendah dalam interaksi antara DNA dan SWNT. Explain how you find the lowest energy interaction conformer between DNA and SWNT. TAMAT END 6/6

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