Hopkins Engineering Applications & Research Tutorials

The 2016 HEART Program: Small Introductions to Big Ideas

The Hopkins Engineering Applications & Research Tutorials (HEART) program provides new undergraduate students with a window on cutting-edge engineering research and its applications to society. These small classes are taught by advanced graduate students and postdoctoral fellows. Students will be introduced to cutting-edge engineering research and learn how that research impacts society. These tutorials will be useful to students as they evaluate their potential role in research projects. To ensure these courses are accessible to entering freshmen (who have priority on registration) they have no prerequisites. The tutorials will be kept small so students will have ample time to interact with their instructor and each other.

Detailed information about the tutorials and instructors will be available here soon; in the meantime, please see the General Engineering course listings for information about the tutorials being taught this semester, including the day and time for each section.

Incoming freshmen can enroll in one of the tutorials when course registration begins on July 6, 2016, Sophomores, juniors, and seniors can register for the tutorials beginning August 1, 2016. The courses have no prerequisites and are open to all JHU undergraduates in both KSAS and WSE. Registration is done through SIS.


Targeting the Gatekeepers: RTKs in Cancer Systems Biology
Sarvenaz Sarabipour
EN.500.111.01 Mon 8:30-9:45 am
EN.500.111.02 Tues 9-10:15 am

Description: This class will provide an overview of the role of receptor tyrosine kinases (RTKs) in cancer systems biology. The course will cover three main topics: systematic measurements of RTKs in the cell and the microenvironment; systems biology approaches (the mathematical models) used to model cancer cells; and RTK targeted cancer therapeutics.

Bio: Sarvenaz Sarabipour is a postdoctoral fellow at Institute for Computational Medicine. She received her PhD on mechanisms of receptor tyrosine kinase (RTK) signal transduction from department of Materials Science and Engineering at Johns Hopkins University. Her current research under Dr.Feilim MacGabhann focuses on computational modeling of Vascular endothelial growth factor receptors (VEGFRs) in human health and diseases.


Printing: Revolutionizing Design and Manufacturing
Mikhail Osanov
EN.500.111.03 Mon 12-1:15 pm
EN.500.111.04 Tues 12-1:15 pm

Description: 3D printing has the potential to revolutionize how we think about design and manufacturing since it makes it possible to fabricate complex parts using fewer components. This course will look at the different 3D printing technologies currently available for plastics and metals and discuss their potential and current applications in the engineering domain. Topology optimization will be introduced as a freeform computational design tool that is capable of designing new parts with optimized performance and leveraging unique possibilities of 3D printing.

Bio: Mikhail Osanov is a PhD student in the Department of Civil Engineering working with Professor Jamie Guest. He joined Hopkins in 2014 to study topology optimization for design of structures with a focus on manufacturability for additive manufacturing. Mikhail was born in Russia where he graduated from high school. He travelled to Baltimore from Bucknell University where he obtained his undergraduate degree.

Introduction to High Performance Computing
Zhangping Wei
EN.500.111.05 Mon 1:30-2:45 pm
EN.500.111.06 Tues 1:30-2:45 pm

Description: This course introduces several scientific programming languages (e.g., FORTRAN, Matlab, C/C++, CUDA C, MPI, and OpenMP) that are widely used in the fields of engineering and science. It is taught by analyzing various programming examples and in-class coding demonstrations. Students will gain hand-on computer programming experience through the course.

Bio: Zhangping Wei is a post-doc fellow in the Department of Civil Engineering. He received his Ph.D. degree in Engineering Science with an emphasis on coastal wave modeling from University of Mississippi. His current research focuses on applying advanced numerical tools to simulate coastal wave processes and wave-related natural disasters under the guidance of Professor Robert A. Dalrymple. He is also interested in high performance computing, in particular, the latest technique utilizing graphics processing units for general-purpose computing.

Challenges in Renewable Power Integration
Cynthia Bothwell
EN.500.111.07 Mon 3-4:15 pm
EN.500.111.08 Wed 3-4:15 pm

Description: As government policies move towards cleaner energy resources, larger amounts of weather dependent wind and sun are needed.  This course will provide an introduction to the electricity system, renewable energy, and optimization.  You will learn optimization techniques useful to everyday life and how these techniques apply to a cleaner energy future.

Bio: Cindy is a PhD student in the Department of Geography and Environmental Engineering working with Benjamin Hobbs.  Her research focuses on optimization and policy development of electricity systems including high penetrations of renewable energy.  She has professional experience working with electric utilities in various planning and policy groups.  She holds a B.S. in Electrical Engineering, an MBA, a M.S. in Statistics, an M.S. in Industrial Engineering and an M.S.E. in Geography and Environmental Engineering.

Economy vs. Environment: Let’s Make Optimal Decisions
Fengwei Hung
EN.500.111.09 Mon 4-5:15 pm
EN.500.111.10 Tues 4-5:15 pm

Description: This class will introduce theories and tools for decision analysis as well as case studies in environmental management and policy. Students are expected to participate in in-class exercises and case study discussions. Topics may include siting hydropower dams, stormwater management with green infrastructure, climate change adaptation, and the applications of game theory in environmental management. Students will be able to formulate linear programming models, elicit preference, identify non-inferior solutions, evaluate risk, and draw decision trees. These capabilities are useful for career in business and government and for personal life decisions.

Bio: Fengwei is a PhD student in Department of Geography and Environmental Engineering. He is interested in developing tools and methods that help inform environmental management decisions. Currently, he is working on a Green Infrastructure planning project for managing stormwater, improving water quality and enhancing city residents’ quality of life.

Decomposing the World: Engineering and Modeling Complex Systems
Gary Lin
EN.500.111.13 Mon 6-7:15 pm
EN.500.111.14 Fri 1:30-2:45 pm

Description: This course will take students through a brief survey of model-based systems engineering (MBSE) methodologies.  Several widely used system modeling tools will be introduced, including agent-based modeling, system dynamics, and network modeling.  In complex systems science, concepts and topics such as game theory, network science, supply and demand, self-organization, and emergent behaviors will be explored.  There are a variety engineering applications that utilize a systems approach: civil infrastructure systems, socio-ecological systems, and large-scale health R&D systems.

Bio: Gary Lin is a PhD student in the Department of Civil Engineering and affiliated with the Systems Institute at Johns Hopkins University.  Gary obtained B.S. in Civil Engineering and B.A. in Economics from the University of Colorado in Boulder.  In collaboration with Professor Tak Igusa, Gary is currently working on integrating systems engineering/science in real-world applications that range from pharmaceutical clinical trials to human population growth.  Prior to joining Johns Hopkins, Gary was working in transportation logistics and planning.  He hopes to apply the systems approach towards large-scale, health and engineering issues that face present and future society.

Manipulating Life: Biomolecular Engineering
Susan Liao
EN.500.111.15 Mon 7-8:15 pm
EN.500.111.16 Thurs 7-8:15 pm

Description: Manipulating life has moved from the realm of science fantasy to pervading everyday life: from the consumption of genetically modified crops to the production of biofuels and pharmaceuticals. Biomolecular engineering applies the principles and methods of engineering to regulating dynamicmolecular processes in living systems. In this tutorial, students will be introduced to fundamental concepts in regulation of biological systems and the techniques used to manipulate these systems. We will survey various fields of biomolecular engineering with an emphasis on genetic/cellular engineering and historical, contemporary, and emerging uses of biological engineering. This seminar course will include assigned readings, lectures, active discussions, student presentations, and guest lectures.

Bio: Susan Liao is a PhD candidate in Biochemistry, Cell, and Molecular Biology Program working in the laboratory of Professor Ryuya Fukunaga (Biological Chemistry Department, School of Medicine). Her research focuses on elucidating the roles of regulatory RNAs and RNA-binding proteins in animal development.

From Seeing Cells to Seeing Atoms
Kelvin Xie
EN.500.111.17 Tues 10:30-11:45 am
EN.500.111.18 Thurs 12-1:15 pm

Description: This course is a journey. We will take you back to the 17th century when the first microscope was invented, and travel all the way to today that we can image individual atoms. By the end of the course, the students are expected to gain fundamental understanding on various microscopy techniques and know which techniques to use to solve materials science and biomedical problems in their future research and/or industrial experiences.

Bio: Kelvin Xie is an Assistant Research Scientist working with Professor Kevin Hemker at Johns Hopkins University. He obtained his Ph.D. at the Australian Centre for Microscopy and Microanalysis under the supervision of Professors Julie Cairney and Simon Ringers. Kelvin’s research interest is to apply advanced microstructural characterization techniques to understand the mechanical properties and functionalities of metals, ceramics and biological materials.

Inspiring Inventions for an Engineering Mind
Santiago Orrego/David Cereceda
EN.500.111.19 Tues 3-4:15 pm
EN.500.111.20 Thurs 6-7:15 pm

Description: The  purpose  of  this  course  is  to  engage  students  in  research  by  exposing them  to  a  series  of  inventions  that  motivated  revolutionary  changes  in  the history of engineering. The course will show students one relevant invention per tutorial selected to cover  the  whole  spectrum  of  the  Engineering  Departments  present  in  the Whiting School of Engineering.  Each tutorial will include a description of what drove scientists to pursue an innovation,  the theory/fundaments behind it, the different experimental/ numerical  approaches  they  tried  to  achieve  their  goal  and  the research evolution based on that idea.

Bios: David Cereceda is a Postdoctoral fellow at Hopkins Extreme Materials Institute, where he is mentored by Prof. Nitin Daphalapurkar and Prof. Lori Graham-Brady. His research at Hopkins is aimed at understanding the dynamic fragmentation of brittle materials under extreme loading conditions. In particular, he is interested in construction materials such as glass, concrete and masonry. His PhD research was focused on the multiscale modeling of materials from atomistic to engineering scales under the guidance of Professor Jaime Marian at UCLA and Lawrence Livermore National Laboratory. Using simulations he was able to understand how to improve the mechanical behavior of brittle materials such as tungsten, one of the main candidates for fusion energy applications.  In his free time he enjoys playing the clarinet, sailing, swimming and dancing cuban salsa.

Santiago Orrego is a Postdoctoral fellow affiliated to the Hopkins Extreme Materials Institute and the Department of Mechanical Engineering. Currently he is working under the guidance of Professor Sung Hoon Kang (The Kang Group) in areas related to functional materials and bio-mineralization. His current research examines wind energy harvesting from the self-sustained flutter of a small piezoelectric membrane. In particular, there is interest in architecting flexible piezoelectric composites to create wind nano-generators. His PhD research was focused on studying the fracture behavior of human dentin, especially after being exposed to oral biofilms. One of his biggest passions are music and scuba diving.

The Right Stuff: Materials Science Challenges for Spacecraft
Steve Thibault
EN.500.111.21 Tues 6-7:15 pm
EN.500.111.22 Thurs 3-4:15 pm

Description: This course will provide an introduction to the unique and interesting challenge of designing spacecraft.  Space is a highly extreme environment in which temperatures can fluctuate hundreds of degrees in seconds, spacecraft are bombarded by radiation and micrometeors, and yet spacecraft must remain functional and powered sometimes for many years.  In this course, case studies will expose HEART students to the challenges of applying their engineering education to spacecraft with real-world examples in component, thermal, mechanical, electrical, and RF engineering.

Bio: Steve Thibault is a member of the JHU Applied Physics Laboratory Principal Professional Staff and Group Supervisor for Space Power and Component Engineering.  He is a part-time PhD student in the JHU Department of Materials Science and Engineering and holds a M.S. in Applied Physics from JHU and a B.S. in Aeronautical Engineering from Rensselaer Polytechnic Institute.  His career spans nearly thirty years in space system development, test, environmental test, launch, and orbital operations of numerous geostationary, science and technology satellite missions.

Vaccine Engineering, in the Post-genomics Era
Mohammad Hossain
EN.500.111.23 Tues 7-8:15 pm

Description: The ‘Vaccine Engineering, in the post-genomics era’ course will focus on understanding the recent technological advances in engineering novel vaccines targeted to eradicate deadly infectious diseases. This course will be a platform to discuss how next-generation sequencing and genomics in combination with novel genome tailoring or manipulating tools are revolutionizing the field of vaccinology. After finishing this course, students will have a broader understanding in biologically inspired engineering approaches that are currently being applied in developing novel vaccines for combating existing and emerging infectious diseases.

Bio: Mohammad Jahangir Hossain is a Postdoctoral Fellow in the Department of Biological Chemistry at Johns Hopkins School of Medicine. Dr. Hossain obtained his PhD in Microbiology from Auburn University under the mentorship of Dr. Mark Liles. He joined laboratory of Dr. Tamara O’Connor at Hopkins in 2015 for studying the disease causing mechanisms of Legionella pneumophila, the causative agent of Legionnaires’ disease, by developing novel molecular biology techniques.

Immunoengineering: Fighting Disease in Developing Countries
John Hickey
EN.500.111.24 Wed 8:30-9:45 am
EN.500.111.25 Fri 8:30-9:45 am

Description: Sometimes you get sick; thanks to engineers and biologists, there are now hundreds of tests that they could do to determine what is wrong with you. But what about within developing countries where resources, money, facilities, and even personnel are limited and a greater risk of disease is present? In this course we will cover these new design challenges and how to create diagnostic devices and therapeutics for developing countries.

Bio: John Hickey is a Biomedical Engineering PhD student under Dr. Jonathan Schneck working to create novel biomaterials for T-cell immunotherapy. He intends to use these materials in both the biophysical characterization of T cells with biomaterials and to improve current T cell immunotherapy. Prior to coming to Johns Hopkins University, he graduated from Brigham Young University with a B.S. in chemical engineering. When not tinkering in lab, he loves to spend time and create adventures with his wife and son.

Steel At It! History, Design, and Innovation of Steel Structures
Dave Fratamico/Deniz Ayhan
EN.500.111.26 Wed 12-1:15 pm
fratamico@jhu.edu/ ayhan@jhu.edu

Description: Why is steel so ubiquitous in civil infrastructure, and how is it evolving? This course presents a tutorial on the history steel structures, as well as current advanced analysis and new construction practices. Students will understand the differences between hot-rolled and cold-formed steel, obtain insight on the assessment of stability and strength via numerical simulations and experimental testing, and gain a research perspective on the ever-evolving cold-formed steel as we discuss current exciting projects undertaken in the Thin Walled Structures Group here at JHU.

Bio: Deniz Ayhan received her M.Sc and Ph.D. from Istanbul Technical University studying the stability of steel members and the nonlinear backbone response of cold-formed steel members, respectively. She was a Visiting Student Scholar at Johns Hopkins during her Ph.D. studies. She developed unique methods for prediction of stiffness and strength deterioration in cold-formed steel members experiencing local and/or distortional buckling – methods that are amendable to ASCE 41 design. She is currently a Postdoctoral Fellow in the Department of Civil Engineering at Johns Hopkins University.

Dave is a Ph.D. candidate and current NDSEG fellow working with Dr. Ben Schafer and the Thin-Walled Structures Group in Civil Engineering. He obtained a B.S. in Architectural Engineering from Drexel University in 2012. He worked as a laboratory technician/intern at CertainTeed Corp., working on the analysis, testing, and quality assurance of exterior building components and enclosures in 2009 and 2010, and also as a structural engineering intern at Thorton Tomasetti in their Philadelphia office in 2011. His research pertains to the experimental and numerical investigation of the stability and behavior of built-up cold-formed steel columns.


The Circle of Life: Networks and How Everything is Connected
David Holland
EN.500.111.27 Wed 1:30-2:45 pm

Description: This course serves as an introduction to network science and its applications to various fields. Topics will include basic graph theory, characterization of network properties, growth models, and network optimization. Common network examples – from the Internet to protein binding networks – will be examined.

Bio: David Holland is a PhD candidate in biomedical engineering working under Dr. Margaret Johnson. His research focuses on protein networks and the effects of protein abundance on misbinding. David received his undergraduate degree in his home state at the University of Virginia. His other interests include taekwondo and tabletop gaming.

Material Supercomputing: Modeling and Design of Materials through Computation
Pandu Wisesa
EN.500.111.28 Wed 4-5:15 pm

Description: In this course we will explore how materials databases are created and utilized to cleverly select and engineer materials for technological applications. The content of this course will focus on showcasing, on a high level, methods and techniques by utilizing softwares that are used in the industry and/or a research environment. By completing this course, students will be familiar with available materials databases and ways to take advantage of them in order to do clever materials selection and engineering; students will have some freedom to focus on applications that are of interest.

Bio: Pandu Wisesa is a graduate student in the Department of Materials Science and Engineering working with Dr. Tim Mueller. His research focus is the use of high-throughput computing to find new materials for protonic fuel cell electrolytes. Other than research, his hobbies are cooking (and eating interesting food), learning a new language, and playing video games.

Prove it to Me: Why Biology Needs Math and Math Needs Biology
Nash Rochman
EN.500.111.29 Wed 5-6:15 pm
EN.500.111.30 Thurs 9-10:15 am

Description: Biology is complicated and hard: complicated because every living thing is an enormous jigsaw puzzle with impossibly many changing pieces; and hard because like a baby, no matter how closely your interests may be aligned, a cell can never adequately express to you why it is distressed. Given that data collection is so time consuming and expensive, we want to take care in deciding just what questions to probe experimentally – thinking long and hard at our desks before we make it to the lab bench. In this course we’ll explore the role of mathematical prediction in the direction of experimental design for problems in biology. No matter how complicated or mysterious the problem, you can always find a related simpler, easier, and analytically soluble statement that will provide valuable insight towards dealing with the messier reality.

Bio: Nash Rochman studied chemical physics and mathematics in college (started at Bard College at Simon’s Rock and transferred to Brown) taking a particular interest in evolutionary dynamics which brought him to the ChemBE department here at Hopkins for my PhD. With his advisor is Sean Sun (MechE), he has become engaged in a variety of problems motivated by exciting analytical predictions that also provide the potential for convincing experimental verification. When not in the office/lab, he likes to play and compose music – playing mostly jazz (trumpet) and writing mostly concert music.

Beyond Explosions: An Introduction to the World of Reactive Materials
Alex Kinsey
EN.500.111.31 Wed 6-7:15 pm

Description: In this course we will explore the field of reactive materials including their fabrication, characterization, and ultimately their utilization in commercial applications. The course will explore the differences between reactive material systems, such as intermetallic formation reactions, thermite reactions (oxidation-reduction), and energetic material systems, such as organic explosives. We will also discuss real world applications of systems such as their use for joining (welding), bio-agent defeat, and propellants.

Bio: Alex Kinsey is a PhD student in the Department of Materials Science and Engineering. He completed his undergraduate degree in physics from Carleton College before coming to Johns Hopkins to work with Professor Timothy P. Weihs. He is studying novel brazing techniques using mechanically processed thermite foils to join dissimilar metals for automotive applications. Outside of lab he coaches the Johns Hopkins Men’s Ultimate Frisbee Team, Dangerzone.

Build a Better Blood Vessel Network
Lindsay Clegg
EN.500.111.32 Thurs 10:30-11:45 am

Description: Blood vessels are essential for growth, health, and healing, but are also involved in atherosclerosis and cancer. In this course, we will explore how computational models and experiments can be used together to study the mechanisms underlying blood vessel growth and remodeling. We will discuss the molecular biology, physiology, and pharmacology of blood vessels, read journal articles, and design experiments, as we explore current strategies to promote therapeutic blood vessel growth.

Bio: Lindsay is a PhD candidate & NDSEG Fellow in the Department of Biomedical Engineering at Johns Hopkins.  She graduated from Purdue University in 2011 with a B.S. in Biomedical Engineering and a minor in German. Lindsay’s thesis, in the lab of Dr. Feilim Mac Gabhann, focuses on developing experimentally-based computational models to study the growth and remodeling of blood vessel networks, facilitating design of more effective therapies. In her free time, Lindsay runs with her dog & mentors a local high school FIRST robotics team.

Making Computers See
Vittal Premachandran
EN.500.111.33 Thurs 1:30-2:45 pm

Description: This course we will begin by discussing the major challenges in computer vision (e.g. image classification, object detection, etc.) and show how deep networks can be used to address some of them. The course will cover certain deep network architectures such as convolutional neural networks and show how they can be trained in a supervised fashion. The material covered in this course will provide the students with the pre-requisites to start playing around with state-of-the-art computer vision technologies.

Bio: Vittal Premachandran is a postdoctoral researcher in the Department of Computer Science at Johns Hopkins University, where he is advised by Prof. Alan L. Yuille. Vittal’s current research focuses on computer vision and machine learning. Previously, he was a postdoctoral researcher at the University of California, Los Angeles, where he co-taught a graduate-level course on Introduction to Machine Learning. He has prior experience in designing courses, engaging with students, and teaching large classes.

Risks Are Everywhere! How Do We Model and Manage Them?
Gonzalo Pita
EN.500.111.34 Thurs 4-5:15 pm

Description: Introduce the attendants to the modeling of hurricane and earthquake risk and the interpretation of risk metrics. Discuss risk mitigation strategies for the building infrastructure.

Bio: Gonzalo L. Pita is an Adjunct Associate Scientist and Lecturer at the JHU’s Civil Engineering Dept. and Sr. Natural Risk and Vulnerability Specialist at the World Bank in Washington, DC.

Drug Shipments: How Medications Move Through the Body
Jayoung Kim
EN.500.111.35 Thurs 5-6:15 pm

Description: The course will cover the broad spectrum of drug delivery system, or an engineered vehicle that carries encapsulated drug cargo to the desired target in the body. The materials include the clinical need, engineering parameters, biological implications, and future directions of such therapeutics. Students will be responsible for reading one or two articles per week, and each session will involve 25-minute lecture and 50-minute group discussion on the topic from the readings.

Bio: Jayoung Kim is a currently a third year BME PhD graduate student (Samsung Fellow) working in Dr. Jordan Green’s laboratory. His primary research focus is on engineering polymeric nano- / microparticles for therapeutic DNA and peptide delivery to various cancer as well as eye diseases. He is the author of 5+ research and review articles, the results of which have been presented at conferences such as Biomedical Engineering Society (BMES) and American Society of Gene and Cell Therapy (ASGCT), and holds the patent on a newly developed nanoparticle system from the Green Lab. He received his B.S. degree from University of California, Berkeley (Bioengineering) and his M.S.E. degree from Johns Hopkins University (BME). He also had a unique experience serving as a military officer in the Republic of Korea for three years, culminating in the U.S. Army Commendation Medal.

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