Master's program

• All students are required to submit their undergraduate transcript to the Director of Masters’ Studies prior to the beginning of their first term to discuss their course plan. (An unofficial copy is sufficient.)
• Full-time registration for MSE students is 9 or more credits per semester.
• In students’ first semester: there will be a mandatory Academic Ethics module and quiz embedded in the online orientation which is part of every graduate student’s degree requirements. This must be completed with a passing grade. You will see the course EN.500.603 added to your SIS enrollments in approximately the third week of the semester; do not drop this course! See https://engineering.jhu.edu/admissions/graduate-admissions/full-time-programs/newlyadmitted-students/graduate-student-orientation/ for more information.
• Students must enroll in at least one semester of Chemical and Biomolecular Engineering Seminar (EN.540.600 in Fall or EN.540.601 in Spring) throughout their tenure.
• Students must complete Responsible Conduct of Research training. For complete information, see  https://engineering.jhu.edu/research/resources-policies-forms/onlinetraining-course-responsible-conduct-of-research/ .
• Students must complete a total of
  • Essay-based Students: 18 credits of coursework and 12 credits of EN.540.801 Graduate Research.
  • Course-based Students: 30 credits of graduate-level (i.e. 600-level and above) coursework approved by  the Director of Masters’ Studies, who is the advisor for all coursework-based MSE students.
• The student and advisor will select these courses to design a curriculum appropriate for the student’s research interests and educational goals.
• The majority of students’ courses should be composed of 3-(or more) credit courses.
• The courses must be taken for a letter grade. These courses cannot include seminars, independent studies, graduate research, or special studies.
• Students are not allowed to count 400-level courses towards their MSE degree unless (1) the course is not offered at the 600 level, and (2) the department offering the course considers it to be a graduate-level course in their program.  A letter from that department’s head, chair, or graduate program director should be included in the submission of graduation materials.
• Courses offered at both the 400 and 600 level must be taken at the 600 level to fulfill MSE course requirements. All ChemBE coursework must be taken at the 600 level.
• The semester before a student’s intended graduation date, they should send the coursework portion of their MSE checklist to their Faculty Advisor for approval.
• Minimum ChemBE credit requirement: At least
  • 12 of the 18 coursework credits (for essay-based and design-based students)
  • 18 of the 30 coursework credits (for course-based students)
    must be from courses in the Chemical and Biomolecular Engineering Department (EN.540.6xx or EN.545.6xx).
    9 of these credits are in the MSE core courses (see below).
• Exceptions to this rule are very rare and must be approved by the Director of Masters’ Studies. A course from a department other than ChemBE may be allowed to count towards these credits only if the course has significant ChemBE content, is 3 credits, and is consistent with the student’s research interests and educational goals as determined by the student’s research advisor and the Director of Masters’ Studies.
• Students in the Design-based MSE track must take Product Design each semester for 3–4 semesters. These courses do not count towards the 18 credits
  *The Design-Based MSE option will be offered in 2025-2026 academic year.

Students must take three core courses; one from each of the following categories:

• Core 1 – Thermodynamics
  • EN.540.671 “Advanced Thermodynamics in Practice”, typically offered in the Spring semester.
  • With approval from the Director of Masters’ Studies and the instructor, this course may be substituted for the more advanced version, EN.540.630 “Thermodynamics & Statistical Mechanics”, typically offered in the Fall semester.
• Core 2 – Transport
  • EN.540.604 “Transport Phenomena in Practice”, typically offered in the Spring semester.
  • With approval from the Director of Masters’ Studies and the instructor, this course may be substituted for the more advanced version, EN.540.652 “Advanced Transport Phenomena”, typically offered in the Fall semester.
• Core 3 – Kinetics (Any one of the following courses)
  • EN.540.602 “Metabolic Systems Biotechnology”
  • EN.540.632 “Project in Design: Pharmacokinetics”
  • EN.540.633 Pharmacokinetics and Phamacodynamics
  • EN.540.638 “Advanced Topics in Pharmacokinetics and Pharmacodynamics I”
  • EN.540.673 “Advanced Chemical Reaction Engineering in Practice”
  • EN.540.681 “Molecular Kinetics and Catalysis”
  • EN.540.695 “Special Topics in ChemBE: Pharmacokinetics and Pharmacodynamics of Food Metabolism”
  • *note that other special topics will not be accepted

Substitutions for core courses are typically granted if students have ChemBE backgrounds.

• Between Core 1 and Core 2, only one of these two Cores may be substituted. (Students in the BS/MSE program may substitute for both Core 1 and Core 2.)
• Students cannot take both versions of the Core 1 courses and have them both count towards their course requirements, and likewise for Core 2. Multiple courses in Core 3 can be taken for course requirements; these excess courses would fall into elective slots.

MSE students in ChemBE may opt to focus their studies within an area of specialization. The program offers three focus areas as of Fall 2024:

1. Cellular, Molecular, and Biopharmaceutical Engineering
2. Chemical and Sustainability Engineering
3. Molecular Modeling, Data Science, and AI

Students completing the essay-based MSE should consult with their advisors to determine which two or more focus area courses best suit their research and interests. Students in the coursework-based MSE consult their advisor to determine which four or more focus area courses best suit their professional interests.

Note that students may also work with their advisors to select an appropriate Kinetics (Core 3) course to enhance their focus area (for example, students in the Cellular, Molecular, and Biopharmaceutical Engineering focus area may choose to take EN.540.602 Metabolic Systems Biotechnology to fulfill their Core 3/Kinetics requirement, and also take two additional courses from the list of focus area courses below).

Students may choose to continue to take courses from the focus area for their additional electives or choose other graduate level courses. Note that the majority of every student’s graduate-level MSE coursework should be in ChemBE, regardless of focus area.

Focus Area 1: CELLULAR, MOLECULAR, AND BIOPHARMACEUTICAL ENGINEERING
Course options:

• EN.540.602 Metabolic Systems Bioengineering
• EN.540.633 Pharmacokinetics and Pharmacodynamics
• EN.540.638 Advanced Topics in Pharmacokinetics and Pharmacodynamics I
• EN.540.640 Micro/Nanotechnology: The Science and Engineering of Small Structures
• EN.540.665 Engineering Principles of Drug Delivery
• AS.030.623 Molecular Synthetic Biology
• EN.540.614 Computational Protein Structure Prediction & Design
• EN.540.618 Cancer Metabolism
• EN.540.626 Fundamentals of Cell Bioengineering
• EN.540.628 Supramolecular Materials and Nanomedicine
• EN.540.637 Application of Molecular Evolution to Biotechnology
• EN.540.667 Targeted Drug Delivery: Mechanistic Concepts
• EN.580.646 Molecular Immunoengineering

Focus Area 2: CHEMICAL AND SUSTAINABILITY ENGINEERING
Course options:

• EN.540.607 Renewable Energy Technologies
• EN.540.673 Advanced Chemical Reaction Engineering in Practice
• EN.540.602 Metabolic Systems Biotechnology
• EN.540.615 Interfacial Science with Applications to Nanoscale Systems
• EN.540.640 Micro/Nanotechnology: The Science and Engineering of Small Structures
• EN.540.681 Molecular Kinetics and Catalysis
• EN.540.658 Modeling and Design of Sustainable Chemical Processes
• EN.510.625 Advanced Materials for Battery
• AS.030.604 Electrochemical Systems for Energy Conversation and Storage
• EN.510.658 Electroanalytical Chemistry and Energy Conversation

Focus Area 3: MOLECULAR MODELING, DATA SCIENCE, AND AI
Course options:

• EN.540.605 Modern Data Analysis & Machine Learning for ChemBEs
• EN.540.614 Computational Protein Structure Prediction & Design
• EN.540.658 Modeling and Design of Sustainable Chemical Processes
• EN.540.635 Software Carpentry

• Many of our students do not have backgrounds in Chemical and Biomolecular Engineering, and it’s great that these students have chosen JHU’s program to start their journey in ChemBE!
  • To help these students excel in their coursework, we recommend that they take some undergraduate-level courses to better prepare themselves for the core courses. For those who are ultimately interested in a Ph.D. program, we especially recommend a solid foundation, as a strong GPA is necessary to compete in the PhD application process. These courses do not count towards your graduate-level course requirements.
    • Core 1 – Thermodynamics
      • EN.540.202 “Introduction to Chemical and Biological Process Analysis”, typically offered both Fall and Spring semesters, recommended to be taken in your first semester. (Students would then take EN.540.671 “Advanced Thermodynamics in Practice” in the Spring semester)
        AND
      • EN.540.203 “Engineering Thermodynamics”, typically offered both Fall and Spring semesters, recommended to be taken in Spring semester after EN.540.202 (concurrently with EN.540.671). Students with sufficient background in Thermodynamics and/or Physical Chemistry, as well as Calculus II, can get approval from the Director of Masters’ Studies to go directly to EN.540.671.
    • Core 2 – Transport
      • EN.540.303 “Transport Phenomena I”, typically offered both Fall and Spring semesters, recommended to be taken in your first semester. Students would then take EN.540.604 “Advanced Transport Phenomena in Practice” in their second semester)
      • Students with sufficient background in Transport, as well as Calculus III and Differential Equations, can get approval from the Director of Masters’ Studies to go directly to EN.540.604.
    • Core 3 – Kinetics
      • EN.540.301 “Kinetic Processes”, typically offered in the Spring semester, recommended to be taken in students’ second semester.
      • Students with sufficient background in Thermodynamics and/or Physical Chemistry, as well as Calculus III and Differential Equations, can get approval from the Director of Masters’ Studies to go directly to EN.540.673 and EN.540.681.
      • Students with sufficient background in the above bullet as well as Kinetics can get approval from the Director of Masters’ Studies to go directly to EN.540.673 and EN.540.681.
    • Some students may find that they wish to supplement their mathematical background prior to taking these undergraduate courses by taking one, or more, of the following to fill in any gaps they have: EN.540.205 Mathematical Methods in ChemBE 1; EN.540.206 Mathematical Methods in ChemBE 2; AS.110.109 “Calculus II (For Physical Sciences and Engineering)”, AS.110.202 “Calculus III”, AS.110.302 “Differential Equations and Applications”, and/or EN.553.291 “Linear Algebra and Differential Equations”. Please consult with the Director of Masters’ Studies to plan your course schedule so that you are sure to finish all your degree requirements on time.

As part of their MSE coursework, students are required to take at least one Technical Writing Course, which they will select from a list of pre-approved options. These courses, which are offered by the CLE Department, have been chosen specifically due to their writing-focused relevance to a professional in the Chemical Engineering field.
These Technical Writing Courses count towards the required 30 credits (Coursework based) or 18 credits (Essay & Design based) of each MSE student’s program.

• Take any one of the following Technical Writing Courses:
  • EN.663.613 – Technical Communication for Scientists and Engineers
  • EN.663.640 – Writing Grant and Contract Proposals
  • EN.663.644 – Writing for Clarity
  • EN.663.645 – Improving Presentation Skills for Graduate Students

• NOTE: For students who completed their undergrad at JHU and took EN.661.315 – Culture of the Engineering Profession, the Technical Writing Requirement is waived.

• Students must enroll in EN.500.601 – Lab Safety in their first semester.
  • Students who attended JHU for their undergrad program are exempt from this requirement if they took EN.540.490 – Introduction to Chemical Process Safety.
• Students must maintain full-time registration for all semesters. This means that students must always be registered for at least 9 credits. In semesters where students are pursuing research, they will register for as many credits as necessary of their advisor’s
  research course (EN.540.801) to maintain the 9 total credits required. (For example, a student taking one 3-credit course would register for 6 credits of research with their advisor to maintain 9 credits for full-time status.)
• Students must remain in good research standing with their research advisor. Failure to do so will result in probation and transfer to the course-based MSE track.
• Students must write an essay based on original research and literature review and present their results at an open seminar attended by faculty and students. The essay must be approved by the departmental graduate committee, which consists of at least (1) the graduate research advisor and (2) a faculty member, one of which must be a faculty member from the Department of Chemical and Biomolecular Engineering (primary or secondary appointment).

• Students must maintain a “B” average (GPA 3.0) in coursework to earn their degree.
• No “D” grade in a ChemBE course can be counted toward their degree requirements.
• In any given semester, receiving a grade of “F”, “D”, or two “C’s” will result in the student being placed on academic probation (“C-”, “C”, and “C+” all count as “C” grades). Once on probation, receiving any additional grade of “C+” or below will result in the student’s termination from the program. A student will remain on academic probation until they are able to improve their “D” or “F” grade upon retake or Director-approved substitution. If no “D” or “F” grades were present, the student attains a “B” average in their coursework.

To broaden the practical training for Master of Science in Engineering (MSE) students in the Whiting School of Engineering, the Institute for NanoBioTechnology (INBT) collaborates with major industry partners to offer a credited and paid co-op opportunity to MSE students in the Chemical and Biomolecular Engineering, Materials Science and Engineering, and Mechanical Engineering programs.

ChemBE students pursuing the essay-based track have the opportunity to choose the co-op program as an alternative to conducting research in JHU laboratories. Students must apply through the INBT office during their first semester. (This application process is separate from, and happens after, being admitted to the ChemBE MSE program.)

Each student who is accepted to the program will be assigned a research advisor/mentor at the sponsoring company. The company is expected to develop a list of goals and development objectives for the student. Once the project has been determined, a few weeks prior to the start of the co-op or within the first week, students must find a faculty advisor with primary or secondary appointment in ChemBE. During the six-month co-op period, students will meet with the faculty advisor at least once every six weeks to provide progress updates. At the end of the co-op internship, students will complete an essay and present their results at an open seminar attended by faculty and students. The company mentor can serve as the student’s second reader as long as they have a PhD or commensurate work experience.
For more information, please visit https://inbt.jhu.edu/masters/.