CHEM649V: Single Molecule Spectroscopy

Syllabus

Instructor: Professor Colin Heyes.

Classroom: CHEM 144

Time: MWF 1:30 – 2:20

Office Hours: Tues: 2:00pm – 3:00pm, Wed: 2:30pm – 3:30pm; Thurs: 2:00pm – 3:00pm or other times by appointment.

Office: CHEM219

Objectives:

Provide an overview of the development, implementation and progress of single molecule spectroscopy and imaging in modern-day research.

Topics:

1.       Interaction of electromagnetic radiation with matter – absorption, emission and scattering.

2.       Statistical thermodynamics and kinetics

3.       Fluorescence Spectroscopy

4.       Statistical Methods to Analyze Single Molecule Signals

5.       Scattering and Dark Field Imaging

6.       Surface-Enhanced and Tip-Enhanced Raman Spectroscopy (SERS, TERS)

7.       Absorption, Photoacoustic and Photothermal Spectroscopy and Imaging

8.       Super-Resolution Imaging (STED, 4-Pi, PALM, STORM)

9.       Force Spectroscopy and imaging (AFM, STM, optical tweezers)

Grading and due dates:

Assigned reading and in-class discussions (10%). Continuous throughout semester

Homework and take-home style exams (20%). Continuous throughout semester

Written Report on a Literature Topic (25%). Due Apr 16

In-Class Presentation of Literature topics and involvement in Q&A portions (20%). Held Apr 18 – May 2

Single Molecule Spectroscopy Proposal (25%). Due Apr 30

Assignments, literature reports and proposals are to be turned in during class on the due date. Assignments not turned in on time will be given zero points

Further information

Assigned reading, in-class discussions and homework/take-home assignments

Book chapters and papers will be assigned for reading throughout the class. We will discuss them in class and grading (10%) will come from these discussions. Questions will be asked by the students to the class and professor as well as the professor asking questions of individual students.

Homework assignments will include questions based on the assigned reading, problems from various textbooks as well as “take-home” style exams that will test problem solving skills. Grading of these assignments will account for 20% of the grade.

Literature Topic

You will perform a literature search on a specific research topic related to single molecule spectroscopy and provide a thorough review of that topic. It will be formatted like a review article in the literature and will include multiple citations – at least 6 main citations (not just filler ones), but probably more will be used once you get going. Don’t just rewrite a review article from the literature. I know most of them; it’s obvious when this happens and, as you know, it is plagiarism. The topic should be discussed with Dr. Heyes and a title decided before March 16th. Come up with a few possibilities on your own before coming to talk to me. The title should be broad enough to encompass a given topic, but specific enough to allow a detailed discussion of the history, methodology and significant advances made in the field. It should be about 5,000-6,000 words in length (excluding references). I’m not going to do a word count, but it needs to be thorough, so will end up being about this length if done correctly.

Presentation

You will prepare a 15-20 minute presentation on your literature topic, which will be followed by a 10 minute Q&A session that will involve questions from students as well as the professor. You will not be able to cover all aspects of your topic in this time, so concentrate on one or two aspects and explain them well. Grading will be based on the presentation (both slide preparation and delivery) as well as the content. Make sure your figures are not too small or pixelated, and that you don’t just read directly from text-only slides. All students must be involved in the Q&A sessions. Some of the grading score (5-10% of the 20%) will be come from this Q&A portion and will be based on the relevance of the questions as well as the relevance and clarity of the answers. The order of presentations will be decided by pulling names out of a hat, and there will be 2 presentations per class.

Proposal

Can be to develop or optimize single molecule methodology/data analysis or to use a specific single molecule technique, or combination of techniques, to address a scientifically important problem. . The topic should be discussed with Dr. Heyes and a title decided before April 1st. You can discuss possible titles with your research advisor and it can be related to your research area but MUST be centered around single molecule spectroscopy, not just be your research project with a small single molecule spectroscopy aspect as an afterthought. For students whose current dissertation is already centered on single molecule spectroscopy (mainly from Dr. Heyes’ group), the proposal for this class must not be the same proposal used for your dissertation. There can be some overlap, but it must be an original proposal that you have not previously submitted. The proposal should be about 5,000-6,000 words in length (excluding references), and contain sections on 2-3 specific aims (What are you planning to do?), background and significance (Why are you doing it?), approach (how are you going to do it?), expected outcomes (What will you get out of it?) and possible pitfalls/alternative strategies (What will you do if it doesn’t work out as you expected?). Grading will be based on importance, feasibility, approach, and clarity of writing. The writing should be formal, as you would see in a published paper. Make sure you read through it and check for this, as the language used by students in such proposals is often too informal.