EGEE 439
Alternative Fuels from Biomass Sources

EGEE 439 Syllabus


EGEE 439: Alternative Fuels from Biomass Sources (Fall 2023)

It is essential that you read this entire document as well as the material covered in the Course Orientation. Together, these serve as our course "contract."


Dr. Hilal Ezgi Toraman

Dr. Hilal Ezgi Toraman
Assistant Professor, Virginia S. and Philip L. Walker Faculty Fellow
John and Willie Leone Family Department of Energy and Mineral Engineering
Department of Chemical Engineering
Institutes of Energy and the Environment
Pennsylvania State University, University Park, PA 16802

  • Email: Please use the Canvas course email system to reach me and the assistant.
  • Phone: 814-863-9261 (Office) - second option, the best way to reach me is by email.
  • Office Hours: Office hours are by appointment on Tuesdays: 15:00-16:30 (Hilal Ezgi Toraman and Do Hyun Lee) and Thursdays: 17:30-18:30 (Do Hyun Lee). Please contact me,, and the assistant of the course: Do Hyun Lee,, to set up a time for the office hour the previous Sunday until 11:59 pm. Please provide the question(s) that you plan to ask during the office hour when you set up a time for the office hour.
  • This semester, EGEE 439 is slated to follow a remote asynchronous format. This means you will be instructed through remote learning.
  • REMOTE ASYNCHRONOUS: EGEE 439 is slated to follow a remote asynchronous format. This means you will be instructed through remote learning. You will be responsible to read course material, taking part in course assignments, and turning in course deliverables according to the due dates listed in Canvas.
  • All students sign and return the Syllabus Acknowledgement Form to the assistant of the course, via email during the first week of the semester.

Course Overview

EGEE 439: Alternative Fuels from Biomass Sources (3 credits)

This course will examine the chemistry of technologies of bio-based sources for power generation and transportation fuels.

Prerequisites and concurrent courses:

  • CHEM 110 or comparable general chemistry course

Students who do not meet these prerequisites may be disenrolled according to Administrative Policy C-5. if they do not have the proper prerequisite override. Students who add the course after being disenrolled according to this policy are in violation of Item 15 on the Student Code of Conduct..

Course Objectives:

When you successfully complete this course, you will be prepared to:

  • describe various biomasses that can be utilized for energy and fuel generation;
  • explain the composition of various processes necessary for biomass processing;
  • utilize the necessary chemistry, as well as mass and energy balances that would be utilized in a biorefining facility;
  • analyze how to utilize biofuels in current fuel infrastructure;
  • illustrate what is required in a biorefinery.


On average, most students spend eight to ten hours per week working on course assignments. Your workload may be more or less depending on your study habits.

Specific learning objectives for each lesson and project are detailed within each lesson. The class schedule is published in Canvas under Syllabus and on the Calendar in the Global Navigation Menu.

Required Course Materials

Required Textbook

You will not be required to purchase a book. There are not all that many biofuel books that cover all of the aspects that I cover in this course. However, there will be excerpts of books and articles posted online for you to read (see 'Reserve materials' below).

Online lesson content

The course materials for the lessons needed for this course are presented online in Canvas. In order to access the online materials, you need to have an active Penn State Access Account user ID and password (used to access the online course resources). If you have any questions about obtaining or activating your Penn State Access Account, please contact the Outreach Helpdesk.

E-Reserve Materials

This course uses library Electronic Reserves (E-Reserves). These can be accessed via Canvas Library Resources.


This course will rely on a variety of methods to assess and evaluate student learning, including:

Homework and Quizzes 35% will include written activities related to the lesson content and supplemental readings. It may include summaries and calculations.
Discussion 5% will allow students to discuss topics related to the lesson content and supplemental readings.
Exams 25% will be given to assess students' understanding of lesson concepts.
Final project reports and presentations 35% will be written biorefinery report and presentations

Citation and Reference Style

You will use the APA citation style.

It is important that your work is submitted in the proper format to the appropriate Canvas Assignment or Discussion Forum and by the designated due date. I strongly advise that you not wait until the last minute to complete these assignments—give yourself time to ask questions, think things over, and chat with others. You'll learn more, do better...and be happier!

Due dates for all assignments are posted on the course calendar in Canvas.

Exams will be conducted at the testing center. Important Note: Questions will be displayed one at a time. You will have only one attempt for each question. No navigation between questions, no backtracking, and no review are allowed. While taking the exam, please consider your answer to each question carefully before you submit it. It is noted that the mode of implementation of the exams can be switched to be conducted using proctoring software, which may listen to you, monitor your computer screen, view you and your surroundings, and record (including visual and audio recordings) all activity during the proctoring process or using Zoom or other technology selected by your instructor which may use your computer’s webcam or other technologies to communicate, monitor, and/or record classes, class activities, and assessment.


I will use the Canvas gradebook to keep track of your grades. Overall course grades will be determined as follows. Percentages refer to the proportion of all possible points earned.

Letter Grade and Corresponding Percentages
Letter Grade Percentages
A 90.0 - 100 %
A- 88 - <90 %
B+ 84.0 - <88 %
B 80 - <84 %
B- 77.0 - <80 %
C+ 75 - <77%
C 65 - <75 %
D 60 - <65 %
F < 60 %
X Unsatisfactory (student did not participate)


I do not usually have a curve. However, depending on circumstances, grade cutoffs may be adjusted.

Late Policy

I do not accept any "late work." In exceptional circumstances, you should contact me. The earlier you contact me to request a late submission, the better. Requests will be considered on a case by case basis. Generally, late assignments will be assessed a penalty of at least 10% and will not be accepted more than one week after the original due date.

Make-up Exam Policy

Make-up exams will only be granted through the approval of the course instructor for legitimate and excused absences. Prior notification and approval for a make-up exam must be obtained by the student at least 72 hours prior to the scheduled exam. Special circumstances will be considered on a case-by-case basis.

EGEE 439 Course Schedule

imagePrintable Schedule

Below, you will find a summary of the primary learning activities for this course and the associated time frames. Each lesson is one week long, with a couple of exceptions. See our Calendar in Canvas for specific lesson time frames and assignment due dates.

Course Orientation
Topics Orientation to Course
Readings Orientation Material

Complete Penn State Academic Integrity Training and upload your Training Certificate to the "Academic Integrity Training Certificate" Assignment.

Lesson 1: Why Alternative Fuels from Biomass?
Topics Why biofuels?

Online course material

Assignments None
Lesson 2: Existing Fossil Fuel Technologies - Transportation
Topics Basics of petroleum refining, Chemistry of liquid fuels for various engines

Online course material

Assignments Quiz #1
Lesson 3: Use of Biomass in Thermal Technologies
Topics Combustion of biomass, gasification of biomass
Readings Online course material
Assignments Homework #11
Lesson 4: Biomass Pyrolysis and Pretreatment
Topics Pyrolysis of biomass, and pretreatment methods
Readings Online course material
Assignments Exam #1
Lesson 5: General Ethanol Production

Biochemistry of enzymes

  • Online course material
  • Lynd, L. R., P. J. Weimer, W. H. Van Zyl, and I. S. Pretorius. "Microbial Cellulose Utilization: Fundamentals and Biotechnology." Microbiology and Molecular Biology Reviews 66.3 (2002): 511-15.
Assignments Quiz #2
Lesson 6: Processing to Produce Ethanol and Butanol From Carbohydrates and Enzymes
Topics Biochemical processing to produced ethanol, Biochemical processing to produce butanol
  • Online course material
  • Robison, D. (2012, March 19). Startup Converts Plastic To Oil, And Finds A Niche. Retrieved December 16, 2014.
  • Bourzac, K. (2009, July 9). Biofuel Plant Opens in Brazil. Retrieved December 16, 2014.
Assignments Discussion #1
Lesson 7: Thermochemical Methods to Produce Biofuels
Topics Chemical processing to produce ethanol, butanol, and other chemicals

Online course material

Assignments Exam #2, Final Project Outline
Lesson 8: Biodiesel Production
Topics Chemistry of fats and oils, Processing of fats and oils to make biodiesel and biojet fuels
  • Online course material
  • Watch 3-part Biodiesel Production Demonstration videos.
Assignments Quiz #3

Lesson 9: Algae as a Source for Fuels

Topics Algae growth and methods of extraction and conversion

Online course material

Assignments Final Project Rough Draft and Presentation(Video recording)
Lesson 10: Economics of Biomass Production – Ethanol, Butanol, and Biodiesel
Topics Economics of Biomass Production – Ethanol, Butanol, and Biodiesel

Online course material

Assignments None
Lesson 11: Additional Processes for Fuels from Biomass
Topics Anaerobic digestion and other gases

Online course material

Assignments Quiz #4, Final Project Report
Lesson 12: Final Project Presentations

Biorefinery project


Online course material

Assignments Final Project Presentations (Video recording)

Course Policies

Technical Requirements

For this course, we recommend the minimum technical requirements outlined on the World Campus Technical Requirements page, including the requirements listed for same-time, synchronous communications. If you need technical assistance at any point during the course, please contact the IT Service Desk (for World Campus students) or Penn State's IT Help Portal (for students at all other campus locations).

Internet Connection

Access to a reliable Internet connection is required for this course. A problem with your Internet access may not be used as an excuse for late, missing, or incomplete coursework. If you experience problems with your Internet connection while working on this course, it is your responsibility to find an alternative Internet access point, such as a public library or Wi-Fi ® hotspot.

Mixed Content

This site is considered a secure web site, which means that your connection is encrypted. We do, however, link to content that isn't necessarily encrypted. This is called mixed content. By default, mixed content is blocked in Internet Explorer, Firefox, and Chrome. This may result in a blank page or a message saying that only secure content is displayed. Follow the directions on our Technical Requirements page to view the mixed content.


This course must be viewed using the latest version of Firefox, Safari, Chrome, or Edge. Internet Explorer is not supported. If you use any other browser, or if you are not using the latest version of your browser, some pages containing equations may not render properly. In addition, javascript must be enabled for equations to render properly. If you have any issues with equations not rendering properly, please update your browser to the latest version or try using a different browser. If you need additional technical assistance at any point during the course, please contact the HelpDesk (for World Campus students) or the IT Service Desk (for students at all other campus locations).

Penn State E-mail Accounts

All official communications from Penn State are sent to students' Penn State e-mail accounts. Be sure to check your Penn State account regularly, or forward your Penn State e-mail to your preferred e-mail account, so you don't miss any important information.

Academic Integrity

This course follows the procedures for academic integrity of Penn State's College of Earth and Mineral Sciences. Penn State defines academic integrity as "the pursuit of scholarly activity in an open, honest and responsible manner." Academic integrity includes "a commitment not to engage in or tolerate acts of falsification, misrepresentation, or deception." In particular, the University defines plagiarism as "the fabrication of information and citations; submitting others' work from professional journals, books, articles, and papers; submission of other students' papers, lab results or project reports and representing the work as one's own." Penalties for violations of academic integrity may include course failure. To learn more, see Penn State's Academic Integrity Training for Students

Course Copyright

All course materials students receive or to which students have online access are protected by copyright laws. Students may use course materials and make copies for their own use as needed, but unauthorized distribution and/or uploading of materials without the instructor’s express permission is strictly prohibited. University Policy AD 40, the University Policy Recording of Classroom Activities and Note Taking Services addresses this issue. Students who engage in the unauthorized distribution of copyrighted materials may be held in violation of the University’s Code of Conduct, and/or liable under Federal and State laws.

For example, uploading completed labs, homework, or other assignments to any study site constitutes a violation of this policy.

Accommodations for Students with Disabilities

Penn State welcomes students with disabilities into the University's educational programs. Every Penn State campus has an office for students with disabilities. The Office for Student Disability Resources website provides contact information for Campus Disability Coordinators at every Penn State campus. For further information, please visit the Office for Student Disability Resources website.

In order to receive consideration for reasonable accommodations, you must contact the appropriate disability services office at the campus where you are officially enrolled. You will participate in an intake interview and provide documentation. See documentation guidelines at Applying for Services from Student Disability Resources. If the documentation supports your request for reasonable accommodations, your campus’s disability services office will provide you with an accommodation letter. Please share this letter with your instructors and discuss the accommodations with them as early in your courses as possible. You must follow this process for every semester that you request accommodations.

Change in Normal Campus Operations

In case of weather-related delays or other emergency campus disruptions or closures at the University, this online course will proceed as planned. Your instructor will inform you if there are any extenuating circumstances regarding content or activity due dates in the course due to these delays or closures. If you are affected by a weather-related emergency, please contact your instructor at the earliest possible time to make special arrangements.

Reporting Educational Equity Concerns

Penn State takes great pride in fostering a diverse and inclusive environment for students, faculty, and staff. Acts of intolerance, discrimination, or harassment due to age, ancestry, color, disability, gender, gender identity, national origin, race, religious belief, sexual orientation, or veteran status are not tolerated (Policy AD29 Statement on Intolerance) and can be reported through Educational Equity via Report Bias.

Counseling and Psychological Services

Many students at Penn State face personal challenges or have psychological needs that may interfere with their academic progress, social development, or emotional well-being.  The university offers a variety of confidential services to help you through difficult times, including individual and group counseling, crisis intervention, consultations, online chats, and mental health screenings.  These services are provided by staff who welcome all students and embrace a philosophy respectful of clients’ cultural and religious backgrounds, and sensitive to differences in race, ability, gender identity, and sexual orientation.  Services include the following:

Counseling and Psychological Services at University Park  (CAPS): 814-863-0395
Counseling Services at Commonwealth Campuses
Penn State Crisis Line (24 hours/7 days/week): 877-229-6400
Crisis Text Line (24 hours/7 days/week): Text LIONS to 741741

Military Personnel

Veterans and currently serving military personnel and/or spouses with unique circumstances (e.g., upcoming deployments, drill/duty requirements, disabilities, VA appointments, etc.) are welcome and encouraged to communicate these, in advance if possible, to the instructor in the case that special arrangements need to be made.

Connect Online with Caution

Penn State is committed to educational access for all. Our students come from all walks of life and have diverse life experiences. As with any other online community, the lack of physical interaction in an online classroom can create a false sense of anonymity and security. While one can make new friends online, digital relationships can also be misleading. Good judgment and decision-making are critical when choosing to disclose personal information to others whom you do not know.

Deferred Grades

If you are prevented from completing this course within the prescribed amount of time for reasons that are beyond your control, it is possible to have the grade deferred with the concurrence of the instructor, following Penn State Deferred Grade Policy 48-40. To seek a deferred grade, you must submit a written request (by e-mail or U.S. post) to the instructor describing the reason(s) for the request. Non-emergency permission for filing a deferred grade must be requested before the beginning of the final examination period.  It is up to the instructor to determine whether or not you will be permitted to receive a deferred grade. If permission is granted, you will work with the instructor to establish a communication plan and a clear schedule for completion within policy.  If, for any reason, the coursework for the deferred grade is not complete by the assigned time, a grade of "F" will be automatically entered on your transcript.


This course will be conducted entirely online. There will be no set class meeting times, but you will be required to complete weekly assignments with specific due dates. Many of the assignments are open for multiple days, so it is your responsibility to complete the work early if you plan to travel or participate in national holidays, religious observances or University approved activities.

If you need to request an exception due to a personal or medical emergency, contact the instructor directly as soon as you are able. Such requests will be considered on a case-by-case basis.

Diversity, Inclusion, and Respect

Penn State is “committed to creating an educational environment which is free from intolerance directed toward individuals or groups and strives to create and maintain an environment that fosters respect for others” as stated in Policy AD29 Statement on Intolerance. All members of this class are expected to contribute to a respectful, welcoming, and inclusive environment and to interact with civility.

For additional information, see:

Mandated Reporting Statement

Penn State’s policies require me, as a faculty member, to share information about incidents of sex-based discrimination and harassment (discrimination, harassment, sexual harassment, sexual misconduct, dating violence, domestic violence, stalking, and retaliation) with Penn State’s Title IX coordinator or deputy coordinators, regardless of whether the incidents are stated to me in person or shared by students as part of their coursework. For more information regarding the University's policies and procedures for responding to reports of sexual or gender-based harassment or misconduct, please visit Penn State's Office of Sexual Misconduct Prevention & Response website.

Additionally, I am required to make a report on any reasonable suspicion of child abuse in accordance with the Pennsylvania Child Protective Services Law.


Please note that the specifics of this Course Syllabus can be changed at any time, and you will be responsible for abiding by any such changes. All changes will be communicated to you via e-mail, course announcement and/or course discussion forum.