Physical BioChemistry: BCHM 485

Spring 2020

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



Quantum Chemistry & Spectroscopy by Thomas Engel
Thermodynamics, Statistical Thermodynamics, and Kinetics by Thomas Engel & Philip Reid
(The Thermodynamics textbook that you might 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
03/12 Ch.7: 7.5-7.8; Ch.9: 9.1-9.2 Qs: 7.2,7.3,7.112,7.14, Prs: 7.6,7.34. Show by direct substitution and calculation that exp(-r/a) is a solution to Shroedinger's Eq. for H-atom when l=0; determine the values of a and E.   The video materials related to lectures 2-4 will be removed from ELMS after March 30th in order to make space for the new lecture materials. If you want to have access to these videos, please download them before that date.
03/10 Midterm Exam #1 Don't forget to bring a pen/pencil and a calculator!  
03/05 Preparation for the midterm exam #1. After the exam: Ch.7: 7.5,7.7 Example problems (with solutions) from the previ ous year Exam #1 are here. A review session for the upcoming midterm exam will be held on Friday March 6 from 4-5 pm in Rm 2118 in Biomolecular Sciences Bldg (2nd floor of the same building where my office is located). Bring your questions. After the exam: Ch.7: Qs: 7.12, 7.14; Pr: 7.7,7.20. Solutions to graded homework #2 pro blems will be posted here.  
03/03 Ch.6: 6.1,6.3,6.4 Ch.6: Example Prs: 6.3, 6.4, Pr: 6.3,6.6,6.7,6.9,6.11,6.23. Prove the genearal relationships for the commutators which I gave you in class. Specifically, evaluate the commutator [A,BC].  
02/27 Ch 7: 7.2, 7.4 Ch.7: Ex.Pr.: 7.4,7.5. Qs: 7.11,7.19. Pr: 7.10,7.21, 7.35(b). Your graded Homework #2 (due on Mar 5, 2020) is here. Example problems from the previous year Exam #1 are here.  
02/25 Ch 7: 7.1,7.3, also 7.2 Ch.7: Ex.Pr.: 7.3; Qs: 7.1,7.6,7.8; Pr: 7 .8,7.15,7.17. Answers to graded Homework #1 problems are here. For those who are curious: here is a calculation of the probability to find quantum mech anical H.O. outside the allowed range for a classical H.O. To download it click here.  
02/20 Ch.4: 4.3; Ch.5: 5.3 Ch.4: Pr: 4.17-19, 4.22, 4.23; Pr. Ch.5: Pr: 5.4, 5.5. Calculate the penetration length for a hydrogen atom and for electron using the same model as we used in class for the Harry Potter and Platform 9 3/4 problem.  
02/18 Ch.5: 5.1-5.2, 5.6-5.8 Ch.5: Qs: 5.6; Pr: 5.7. Happy Potter and the Basilisk problem.  
02/13 Ch.4: 4.2,4.4; also Ch. 2.1 Ch.4: Ex.Pr.4.1-4.3; Pr: 4.12,4.16. Think of the Happy Potter and the Basilisk problem.  
02/11 Ch.4: 4.2 Ch.4: Qs: 4.1-2,4.9-10,4.14-15,4.18-20; Pr: 4.9,4.10,4.28,4.29.Do the Schroedinger's cat problem from the last assignment. Your graded Homework #1 (due on Feb 18, 2020) is here. Some useful trigonometric equations and and identities are here.  
02/06 Ch.4: 4.1. A video recording of a last year ecture containing some of the mateal covered today is available on ELMS (BCHM485_L_4.mp4) along with a PDF version of that lecture notes. Ch.4: Qs: 4.3-5,4.11; Pr: 4.4-4.6,4.13. Question: Schroedinger's cat was found alive in 64% experiments and dead in 36%. Reconstruct the wavefunction of the cat.  
02/04 Ch.3: 3.1-3.5 (3.6) A video recording of this and the previous lecture is available on ELMS (BCHM485_L2_3.mp4). A PDF version of the lecture notes from that video is also available on ELMS as well as here. Ch.3: Qs: 3.9-3.10; Pr: 3.12,3.16. Question: How can you tell from the outcome of your experiments if the QM system is in a pure state or in a superposition state?  
01/30 Ch.2: 2.6,2.7; Ch.3: 3.1-3.3. Ch.2: Ex.Pr. 2.3,2.4; Pr: 2.12, 2.14; Ch.3: Qs:3.2-3.9; Pr: 3.1,3.2,3.8,3.9  
01/28 QCS: Ch.1 & Ch.2: 2.2-2.3 Ch.1: Do Example problem: 1.3 from Ch.1: determine the radius of the lowest-energy orbit of electron in Bohr's planetary model of the hydrogen atom.
Using Wien's displacement law, λmax*T=1.44/5 cm*K, perform the following calculations: (1) estimate λmax for your body radiation, and (2) assuming that the maximum of Sun's radiation is in the yellow range, i.e. λmax ~ 580 nm, estimate the temperature of the Sun's surface.
It's not too late to prepare yourself for the course. The relevant information can be found below and also at ELMS. 
before 01/28 Prepare yourself for the course. The relevant information can be found here.  Pepare 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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