585.710.81 - Biochemical Sensors

Course Structure

The course materials are divided into modules which can be accessed by clicking Course Modules on the course menu. A module will have several sections including the overview, content, readings, discussions, and assignments. You are encouraged to preview all sections of the module before starting. Most modules run for a period of seven (7) days, exceptions are noted in the Course Outline. You should regularly check the Calendar and Announcements for assignment due dates.

Course Topics

Module 1 - Introduction to Biochemical Sensors/Sensor Principles
Module 2 - Thermodynamics, Kinetics
Module 3 - The Basic Properties of Biosensors/Examples of Biosensors
Module 4 - Optical Techniques
Module 5 - Top-down and Bottom-up Processing, Self-assembled Monolayers (SAMS) of Recognition Elements
Module 6 - Mass Sensitive Sensors
Module 7 - Mid Term Exam and Project
Module 8 - Electrochemistry, Galvanic Cells, Electrochemical Sensors
Module 9 - Thermal Sensors
Module 10 - Molecular Biology Techniques, Biomolecular Recognition
Module 11 - Biochemical Agent Sensors - Part 1
Module 12 - Biochemical Agent Sensors - Part 2
Module 13 - Neuron-Based Biosensors and DNA Microarrays
Module 14 - Final Exam and Project

Course Goals

This course covers the fundamental principles and practical aspects of chemical sensing of physiological signals. The focus of the course is on the electrochemistry and biophysical chemistry of biological sensing elements and their integration with signal transducers. Other topics covered include design and construction of practical sensors, processing and interpretation of signal outputs, and emerging technologies for biosensing.

Course Learning Outcomes (CLOs)

• Demonstrate an understanding of the basic principles of how to design and construct a wide range of chemical and biochemical sensors
• Utilize the basic principles that thermodynamics, kinetics, solid-state physics, electrochemistry, analytical chemistry, materials science, and molecular biology play to build chemical and biological sensors
• Recognize the role of engineering in the design and construction of making biosensors practical, processing and interpretation of signal outputs and emerging technologies for biosensing
• Describe how immobilization procedures can be used to bind biological components to electrical and optical sensing elements
• Understand how living microorganisms can be incorporated into biochemical sensors to identify complex analysis
• Show how recognition, transduction and signal processing can be combined to fabricate biochemical sensors
• Appreciate the important role that biosensors play in modern medicine

Textbooks

Eggins, B. R. (2002). Chemical sensors and biosensors. Chichester: John Wiley. ISBN-10: 0471899143 ISBN-13: 978-0471899143

Required Software

There are no software requirements for this course.

Student Coursework Requirements

It is expected that each module will take approximately 7–10 hours per week to complete. Here is an approximate breakdown: reading the assigned sections of the texts (approximately 3–4 hours per week) as well as some outside reading, listening to the audio annotated slide presentations (approximately 2–3 hours per week), and writing assignments (approximately 2–3 hours per week). This course will consist of the following basic student requirements:

Preparation and Participation (7% of Final Grade Calculation)
You are responsible for carefully reading all assigned material, watching the instructor lectures and being prepared for discussion. The majority of readings are from the assigned articles and course text. Additional reading may be assigned to supplement these readings. Students will be asked to discuss a review article and point out ideas that were not mentioned or elaborate on the evaluations of the selected assessment. Everything will need to be referenced so that there are no comments such as "good point". You will also be asked to comment and provide constructive criticism on classmates' presentations. You are expected to be respectful and provide useful feedback. We will monitor module discussions and will respond to some of the discussions as discussions are posted. Evaluation of preparation and participation is based on contribution to discussions.

Preparation and participation is evaluated by the following grading elements:

1. Timeliness (50%)
2. Critical Thinking (50%)

Preparation and participation is graded as follows:

• 100–90 = A—Timeliness [regularly participates; all required postings; early in discussion; throughout the discussion]; Critical Thinking [rich in content; full of thoughts, insight, and analysis].
• 89–80 = B—Timeliness [frequently participates; all required postings; some not in time for others to read and respond]; Critical Thinking [substantial information; thought, insight, and analysis has taken place].
• 79–70 = C—Timeliness [infrequently participates; all required postings; most at the last minute without allowing for response time]; Critical Thinking [generally competent; information is thin and commonplace].
  

Lecture Quizzes (6% of Final Grade Calculation)
This is essentially a quiz of the material covered in each week's lectures. All the information will come from the lecture itself. These are to ensure that students are watching the lectures and understand the key points of each module.

Reading Problem Sets (6% of Final Grade Calculation)
The assigned text has problems included. The instructor has selected a few of these for students to complete.

Technical Paper Evaluations (12% of Final Grade Calculation)
Students will read an assigned scientific paper in a subject matter related to the current module and then do an evaluative assessment of the paper. Evaluations will be graded as follows:

• 100–90 = A—All parts of question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [rich in content; full of thought, insight, and analysis].
• 89–80 = B—All parts of the question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [substantial information; thought, insight, and analysis has taken place].
• 79–70=C—Majority of parts of the question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [generally competent; information is thin and commonplace].
• <70=F—Some parts of the question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [rudimentary and superficial; no analysis or insight displayed].

Mid-term Project (24% of Final Grade Calculation)
A course project will be assigned at the beginning of the course. The week of the mid-term exam will be devoted to this project. Students will have to develop a presentation to a "venture capitalist" selling a biosensor. Students will look through current literature to find something new and innovative in the current art. Students will then create a technical "pitch" to a mock venture capitalist and will present this as a presentation to the class. A proposal paper will also be turned in via Canvas. The project will be evaluated by the following elements, criteria for each is explained in the assignment:

1. Thoroughness in topic of research (20%)
2. Presentation (40%)
3. Paper (40%)

1. Thoroughness in topic of research (40%)
2. Presentation (40%)
3. Template (20%)

Grading Policy

Course Policies

Late submissions. Drs. Potember and Bryden do not accept late submissions.  Assignments will close at 11:59 PM on the date due and will not be accepted.   Students should not wait until the last minute to submit assignments because large files (which many submissions will be) can take many minutes to upload to Canvas and students may not be able to submit if the files are not completely loaded by 11:59PM.   If students run into technical difficulties, they may (as a matter of last resort and not to be used for every assignment) e-mail their assignment to the instructor as long as it is received in Drs. Potember and/or Bryden’s inbox before 11:59PM on the due date.  Assignments received after this time will not be accepted or graded and will result in a 0 for that assignment. 

Academic Policies

Deadlines for Adding, Dropping and Withdrawing from Courses

Students may add a course up to one week after the start of the term for that particular course. Students may drop courses according to the drop deadlines outlined in the EP academic calendar (https://ep.jhu.edu/student-services/academic-calendar/). Between the 6th week of the class and prior to the final withdrawal deadline, a student may withdraw from a course with a W on their academic record. A record of the course will remain on the academic record with a W appearing in the grade column to indicate that the student registered and withdrew from the course.

Academic Misconduct Policy

All students are required to read, know, and comply with the Johns Hopkins University Krieger School of Arts and Sciences (KSAS) / Whiting School of Engineering (WSE) Procedures for Handling Allegations of Misconduct by Full-Time and Part-Time Graduate Students.

This policy prohibits academic misconduct, including but not limited to the following: cheating or facilitating cheating; plagiarism; reuse of assignments; unauthorized collaboration; alteration of graded assignments; and unfair competition. Course materials (old assignments, texts, or examinations, etc.) should not be shared unless authorized by the course instructor. Any questions related to this policy should be directed to EP’s academic integrity officer at ep-academic-integrity@jhu.edu.

Students with Disabilities - Accommodations and Accessibility

Johns Hopkins University values diversity and inclusion. We are committed to providing welcoming, equitable, and accessible educational experiences for all students. Students with disabilities (including those with psychological conditions, medical conditions and temporary disabilities) can request accommodations for this course by providing an Accommodation Letter issued by Student Disability Services (SDS). Please request accommodations for this course as early as possible to provide time for effective communication and arrangements.

For further information or to start the process of requesting accommodations, please contact Student Disability Services at Engineering for Professionals, ep-disability-svcs@jhu.edu.

Student Conduct Code

The fundamental purpose of the JHU regulation of student conduct is to promote and to protect the health, safety, welfare, property, and rights of all members of the University community as well as to promote the orderly operation of the University and to safeguard its property and facilities. As members of the University community, students accept certain responsibilities which support the educational mission and create an environment in which all students are afforded the same opportunity to succeed academically. 

For a full description of the code please visit the following website: https://studentaffairs.jhu.edu/policies-guidelines/student-code/

Classroom Climate

JHU is committed to creating a classroom environment that values the diversity of experiences and perspectives that all students bring. Everyone has the right to be treated with dignity and respect. Fostering an inclusive climate is important. Research and experience show that students who interact with peers who are different from themselves learn new things and experience tangible educational outcomes. At no time in this learning process should someone be singled out or treated unequally on the basis of any seen or unseen part of their identity. 
 
If you have concerns in this course about harassment, discrimination, or any unequal treatment, or if you seek accommodations or resources, please reach out to the course instructor directly. Reporting will never impact your course grade. You may also share concerns with your program chair, the Assistant Dean for Diversity and Inclusion, or the Office of Institutional Equity. In handling reports, people will protect your privacy as much as possible, but faculty and staff are required to officially report information for some cases (e.g. sexual harassment).

Course Auditing

When a student enrolls in an EP course with “audit” status, the student must reach an understanding with the instructor as to what is required to earn the “audit.” If the student does not meet those expectations, the instructor must notify the EP Registration Team [EP-Registration@exchange.johnshopkins.edu] in order for the student to be retroactively dropped or withdrawn from the course (depending on when the "audit" was requested and in accordance with EP registration deadlines). All lecture content will remain accessible to auditing students, but access to all other course material is left to the discretion of the instructor.