2024 Projects
Breaking the Mold
Principal Investigator: Thomas Bifano
Mentor: Ruifeng Hu
Project Description: BU is known for developing scaffolds that support self-assembled engineered cardiac tissue (ECT) derived from human induced pluripotent stem cells. Most of these scaffolds feature pairs of identical compliant pillars between which the ECT is suspended.Spontaneous contraction of the ECT bends the pillars, and contractile force can be inferred from video images of pillar deflections. A higher resolution of this force measurement could be obtained by narrowing the field of view to observe deflection of only one pillar, and assuming that the other pillar deflection was identical. Even better would be to create a scaffold with one rigid pillar and one compliant pillar, so that all deflection could be observed in a narrow field of view around the compliant pillar. In this project, the REU student will design, fabricate, and test such a scaffold, comparing results with that of a conventional scaffold.
Mentor: Ruifeng Hu
Project Description: BU is known for developing scaffolds that support self-assembled engineered cardiac tissue (ECT) derived from human induced pluripotent stem cells. Most of these scaffolds feature pairs of identical compliant pillars between which the ECT is suspended.Spontaneous contraction of the ECT bends the pillars, and contractile force can be inferred from video images of pillar deflections. A higher resolution of this force measurement could be obtained by narrowing the field of view to observe deflection of only one pillar, and assuming that the other pillar deflection was identical. Even better would be to create a scaffold with one rigid pillar and one compliant pillar, so that all deflection could be observed in a narrow field of view around the compliant pillar. In this project, the REU student will design, fabricate, and test such a scaffold, comparing results with that of a conventional scaffold.
An In Vitro Model of the Infarct Border Zone
Principal Investigator: Christopher Chen
Mentor: Claudia Varela
Project Description: The severity of a heart attack is determined by the area of heart muscle affected by the occluded vessel, but also by a ‘border zone’ (BZ) that separates the infarct region from the unaffected heart muscle. The BZ has been implicated in adverse remodeling that occurs after a heart attack, but because the region is difficult to isolate and study using animal models, how BZ biology contributes to disease progression remains largely unknown. To study BZ biology, the Chen lab is engineering a cardiac microtissue model that recapitulates BZ biology and biomechanics. Together with Claudia Varela, a postdoctoral researcher in the Chen lab, the REU student will help with the design and manufacturing of prototypes of the culture system and conduct experiments to assess BZ induction into the cardiac microtissues. This model will enable studies that elucidate how the region evolves and provide key design criteria for interventions that need to interface with that region, such as the cardiac patches being engineered in CELL-MET.
Mentor: Claudia Varela
Project Description: The severity of a heart attack is determined by the area of heart muscle affected by the occluded vessel, but also by a ‘border zone’ (BZ) that separates the infarct region from the unaffected heart muscle. The BZ has been implicated in adverse remodeling that occurs after a heart attack, but because the region is difficult to isolate and study using animal models, how BZ biology contributes to disease progression remains largely unknown. To study BZ biology, the Chen lab is engineering a cardiac microtissue model that recapitulates BZ biology and biomechanics. Together with Claudia Varela, a postdoctoral researcher in the Chen lab, the REU student will help with the design and manufacturing of prototypes of the culture system and conduct experiments to assess BZ induction into the cardiac microtissues. This model will enable studies that elucidate how the region evolves and provide key design criteria for interventions that need to interface with that region, such as the cardiac patches being engineered in CELL-MET.
Cardiac Cell Engraftment in a Cardiac Slice Culture System
Principal Investigator: Christopher Chen
Mentors: Xining Gao and Claudia Varela
Project Description: A myocardial infarction (MI) occurs when blood flow to a region of heart muscle is interrupted, depriving cardiomyocytes of oxygen, leading to cell death and thus a loss of contraction in the area. The damaged muscle is replaced by a dense collagenous scar often leading to adverse remodeling and ultimately heart failure. One of the main goals of CELL-MET is to engineer a vascularized cardiac patch that can be grafted onto scar tissue to assist the heart recover some of the lost function. To ensure successful engraftment of the cardiac patch, the engrafted cells need to integrate with the host tissue in a way that benefits cardiac function. However, knowledge about this biological integration is lacking. To study cardiac muscle cell engraftment, the Chen lab is currently adapting a cardiac slice culture system to study how engrafted cells biologically interact with host tissue, with the aim of optimizing graft-host integration. Together with Xining Gao, a graduate student, and Claudia Varela, a postdoctoral researcher in the Chen lab, the REU student will help with the initial set-up of such a platform by aiding with the development and characterization of this ex vivo culture system.
Mentors: Xining Gao and Claudia Varela
Project Description: A myocardial infarction (MI) occurs when blood flow to a region of heart muscle is interrupted, depriving cardiomyocytes of oxygen, leading to cell death and thus a loss of contraction in the area. The damaged muscle is replaced by a dense collagenous scar often leading to adverse remodeling and ultimately heart failure. One of the main goals of CELL-MET is to engineer a vascularized cardiac patch that can be grafted onto scar tissue to assist the heart recover some of the lost function. To ensure successful engraftment of the cardiac patch, the engrafted cells need to integrate with the host tissue in a way that benefits cardiac function. However, knowledge about this biological integration is lacking. To study cardiac muscle cell engraftment, the Chen lab is currently adapting a cardiac slice culture system to study how engrafted cells biologically interact with host tissue, with the aim of optimizing graft-host integration. Together with Xining Gao, a graduate student, and Claudia Varela, a postdoctoral researcher in the Chen lab, the REU student will help with the initial set-up of such a platform by aiding with the development and characterization of this ex vivo culture system.
PCR Protocol for Preparing 'sticky end' DNA Handlesfor Single Molecule Force Spectroscopy Measurements
Principal Investigator: Masha Kamenetska
Mentor: Favian Liu
Project Description Single molecule force spectroscopy measurements using optical tweezers (OT) allow for insights into the molecular mechanisms of biological processes. In our lab and in collaboration with the lab of Adrian Whitty, we use OT techniques to study the structure and dynamics of the protein, NF-kappa-B essential modulator (NEMO), whose misregulation has a role in many human diseases. As is common in the field, we use extended polymer handles, made out of DNA, to attach the protein to the microscopic beads, which are required for OT measurements. However, because of the unique structure of NEMO and how it must be immobilized for experimentation, we require custom handles that contain single stranded DNA overhangs on one end. The protocol for creating such structures has been published by others, but is not trivially extended to the DNA sequences we require. In this project, Shanen Arellano will adapt the protocol to generate DNA handles with sticky overhangs for single molecule measurements of NEMO. She will then use these constructs to begin studying NEMO using OT methods.
Mentor: Favian Liu
Project Description Single molecule force spectroscopy measurements using optical tweezers (OT) allow for insights into the molecular mechanisms of biological processes. In our lab and in collaboration with the lab of Adrian Whitty, we use OT techniques to study the structure and dynamics of the protein, NF-kappa-B essential modulator (NEMO), whose misregulation has a role in many human diseases. As is common in the field, we use extended polymer handles, made out of DNA, to attach the protein to the microscopic beads, which are required for OT measurements. However, because of the unique structure of NEMO and how it must be immobilized for experimentation, we require custom handles that contain single stranded DNA overhangs on one end. The protocol for creating such structures has been published by others, but is not trivially extended to the DNA sequences we require. In this project, Shanen Arellano will adapt the protocol to generate DNA handles with sticky overhangs for single molecule measurements of NEMO. She will then use these constructs to begin studying NEMO using OT methods.
Studying Thermal Properties of Direct Air Capture Adsorbents with Hot Disk Instruments
Principal Investigator:Sean Lubner
Mentor: Savannah Schisler
Project Description: Climate change is among the most critical challenges facing humanity today. Society’s infrastructure, agriculture, and health are threatened by global warming, which leads to floods, unprecedented weather patterns and damaging natural disasters. No amount of emissions reductions alone will be able to reduce emissions enough to stop irreparable global warming. Thus, Direct Air Capture (DAC) of Carbon Dioxide (CO2) is needed to help remove existing emission in our environment. But there remain significant unknowns, from the system design to adsorbent material to plant implementation. This project aims to study the thermal properties of adsorbent materials for DAC of CO2 through Hot Disk thermal conductivity and heat capacity measurements. REU student will take thermal conductivity and heat capacity measurements for a Direct Air Capture (DAC) adsorbent material on a Hot Disk Instrument. Student will develop DAC adsorbent sample preparation methods compatible for Hot Disk measurements. Additionally, sample holders for Hot Disk measurements may be designed and fabricated in EPIC. Additionally, the student will help calibrate the Hot Disk Instrument using known samples to verify its proper operation, and quantify measurement variance due to differently sized sensors. If time remains in the program, the student will investigate the effects of temperature and carbon dioxide loading on the DAC adsorbent thermal properties.
Mentor: Savannah Schisler
Project Description: Climate change is among the most critical challenges facing humanity today. Society’s infrastructure, agriculture, and health are threatened by global warming, which leads to floods, unprecedented weather patterns and damaging natural disasters. No amount of emissions reductions alone will be able to reduce emissions enough to stop irreparable global warming. Thus, Direct Air Capture (DAC) of Carbon Dioxide (CO2) is needed to help remove existing emission in our environment. But there remain significant unknowns, from the system design to adsorbent material to plant implementation. This project aims to study the thermal properties of adsorbent materials for DAC of CO2 through Hot Disk thermal conductivity and heat capacity measurements. REU student will take thermal conductivity and heat capacity measurements for a Direct Air Capture (DAC) adsorbent material on a Hot Disk Instrument. Student will develop DAC adsorbent sample preparation methods compatible for Hot Disk measurements. Additionally, sample holders for Hot Disk measurements may be designed and fabricated in EPIC. Additionally, the student will help calibrate the Hot Disk Instrument using known samples to verify its proper operation, and quantify measurement variance due to differently sized sensors. If time remains in the program, the student will investigate the effects of temperature and carbon dioxide loading on the DAC adsorbent thermal properties.
Imaging Cardiac Organoids with Laser Speckle
Principal Investigator: Jerome Mertz
Project Description: The Mertz lab has been working on an optical imaging method to monitor tissue dynamics (vascularization, blood flow, perfusion, viscoelasticity, etc.) that is simple and can work at frame rates greater than 100 Hz. The technology is based on laser speckle contrast imaging (LSCI) requires no labeling, is non-contact, and is designed to work in thick scattering media, making it ideal for non-invasive assessment of living cardiac tissue health. The goal of this project is to test improved LSCI processing algorithms and apply these to the monitoring of vascularization of cardiac organoid grafts in mouse tissue.
Project Description: The Mertz lab has been working on an optical imaging method to monitor tissue dynamics (vascularization, blood flow, perfusion, viscoelasticity, etc.) that is simple and can work at frame rates greater than 100 Hz. The technology is based on laser speckle contrast imaging (LSCI) requires no labeling, is non-contact, and is designed to work in thick scattering media, making it ideal for non-invasive assessment of living cardiac tissue health. The goal of this project is to test improved LSCI processing algorithms and apply these to the monitoring of vascularization of cardiac organoid grafts in mouse tissue.
iCoagLab Platform
Principal Investigator: Seemantini Nadkarni
Mentor: Brian Koker
Project Description: TThe iCoagLab Platform is based on patented technology developed by scientists at the Massachusetts General Hospital. iCoagLab uses an optical sensor that detects intensity fluctuations of laser scattering patterns to measure blood clot stiffness over time. Acute bleeding or hemorrhage is a major cause of preventable death in hospitalized patients. Conventional laboratory tests can be costly, cumbersome and take too long. Delays in detecting and managing impaired coagulation are associated with poor outcomes. Coalesenz seeks to solve this problem by providing rapid viscoelastic coagulation profiling at the point of care. Currently, a device is in development with a greatly reduced form factor and instrument cost, with a disposable cartridge that uses a very small blood volume and provides rapid results in about 10 minutes.
Mentor: Brian Koker
Project Description: TThe iCoagLab Platform is based on patented technology developed by scientists at the Massachusetts General Hospital. iCoagLab uses an optical sensor that detects intensity fluctuations of laser scattering patterns to measure blood clot stiffness over time. Acute bleeding or hemorrhage is a major cause of preventable death in hospitalized patients. Conventional laboratory tests can be costly, cumbersome and take too long. Delays in detecting and managing impaired coagulation are associated with poor outcomes. Coalesenz seeks to solve this problem by providing rapid viscoelastic coagulation profiling at the point of care. Currently, a device is in development with a greatly reduced form factor and instrument cost, with a disposable cartridge that uses a very small blood volume and provides rapid results in about 10 minutes.
Machine Learning Optimization of OAM-mediated Nonlinear Fiber Optics
Principal Investigator: Siddharth Ramachandran
Mentors: Purva Bhumkar; Jeff Demas
Project Description: Structured light – i.e. light with spatially-tailored intensity, phase, or polarization properties – has become a ubiquitous tool across myriad applications in optics; including biological imaging, quantum optics, telecommunications, and more. In particular, it has been shown that light beams which carry orbital angular momentum (OAM) can propagate for kilometer-scale distances in both free-space and optical fibers, opening up many new avenues for linear and nonlinear photonics due to the robustness and multiplicity of this, in principle, infinite basis. Targeting specific single, or superpositions of, OAM modes generally requires the use of digital holograms encoded by spatial light modulators (SLMs). These SLM-based generation systems can flexibly excite pure OAM modes; however, optimization and alignment of these systems is non-trivial, and they are often plagued by alignment drift during long-duration experiments. Recently, the High Dimensional Photonics Lab has had encouraging results that indicate that the combination of Multi-Plane Light Conversion (MPLC) – a spatial phase modulation technique for exciting OAM modes with nearly zero theoretical loss – and machine learning methods can be combined to facilitate automatic optimization and alignment of OAM excitation systems. In this project, we will build upon these results to directly apply machine learning algorithms to optimize and stabilize high power laser generation at novel colors using the nonlinear interaction between OAM modes in optical fibers.
Mentors: Purva Bhumkar; Jeff Demas
Project Description: Structured light – i.e. light with spatially-tailored intensity, phase, or polarization properties – has become a ubiquitous tool across myriad applications in optics; including biological imaging, quantum optics, telecommunications, and more. In particular, it has been shown that light beams which carry orbital angular momentum (OAM) can propagate for kilometer-scale distances in both free-space and optical fibers, opening up many new avenues for linear and nonlinear photonics due to the robustness and multiplicity of this, in principle, infinite basis. Targeting specific single, or superpositions of, OAM modes generally requires the use of digital holograms encoded by spatial light modulators (SLMs). These SLM-based generation systems can flexibly excite pure OAM modes; however, optimization and alignment of these systems is non-trivial, and they are often plagued by alignment drift during long-duration experiments. Recently, the High Dimensional Photonics Lab has had encouraging results that indicate that the combination of Multi-Plane Light Conversion (MPLC) – a spatial phase modulation technique for exciting OAM modes with nearly zero theoretical loss – and machine learning methods can be combined to facilitate automatic optimization and alignment of OAM excitation systems. In this project, we will build upon these results to directly apply machine learning algorithms to optimize and stabilize high power laser generation at novel colors using the nonlinear interaction between OAM modes in optical fibers.
User Interface for Electronic Control of a Biospired Soft Robot
Principal Investigator:Tom Ranzani
Mentor:Vi Vo
Project Description:The project will entail developing a graphical user interface for controlling electropermanent magnets-based valves.
To select the fluid lines that will activate the channel of our soft actuators, we configure electropermanent magnets (EPMs) as pinch valves that are electronically activated. These are sued to control an octopus inspired soft robot for underwater exploration. The project will be focused on creating a graphical user interface that allows us to both select the EPMs to turn on/off in real time and to create a sequence of actuation.
Mentor:Vi Vo
Project Description:The project will entail developing a graphical user interface for controlling electropermanent magnets-based valves.
To select the fluid lines that will activate the channel of our soft actuators, we configure electropermanent magnets (EPMs) as pinch valves that are electronically activated. These are sued to control an octopus inspired soft robot for underwater exploration. The project will be focused on creating a graphical user interface that allows us to both select the EPMs to turn on/off in real time and to create a sequence of actuation.
Speckle Contrast Optical Spectroscopy for Cuffless Blood Pressure Measurements
Principal Investigator: Darren Roblyer
Mentor: Ariane Garrett
Mentor: Ariane Garrett
Project Description: Hypertension affects more than half of all adults in the United States, but one in five adults with hypertension remain undiagnosed. The current gold standard for non-invasive blood pressure estimation is the cuff-based sphygmomanometer, which can only provide discrete, intermittent measurements of blood pressure. Continuous, cuff-less blood pressure measurements would enable blood pressure measurements outside of the clinic during daily life, which can provide a more accurate assessment of blood pressure. Speckle contrast optical spectroscopy (SCOS) is a technique that utilizes long coherence lasers to measure relative blood flow changes in tissue. When speckle images are acquired at a sufficient frame rate, blood flow and volume changes within each cardiac pulse can be resolved. We have previously shown that SCOS improves cuffless blood pressure estimation. This project will focus on continuing the development of our SCOS device.
Simulation of the Lung Environment for Validation of Soft Robot Bronchoscopy
Principal Investigator: Sheila Russo
Mentor: Daniel Van Lewen
Mentor: Daniel Van Lewen
Project Description: Lung cancer remains as the leading cause of cancer-related deaths in the United States due to the difficulty to treat and diagnose early-stage lung tumors. The main reason for this difficulty is that during a bronchoscopy procedure the surgeon must navigate tortuous paths to the periphery of the lung where early tumors form. The flexibility offered by soft robots make them inherently safe for interacting with tissue and allow for the creation of dexterous degrees of freedom which can be used to ease navigation into these regions of the lung. This project will focus on creating validation rigs for use in ex-vivo experiments with a previously developed soft robot. The validation rigs must account for tissue deformability and breathing motion in the lungs without hindering normal operation of the robot. Breathing motion will be simulated through tissue displacement and the control of pressure in a closed environment. The validation rig will be configurable to suit potential differences in the frequency of breathing. Two validation rigs are envisioned for this project which will assess both the ability to interact with in-vitro simulated tissue and ex-vivo tissue through soft robotic biopsy tools and the ability of the soft robot to navigate through the tortuous paths of the lungs. The main goal of this project is to capture the dynamic environment of the lungs in actual bronchoscopy procedures.
Population Responses of Living Neural Networks to Periodic Drive
Principal Investigator: John White
Mentor: Brandon Williams
Project Description: The hippocampal formation (HF) in mammals is responsible for collecting information about the sensory world and, if appropriate, storing that information as memories, to be offloaded to other brain structures later. The HF has a number of notable response properties, including nested, quasi-periodic activity. In this project, the student will work with us to collect and analyze data related to responses to periodic drive, collected via novel microscopy and voltage-imaging methods.
Mentor: Brandon Williams
Project Description: The hippocampal formation (HF) in mammals is responsible for collecting information about the sensory world and, if appropriate, storing that information as memories, to be offloaded to other brain structures later. The HF has a number of notable response properties, including nested, quasi-periodic activity. In this project, the student will work with us to collect and analyze data related to responses to periodic drive, collected via novel microscopy and voltage-imaging methods.