Enroll in CSCE 458/858: Molecular and Nanoscale Communication

Enroll in CSCE 458/858: Molecular and Nanoscale Communication.
Enroll in CSCE 458/858: Molecular and Nanoscale Communication.

Add another course to your spring 2021 semester and enroll in CSCE 458/858: Molecular and Nanoscale Communication.

CSCE 458/858: Molecular and Nanoscale Communication

Online Course with Remote Access through Canvas
Synchronous Lectures from 01/25
MWF 2:30PM – 3:20PM (Recorded and Posted on Canvas)
Zoom Link: TBD
Zoom Password: TBD

Instructor: Dr. Massimiliano Pierobon, Associate Professor
Department of Computer Science and Engineering
University of Nebraska-Lincoln
Lincoln, NE 68588

Office: 104 Schorr Center
Office Hours: @ same Zoom link as lectures on M W 2:30PM – 3:30PM or by appointment.
Tel: (402) 472-5021
Fax: (402) 472-7767
Web: http://cse.unl.edu/~pierobon/
E-mail: pierobon@cse.unl.edu

Office Hours: Monday, Wednesday 3:30PM – 4:30PM (after lecture) or by appointment.

Description: Develop an understanding of the different options to realize communication at the nanoscale among nano-precise entities, or nanomachines, being they genetically engineered biological cells or man-made nano-devices. The specific focus will be on bio-inspired communication through molecule exchange and biochemical reactions. Different techniques to realize nanomachines will be surveyed in the course, with particular attention to the tools provided by synthetic biology for the programming of biological cooperative systems. This course will give a chance to be initiated to a very exciting cutting-edge research field, which will soon influence many diverse research fields, such as engineering, chemistry, biology, and medicine.

Prerequisites: A grade of "P" or "C" or better in CSCE 310, CSCE 310H, CSCE 311, SOFT 260, SOFT 260H or RAIK 283H; STAT 380, ECEN 305 or RAIK 270H. Completing CSCE 462/862 and CSCE 465/865 prior to taking this course is recommended. Exceptions can be granted on a per-student basis by the instructor.

Good standing undergraduate/graduate student from Computer Science and Engineering, Electrical Engineering, Chemical Engineering, Biology, Chemistry, Chemical and Biomolecular Engineering, and Mathematics, or upon instructor permission.

Most of the necessary concepts from physics, chemistry, and biology, as well as from systems and communication engineering, will be provided during the lectures to accommodate students with different backgrounds, and let them benefit from a truly interdisciplinary approach. Student creativity, passion, and open-minded attitude will be highly appreciated and rewarded.

Required Textbook:
"Fundamentals of Diffusion-Based Molecular Communication in Nanonetworks"
by Massimiliano Pierobon,‎ Ian F. Akyildiz
Now Publishers Inc (April 30, 2014)
ISBN-10: 1601988168
ISBN-13: 978-1601988164

Selected lectures of this course will be based on the following additional textbooks (not required):
• Synthetic Biology — A Primer
by Paul S Freemont and Richard I Kitney
• Communication Systems Engineering
by John G. Proakis and Masoud Salehi

Lecture slides (PDF) will be available on the course’s homepage.

A list of reference books and research papers will be given throughout the semester.

Some of the research papers and reports will be distributed via the course’s homepage.

HOMEWORKS and EXAMS will be based on what explained during the lectures and supplemental reading materials.

Course Topics:
0. Course Presentation
1. Overview of Molecular and Nanoscale Communication: from Motivation to Application
2. Introduction to Molecular Communication Theory
3. Analysis of Molecular Communication Systems
4. Molecular Communication and Biochemical Pathways
5. Molecular Communication and Electrochemistry
6. Design/Engineering of Molecular Communication Systems
7. Molecular Communication and Neurons
8. Molecular Communication and Synthetic Biology
9. Towards the Internet of Bio-Nano Things

458 vs. 858: This course will not have major differences between the 458 and 858 versions in the delivery of the content. Instead, some selected questions in the exams and virtual lab assignments will be mandatory for 858 students, and optional for 458 students.

Course Organization:
• Lectures
o Lectures will be delivered through Zoom videoconferencing and recording of all the lectures will be made available in Canvas.

• TWO Exams
o Midterm Exam
o Final Exam

• 4 Homework Assignments
o To be solved individually

• 4 Virtual Lab Assignments
o Based on the iBioSim, Matlab SimBiology (and others) simulation environments
o To be solved individually
o Will help you consolidate the concepts seen in class in a more practical and engaging way

• Course Project (optional for undergrads)
o Create small projects using simulators, code etc. applying the theory learned in class
o Term papers on a hot topic of recent interest in the field
o To be worked on by groups of 2-3 people (for project) and individually (for term paper)
o Will help you consolidate the concepts seen in class in a more practical and engaging way

Grade Distribution:
Homework Assignments: 15%
Virtual Lab Assignments: 5%
Midterm Exam: 20%
Final Exam (OPEN NOTES): 20%
Project or Term Paper: 35%
In-class Participation and Professionalism: 5%

458 students who turn in the non-mandatory questions in the assignment will receive a maximum bonus of 10% (10% of the average question scores) on the final grade.

Final letter grades will be assigned tentatively based on the following scale:

A+: ≥ 100 A: 97% to 100% A−: 94% to 96%
B+: 90% to 93% B: 87% to 89% B−: 84% to 86%
C+: 80% to 83% C: 77% to 79% C−: 74% to 76%
D+: 70% to 73% D: 67% to 69% D−: 64% to 66%
F: ≤ 63%

Communication and Remote Teaching Plan:
• Course official announcements and messages will be delivered through Canvas.
• Lectures are PowerPoint-slide-based and will be delivered through PowerPoint presentation recording (Audio/Video + animated annotations).
• Homework assignments and quizzes will be posted and submitted online through Canvas.
• Exams will be delivered online through Canvas timed quiz + Zoom-enabled view of participants and their computer screen monitored real-time by the instructor/proctors. Students are expected to have a broadband connection available at the time of the exam to enable Zoom proctoring.
• Office hours are held on Zoom at selected times or schedule by appointment (agreed via email), as well as through the Discussions functionality in Canvas.

Back-up Plan: In case of problems for the instructor to establish a proper Zoom videconference at the time of the lecture, the instructor will record the lectures and distribute the video through Canvas.

Alternative accommodation for the exams will be provided to students experiencing connection problems.

Assessment Plan:
• Homework Assignments
Homework submissions will be through Canvas. Late homework is penalized 10% per day, and no homework will be accepted after the solution is posted online
• Exams
There will be TWO exams that will be delivered online through Canvas timed quiz + Zoom-enabled view of participants and their computer screen monitored real-time by the instructor/proctors. The exams will be OPEN NOTES: students are allowed to used class notes on your computer but are not allowed to use Internet (Google, etc.). The exam will include both open-ended, and multiple-choice questions.
• Homework Assignments and quizzes
Homework submissions will be through Canvas. Late homework is penalized 10% per day, and no homework will be accepted after the solution is posted online
• Project
There will be half-semester-long projects, focused on the research of material from the available literature, analysis and presentation to the class (at the end of the semester) of a specific topic chosen from those introduced in the class. The project will be assigned to students divided into teams according to the class size and should be executed through a review-style paper and an oral presentation (via Zoom or alternative means) at the end of the course. The presentation will be performed within the dead week, and it will be followed by technical questions from the instructors (oral exam).

Additional Materials:
All the following additional materials will be available in Canvas:
• Lecture slides
• Additional reading resources
• Homework assignments and quizzes
• Programming assignments and software

Attendance: Attendance at all officially scheduled class meetings in Zoom is expected but not mandatory. Students are responsible for knowing all materials discussed in class meetings. Changes to class and assignments will be announced on Canvas.

Academic Integrity: All homework assignments, quizzes, exams, etc. must be the student’s own work. No direct collaboration with fellow students, past or current, is allowed unless otherwise stated. The Computer Science & Engineering department has an Academic Integrity Policy:


All students enrolled in any computer science course are bound by this policy. You are expected to read, understand, and follow this policy. Violations will be dealt with on a case-by-case basis and may result in a failing assignment or a failing grade for the course itself.

Dealing with Stress and Adversity: UNL offers a variety of options to students to aid them in dealing with stress and adversity. Counseling and Psychological Services (CAPS) is a multidisciplinary team of psychologists and counselors that works collaboratively with Nebraska students to help them explore their feelings and thoughts and learn helpful ways to improve their mental, psychological and emotional well-being when issues arise. CAPS can be reached by calling 402-472-7450. Big Red Resilience & Well-Being provides fun events, innovative education, and dynamic services to help students understand emotions, manage stress, build strength, connect with others, develop grit and navigate transitions.

Students with Disabilities: Students with disabilities are encouraged to contact the instructor for a confidential discussion of their individual needs for academic accommodation. This includes students with mental health disabilities like depression and anxiety. It is the policy of the University of Nebraska-Lincoln to provide individualized accommodations to students with documented disabilities that may affect their ability to fully participate in course activities or to meet course requirements. To receive accommodation services, students must be registered with the Services for Students with Disabilities (SSD) office, 232 Canfield Administration, 472-3787.

Suggestion Box: The CSE Department has an anonymous suggestion box (http://cse.unl.edu/department/suggestion.php) that you may use to voice your concerns about any problems in the course or department if you do not wish to be identified.

Stay Up-to-Date: It is CSE Department policy that all students in CSE courses are expected to regularly check their email so they do not miss important announcements.

CSE Resource Student Center: The CSE Student Resource Center (Avery Hall Rm 12) is intended to provide UNL Computer Science and Computer Engineering majors who are new to the program with a set of resources that will help them assimilate to college life and encourage them to continue their study of Computer Science and Computer Engineering (http://cse.unl.edu/src).

This syllabus will be updated and expanded as the semester progresses.