Physical BioChemistry: BCHM 485

Spring 2016

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 still have from the 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
05/13 Final Exam: Friday, 8:00am(!!!).    
05/10 Review session. Bring your questions! Don't forget to do the online course evaluation!!!

Equations help sheet for the final exam is here.  
Examples from previous final exams can be found here . The statistics of you current total scores (prior to the final exam) are posted below under Exam #2 Statistics. 
05/05 Read the material on polymer chain statistics to the end. Do homework problems 4-8. Solutions to HW4 can be found here.  
05/03 Read pages 1-4 of the text on statistics of polymeric chains( Polym_text.pdf posted on canvas), and the handout notes on 1-D random walk model (can be downloaded from here ). Problems 1-3 from the homework problems (can be downloaded from here )  
04/28 TSK: Ch.14: 14.3,14.4,14.5(1-2),14.7 and Ch.15: 15.1-3, 15.6 Ch.14: Pr: 14.2, 14.4, 14.13, 14.26 + Example problems from that chapter including 14.4. Pr. 15.12 from Ch. 15  
04/26 TSK: Ch.13 till the end; and Ch. 15.4. Ch.13: Qs: 13.6,13.9-11; Pr: 13.9,13.10,13.14 and 15.3. Your graded Homework #4 (due Thu May 3, 2016) is here.  
04/21 TSK: Ch.12 (refresh your knowledge of probabilities); Ch.13: 13.1-13.5. In McQuarrie: Ch.3.1-3.2, and MathChapters B, E 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 and scores statistics are posted below. 
04/19 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]. Slides from today's lecture lllustrating the use of NMR spectroscopy in Biochemistry and Structural Biophysics can be found on the course canvas website ( under Files.  
04/12 Ch.17: 17.3, [17.13]. Ch.17: Qs: 17.14; Here is the link to educational videos illustrating various aspects of Nuclear Magnetic Resonance: You want to watch videos 1, 2, and 4. For those who are curious how matrix/vector representation of quantum mechanics works: do problems 17.4,17.7.  
04/07 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 midterm exam will take place on Mon, April 11, at 6pm in Rm 2118 Biomolecular Sciences Bldg. Tentative 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 are here.
04/05 Ch.8: 8.3-8.6, (for those who are curious: 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.   Reveiw session for the upcoming midterm exam #2 will be held on April 11 at 6pm in Rm 2118 BMS building. Bring your questions.
03/31 Ch.8: 8.1,8.2,8.9 Do Example problem 8.1. Q: 8.4. Do the electron-neutron atom problem from the previous assignment. Your graded Homework #3 (due April 7, 2016) is here.  
03/29 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, 10.3, 10.10, [10.6, 10.7]. Determine Bohr's radius (ao) for a hypothetical atom formed by an electron and a neutron (i.e. being held by the gravitational force). What can you conclude about the possibility for such an atom to exist?  
03/24 Ch.9: 9.4-9.6; Ch.10: 10.1 Ch.9: Example Problems: 9.4,9.6; Qs: 9.1,9.13; Pr: 9.5-9.7.  
03/22 Ch.9: 9.1-9.4 Ch.9: Example Problems: 9.1-9.2; Qs: 9.2, 9.4,9.7-9.10, 9.16; 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.  Solutions to Exam #1 problems and scores statistics are posted below.
03/10 Midterm Exam #1 Don't forget to bring a pen/pencil and a calculator!  
03/08 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.  
03/03 Ch 7: 7.2, 7.4 Ch.7: Ex.Pr.: 7.4,7.5; Q: 7.11,7.15,7.19; Pr: 7.10,7.21,7.35(b). Review session for the upcoming exam will be held in Rm 2118 Biomol Sciences Bldg on Tue 03/08 at 6pm. Bring your questions! Example problems (with solutions) from Exam #1 from the last year are here. The equations help sheet for the upcoming midterm exam is here  
03/01 Ch.5: 5.3; Ch 7: 7.1, 7.3 Ch.5: Pr: 5.4,5.5; Ch.7: Ex.Pr.: 7.1, 7.3; Qs: 7.1,7.5,7.6,7.8. Pr: 7.8, 7.11,7.13,7.14,7.16. Your graded Homework #2 (due March 8, 2016) is here. You can find some useful formulae and table integrals here. 
02/25 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. Evaluate the commutator [A,BC]. Using Heisenberg's equation, estimate the minimum uncertainty in the velocity ofa particle (piece of chalk) with mass of 1 g if its position is known with 1 micrometer precision. Will you be able to notice such an uncertainty? Perform the same calculation for the hydrogen atom.  Answers/solutions to HW#1 problems can be found here.
02/23 Ch.5: 5.1-5.2, 5.6-5.8 Ch.5: Qs: 5.6; Pr: 5.7.  
02/18 Ch.4: 4.2-4.4 Ch.4: Qs: 4..9,4.11,4.14,4.15,4.18,4.20; Pr: 4.11,4.28,4.32,4.34. Find a non-trivial soluition to the Happy Potter and the Deadly Snake problem. Your graded Homework #1 (due Feb 25, 2016) is here.
02/11 Ch.4: 4.1-4.2 Ch.4: Ex.Pr. 4.1; Qs: 4.1-5; Pr: 4.4,4.5,4.9,4.10,4.12,4.27,4.29.  
02/09 Ch.3: 3.1-3.5 (3.6) Ch.3: Qs: 3.8-3.12; Pr: 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?  
02/04 Ch.2: 2.6,2.7; Ch.3: 3.1-3.3(3.4). Ch.2: Pr: 2.12, 2.14; Ch.3: Qs:3.2-3.7; Pr: 3.1,3.2,3.8,3.9  
02/02 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. Ch.2: Example problems 2.3-2.4. Using Wien's displacement law, λmax*T=1.44/5 cm*K, do the following calculations: (1) estimate λmax for your body radiation, and (2) assuming that λmax ~ 550 nm for the Sun's radiation, estimate the temperature of the Sun's surface. Also, using de Broglie relationship between the momentum and the wavelength, estimate your wavelength assuming that you move with a speed of 10 m/sec.  
01/28 Cancelled due to weather.   QCS: Ch.1.   
01/26 Cancelled due to weather.   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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