PNG 550
Reactive Transport in the Subsurface

PNG 550 Syllabus


PNG 550 Reactive Transport Processes in the Subsurface

This syllabus is divided into several sections. You can read it sequentially by scrolling down the length of the document or by clicking on any of the links below to “jump” to a specific section. It is essential that you read the entire document as well as material covered in the Course Orientation. Together these serve as our course "contract."


Name: Li Li
Title: Professor
154 Hosler Bldg.
College of Earth and Mineral Sciences, The Pennsylvania State University

Note: I will read and respond to e-mail and discussion forums at least once per day during the work week (Monday through Friday). You may see me online occasionally on the weekends, but please don't count on it!

Teaching Assistant

Name: Han Wen
Title: Grading Assistant
Campus address: 158 Hosler Bldg.
College of Earth and Mineral Sciences, The Pennsylvania State University

NOTE: I will read and respond to e-mail and discussion forums at least once per day during the work week (Monday through Friday). You may see me online occasionally on the weekends, but please don't count on it!

Class Support Services

Penn State Online offers online tutoring to World Campus students in math, writing, and some business classes. Tutoring and guided study groups for residential students are available through Penn State Learning.

Course Overview


This course targets graduate students from various disciplines that work with chemical and physical processes in natural subsurface. This includes, for example, petroleum and natural gas engineering, geosciences, environmental engineering, agricultural engineering, civil engineering, chemical engineering, and applied mathematics. The course teaches fundamental concepts that are important in understanding subsurface reactive transport processes, as well as their quantitative representation and application. Covered topics include, for example, (bio)geochemical thermodynamics and kinetics, contaminant transport, and reactive transport coupling. Depending on the students’ interests, the course will discuss the applications of the principles in understanding and quantifying chemical weathering processes, environmental (bio)remediation, geological carbon sequestration, and reservoir souring. 

Prerequisites and concurrent courses:

Some chemistry and hydrogeology background would help however are not required. No experiences on numerical methods are required. This course teaches how to use a reactive transport code CrunchFlow, instead of solving for reactive transport equations.

Students who do not meet these prerequisites may be dis-enrolled during the first 10-day free add-drop period after being informed in writing by the instructor (see Senate policy 34-60, Prerequisites and Concurent Courses). If you have not completed the listed prerequisites, then promptly consult with the instructor if you have not done so already. Students who re-enroll after being dis-enrolled according to this policy are in violation of Item 15 on the Student Code of Conduct.

Course Objectives

The learning outcomes for the students are to:

  1. understand the reaction thermodynamics and kinetic of important geochemical reactions, including mineral dissolution and precipitation, aqueous complexation, surface complexation, and ion exchange;
  2. understand concepts of advective and dispersive/diffusive transport;
  3. understand the concept of spatial heterogeneity and how they affect reactive transport processes;
  4. acquire skills to model coupled flow, transport, and reactions using the reactive transport code CrunchFlow;
  5. develop the ability to communicate and collaborate within interdisciplinary teams.

The course will be taught through a combination of online lectures that discuss general principles and reactive transport equations, video demos, discussion forums, homework assignment, and a final project that requires the use of CrunchFlow. Students decide the content of the final project. Ideally the student will be able to integrate the project as part of their research.


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.

I have worked hard to make this the most effective and convenient educational experience possible. The Internet may still be a novel learning environment for you, but in one sense it is no different from a traditional college class: how much and how well you learn is ultimately up to you. You will succeed if you are diligent about keeping up with the class schedule and if you take advantage of opportunities to communicate with me as well as with your fellow students.

Specific learning objectives for each lesson and project are detailed within each lesson. The class schedule is published in the Calendar in Canvas (the course management system used for this course).

Required Course Materials

Required textbook: None

Online lesson content (not required, all are on reserve in EMS library):

  1. Geochemistry, groundwater, and pollution, by C. A. J. Appelo and D. Postma, 2nd edition, 2005.
  2. Reactive transport in porous media, edited by P. C. Lichtner, C. I. Steefel, and E. H. Oelkers, 1996.
  3. Principles and applications of aquatic chemistry. By F. M. M. Morel and J. G. Hering, 1993.
  4. Aqueous environmental geochemistry, by D. Langmuir, 1997.
  5. Contaminant hydrogeology, by C. W. Fetter, 2nd edition, 1999 / 2008
  6. The geochemistry of natural waters: surface and groundwater environments. 3rd edition. By J. I. Drever. 1997.
  7. Applied contaminant transport modeling. 2nd ed. Chunmiao Zheng. 2002.
  8. Additional reading materials posted in Canvas

All other materials needed for this course are presented online through our course website and 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 World Campus Helpdesk.

Reserve materials
This course uses library Electronic Reserves (E-Reserves). More information about how to access this content is available in the course orientation.


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

  • Homework: There will be approximately 9 homework assignments, one of which is optional. Students are required to submit homework via Canvas.
  • Exams: There will be one final exam in the final week.
  • Project: Each student will work on a research project that uses CrunchFlow. Ideally, this would be a topic that would be relevant to your thesis. An abstract of the project (3 pages, single space) will be due in the mid of the semester. An abstract template will be handed out in early February. Students are welcome to discuss ideas with the instructor before the abstract is due.
  • Presentation: At the end of the semester, each student will give a 15 minutes presentation to classmates and will submit a project report.

It is important that your work is submitted in the proper format to the appropriate Canvas assignment drop-box 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.


Breakdown of each assignment's value as a percentage of total course grade.
Assignment Percent of Grade
Homework 40%
Final exam 20%
Project 40%

I will use the Canvas gradebook to keep track of your grades. You can see your grades in the gradebook, too, by clicking "Grades" in Canvas. Overall course grades will be determined as follows. Percentages refer to the proportion of all possible points earned.

Letter Grade and Corresponding Percentage
Letter Grade Percentages
A 93 - 100 %
A- 90 - 92.9 %
B+ 87 - 89.9 %
B 83 - 86.9 %
B- 80 - 82.9%
C+ 77 - 79.9 %
C 70 - 76.9 %
D 60 - 69.9 %
F < 60 %

Unsatisfactory (student did not participate)

PNG 550 Course Schedule

imagePrintable Schedule

Below you will find a summary of the primary learning activities for this course and the associated time frames. This course is 16 weeks in length. Each lesson is 1 week long. See our Calendar in Canvas for specific lesson time frames and assignment due dates.

NOTE:See the Canvas Calendar tab for a full semester calendar of events.

Week 1 - Lesson 0
Topics: Lesson 0: Orientation
Readings: Check "Lessons Roadmap" section of the first page of the lesson.
Assignments: To do list for lesson 0
Week 2 - Lesson 1
Topics: Lesson 1: Aqueous complexation
Readings: Check "Lessons Roadmap" section of the first page of the lesson.
Assignments: Assigned: Homework #1 in lesson 1
Week 3 - Lesson 2
Topics: Lesson 2: Mineral dissolution and precipitation
Readings: Check "Lessons Roadmap" section of the first page of the lesson.
Assignments: Due: Homework #1 due on Monday
Assigned: Homework #2 in lesson 2
Week 4 - Lesson 3
Topics: Lesson 3: Surface complexation
Readings: Check "Lessons Roadmap" section of the first page of the lesson.
Assignments: Due: Homework #2 due on Monday
Assigned: Homework #3 in lesson 3
Note: Project abstract template will be handed out this week.
Week 5 - Lesson 4
Topics: Lesson 4: Ion exchange
Readings: Check "Lessons Roadmap" section of the first page of the lesson.
Assignments: Due: Homework #3 due on Monday
Assigned: Homework #4 in lesson 4
Note: Discussion Session - Time and location TBA
Week 6 - Lesson 5
Topics: Lesson 5: Flow and transport in 1D homogeneous porous media
Readings: Check "Lessons Roadmap" section of the first page of the lesson.
Assignments: Due: Homework #4 due on Monday
Assigned: Homework #5 in lesson 5
Week 7 - Lesson 6
Topics: Lesson 6: Flow and transport in 1D heterogeneous porous media (Phreeqc, optional)
Readings: Check "Lessons Roadmap" section of the first page of the lesson.
Assignments: Due: Homework #5 due on Monday
Assigned: Homework #6 in lesson 6
Note: Project abstract due on Friday
Week 8 - Lesson 7
Topics: Lesson 7: Flow and transport in 2D heterogeneous porous media
Readings: Check "Lessons Roadmap" section of the first page of the lesson.
Assignments: Due: Homework #6 due on Monday
Assigned: Homework #7 in lesson 7
Note: Discussion Session - Time and location TBA
Week 9 - Spring Break
Topics: None
Readings: None
Assignments: None
Week 10 - Lesson 8
Topics: Lesson 8: Reactive transport coupling: chemical weathering
Readings: Check "Lessons Roadmap" section of the first page of the lesson.
Assignments: Due: Homework #7 due on Monday
Assigned: Homework #8 in lesson 8
Week 10 - Lesson 9
Topics: Lesson 9: Reactive transport coupling: Marcellus Shale waters leakage
Readings: Check "Lessons Roadmap" section of the first page of the lesson.
Assignments: Due: Homework #8 due on Monday
Assigned: Homework #9 in lesson 9
Week 11-14 - Final Project
Topics: Work on Final Project
Readings: None
Assignments: Homework #9 due on March 27
Note: Discussion Session - Time and Location TBA
Week 15 - Project Presentation
Topics: Final Project Presentation
Readings: None
Assignments: Project Presentation
Final project report due on Friday, April 29th

Course Policies

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.

Technical Requirements

For this course, we recommend the minimum technical requirements outlined on the Dutton Institute 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 Outreach Helpdesk (for World Campus students) or the ITS Help Desk (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 one of the following browsers: Firefox (any version), Safari (versions 5.1 or 6.0), Chrome (0.3 or later), or Internet Explorer with the MathPlayer PlugIn. If you use any other browser, there will be pages containing equations that do not render properly. If you need technical assistance at any point during the course, please contact the Outreach 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 the Penn State World Campus 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 guidelines 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 "Plagiarism Tutorial 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 Student Disability Resources (SDR) website provides contact information for every Penn State campus: Contacts for Disability Resources at all Penn State Campuses. For further information, please visit the Student Disability Resources (SDR) 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 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.

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 wellbeing.  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 and Psychological 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

Reporting Bias-Motivated Incidents

Penn State takes great pride to foster 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.

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.

Inclement Weather

In case of weather-related delays 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 weather delays. If you are affected by a weather-related emergency, please contact your instructor at the earliest possible time to make special arrangements.

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 with others whom you do not know.

Deferred Grades

If you are prevented from completing this course within the prescribed amount of time, it is possible to have the grade deferred with the concurrence of the instructor. To seek a deferred grade, you must submit a written request (by e-mail or U.S. post) to your instructor describing the reason(s) for the request. It is up to your instructor to determine whether or not you will be permitted to receive a deferred grade. If, for any reason, the course work 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 and 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 with you via e-mail, course announcement and/or course discussion forum.