2020

2020-21 Rocky Mountain Mechanics Seminar Series

Anonymous — Mon, 18 Jan 2021 18:51:05 +0000

2020-21 Rocky Mountain Mechanics Seminar Series Anonymous (not verified) Mon, 01/18/2021 - 11:51

The Rocky Mountain Seminar Series provides �鶹��Ѱ��Boulder faculty, staff and students with the opportunity to hear from researchers across disciplines from various institutions.

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Outstanding Student Q&A: Shankar Lalitha Sridhar, Outstanding Dissertation Award

Anonymous — Wed, 02 Dec 2020 04:03:17 +0000

Outstanding Student Q&A: Shankar Lalitha Sridhar, Outstanding Dissertation Award Anonymous (not verified) Tue, 12/01/2020 - 21:03

Outstanding Dissertation Award winner Shankar Lalitha Sridhar.

Share about your background. What led you to study engineering?

My undergraduate background is in Civil Engineering and I have a master's in structural engineering from the Indian Institute of Technology Madras in South India. My master's thesis was focused on developing a computational tool for a complex material model that was relevant for a variety of different materials ranging from concrete to soft tissues. This piqued my interest in describing the mechanical behavior of materials using concepts of physics and mathematical tools. I eventually transitioned into mechanical engineering when I moved to the United States for my master's at Texas A&M before joining �鶹��Ѱ��Boulder for my PhD.

There is a funny saying in India that a child is designated as either a doctor or engineer as soon as they are born. I guess in my case, I became both. But jokes aside, I really enjoyed learning physics and mechanics in high school and engineering seemed a natural choice to pursue a technological career that is open-ended enough to offer paths to a variety of different careers. And after 11 years in engineering school, I’d say I have indeed found that to be true.

What is the title of your dissertation? Can you give a brief summary of your findings?

The title of my dissertation is Mechanics of transient networks: an interplay of dynamics and microstructure.

The main topic of my dissertation relates to developing theoretical models that describe and predict the mechanical behavior of soft materials. Particularly, the focus was on polymer networks whose microstructure is dynamic and continuously reconfiguring itself in real-time. Many biological systems rely on such polymers (e.g., proteins, DNA, etc.) for achieving most of the key functions of life including growth, reproduction, locomotion, self-repair, etc. A particularly difficult aspect of modeling such materials is connecting the average properties of the polymer configuration to macroscopic aspects like stress, mechanical stiffness or viscosity and their evolution with time. In my dissertation, I present computational/theoretical models to explore the emerging mechanical behavior of transient polymers arising from: (a) spatial heterogeneity of degradation and growth in a polymer network with applications to holographic photopolymers and tissue engineering, (b) reversible cross-linking to produce nonlinear behavior such as shear thickening, and (c) molecular ordering to produce interesting anisotropic behavior with applications to the cell wall mechanics of fungi, and programming liquid crystal elastomers for actuation.

Understanding the interplay between structural components of a material and its dynamics through theory and modeling can deepen our understanding of the biological machinery. Importantly, they can inspire smart synthetic counterparts that have far-reaching impacts in the field of biomedicine, soft robotics, 3D printing, etc.

Shankar Lalitha Sridhar learned to ski while studying in Colorado.

What have you enjoyed most about your research?

I love learning new things. And coming into my PhD, I did not have much of a background in biological processes or polymeric materials. I enjoyed the challenge and loved learning about biopolymers and bringing skills from my training on strength of materials as a civil/mechanical engineer.

Having mostly been a user of existing theoretical models in my undergraduate and master's programs, I found it very satisfying to be on the side of proposing new models. And seeing it come to life through predictions and graphical simulations was icing on the cake.

Last but certainly not least, learning to put my work in perspective to understand why it would matter to other people and the skills to communicate that effectively was definitely the most meaningful aspect of research to me.

Who is your research advisor and what lessons have you learned from them?

My advisor was Prof. Franck Vernerey. The most important thing I have learned from him is thinking big and cultivating self-confidence. He helped me set high bars for myself that I hope I will be able to raise even higher in the coming years. He has a major contribution in motivating me to think bigger, smarter and bolder. He has also helped me develop useful time management techniques and cultivate self-confidence by involving me in multiple projects, proposal writing, preparing course content and preparing presentations for esteemed research conferences. And finally, the art of making connections and collaborating with fellow researchers in a diverse field is something for which I will be eternally grateful to him.

What accomplishment from your time at �鶹��Ѱ��Boulder are you most proud of and why?

If I have to decide on one accomplishment that I am most proud of, it will have to be my skiing skills. I had not set foot on a ski resort in my life before joining �鶹��Ѱ��Boulder. And the first time I did, it was actually with my research advisor and our team. And like his teaching style with scientific research, I was essentially taken on the ski lift and asked to jump off. And I picked up skiing fairly quickly after that. It showed me that taking a leap of faith and the passion/mindset to learn something no matter what are all you need to succeed, and a strong presence of this quality almost always underlies success in scientific research. The most significant obstacles in our path to success are often the ones we create in our heads.

Do you have any plans for the future after you graduate? If so, what are they?

I would like to remain in STEM and pursue research on materials science and explore new types of materials to develop a deep understanding of their behavior. Currently, I am a postdoctoral research associate in the BioFrontiers Institute under the supervision of Dr. Loren Hough from Physics. I am open to and pursuing opportunities in R&D in the biomedical and polymer industries, in addition to a research career in national labs like NREL, Oak Ridge and Lawrence Livermore. I think I’d like to return to academia one day and take up teaching to give back to the community, but right now what excites me is the opportunity to work on a large-scale project with a huge team of expert researchers.

What is the impact you hope to have on the world one day?

I think I would be satisfied if my work results in incremental progress in the lives of other beings in this world. I believe that is one of the most amazing features of the scientific revolution where each generation gets to add to the collective knowledge of humankind to make the world a little bit better than it was before. An immediately obvious path I can see for my scientific research background is the field of biomedicine to have an impact on the health of so many people. However, my horizon is wide open, and I see myself contributing toward causes I care about, even if not directly scientific in nature, including tackling climate change, animal cruelty and human suffering in this world. At the end of the day, it is our connection to and care for each other that should matter the most and is at the core of a life well-lived.

Is there anything else you would like to add?

My family that includes my parents, brother and sister have been my rock during my PhD, and their role in making this happen cannot be emphasized enough. My advisor has been an invaluable ally in my path to a doctoral degree and his guidance will have a long-lasting impact on me. Finally, I am eternally grateful to my friends and partner who made my time in Boulder that much more enjoyable. The PhD journey is never an easy one, and I think I found a lot of meaning in the relationships I developed and learned a lot about myself in the process. And if I had to, I would do it all over again with no hesitation.

Shankar Lalitha Sridhar is being awarded an Outstanding Dissertation Award from the College of Engineering and Applied Science. Check out his Q&A to learn more.

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Undergraduate researchers learn valuable lessons from remote research

Anonymous — Thu, 24 Sep 2020 17:23:35 +0000

Undergraduate researchers learn valuable lessons from remote research Anonymous (not verified) Thu, 09/24/2020 - 11:23

During campus closures due to COVID-19, Senior Professional Development Advisor Katherine McConnell contacted Director of Active Learning Sharon Anderson, who leads a summer program for undergraduate research, to see if they could work together to provide an opportunity for students seeking to gain research experience. Undergraduate researchers share their experiences as participants in the new ME SPUR Program which enabled them to work with mechanical engineering faculty on research that could be conducted remotely during summer 2020.

Undergraduate researchers share their experiences as participants in the ME SPUR Program. ME SPUR, modeled after �鶹��Ѱ��Summer Program for Undergraduate Research, enabled undergraduate students to work with mechanical engineering faculty on research that could be conducted remotely.

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The ME SPUR Experience: Hodgkins, Kirk and Pérez research air quality impacts of Stay-at-Home and Safer-at-Home orders

Anonymous — Wed, 23 Sep 2020 06:00:00 +0000

The ME SPUR Experience: Hodgkins, Kirk and Pérez research air quality impacts of Stay-at-Home and Safer-at-Home orders Anonymous (not verified) Wed, 09/23/2020 - 00:00

Mechanical engineering undergraduate researchers, Kirsty Hodgkins (left), Paula Pérez (center), and Evan Kirk (right).

The ME SPUR Program, modeled after �鶹��Ѱ��Summer Program for Undergraduate Research, enabled undergraduate students to work with mechanical engineering faculty during summer 2020 on research that could be conducted remotely. As participants, Kirsty Hodgkins, Evan Kirk and Paula Pérez worked with Professor Jana Milford to understand how reduced traffic, telecommuting and reduced industrial activity during Colorado's Stay-at-Home and Safer-at-Home orders have affected air quality with goals that the project would inform future strategies for improving air quality in the region beyond the timeframe of the COVID-19 pandemic. Their summer research project was titled, Impacts of Colorado’s Stay-at-Home and Safer-at-Home Orders on Air Quality.

Hodgkins is a rising fifth-year mechanical engineering student with minors in business and engineering management and a current member of the �鶹��Ѱ��Women’s golf team. She is not yet sure what field of mechanical engineering she would like to pursue after graduating. Kirk is a fourth-year mechanical engineering student with career interests including public health and medicine. After completing his undergraduate studies, he plans to attend medical school to pursue a career in family medicine. Pérez is a fourth-year mechanical engineering student with an energy engineering minor. She is focusing her career on water and energy insecurity in underserved communities, supported by experience in data analysis, rural development projects and entrepreneurship.

Hodgkins, Kirk and Pérez's insights below provide a window into their research experience with ME SPUR.

Describe your summer research.

A visualization of average daily traffic levels taken over a week-long period, comparing Denver I-70 traffic levels in 2020 to traffic levels in years prior. It highlights the a reduction in traffic following the WHO declaring COVID-19 a global pandemic and the Colorado Stay-at-Home declaration.

A time series that shows how nitrogren dioxide changed week by week across five monitors by calculating medians for each week. This visualization shows a downward trend for nitrogen dioxide, mainly caused by normal seasonal effects with some weeks increasing or decreasing across most monitors more sharply.

Our project focused on understanding the impacts of the COVID-19 Stay-at-Home and Safer-at-Home orders on air quality in Colorado.The purpose of the study is to report to policymakers and the general public about our research topic in ways that might inform future pollution control strategies. Our team focused on three pollutants: Ozone, NO2 and PM2.5. We were each responsible for studying one of these pollutants. The goal of the project was to determine if these pollutants experienced changes in 2020 and to try to explain the observed trends by analyzing traffic data, oil and gas activity and meteorological impacts.

Pérez: It was my first time working so closely with data on different social and environmental factors, which for me revealed how important our assumptions are in analyzing said factors and how the relationships between them are rarely straightforward.

What was the end result of your research project?

Overall, all of the pollutants saw small differences in 2020 when compared to previous years. We were unable to find that these discrepancies were necessarily correlated to the decrease in traffic levels, and further analysis of explanatory variables would need to be studied to understand why we didn’t see the expected pollutant behavior. Studying meteorological values we determined that the temperature and humidity levels had a large effect on the pollutant levels which could have counteracted the effects from traffic reduction. However, further research is needed to provide a definitive answer as to why levels were only slightly different.

What was it like working on a research project remotely?

Working on a project remotely is always a difficult task; this was no different. Someone described the COVID-19 situation as "more like living at work than it is working from home” which feels very relatable. It was difficult not always being able to meet or talk with the other members regularly as you would in an office, but a weekly Zoom meeting helped to make sure we were all on the same page, and we were still able to communicate over email and Slack continuously. The upside was the flexibility of working under our own schedule and knowing we could always reach out to the group with questions.

What about this project was rewarding?

The most rewarding part of this project was seeing the final results and creating the report for the study after going from basic knowledge of air pollution to having a fairly solid understanding of the problem. It is challenging to summarize the work that goes into research concisely, and after doing so many different graphs, looking at so many different variables, it all seems to blend into one. However, looking back over, it was really interesting to see the connections that had been made, and it was satisfying to see everyone’s work compiled into a final deliverable. It’s a particularly tangible way to see all of your hard work from the summer.

What advice would you share with other students considering getting involved in research?

Hodgkins: Research is definitely something every engineering student should be a part of, especially mechanical students. Definitely keep an open mind heading into it, as engineering students we’re very much used to having an answer or a solution to a problem but research isn’t always like that. Sometimes you just have to accept the fact that maybe there wasn’t a change in anything or that the results were insignificant. Even insignificant results can mean something.

Kirk: The recommendation I would make to students who are thinking about getting involved in research is simply to be patient. It is best to move slowly, working meticulously to ensure you are drawing reasonable conclusions and are not making mistakes. Take the time to double- and sometimes triple-check your work. You will be happy you did later.

Pérez: It is truly a great learning experience as you quickly gain hard skills as well as soft skills like collaborating with a team and communicating your findings. You will also likely gain more depth in your understanding of the research subject that you might not get in classes.

As ME SPUR participants, Kirsty Hodgkins, Evan Kirk and Paula Pérez worked with Professor Jana Milford to understand how reduced traffic, telecommuting and reduced industrial activity during Colorado's Stay-at-Home and Safer-at-Home orders have affected air quality with goals that the project would inform future strategies for improving air quality.

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The ME SPUR Experience: Smith models the human abdomen for ultrasound simulation

Anonymous — Mon, 21 Sep 2020 06:00:00 +0000

The ME SPUR Experience: Smith models the human abdomen for ultrasound simulation Anonymous (not verified) Mon, 09/21/2020 - 00:00

Mechanical engineering undergraduate researcher, Ryan Smith.

The ME SPUR Program, modeled after �鶹��Ѱ��Summer Program for Undergraduate Research, enabled undergraduate students to work with mechanical engineering faculty during summer 2020 on research that could be conducted remotely. As a participant, Ryan Smith worked with Assistant Professor Nick Bottenus to use medical image data to develop 3D finite element models of the abdominal wall and perform various compressions to mimic clinical practice. His summer research project was titled, Modeling the Human Abdomen for Ultrasound Simulation.

Smith will be finishing his final semester in mechanical engineering at �鶹��Ѱ��Boulder this fall. His interests include numerical methods/analysis, computer modeling and fluid mechanics. His insights below provide a window into his research experience with ME SPUR.

Describe your summer research.

Ultrasound is commonly used to image structures within the abdomen; however, these images are often degraded by acoustic clutter such as aberration and reverberation. Interestingly, it is observed that compressing the ultrasound transducer into the abdomen improves image quality. However, it is not fully understood why. Simulations may help to better understand this effect. The goal of this project is to predict the deformation of the abdomen under compression using FEA. These results can then be used in Fullwave, a tool for modeling nonlinear propagation and multiple scattering of ultrasound through heterogeneous tissues.

Top: Cross section of an abdominal wall.
Bottom: The results of the finite element analysis are used to construct an image of the compressed abdomen.

What was it like working remotely?

This project was well suited for remote work. I was able to interact with my research supervisor, Professor Bottenus during weekly meetings which helped to guide my efforts and at certain points, received feedback and improvements on my code. Moreover, I received some helpful tips on the FE part of the problem from Professor Mark Palmeri at Duke and Boyuan Liu, a member of Professor Maureen Lynch’s lab.

What challenges did you encounter and work through as part of your project?

Converting a 3D medical image into a mesh is no simple task. Before coming across iso2mesh, I had multiple attempts at this problem. At first, I tried constructing a surface mesh for the outer shape of the abdomen, generating an internal mesh based on this surface mesh, and then assigning materials to elements in the mesh based on the 3D image. The problem with this method is that the internal boundaries separating the various tissue domains are not modeled well, as the mesh was generated with no knowledge of the internal structures. In an attempt to improve upon this, I developed two additional methods, each with its own issues before finding iso2mesh.

What about this project was rewarding?

For me, the most rewarding part of the project was writing the code to map between the original and deformed images. I was able to use my knowledge of shape functions which I learned about in Professor Debanjan Mukherjee’s CFD class, to map coordinates between the undeformed and deformed meshes. Moreover, this part of the project was a lesson in the computational expense of code. Originally, using a test mesh, the mapping took over eight hours to complete. With the aid of Professor Bottenus, and by making some modifications to the algorithm myself, this time was reduced to around three hours.

What advice would you share with other students considering getting involved in research?

Learn how to find and use manuals/documentation for software you are unfamiliar with. Most software will have these sorts of resources if you look. Moreover, create the same resources for anything you come up with so that others can easily learn and follow what you have done.

As an ME SPUR participant, Ryan Smith worked with Assistant Professor Nick Bottenus to use medical image data to develop 3D finite element models of the abdominal wall and perform various compressions to mimic clinical practice.

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The ME SPUR Experience: DiTomas explores minimum energy requirements for robotic missions

Anonymous — Fri, 18 Sep 2020 06:00:00 +0000

The ME SPUR Experience: DiTomas explores minimum energy requirements for robotic missions Anonymous (not verified) Fri, 09/18/2020 - 00:00

As an ME SPUR participant, Paul DiTomas worked with Research Professor John Pellegrino to perform analysis for scenarios of the minimum energy requirement for robotic missions that will be used in a review article about portable power devices for next-gen robots.

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The ME SPUR Experience: Evans tests a miniature tank-tread robot

Anonymous — Wed, 16 Sep 2020 06:00:00 +0000

The ME SPUR Experience: Evans tests a miniature tank-tread robot Anonymous (not verified) Wed, 09/16/2020 - 00:00

Mechanical engineering undergraduate researcher, Sydney Evans.

The ME SPUR Program, modeled after �鶹��Ѱ��Summer Program for Undergraduate Research, enabled undergraduate students to work with mechanical engineering faculty during summer 2020 on research that could be conducted remotely. As a participant, Sydney Evans worked with Assistant Professor Kaushik Jayaram to develop a novel robot capable of sticking to and navigating virtually any surface, leveraging adhesion mechanisms involving electrostatic attraction. The first stage of the project would involve extensive literature review, building on an existing design and developing a modeling framework for scalable fabrication. Her summer research project was titled, Miniature Tank-Tread Robot Capable of Vertical and Inverted Climbing.

Evans is a third-year student at �鶹��Ѱ��Boulder studying mechanical engineering and applied mathematics. She is actively engaged on campus through the club swim team, Global Engineering RAP and as president of CU’s chapter of Engineers in Action. Her insights below provide a window into her research experience with ME SPUR.

Describe your summer research.

My research project is through the Animal Inspired Motion and Robotics Lab (AIM-RL) which was created by Professor Kaushik Jayaram. The goal of the project is to create a small robot that utilizes electroadhesion (which takes advantage of the attractive forces generated between electrically-induced opposite charges) to climb inclined conductive surfaces. This course of action will allow us to engage in the developing fields of electroadhesion and micro-robotic technologies.

This summer, my pursuit of this project involved reading a lot of literature about electroadhesion and robotics, as well as coding in Arduino and using Solidworks to make 3D models. I also designed an experimental “arena” that will be used to test the robot. I am really excited about this project, because I will continue working on it this fall as part of an independent study. This means that I will be able to follow through with my designs and code and integrate them into a functional version of the robot.

What was it like conducting research remotely?

I had a lot of opportunities to engage with the other members of my lab group; this was one component of my experience that stood out to me from the beginning. Working together and using each other’s expertise was highly encouraged by Dr. Jayaram. In one of our meetings early this summer, we did a mini-symposium within our lab so that everyone could present what they were working on, their background and experiences. I had multiple meetings with my lab members who gave me feedback and assisted with my coding and designing my testing space. While remote work was not ideal, it was well managed and now I can take advantage of the upcoming opportunity to be on campus and utilize our lab space.

What about this project was rewarding?

The miniature tank tread robot ascending an incline.

At the very beginning of this project, I was trying to practice and remember CAD, read papers and wait for Dr. Jayaram to provide instructions. One day, I read a paper about electroadhesive pad designs. I came to a section where I started jotting down questions and thoughts about the tread design of our robot. I went into my next meeting with Dr. Jayaram excited about this paper and with a lot of questions. I loved feeling like my engineering education was kicking into gear and having a real-life effect. I gained just enough confidence in myself and what I was trying to do so that when I went through all of the other difficult and daunting moments of the summer, instead of feeling like I was too inexperienced for the job, I felt as if they were normal obstacles any undergraduate engineer in research would face.

As a student new to conducting research, what skills did you bring to the project that helped you be successful?

Prior to this, I did not have any experience in engineering research. I was surprised at how often I drew on the material from my classes (I actually drew a free body diagram at one point!) such as physics, dynamics, and material science. The skills that have been most useful were Solidworks, LaTeX, and googling coding solutions and functions. These were all skills that I developed during my first two years at �鶹��Ѱ��Boulder, and I don’t think my experience would have been as fun or meaningful if I had done it earlier in my career without some of these basics.

What advice would you share with other students considering getting involved in research?

Try it. I was a little intimidated and turned off by research initially, because I thought it was more about reading and writing papers and took too much time to make any interesting progress. This can be more true of research in other fields, but that shouldn’t be a reason to forego a learning experience in a research lab. Also, professors really like to share their research and are looking for students who are interested in the same things, not necessarily those who have all of the skills they need. Sitting down with a professor and hearing about their research does not obligate you to engage with it, you can walk away and find something different, or even better, have them help you connect with an alternative lab you are more interested in.

As an ME SPUR participant, Sydney Evans worked with Assistant Professor Kaushik Jayaram to develop a novel robot capable of sticking to and navigating virtually any surface, leveraging electrostatic attraction.

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The ME SPUR Experience: Gruener researches magnetic field design

Anonymous — Mon, 14 Sep 2020 06:00:00 +0000

The ME SPUR Experience: Gruener researches magnetic field design Anonymous (not verified) Mon, 09/14/2020 - 00:00

Mechanical engineering undergraduate researcher, Jonathon Gruener.

The ME SPUR Program, modeled after �鶹��Ѱ��Summer Program for Undergraduate Research, enabled undergraduate students to work with mechanical engineering faculty during summer 2020 on research that could be conducted remotely. As a participant, Jonathon Gruener worked with Associate Professor Svenja Knappe to create a testing environment for highly-sensitive miniature magnetic field sensors with non-invasive brain imaging, space and industrial applications. The goal of the project was to first model the desired field environment, and once the coil geometries were defined, design, print, and assemble magnetic field coils, with the final step being to measure and compare with the model. Gruener's summer research project was titled, Magnetic Field Design.

Gruener is a second-year student in the mechanical engineering department at �鶹��Ѱ��Boulder. He is a passionate learner and especially excited to participate in projects that focus on mechanical engineering and computer science. His insights below provide a window into his research experience with ME SPUR.

Describe your summer research.

The purpose of the research project I have been working on has been to create a model of the magnetic field produced by an octagonal array of rectangular wire coils to determine the percent homogeneity. Originally, I was trying to model a cylindrical coil of wire but the math and requisite time to model that design proved to be overly complex, so my professor and I decided to attempt the octagonal shape instead. For me, the majority of this process has taken place using Mathematica to create various graphs and equations to model the magnetic fields. I have also spent time searching for academic papers that could apply to the research.

The result of my project was a working model of an octagonal array of rectangular coils with the potential for variation of almost every aspect of the coils: from length and width to individual currents. Additionally, I created various functions to test the homogeneity with different criteria. This model will be used to inform whether Professor Knappe and her researchers will attempt to build an octagonal array of coils for testing their microfabricated sensors or try a different shape.

Visual model of octagonal coil array and the resulting magnetic field.

What challenges did you encounter and work through as part of your project?

The challenges I faced most often this summer surrounded Mathematica. While there is a lot of documentation available from Wolfram Alpha, it often explains only the use of the function and not the behind-the-scenes workings of it. This often resulted in small errors that eventually compounded into a very unexpected result. An example of this was using a function to plot vectors in three dimensions. When creating my methods of testing homogeneity, I needed to measure and compare the z-component of each vector. However, while plotting the vectors, Mathematica scaled them in an unexpected way that didn’t appear to be explained in their documentation. To solve that issue, I created a mock graph that allowed me to access and manipulate the scaled vectors and then apply them to my final graph and comparisons.

What about this project was rewarding?

The most rewarding part of the project for me was seeing the final model and verifying that the digital representation concurred with the equations I had been given. It took a lot of modification of existing equations and research to create my model, and it felt great to see it all come together visually.

What advice would you share with other students considering getting involved in research?

Some advice I would share with other students considering getting involved in research is to trust your abilities to learn and adapt on the fly. Just because you don’t understand a component of the project doesn’t mean you will never understand it.

As an ME SPUR participant, Jonathon Gruener worked with Associate Professor Svenja Knappe to create a testing environment for highly-sensitive miniature magnetic field sensors with non-invasive brain imaging, space and industrial applications.

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The ME SPUR Experience: Beiter researches image-based modeling for cardiovascular systems

Anonymous — Fri, 11 Sep 2020 06:00:00 +0000

The ME SPUR Experience: Beiter researches image-based modeling for cardiovascular systems Anonymous (not verified) Fri, 09/11/2020 - 00:00

Mechanical engineering undergraduate researcher, Andrew Beiter.

The ME SPUR Program, modeled after �鶹��Ѱ��Summer Program for Undergraduate Research, enabled undergraduate students to work with mechanical engineering faculty during summer 2020 on research that could be conducted remotely. As a participant, Andrew Beiter worked with Assistant Professor Debanjan Mukherjee to develop an in-house library of models for arterial hemodynamics in human patients, using CT and MRI scans and microscopy image data. His summer research project was titled, Image-Based Modeling for Cardiovascular Systems.

Beiter is a third-year student at �鶹��Ѱ��Boulder studying mechanical engineering who is also pursuing minors in philosophy and astrophysical and planetary sciences. His insights below provide a window into his research experience with ME SPUR.

Describe your summer research.

Left Ventricular Assist Devices (LVADs) are a primary treatment modality for end stage heart failure patients. LVADs are mechanical pumps that are surgically attached to the heart and the aorta. The end goal of the project I’ve been working on this summer is to use embolus transport simulations on patient-specific models of various surgical attachment configurations of LVADs to the human aorta to see how the attachment influences blood flow and embolus (or blood clot) distribution. The purpose of this is to compare how differences in surgical attachment affect the likelihood of embolic particles going from the aortic arch up the carotid arteries towards the brain. This information can then be used by surgeons in determining how to attach the LVAD to best mitigate the risk of stroke.

The end result of my work this summer was the development of a computer simulation pipeline which can be used to run embolus transport simulations on patient-specific models that can accurately report the distribution of embolic particles to each possible arterial branch of the aortic arch. This work is part of a larger continuing research project in Professor Mukherjee’s group, where I plan to use this pipeline to determine ideal or optimal surgical attachment options to minimize stroke risk in patients who need LVADs, providing valuable information to surgeons. Eventually, a similar process can be used for any situation involving particle transport in blood vessels and stroke mechanics for other physiological interventions as well.

What was it like conducting research remotely?

Working on this project remotely didn’t prove to be too much of a challenge, as all of the work I did was computational by nature. The models and flow profiles I used were developed by another graduate student in the group that I worked with regularly, and I had quite a few questions for Professor Mukherjee while becoming familiar with the VCPrePost package. Also, there were a lot of opportunities associated with just being a member of the group, more than my project specifically, such as participating in a lab journal club and having a valuable resource to experience new things in group learning sessions.

What about this project was rewarding?

The most rewarding aspect of this project for me was knowing that the work I was doing could potentially be used to help save people’s lives by lowering their risk of stroke. The project is part of a clinical collaboration, and it’s good to know that the work I’m doing provides valuable information that can be used by clinicians. Also, I’m really proud of how much I’ve learned this summer, as I had no prior experience with anything similar to the framework I used, and running the simulations is a very advanced task.

Did you have any research experience prior to ME SPUR?

I had no research experience prior to joining Professor Mukherjee’s group and found it to be a very valuable experience. Problem solving and communication skills turned out to be the biggest assets I had in completing my project, as I was working with new and unfamiliar software and also had very little background in the biomedical field in general. Being able to tap into the knowledge and experience of my professor and other group members was hugely beneficial to making what at times felt like a daunting task much more doable.

What advice would you share with other students considering research?

I’d say that anybody considering getting involved in research should definitely go for it. The nature of research involves working on often entirely new problems and using novel software/tools/equipment that might not even be fully out of the development stage, which makes it a very unique experience that you can’t get by taking classes. It can also make it seem intimidating at times, and you might feel as though you run into a lot of difficulties, but your research group and advisors are there to help you succeed and ensure that it’s a valuable learning experience. I’ve learned a huge amount of new things and developed many new skills in a fairly short timeframe. Worst case scenario, you decide you don’t like research, but even then, that’s a worthwhile thing to find out, and you’ll still get a lot from the experience.

[video:https://youtu.be/nLdG8a7Meho]

As an ME SPUR participant, Andrew Beiter worked with Assistant Professor Debanjan Mukherjee to develop an in-house library of models for arterial hemodynamics in human patients, using CT and MRI scans and microscopy image data. His summer research project was titled, Image-Based Modeling for Cardiovascular Systems.

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The ME SPUR Experience: Beattie researches image-based elastography in the deforming cell nucleus

Anonymous — Wed, 09 Sep 2020 06:00:00 +0000

The ME SPUR Experience: Beattie researches image-based elastography in the deforming cell nucleus Anonymous (not verified) Wed, 09/09/2020 - 00:00

Mechanical engineering undergraduate researcher, Julia Beattie.

The ME SPUR Program, modeled after �鶹��Ѱ��Summer Program for Undergraduate Research, enabled undergraduate students to work with mechanical engineering faculty during summer 2020 on research that could be conducted remotely. As a participant, Julia Beattie worked with Professor Corey Neu to measure intranuclear mechanics. The goal was to provide a non-invasive framework to investigate the mechanobiological function of subcellular and subnuclear domains limited only by the spatiotemporal resolution of the image acquisition method. Her summer research project was titled, Image-Based Elastography of Heterochromatin and Euchromatin Domains in the Deforming Cell Nucleus.

Beattie is a third-year student from Centennial whose area of focus in the mechanical engineering department is in biomedical engineering. Beattie hopes to use her engineering education to work on medical devices or research to improve people’s quality of life. Her insights below provide a window into her research experience with ME SPUR.

Describe your summer research.

The goal of my project was to assist the Neu Lab in automating their deformation microscopy code and also, to beta test their new graphical user interface (GUI). Deformation microscopy is a technique that utilizes conventional imaging and a hyperelastic warping algorithm to analyze deformation and strain patterns within cell nuclei. In the GUI, the user inputs images of a cell nucleus before and after a mechanical deformation. Then, the program processes the images, runs a warping algorithm and creates a map of intranuclear strains. I have been running images through the program to look for errors and ways to improve it.

We made progress towards an automated, user-friendly program. The goal is for the program to be published for use in other labs where it will hopefully be used to contribute to further research of cell mechanobiology. The Neu Lab also plans to continue using deformation microscopy in future work in intracellular elastography which could potentially help in many mechanobiological applications.

What was it like conducting research remotely?

It was surprisingly uncomplicated to work in a remote format. I did most of the work on a remote desktop that I accessed from my computer. I had weekly Zoom meetings with my supervisor and other lab members. Between meetings, I regularly communicated and shared my findings with the other lab members via email and Slack.

What challenges did you encounter and work through as part of your project?

One of the main challenges was working with a Mac while the rest of the lab had PCs. Certain software packages function differently (or not at all) on my computer compared to theirs. However, the remote desktop helped, and this obstacle ultimately turned into an opportunity: my ability to run the deformation microscopy code on my computer allowed the team to start developing code that is compatible with macOS.

What about this project was rewarding?

It was very rewarding to see my findings and suggestions implemented. This program will someday be used in a variety of mechanobiological research labs, and I can say I helped make it usable.

Did you have any research experience prior to ME SPUR?

I had no experience with research prior to this program. My experience with MATLAB from past classes helped me understand the program I was working with. Additionally, my modest knowledge of cellular biology from past courses (I used to be a chemical and biological engineering major) helped me grasp the biological concepts of cell mechanics more quickly.

What advice would you share with other students considering getting involved in research?

I would highly recommend applying, even if you feel like your qualifications are not good enough. I almost didn’t apply for that reason, but I’m glad that I did. You will learn technical skills, develop communication and teamwork skills and make new connections.

Images from Beattie's research showing an analysis of deformation and strain patterns within a cell nucleus. Inputs are shown in the left two images and results are shown in the right two images.

As an ME SPUR participant, Julia Beattie worked with Professor Corey Neu to measure intranuclear mechanics. The goal was to provide a non-invasive framework to investigate the mechanobiological function of subcellular and subnuclear domains limited only by the spatiotemporal resolution of the image acquisition method.

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