Physical BioChemistry: BCHM 485

Spring 2015

Course meets in Chem 2201, TuTh 9:30 am
Professor: David Fushman
Office: Room 1121 Biomolecular Sciences Bldg (#296)
Office Hours: (tentatively) Tuesday, 12:30 - 2:30 pm



Quantum Chemistry & Spectroscopy by Thomas Engel
Thermodynamics, Statistical Thermodynamics, and Kinetics by Thomas Engel & Philip Reid
(The Molecular Thermodynamics textbook by McQuarrie & Simon that you might have from the Fall 2014 CHEM481 course could be sufficient.)
Physical Chemistry by Peter Atkins and Julio de Paula, Vol.2 Quantum Chemistry, Spectroscopy, and Statistical Thermodynamics;
Physical Chemistry with Applications to the Life Sciences by David Eisenberg and Donald Crothers;
Principles of Physical Biochemistry by van Holde, Johnson & Ho;
Molecular Driving Forces by Dill & Bromberg;
Biophysical Chemistry by Cantor & Schimmel.
Reading and problems are either from Quantum Chemistry & Spectroscopy [QCS] or from Thermodynamics, Statistical Thermodynamics, and Kinetics [TSK]
Date Reading Problems Q&A
05/15 Final Exam: Friday, 8:00am(!!!).    
05/12 The second part of the class today will be a mini-review session to help you prepare for the final exam: please bring your questions!!! Equations help sheet for the final exam is here Don't forget to do the online course evaluation!!! Equations help sheet for the final exam is here
05/07 TSK: Ch.14: 14.1,14.2; Ch.15: 15.1-15.3,15.6 (skip 15.3.6) Ch.15: Pr: 15.3,15.5,15.12,15.22. Solutions to HW#4 problems are here Statistics of the distribution of the current total scores (before the final exam) are posted below (together with the Exam #2 Statistics) .
05/05 TSK: Ch.14: 14.3,14.4,14.5(1-3),14.7 and 15.4 Ch.14: Pr: 14.2, 14.4, 14.13, 14.26 + Example problems Statistics of Exam 2 scores and of current total scores are posted below.  
04/30 TSK: Ch.13 till the end. Ch.13: Qs: 13.6,13.9-11; Pr: 13.9,13.10,13.14. Your graded Homework #4 (due Thu May 7, 2015) is here. Examples of Homework #4 problems with solutions from a previous year are here.  
04/29 TSK: Ch.12 (refresh your knowledge of probabilities); Ch.13: 13.1-13.5. In McQuarrie: Ch.3.1-3.2, and MathChapter B TSK: Ch.13: Qs: 13.1-13.3,13.5; Pr: 13.1,13.7,13.12,13.19; Example Probl.13.5, 13.6. In McQuarrie: Pr.3.8. Using a calculator, assess the accuracy of Stirling's approximation for N!: at what value of N the accuracy becomes better than 10%? better than 1%? Do this for both complete formula and for ln(N!) = Nln(N)-N. Solutions to exam #2 problems are posted below.  
04/23 Midterm exam #2 Exam #2 problems posted here. Do them as your new homework.  
04/21 Ch.17: 17.3-17.6, [17.12-17.13]. Ch.17: Qs: 17.3,17.4,17.14,17.15; Pr: 17.6,17.13,[for those who are curious how matrix/vector representation of quantum mechanics works: 17.4,17.7]. Here is the link to educational videos illustrating various aspects of Nuclear Magnetic Resonance: You want to watch videos 1 and 2.  
04/16 Ch.17: 17.1-17.2, 17.11. Ch.17: Ex.Pr 17.1; Pr: 17.3, [17.4,17.7]. A review session for the next m idterm exam will take place on Tue, April 22, at 6pm in Rm 2118 Biomolecular Sciences Bldg. Equations sheet for Exam #2 is here. Make yourself familiar with these equations. An example of midterm exam #2 problems (with solutions) from last year is here.. Solutions to HW#3 problems can be downloaded from here.
04/14 Ch.8: 8.3-8.6, (8.7). Ch.8: Ex.Pr: 8.2-8.6; Qs: 8.1,8.2,8.7,8.9,9.10,8.12,8.13; Pr: 8.7, 8.14, 8.15, 8.20.  
04/09 Ch.8: 8.1,8.2,8.9 Do Example problem 8.1. Q: 8.4.  
04/07 Ch.10: 10.1-10.3 [10.5-10.6]; Ch.12: 12.2-12.4. Ch.10: Pr: 10.3,10.10. Ch.12: Q: 12.15,19. Your graded Homework #3 (due April 14, 2014) is here. An example (with solutions) of HW3 from the previous years is posted here Solutions to Exam #1 problems and scores statistics are posted below.  
04/02 Ch.10: 10.1-10.3, Ch. 6.2 Ch.10 Ex.Problems: 10.1-10.2; Qs: 10.1,10.5,10.7,10.12,10.16; Pr: 10.2. What is the degeneracy of the energy level n H atom with the principal quantum number n? Determine Bohr's radius (ao) for a hypothetical atom formed by an electron and a neutron (i.e. being held by the gravitational force). Do the same calculation f or a proton-neutron or neutron-neutron pair. What can you conclude about the pos sibility for such an atom to exist?  
03/31 Ch.9: 9.4-9.6 Ch.9: Example Problems: 9.4,9.6; Qs: 9.1,9.2,9.13,9.15,9.16; Pr: 9.5-9.7; Determine Bohr's radius (ao) for a hypothetical atom formed by an electron and a neutron (i.e. being held by the gravitational force). Do the same calculation for a proton-neutron or neutron-neutron pair. What can you conclude about the possibility for such an atom to exist?  
03/26 Midterm Exam #1 Don't forget to bring a pen/pencil and a calculator!  
03/24 Ch.9: 9.1-9.3 Ch.9: Example Problems: 9.1-9.2; Qs: 9.4,9.7-9.10; Pr: 9.2, 9.4, 9.24. Show that exp(-r/a) is a solution to the Shroedinger Eq. for H-atom; determine a and E. Compute the degeneracy of the energy level corresponding to the principal quantum number n.  
03/12 Ch.7: 7.5-7.8 Ch.7: Qs: 7.2,7.3,7.4,7.12,7.14; Pr: 7.2,7.4,7.6,7.7,7.20. Answers/solutions to graded Homework #2 problems are here. Example problems (with solutions) from Exam #1 from the last year are here. The equations help sheet for the upcoming midterm exam is here  
03/10 Ch 7: 7.2, 7.4 Ch.7: Ex.Pr.: 7.4,7.5; Q: 7.5,7.6,7.11,7.15,7.19; Pr: 7.10,7 .21,7.35(b).  
03/05 Snowday   Graded HW#2 is now due on March 12, 2015. An example of HW#2 problems (with solutions) previous years can be found here.
03/03 Ch.7: 7.1, 7.3, 5.3 Ch.7: Ex.Pr.: 7.3; Pr: 7.8, 7.11,7.13,7.14,7.16; 5.4,5.5. Your graded Homework #2 (due March 10, 2015) is here. You can find some useful formulae and table integrals here. 
02/26 Snowday. Read Ch.5.3 Ch.5: Pr: 5.4,5.5  
02/24 Ch.6:6.1,6.3,6.4, (6.5,6.6) Ch.6: Example Prs: 6.3, 6.4, Qs: 6.5,6.6,6.8,6.14,6.15; Pr: 6.3,6.6,6.7,6.9,6.11,6.16,6.23  
02/19 Ch.5: 5.1-5.2, 5.6-5.8 and Ch.2.1 Ch.5: Qs: 5.5,5.6,5.8,5.13,5.14; Pr: 5.7. Answers/solutions to graded Homework #1 problems are here.
02/17 Snowday. Read: Ch.4.3 Ch.4: Pr: 4.18.  
02/12 Ch.4: 4.2,4.4 Ch.4: Qs: 4.15,4.18,4.20; Pr: 4.11,4.18,4.28,4.32,4.34. Happy Potter and the Basilisk question.   An example (with answers) of HW#1 from the previous years is here.
02/10 Ch.4: 4.1-4.2; Ch.4: Ex.Pr. 4.1; Qs: 4.1-5,4.9,4.11,4.12,4.14; Pr: 4.4,4.10,4.12,4.27,4.29. Your graded Homework #1 (due Feb 17, 2015) is here.  
02/05 Ch.3: 3.1-3.5 (3.6) Ch.3: Qs: 3.9-3.10; Pr: 3.5,3.6,3.12,3.16. Q#1: Schroedinger's cat was found alive in 60% experiments and dead in 40%. Reconstruct the wavefunction. Q#2: How could you tell from the outcomes of your experiments if the QM system is in a pure state or in a superposition state?  
02/03 Ch.2: 2.3,2.6,2.7; Ch.3: 3.1-3.4. Ch.2: Example Probl: 2.3,2.4; Pr: 2.12, 2.14; Ch.3: Qs:3.2-3.8; Pr: 3.1,3.2,3.8,3.9  
01/29 QCS: Ch.1 & Ch.2: 2.2-2.3 Ch.1: Example probl: 1.3. Questions in the end of Ch.1: 1.1-1.3,1.5. Using Wien's displacement law ( λmax*T=1.44/5 cm*K ), do the following: (1) estimate λmax for your body radiation, and (2) assuming that λmax ~ 600 nm for the Sun's radiation, estimate the temperature on the Sun's surface  
01/27 Snowday   It's not too late to prepare yourself for the course. The relevant information can be found here.   
Exam # 1: Exam # 2: Final Exam:
Statistics Statistics Statistics
Solutions Solutions Solutions

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