CHEME 7130 Chemical Kinetics & Transport School of Chemical and Biomolecular Engineering, Cornell University, Spring 2012

Time & Place: Instructors: Tu, Thu 10:10-12:05 PM in Olin Hall 218 Susan Daniel (OH 256, sd386@cornell.edu) Fernando Escobedo (OH 377, fe13@cornell.edu) Sushmit Goyal (sg663@cornell.edu) Mon 5:00 6:00 PM, Wed 4:00 5:00 PM, or by appt. (TA) Fri 4:00 5:00 PM, or by appointment (Prof. Daniel) Fri 3:00 4:00 PM, or by appointment (Prof. Escobedo) 15 % Class participation + literature presentations 16 % Homework sets 22 % Exam 1 22 % Exam 2 25 % Project www.blackboard.cornell.edu self enroll

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Course Description Lectures: (13 weeks: Jan. 26 April 19). Introduction to the fundamental concepts and applications of physical and chemical kinetics. In particular, the course will cover theories that allow macroscopic rate constants and transport coefficients to be predicted from considerations of molecular-scale dynamics. Examples from current literature in biological engineering, polymer science, reaction engineering, micro and nano-technology will be treated in seminar-style discussion and in homework problems. Some of these case studies will require the use of specialized software which will be made available to the class; students will have to either learn how to use or modify a core program to get the results needed for the class discussions. NOTE THAT CLASS WILL BE HELD ON WEDNESDAY FEBRUARY 22 ALSO. Literature discussions: (Sign up on schedule posted outside 256 Olin Hall by the end of 1/24). Each Thursday we will use the last 40 minutes of the class period to discuss a paper from the literature that relates to the concepts treated in lecture. These papers will be listed on Blackboard, but if you find an article that you would like to discuss instead, you may inquire with the instructors about substituting. All substitutions must be cleared one week prior to the discussion. The discussions will be led by students and presented in pairs. Each student must participate in leading at least one discussion during the semester. Homework: Homework will be given approximately once per week. Assignments and due dates will be posted on Blackboard and will be collected in class. Exams: Exam 1 will be given at the end of Prof. Daniels lectures (March 1st) and Exam 2 will be given at the end of Prof. Escobedos lectures (April 20).

CHEME 7130 Chemical Kinetics & Transport School of Chemical and Biomolecular Engineering, Cornell University, Spring 2012 Project: (3 weeks: April 21 May 11): Development of a research project by each student. The projects will conclude with a written report and an oral presentation to the class. See end of syllabus for more information. Collaboration Policy: You are encouraged to discuss the problem sets with your fellow students in this class, but not other classes or previous students of this course. Discussions should be limited to the conceptualization stage only. Your written solutions must be 100% your own work. Work on examinations is expected to be entirely your own, without discussion with any other students from this or prior years. Academic Integrity: Please review Cornells academic integrity policy if you are not already familiar with it at: http://cuinfo.cornell.edu/Academic/AIC.html Reference List Course textbook: None officially you will be provided print-outs as necessary and may get the full texts at the library on reserve when needed. Useful texts: (on reserve in Carpenter) Analysis of Transport Phenomena, Deen (Oxford, 1998). Statistical Mechanics, McQuarrie (Harper & Row, 1976). Diffusion Mass transfer in fluid systems, Cussler (1984 or 1997). Transport Phenomena, Bird, Stewart & Lightfoot (Wiley, 2nd ed. 2002). Physicochemical Hydrodynamics, Probstein (Wiley, 1994) Chemical Kinetics and Dynamics, Steinfeld, Francisco, and Hase (Academic Press, 1999). Colloidal Dispersions, Russel, Saville, and Schowalter (Cambridge, 1989) Foundations of Colloid Science, Hunter (1989). Molecular Theory of Gases and Liquids, Hirschfelder, Curtiss, & Bird. (Wiley 1964) Modern Quantum Chemistry, Szabo and Ostlund (Dover, 1989). Understanding Molecular Simulation, Frenkel & Smit, (2nd ed. Academic Press, 2002). Physical Chemistry, Berry, Rice, and Ross (full text from which Physical and Chemical Kinetics was extracted)

CHEME 7130 Chemical Kinetics & Transport School of Chemical and Biomolecular Engineering, Cornell University, Spring 2012 Course Outline Part I: (Daniel) I. Introduction to course A. What? Physical & chemical kinetics non-equilibrium processes B. Why? C. Approach: bridging macroscale to microscale phenomena, integrating physical and chemical kinetics II. Continuum Mass Transfer with Reactions [Cussler 1-3, 13, 15, & 16; Deen 1, 2, 4, & 9; McQuarrie 17, 20, & 21] A. Introduction: 1. Flux of material & rate laws (constitutive relationships) 2. Governing equations (dilute and concentrated regimes) a. Mass different than heat B. Diffusive mass transfer 1. Time-independent a. Greens function & convolution, method of images, similarity solution 2. Time-dependent a. Greens function & Fourier transforms b. Applications: Fluorescence recovery after photobleaching 3. Einsteins picture of diffusion (connecting macroscale diffusion to microscale) a. Applications: Single particle tracking techniques C. Mass transfer with reactions 1. Homogeneous reactions 2. Heterogeneous reactions D. Convective mass transfer 1. Scaling (down) 2. Dispersion (bridging macroscale to microscale) III. Basic molecular-scale models of physical and chemical kinetics [Russel 4 & 7; Pilling 6; McQuarrie 15 & 16; Berry 27, 28, 30; Steinfeld 4] A. Solution phase physical and chemical kinetics 1. Transport a. External forces on mass transfer mobility: Stokes-Einstein i. Applications: sedimentation, electrophoretic separation b. Electrokinetic phenomema i. Poisson-Boltzmann ii. Debye-Huckle iii. Electroosmosis/Electrophoresis 2. Reaction-diffusion a. Diffusion limitations in solution b. Electrostatic effects on reaction kinetics in solution

CHEME 7130 Chemical Kinetics & Transport School of Chemical and Biomolecular Engineering, Cornell University, Spring 2012 Part II: (Escobedo) B. Gas phase kinetic theory [Steinfeld 4, Berry 28, McQuarrie 15-16] 1. Overview of Maxwell Boltzmann distribution 2. Simple collision theory 3. Transport: prediction of diffusivity, viscosity, thermal diffusivity 4. Chemical rates with kinetic theory: prediction of rate constants V. Potential energy surfaces and molecular dynamics [Steinfeld 7-8 & 10; Berry 29-30, Frenkel & Smit 4, McQuarrie18-19, 21] A. Potential energy surfaces (PES) B. Classical mechanics C. Non-reactive two-body collisions (scattering) D. Simple (3-body) reactive collisions E. Many body classical collisions: Numerical and analytical treatments 1. Time-correlation functions 2. Transport properties 3. Applications. VI. Transition state theory (TST) and nucleation theory [Berry 30, Steinfeld 10] A. Statistical and thermodynamic approaches to TST B. Application of TST to chemical and physical kinetics C. Classical nucleation theory. D. Application to homogeneous liquid phase and vapor phase nucleation E. Measurement of kinetic properties VII. Stochastic description of diffusion: Master and Langevin equations [McQuarrie 20] A. Revisiting Einstein approach to Brownian motion and diffusion B. Markov properties and more general Master and Fokker-Planck equations C. Langevins approach D. Fokker-Planck equation E. Continuous and discrete Master equations VIII. Stochastic description of chemical kinetics A. Master Equation approach B. Stochastic approach [Steinfeld] C. Gillespies Kinetic Monte Carlo (KMC) method D. KMC for dynamic processes with coupled space and reaction coordinates E. Other advanced topics and applications

CHEME 7130 Chemical Kinetics & Transport School of Chemical and Biomolecular Engineering, Cornell University, Spring 2012

Kinetics Project Guidelines General Objectives: Provide a setting where knowledge from the core ChemE disciplines (transport and kinetics in particular) is applied so as to stress their synergism and integration. Provide concrete, hands-on experience on open-ended problems. Continue to develop skills for critical reading and analysis of technical literature. Give the students the opportunity to be active participants in the learning process by teaching themselves and the class a particular subject of interest. Specific Objectives: Demonstrate ability for critical interpretation and analysis of current literature. Demonstrate ability to apply concepts, methods, and lessons learned throughout the course to specific problems (beyond what may be given in a selected publication). Demonstrate ability to set and redefine goals, and to achieve results under the prevailing constraints of time and resources. The first specific objective will build upon the literature critiquing skills learned throughout the course. The second specific objective entails the pursuit of some aspect of a problem that is new, even if just incrementally so. The novelty of the project may be due to features of the system of interest which are different from those treated in the literature, or due to distinctive features of the method of analysis. The project may emphasize theoretical, computational modeling, or experimental aspects (e.g., experimental design and analysis) of a problem. Projects should not involve actual experimental work. The final objective will be achieved during the process of defining your project and conducting your planned extension. Output: Part I: Students are expected to select a project topic, select one or two key papers which more closely or completely embody the problem of interest, learn this (these) paper(s), give a brief (~5-7 min) presentation on the subject to the class, with an introduction to the part of the problem that the student will extend. The presentation should end with a very brief progress report, pointing out the difficulties that may have been encountered thus far. Following this presentation, students will get feedback from the instructors. Part II: Students should generate results or extend analysis on that problem, and then prepare a final written report and associated oral presentation. The first introductory presentation (Part I) should not exceed 7 min including questions and discussion. Plan for about 3-5 PowerPoint slides per presentation. The final presentation (Part II) should not exceed 10 min plus a minute or two for a few questions and discussion. The maximum number of PowerPoint slides is 6 per presentation. The final written paper should contain the typical sections of peer-reviewed papers, e.g., title, abstract, introduction, methodology, results-discussion, conclusions, acknowledgements, references, and appendix (if needed). The paper should be concise, making sure to stress primarily the most important points and results. The paper should not exceed 6 pages. Any additional materials can be included in an appendix.

CHEME 7130 Chemical Kinetics & Transport School of Chemical and Biomolecular Engineering, Cornell University, Spring 2012

Timeline: (tentative dates and times) Selection of theme of project: Tuesday, April 24 (or sooner). Provide key paper(s) to instructors (preferably via e-mail): Friday, April 27. Presentation of key papers & topic: Tuesday, May 1 (possible May 3 if we do not complete all) Final written reports due: Wednesday, May 9. Final oral presentation: Friday, May 11 (time TBA, depending on enrollment number). Grading: The project constitutes 25 % of the total grade (including a class participation component). The evaluation will be based on the following criteria: Mastery of the subject presented Depth of analysis Novelty or significance of results attained Organization and clarity of both written and oral presentations Class participation during presentations and discussions, including questions and suggestions to others. Examples of project topics: Use of Transition State Theory to study selectivity in micro-porous materials Diffusion and shear assisted transport of drugs in tissue Analysis of thin film oxide formation on silicon Analysis of homogeneous and heterogeneous nucleation processes Transport of small-molecule additives in polymers or solids Electrokinetics and transport of charged molecules in nanochannels Kinetics of the self assembly of red blood cells Transition State Theory model of a molecular motor Modeling of enzymatically activated reactions Application of commercial or software such as Gaussian (quantum) or freeware to study Potential Energy Surfaces or the classical dynamics of molecular processes Analysis of theoretical basis of experimental methods that probe microscopic dynamics Stochastic simulation of chemical reactions, polymerization, diffusion, mixing processes, etc. The topic can have some relation to the students thesis research area but should be a small subset or piece to fit within the constraints of time and resources. You may also choose a topic in a different or complementary area. However, all topics must be cleared with the Instructors.