MDP Research Projects

The MDP is committed to offering students novel and creative design opportunities exploring the diverse, multidisciplinary fields of energy, environment, healthcare, and culture. Student design teams will be fully immersed in the research laboratory, collaborating with their faculty co-mentors, and using state-of-the-art equipment. These projects will fully engage the students and provide them the opportunity to see how multidisciplinary collaboration can lead to innovative results.

The following faculty-mentored design projects are available during the 2018-2019 MDP. Select a link for an overview of the project, associated faculty co-mentors, project prerequisites, and related publications.

MDP Design Projects

    1) “MUGIC” Development of an Interactive Device Interpreting Musical Performance Gesture and Expression 

    2) Continuous Flow Biosynthesis 

    3) Contribution of Phyllosphere Microbes to Total Biogenic Volatile Emissions from Native Plants of the Coastal Sage Scrub 

    4) Enhancing the Efficacy of Drug Released from Loaded Fibrin Glue by Photochemical Internalization (PCI) 

    5) Experimental Test of Energy Efficiency Annoyance Thresholds 

    6) Formation and Evolution of Ideology: A Cultural Consensus Model Approach for Mapping Religious Ideologies 

    7) Greensteam: Rethinking External Combustion for a Sustainable Future 

    8) Investigating Interpersonal Comparisons of Utility 

    9) Oman Humanitarian Desalination Challenge: Passive Solar Desalination Water Bottles 

    10) Quantitative Evaluation of Visual Function Using Cone Contrast Thresholds in Patients with Different Cone Opsin Genotypes or Eye Disease 

    11) Robust, User-Friendly Optical Platform for Long-Term In Vivo Neuroimaging 

    12) Seeing the World Through the Sewage Microbiome 

    13) Smart Multimedia Technology for Understanding and Guiding Human Behavior 

    14) VR Digital Audio Workstation (VirDAW) 




 Project #1:  “MUGIC” Development of an Interactive Device Interpreting Musical Performance Gesture and Expression
Faculty Mentors:  
Professor Mari KimuraMusic

Dr. Michael KlopferBiomedical Engineering

Description:  MUGIC is comprised of a glove worn sensor, a communications system, and a software interface that provides unique artistic applications for performance artistry. We took part in last year’s MDP, achieving our goal of building a proof-of-concept project called MUGIC. We seek to a second round of MDP sponsorship to finish the product design cycle to the final prototype level. This year, we will be building off the success of last year’s work, in order to push ahead for completing a solid prototype ready for mass production. The ‘endpoint’ for the project would be 1) add more features, finish and test the PCB board we developed last year, 2) add more features, finish and test the firmware from last year, 3) develop a durable, secure yet as small-as-possible casing design to house the PCB board, 4) perfect the software design to interface with existing commercial software and 5) develop the wearables and glove designs to house MUGIC. The foremost initial priority is to finish the PCB board and the firmware in order to professionally manufacture MUGIC in bulk.

MUGIC system involves the development of an integrated device to interpret and extract expressive gestures, and provide performance control, enabled by the latest generation of low power wearable sensors when paired with reliable wireless links. A number of solutions using gesture control have been envisioned and are in production, but many lack the focused, interdisciplinary development required to produce solutions for disruptive musical training and enhancement of musical performances. Through the support of the 2nd year of the MDP program, this team intends to push ahead, completing a new generation gesture control solution with numerous potential applications for musical performance and education as well as in other fields of the arts.

Last year, Dr. Kimura provided her PhD students at ICIT, the previous proof-of-concept model of MUGIC (prototype 0) in her Graduate Seminar. The students were so inspired by the MUGIC that they purchased the sensors after the class was completed, and continued their creative activities using them. Dr. Kimura also co-authored a paper entitled “Gestural Envelopes: Aesthetic Considerations for Mapping Physical Gestures Using Wireless Motion” with two PhD students at ICIT who also composed and performed their works using MUGIC. The musical compositions by the students, Alex Lough and Mark Micchelli, along with the aforementioned paper, were accepted by the International Computer Music Conference (ICMC), the premier conference of computer music which took place this year in Daegu, Korea. Mr. Lough and Mr. Micchelli attended ICMC in August, and presented the paper and their works.

The system is implemented as a specialized controller for this software to provide musical processing with highly specialized gesture control. The movements are reported by the sensorover a wireless link. The software then detects and analyzes characteristics of the user’s movements using a mapping engine. The output of this mapping engine is used to control inputs to commercial music software that allows real time interaction, such as Max(Cycling74.com) or Ableton LIVE (ableton.com), to permit relevant and direct gesture control of specific performance parameters while reducing cross-talk from non-intended motions. The system provides the capability to allow dynamic modification of the performance experience by the artist. The performer may use this device to control the rate or style of pre-recorded accompaniment, add performance audio/visual effects, or even create a new method for expanding artistic and human expression. In the current version, it is focused towards music but could be applied to different forms of artistic expression and specialized interactive gaming. It could also be attached to another non-electronic device such as a paint brush, tablet pen, mouse or inserted inside a ball or a toy.

Over this summer, Dr. Kimura continued to concertize in USA and in her festival performances in Italy, Denmark and Iceland using MUGIC (prototype 0). In July, she directed her annual music program “Future Music Lab” at the Atlantic Music Festival in Maine, where aforementioned PhD student from ICIT, Mark Micchelli joined as a Research Associate, making considerable improvement for the MUGIC software working with Dr. Kimura. In December 2018, Dr. Kimura and her students will present performance events specifically using MUGIC at the Experimental Media Performance Lab (XMPL) at CTSA. Also in December, Ableton, one of the most popular music software companies today, will sponsor an educational tour for Dr. Kimura in Japan for institutions such as Waseda University, where she will present MUGIC. Dr. Kimura is also working with a renown Japanese composer Dai Fujikura, who is composing a work for violin and MUGIC, which will be premiered in the 2019-2020 season.

Beyond performance, development of this device can hold great benefit for musical education. To take an example for violin playing the device could be worn as a wearable glove on the right hand. A teacher for a group of students could use a version of this system to detect and characterize elements of technique to offer specialized guidance on not just a specific point, but common patterns in technique that characterize poor habits. Tracking of specific “proper” pattern can also be accomplished allowing this to help train good habits in addition to identifying bad ones. Other applications in art and beyond are possible.

Students' Involvement and Expected Outcomes:
For this project, students from both art and engineering are involved in product design for this highly interdisciplinary project. Under mentorship lead from Departments of Music and Engineering, two students from each department will brain-storm, collaborate and work in tandem, in order to providing design input and product refinement feedback. Graduate student, Mark Micchelli will act as a day-to-day project manager under Dr. Kimura and Dr. Klopfer. This would provide a management experience for him to keep track of the assignments to undergraduates, adding another learning opportunity inside this project. In addition, students in Costume Design at the Theater Dept. of the CTSA will participate in designing the gloves, and other ‘wearables’ for MUGIC, gaining the experiences working in the field of fashion technology.

The two dedicated engineering students will be reducing product design aspects to a device which will be constructed at Calit2. A graduate seminar taught by Dr. Kimura will serve as a testbed for the new developed “MUGIC” device. In the class, she will further develop and research the relationship between relevant movements generated for artistic purposes. The MDP student team in consultation with Dr. Klopfer and Dr. Kimura, will help complete a ‘turn-key’ version of MUGIC with user-friendly software control with the wearable as a complete package, ready for final design for manufacture development and commercial production. The goal is to take the students from proof of concept development through the design refinement, sourcing constraints, testing, and design freezing process.

Prerequisites: This project is highly interdisciplinary; we are looking for students with interests in several fields; music, product design, visual artistry, electrical engineering, and computer science. The firmware development is based in the C programming language, while the interfacing software is currently written in a combination of C and interfaced using a visually driven programming interface using the interactive music software Max (cycling74.com). Development of the physical interface involves textile design and electronics development. A key aspect of this project is reducing the electronics footprint, decrease in size and cost while increasing in device reliability, robustness and utility which relies on the design of a custom printed circuit board (PCB). Experience in printed circuit board and basic electronics is a must for some team members. Innovative thinkers with relevant experience are encouraged to apply. Hands on experiences in graphic design (Photoshop, Illustrator) are preferred for students majoring in art who would like to participate in the design of the user interface and product development.

Recommended Web sites and publications: 
  
A. Lough, M. Micchelli, and M. Kimura, “Gestural Envelopes: Aesthetic Considerations for Mapping Physical Gestures Using Wireless Motion”, International Computer Music Conference (ICMC) unpublished conference proceedings, Daegu, Korea, 2018.: https://drive.google.com/file/d/1-6VT2SgwLqDClX1bmb0bItrWZKDY4F0e/view
  
B. Zamborlin, F. Bevilacqua, M. Gillies, and M. d’Inverno, Fluid gesture interaction design: applications of continuous recognition for the design of modern gestural interfaces , ACM Transactions on Interactive Intelligent Systems, 3(4), pp. 30-45, 2014.:
  
S Fdili Alaoui, C Jacquemin, F Bevilacqua, Chiseling bodies: an augmented dance performance, CHI’13 EA on Human Factors in Computing Systems, 2915-2918, 2013.:
  
Frédéric Bevilacqua, Nicolas Rasamimanana, Emmanuel Fléty, Norbert Schnell, and M. Kimura, "Extracting Human Expression For Interactive Composition with the Augmented Violin", New Instruments for Musical Expression conference proceedings at University of Michigan, Ann Arbor, pp. 99–102, 2012.:
  
F Bevilacqua, F Baschet, S Lemouton, The Augmented String Quartet: Experiments and Gesture Following , Journal of New Music Research 41 (1), 103-119, 2012.:
  
M. Kimura, “Making of Vitessimo for Augmented Violin: Compositional Process and Performance", New Instruments for Musical Expression conference proceedings in Genova, Italy, pp. 219-220, 2008:
  
“Future Music Lab” at Atlantic Music Festival, where the ‘proof of concept’ prototype has been used by Dr. Kimura and her students:
https://www.atlanticmusicfestival.org/the-institute/programs/future-music-lab/
https://www.youtube.com/watch?v=X3Y0RWu8iOQ
https://www.youtube.com/watch?v=8CthR5MOr1E:
  
“Eigenspace” by Mari Kimura: https://www.youtube.com/watch?v=kYfGCwKN6VY



 Project #2:  Continuous Flow Biosynthesis
Faculty Mentors:  
Professor Gregory Weiss Chemistry

Professor Shiou-Chuan (Sheryl) TsaiMolecular Biology & Biochemistry

Dr. Sudipta MajumdarChemistry

Description:  Additional Mentor: Joshua Kim

Continuous flow is increasingly a prevalent industrial process. The technique can accelerate the synthesis of commercial products, including pharmaceuticals, beer, and wine. In essence, starting materials are continuously pumped through reactors to yield products.1 Continuous flow systems may be constructed from an array of materials; perfluoroalkoxy tubing is common and accessible, and metal reactors can endure a wide range of temperatures.2, 3, 4 A back-pressure regulator precisely monitors the internal pressure of the system; these devices enable usage of superheated solvents and steady outflow at specific temperatures.

Continuous flow systems can optimize and expedite chemical and biocatalytic processes. For example, the synthesis and purification of multiple active pharmaceutical ingredients were completed in continuous flow.5 Biosynthesis applies catalytic proteins termed enzymes, and works especially well in flow synthesis. Purified proteins are typically expressed in E. coli bacteria and subsequently purified. The resultant enzymes exhibit exquisite specificity for substrates and products. This process can be cost effective and operational without supplemental co-factors, while circumventing issue typically associated with in vitro biocatalysis.6, 7 Whole cell biosynthesis with overexpressed enzymes has disadvantages, including: errant metabolic pathways that may produce undesirable byproducts or chemicals, cell membranes that limit the penetration of chemicals involved in the reaction, and cell debris that may contaminate the product.6, 8, 9

In continuous flow biocatalysis, enzymes are typically adsorbed onto solid supports. A plethora of supports are available, such as coconut fibers, 10, 11 cellulose, 12 kaolin, 13, 14 and molecular sieves.15, 16 Immobilization can hinder the lifetime and efficiency of the protein. Thus, exploration of enzyme immobilization typically requires extensive efforts.

In this project, a library of enzymes will be expressed and purified using E. coli. Gene inserts encoding for the protein of interest will be subcloned into expression vectors. After transformation, growth, and expression in E. coli, Ni-NTA chromatography will remove contaminants. Once a suitable quantity of proteins is obtained, our team will optimize conditions for binding proteins to resins. The binding conditions, such as the concentration of protein, solution to resin ratio, salt concentration, and pH, will be optimized. High-throughput assays will also be developed to screen the activity of immobilized proteins.

Once a continuous flow system is properly established, acoustic amplification of enzyme activity will also be explored. We plan to accelerate enzyme activity using different sound wave frequencies. This experiment is based on prior results from the mentor’s lab.17

The team will also synthesize necessary substrates for enzymes in continuous flow. Most substrates are costly and expensive, and inexpensive fabrication of components of the reactions will be a crucial aim of the project.

Students Involvement and Expected Outcomes:
The student will subclone the gene of interest into the pET expression vector using ligation independent cloning. After obtaining correct sequencing data, the gene will be over-expressed in E. coli. He/she will optimize the conditions for over-expression by varying different parameters, such as temperature and IPTG concentration. The student will then isolate and purify the protein using Ni-NTA chromatography. Active enzymes will be immobilized on a range of resins and tested for enzymatic activity. The conditions for attachment will be optimized for each resin using the mentor’s lab experience with high-throughput screening.

The primary goal of this project will be to reduce chemical waste and expensive reagents required to fuel reactions. Binding enzymes to resins significantly reduces the quantity required for synthesis.1 Furthermore, continuous flow biosynthesis can process greater volumes than batch reactions processed under similar conditions. For example, the synthesis of an enantiopure (5R)-hydroxyhexane-2-one in immobilized Lactobacillus kefiri strains was, on average, amplified by a factor of 19 in continuous flow.1 This particular system independently operated for six days, demonstrating the autonomy that such systems offer.

This project seeks to accentuate the benefits of continuous flow synthesis by optimizing residual enzymatic activity by uncovering efficient immobilization techniques. Exploring the lifetime and efficiency of such systems will prevent copious consumption of reagents, leading to greener, more cost effective chemistry.1

Prerequisites: Any undergraduate from any STEM discipline and any level may pursue this research.

Recommended Web sites and publications: 
  
Continuous flow biocatalysis. J. Britton, S. Majumdar, and G. A. Weiss, Chem. Soc. Rev., 2018, 47, 5891:
  
Continuous Flow Coupling and Decarboxylation Reactions Promoted by Copper Tubing. Y. Zhang, T. F. Jamison, S. Patel and N. Mainolfi, Org. Lett., 2011, 13, 280–283.:
  
The utilization of copper flow reactors in organic synthesis. J. Bao and G. K. Tranmer, Chem. Commun., 2015, 51, 3037–3044.:
  
Facile azide formation via diazotransfer reaction in a copper tube flow reactor. K. Nuyts, M. Ceulemans, T. N. Parac-Vogt, G. Bultynck and W. M. De Borggraeve, Tetrahedron Lett., 2015, 56, 1687–1690.:
  
On-demand continuous-flow production of pharmaceuticals in a compact, reconfigurable system. A. Adamo, R. L. Beingessner, M. Behnam, J. Chen, T. F. Jamison, K. F. Jensen, J.-C. M. Monbaliu, A. S. Myerson, E. M. Revalor, D. R. Snead, T. Stelzer, N. Weeranoppanant, S. Y. Wong and P. Zhang, Science, 2016, 352, 61–67.:
  
Whole-cell biocatalysts by design. B. Lin and Y. Tao, Microb. Cell Fact., 2017, 16, 106.:
  
Whole-cell biocatalysis for selective and productive C–O functional group introduction and modification. M. Schrewe, M. K. Julsing, B. Buhler and A. Schmid, Chem. Soc. Rev., 2013, 42, 6346–6377.:
  
Programmable bacterial catalysis – designing cells for biosynthesis of value-added compounds. C. M. C. Lam, M. Su ́arez Diez, M. Godinho and V. A. P. Martins dos Santos, FEBS Lett., 2012, 586, 2184–2190.:
  
S. Lee, Encyclopedia of Chemical Processing, Taylor & Francis Group, New York, 2006, vol.1.:
  
Immobilization of commercial laccase onto green coconut fiber by adsorption and its application for reactive textile dyes degradation. R. O. Cristóvão, A. P. M. Tavares, A. I. Brígida, J. M. Loureiro, R. A. R. Boaventura, E. A. Macedo and M. A. Z. Coelho, J. Mol. Catal. B: Enzym., 2011, 72, 6–12.:
  
Immobilization of Candida antarctica Lipase B by Adsorption to Green Coconut Fiber. A. I. S. Brígida, Á. D. T. Pinheiro, A. L. O. Ferreira and L. R. B. Gonçalves, Appl. Biochem. Biotechnol., 2008, 146, 173–187.:
  
Adsorption of high-purity endo-1,4-β-glucanases from Trichoderma reesei on components of lignocellulosic materials: Cellulose, lignin, and xylan. V. M. Chernoglazov, O. V. Ermolova and A. A. Klyosov, Enzyme Microb. Technol., 1988, 10, 503–507.:
  
Immobilization of horseradish peroxidase onto kaolin. N. Ž. Sekuljica, N. Ž. Prlainović, J. R. Jovanović, A. B. Stefanović, V. R. Djokić, D. Ž. Mijin and Z. D. Knežević-Jugović, Bioprocess Biosyst. Eng., 2016, 39, 461–472.:
  
Immobilization of Candida antarctica lipase B on kaolin and its application in synthesis of lipophilic antioxidants. S. Jakovetić Tanasković, B. Jokić, S. Grbavćić, I. Drvenica, N. Prlainović, N. Lukovíc and Z. Knežević-Jugović, Appl. Clay Sci., 2017, 135, 103–111.:
  
Adsorption of Lysozyme over Mesoporous Molecular Sieves MCM-41 and SBA-15: Influence of pH and Aluminum Incorporation. A. Vinu, V. Murugesan and M. Hartmann, J. Phys. Chem. B, 2004, 108, 7323–7330.:
  
Recent progress on immobilization of enzymes on molecular sieves for reactions in organic solvents. A.-X. Yan, X.-W. Li and Y.-H. Ye, Appl. Biochem. Biotechnol., 2002, 101, 113–129.:
  
Accelerating Enzymatic Catalysis Using Vortex Fluidics. Britton J, Meneghini LM, Raston CL, Weiss GA. Angewandte Chemie (International ed in English). 2016;55(38):11387-11391. doi:10.1002/anie.201604014.:



 Project #3:  Contribution of Phyllosphere Microbes to Total Biogenic Volatile Emissions from Native Plants of the Coastal Sage Scrub
Faculty Mentors:  
Professor Celia FaiolaEcology & Evolutionary Biology

Professor Alex GuentherEarth System Science

Description:  The largest source of volatile organic compounds in the atmosphere is emitted by terrestrial ecosystems. Volatile organics play an important role in determining atmospheric constituents, including ozone and aerosols, that control air quality and climate. There is widespread recognition that accurate volatile emission estimates are needed as quantitative inputs to numerical air quality and climate models and yet simulations of these emissions remain highly uncertain. The presence of phyllosphere microbes on foliage has the potential to exert substantial control over these volatile emissions and yet their role has been completely ignored in these models. Our proposed research will be the first step in demonstrating the importance of leaf microbes for ecosystem-scale volatile emissions into the atmosphere.

Our central hypothesis is that microbes substantially modify plant volatile emissions from terrestrial ecosystems into the atmosphere and the omission of this process in numerical Chemistry and Transport Models (CTMs) significantly reduces their predictability of air quality and climate. Our proposed pilot program will be the first step in demonstrating the importance of leaf microbes for ecosystem-scale organic emissions into the atmosphere. This will be accomplished by 1) performing experiments characterizing volatile emissions from control plants and plants treated with an anti-microbial spray and 2) culturing phyllosphere microbes from the plant leaf surfaces and characterizing emissions directly from the microbes. The model study plant we will use is a native keystone species in Southern California, Salvia mellifera (black sage). These tasks will be a first step to determine the contribution of phyllosphere microbes to total plant volatile emissions of plants native to the coastal sage scrub ecosystem in southern California. The results could transform our current view of processes controlling air quality and climate and establish the need for interdisciplinary research collaborations with microbial, plant physiology, and atmospheric chemistry expertise.

Students’ Involvement and Expected Outcomes: The undergraduate researcher will care for the plants in the UCI greenhouse and develop methods for growing phyllosphere cultures. The graduate researchers will assist with volatile sample collection and analysis on the Guenther and Faiola lab GC systems. The primary research goal for the undergraduate researcher will be focused on developing microbial culture techniques from plant leaf washes and an introduction to gas chromatography.

The outcome of the project will provide information on links between phyllosphere microbes and plant volatile emissions. The project will help the undergraduate researcher develop technical skills including plant propagation, anti-microbial treatment application, culturing, and sample analysis with two different types of gas chromatography techniques (TD-GC-ToF-MS and TD-GC-FID). The graduate researchers will gain experience mentoring the undergraduate researcher. Furthermore, the students will attend regular weekly meetings including all study participants which will help the students gain a broader understanding of how their research relates to the overall objectives of both laboratory groups. This experience will help develop skills in collaborative, interdisciplinary research.

Prerequisites: Open to undergraduate students pursuing a degree in either Earth System Science or the Biological Sciences.

Recommended Web sites and publications: 
  

Kharwar R.N., Gond S.K., Kumar A., Mishra A. (2010) A comparative study of endophytic and epiphytic fungal association with leaves of Eucalyptus citriodora Hook., and their antimicrobial activity. World Journal of Microbiology and Biotechnology, 26, 1941–1948.Lindow S. and M. Brandl (2003) Microbiology of the Phyllosphere. Applied and Environmental Microbiology, 69, 1875–1883.:
  
Peñuelas, J., G. Farrė-Armengol, J. Llusià, A. Gargallo Garriga, L. Rico, J. Sardans, J. Terradas, and I. Filella (2014) Removal of floral microbiota reduces floral terpene emissions. Nature, Scientific Reports, 4, 6727, doi: 10.1038/srep06727.:



 Project #4:  Enhancing the Efficacy of Drug Released from Loaded Fibrin Glue by Photochemical Internalization (PCI)
Faculty Mentors:  
Professor Eric PotmaChemistry

Dr. Henry HirschbergBeckman Laser Institute

Description:  Additional Mentors: Lina Nguyen, Mai Le, Richard C. Prince

Although gross total resection of gliomas, as evaluated on post-operative MRI, is often possible with current available techniques, almost all tumors recur due to the infiltrative nature of these tumors. Conventional therapy consisting of post-operative radiation and chemotherapy have been largely ineffective resulting in an average of 14 months overall survival. Infiltrative tumor cells are supplied with nutrients and oxygen by the normal brain vasculature and consequently protected by the blood brain barrier (BBB): few anti-cancer drugs are capable of crossing this barrier to target these infiltrating cells. Localized methods of drug delivery that bypass the BBB altogether, applied during surgical tumor resection, would circumvent this problem. Although fibrin glue (FG) has shown promise in several areas in delivering a depot of drugs, the quantity and release kinetics attainable for a variety of anti-cancer agents was not adequate [1]. Methods to increase the efficacy of the released agents are therefore of considerable value.

Photochemical internalization (PCI) has been shown to improve the cytosolic delivery of drugs in a site-specific manner [2, 3]. The concept of PCI is based on using photosensitizers, which will localize in the membranes of endocytic vesicles. When light is applied, the photosensitizer will react with oxygen causing membrane rupture releasing the trapped macromolecules into the cell cytosol, avoiding lysosomal degradation. The ability to enhance the efficacy of the drug released from FG by PCI, in a site specific manner, forms the basis of the experiments presented here. The aim of the present research is designed to evaluate and optimize the ability of PCI to enhance the effectiveness of FG released drug on multi-cell 3 dimensional tumor spheroids formed from glioma tumor cells. The proposed project is an in vitro proof of principle study.

Specific Aims:
1. Optimize the FG drug release. The concentration and release kinetics of the drug bleomycin and doxorubicin will be studied with advanced microscopic technology (Richard C. Prince (BME student Dr. Potma’s lab) Mai/Lina (Dr. Hirschberg’s lab)
2. Optimize the PCI-enhanced growth inhibitory effects of the released drugs using an in vitro multi-cell 3 dimensional tumor model (Lina/ Mai Dr. Hirschberg’s lab).

Prerequisites: The students involved have extensive previous experience in the laboratory skills necessary for this project. They will be responsible for all the hands-on experimental procedures and all lab work.

Recommended Web sites and publications: 
  
Patrick P. Spicer and Antonios G. Mikos, Fibrin Glue as a Drug Delivery System. J Control Release. 2010 November 20; 148(1): 49–55.:
  
Mathews MS, Blickenstaff JW, Shih EC, Zamora G, Vo V, Sun CH, Hirschberg H, Madsen SJ. Photochemical internalization of bleomycin for glioma treatment. J Biomed Opt. 2012 May; 17(5):
  
Diane Shin, Catherine Christie, David Ju, Rohit Nair, Stephanie Molina, Kristian Berg, Tatiana B Krasieva, Steen Madsen, Henry Hirschberg. Photochemical Internalization Enhanced Macrophage Delivered Chemotherapy. Photodiagnosis Photodyn Ther. 2017 Dec 5. pii: S1572-1000(17)30478-7.:



 Project #5:  Experimental Test of Energy Efficiency Annoyance Thresholds
Faculty Mentors:  
Dr. Michael KlopferBiomedical Engineering

Dr. Sergio Gago-MasagueBiomedical Engineering

Professor Joy E. PixleySocial Science

Description:  One strategy for reducing energy waste in plug load devices (such as computers or televisions) is to design a low-power mode (e.g., sleep or standby) that the device can automatically transition to when it is not being used. The inherent challenge is finding the optimal balance between saving energy and user satisfaction. That is, we want to have the device spend as much time as possible in the low-power state, but we also want to avoid annoying the user so much that they disable the power management feature. When asked why they don’t enable sleep on their computers, many users report that their computer takes too long to restart from sleep mode (Pixley and Ross 2014). This is undoubtedly a factor with other devices as well. If the user has an urgent desire to access their television or other entertainment device, but the lag time for it to power up is longer than desired, this might motivate them to figure out how to disable the sleep setting altogether. Thus, figuring out how long is “too long” to wait for a particular device to power back up is important when designing energy efficiency features in plug-load devices. The study of waiting times is of great interest to social scientists (e.g., cultural norms about waiting in lines, and psychological stress related to doing so) and service businesses (e.g., how long will customers stay on hold). And a good deal of research has been done on users’ tolerance of slow web page uploads. Yet, surprisingly, there is relatively little experimental research that directly tests the “annoyance threshold” for waiting for entertainment or office devices to power up from sleep mode.

The current project will involve a laboratory experiment, conducted in the Human Subjects Lab at the UCI School of Social Sciences, which supplies undergraduate students as subjects. Subjects will be asked to do a task on a device (to be determined – e.g., a game console, television, or audio system). The experiment will involve deception, in that it will appear to be asking subjects to do some other task, when our main purpose will be seeing how they react when they have to wait an unusually long time for the device to power up from sleep mode. That is, we will measure how long they wait before pushing the “on” button again, and whether this differs depending on which treatment group they are in (what statements or instructions they were exposed to earlier) or by characteristics of the subject.

Students' Involvement:
The students mentored in this project will work in a proactive research team guided by the faculty listed above to design the experiment, administer it, and analyze the results. The project includes the following components:
1. Reviewing the literature on the topic.
2. Brainstorming ideas for how to design the experiment, and designing it.
3. Helping to write materials for the experiment, such as the informed consent document and a questionnaire.
4. Being trained on experimental methods for testing user behavior, as well as more general human subjects training, such as confidentiality and obtaining informed consent.
5. Developing the testing methodology – e.g., designing or adapting a device that will measure and record the subjects’ behaviors.
6. Administering the experiment at the Human Subjects Lab.
7. Helping to analyze and interpret the results.
8. Presenting the results at a series of MDP and UROP sessions.

Students' Expected Outcomes: The students will benefit from working in an interdisciplinary team environment that meets on a regular basis and will receive detailed, direct feedback and mentoring from experts in this area. In addition, they will:
1. Get hands-on experience with scientific behavioral testing methods and experimental methodology.
2. Learn how to design and implement metering technology (for measuring subject reaction times).
3. Learn about how user behavior affects the energy efficiency of devices, as well as more general issues about device-user interface and interaction.

Prerequisites: We are looking for students with interests in several fields; Sociology or Psychology, Computer Sciences, and Engineering. Students should be good problem solvers, goal oriented, and innovative. An interest in energy efficiency and/or user behavior is beneficial but not required.

Recommended Web sites and publications: 
  
Chien, S. Y., and Y. T. Lin. 2015. "The effects of the service environment on perceived waiting time and emotions." Human Factors and Ergonomics In Manufacturing 25(3):319-28.:
  
Nah, Fiona Fui-Hoon. 2004. "A study on tolerable waiting time: how long are Web users willing to wait?" Behaviour & Information Technology 23(3):153-63.:
  
Pixley, Joy E., Stuart A. Ross, Ankita Raturi, and Alan C. Downs. 2014. "A Survey of Computer Power Modes Usage in a University Population." Sacramento, CA: California Energy Commission.:



 Project #6:  Formation and Evolution of Ideology: A Cultural Consensus Model Approach for Mapping Religious Ideologies
Faculty Mentors:  
Dr. Sergio Gago-MasagueBiomedical Engineering

Professor Louis NarensCognitive Sciences

Dr. Kimberly JamesonInstitute for Mathematical Behavioral Sciences

Dr. Jean-Paul CarvalhoEconomics

Description:  Additional Mentor: Maryam Gooyabadi

This project is a multidisciplinary approach to the topic of ideology, culture, and norms. Ideology is and has been a central topic to many fields within the social sciences where it is credited with the creation of much of our social reality today. Yet, very little agreement exists for what constitutes an ideology, how it relates to culture and norms, and its emergence, role, and evolution. This study attempts to remedy this age-long struggle in a novel way by drawing from appropriate quantitative methodologies in anthropology (multidimensional scaling and cultural consensus analysis), sociology (networks), evolutionary game theory (cultural transition models), and machine learning (natural language processing). This project will gather data from various religious ideologies and develop new mathematical modeling techniques in order to infer key features of such ideologies. In particular, a system must be developed to show how knowledge is distributed amongst members of a group, religious texts analyzed in order to customize and administer its corresponding survey, and the data processed using a variety of mathematical techniques. This data will guide modeling in an evolutionary game theoretic approach.

Students’ Involvement and Expected Outcomes:
With faculty guidance, students will be involved in the implementation of the mathematical models (i.e. cultural consensus model), survey design, label and codify ideological text for textual analysis, participate in the early development stages of the evolutionary dynamic model, and gain experience in data gathering and statistical analysis. This is a highly collaborative project where students will be able to focus on areas that best fits their interests and propose novel ideas of exploration. Students will gain an intimate knowledge of sophisticated quantitative methods and acquire experience developing dynamic computation models for artificial agents over networks. Specifically students can choose from the following activities:
• Develop a cultural consensus framework for data analysis
• Codify and label religious text for textual analysis
• Assist in survey design and data gathering
• Design, develop, and implement algorithms for understanding the dynamics involved in the formation, transmission, and evolution of ideology
• Learn how to write about the processes, procedures, findings, and implications of such research
• Develop creative graphics for displaying the results which can include
• Create evolving network

Prerequisites: Individuals with strong computing skills, with preferably training in computer programing and algorithm design, interests in STEM careers (science, technology, engineering, and mathematics), dynamical game theory and modeling, sociology, and culture. Innovative thinkers with real-world experiences or relevant experience are encouraged to apply. Knowledge of Mathematica, Python, or other computing languages.

Recommended Web sites and publications: 
  
Batchelder, W. H., & Anders, R. (2012). Cultural consensus theory: Comparing different concepts of cultural truth. Journal of Mathematical Psychology, 56(5), 316-332.:
  
Bisin, A., & Verdier, T. (2001). The economics of cultural transmission and the dynamics of preferences. Journal of Economic theory, 97(2), 298-319.:



 Project #7:  Greensteam: Rethinking External Combustion for a Sustainable Future
Faculty Mentors:  
Professor Simon PennyStudio Art

Professor Michael McCarthyMechanical & Aerospace Engineering

Description:  Buildup of Greenhouse gases and reliance on fossil fuels are two major contributors to climate change (global warming). This, as most humans on the planet now understand, is an existential crisis. Project Greensteam aims to address both these issues while attending to the needs of people in third world, isolated and off-the-grid locations, by developing simple and efficient external combustion (steam) engines for cogeneration of heat, mechanical and electric power, that efficiently and cleanly burn low-grade and mixed solid, liquid and gas fuels, (as well as leveraging solar and geothermal where appropriate).

Project Greensteam aims to develop a new generation of steam engines, leveraging advances in power machinery engineering, metallurgy, synthetic and composite materials, and digital, electromechanical and sensor solutions that have been developed in the 100 years since steam engine development essentially stopped.

Greensteam addresses sustainability issues by making small scale stationary power plants with clean and efficient engines and boilers, exploiting low grade solid fuels such as agricultural waste, biogas and plastic trash incineration. Greensteam rethinks conventional wisdom regarding (internal) combustion-based energy and power, decoupling power stroke from combustion to permit simpler, clean burning solutions.

Greensteam Research Program
The research project will advance on several fronts:

Greensteam Mechatronics - to develop sensor based, microcontroller driven, electromagnetically actuated steam engines. Greensteam ME1 will be a central project of 18/19 MDP, to be completed by end of spring quarter 2019.

Greensteam Combustion - to develop safe, clean, efficient furnace/boiler systems using low grade fuels and domestic, industrial and agricultural waste, deploying automated sensor/microcontroller management. This will involve sophisticated combustion science, physical prototyping, safety testing, instrumenting and sensor/microcontroller design for combustion and steam supply control.

Greensteam Design and Materials Research (DMR). Reviewing 250 years of steam and internal combustion technology, innovative engine that address traditional problems and inefficiencies will be designed and prototyped. This will involve basic research in metallurgy, steam systems, high pressure valve systems, mechatronics, sensors etc. Research into new materials and methods, (such as piezo electrics) and into existing technologies that might be adapted/repurposed, such as components from hydraulics, pneumatics, automotive, power industries and industrial fluid metering and processing. DMR will give rise to new engine projects like ME1

Greensteam Testing and Calibration (T+C). The goal of Greensteam is to create clean, efficient power systems. It is therefore crucial that claims of cleanliness and efficiency be backed up with hard testing data. This will demand instrumentation, monitoring and protocol development.

Greensteam Documentation and publication. Participants in projects will take part in documentation and preparation of technical reports and papers. Greensteam will require a coordinating information management officer to manage website, coordinate presentations, prepare graphics and prepare applications and reports. A clear program of mentoring, briefing and debriefing will be established.

Greensteam plant and skill building. Development of production facilities and skills and knowledge of team members (for prototyping electronic, mechanical and combustion/thermal aspects) is a key part of any educational/research project. Students will learn general use of machine and hand tools, metalworking, precision machining, electronics, and working with composites and plastics. Most prototypes will be developed from basic materials and components. Greensteam homebases are the CTSA Art Dept Mechatronic Art lab and CTSA Arts Annex machine shop.

Students will be involved in all aspects of research, theoretical modelling, design, building prototypes and testing, in a vertically integrated environment, grappling with fundamentals of machine design and thermodynamics where application of physics and engineering theory meets hands-on fabrication. Students will experience a ‘soup to nuts’ understanding of the R+D process, the iterative process of design elaboration, building and testing of prototypes, involving skill development and understanding of materials and manufacturing processes. Students will gain a detailed and holistic understanding of the realities of power generation machinery and the integration of electronic and mechanical components.

Students in the team will receive a series of introductory and training classes covering the technical history and design of steam engines, identifying engineering problems, efficient and unusual designs. We will discuss including general engine topologies (multi-cylinder, single and double acting, unaflow etc), valve systems, linkage and crank arrangements, materials and metallurgy, bearings and seals, boiler design, regulation and safety issues for high pressure, high temperature environments. There will also be briefing and training in relevant electronics and mechatronics.

Depending on skill profiles and interests of participating students, small development teams will be formed to pursue different aspects including:
• sensor research and prototyping,
• mechatronics, electronics, and coding,
• electromagnetic and fluid flow modelling,
• modelling and design of electro-magnetic valve actuators
• modelling and design of valve, valve seat and steam passages.
• boiler design and construction
• solidworks modelling of several prototype engines,
• solidworks design piston and mechanical linkages
• bearing and linkage R+D
• sensor-based combustion and emissions control
• precision fabrication in metals and (custom) epoxy-based composites,
• precision machining on lathe and mill

Expected Outcomes (2018/19)
• Fully functioning small scale steam engine, Greensteam ME1 (small scale). This first prototype engine is a custom two-cylinder unaflow scotch yoke design developed by Professor Penny, with sensor driven, magnetically actuated inlet valves. Bench testing will be done using compressed air.
• A prototype clean, efficient furnace/boiler.
(Depending on progress and test results, further prototypes and scaled up versions will be built.)
• Jointly authored UROP technical paper(s)
• Presentation of project and papers at relevant events off campus
• Fully built-out website

Prerequisites: Students of all levels are welcome. Students must be ready to pursue research in a self-directed manner, in teams or alone. Students must be ready to do hands-on work, to get dirty, and have the patience to learn from their mistakes. Students must be ready to play a role in all levels form the most (seemingly) menial to the most intellectual. Background in practical mechanics and precision machining is desirable. Solidworks and kinematic and thermal modelling experience desirable. Some members of the team should have grounding some or all of: fluid mechanics, electromagnetic design, metallurgy and materials science.

Recommended Web sites and publications: 
  
Greensteam Project outline: simonpenny.net/greensteam
  
Uniflow power (Australia): http://www.uniflowpower.com/technology/uniflow-stationary-steam-generator.aspx
  
See also Ted Pritchard – steam engineer: https://en.wikipedia.org/wiki/Edward_Pritchard_(engineer)
  
Janicki Omniprocessor -Steam power from sewage in Senegal: https://www.janickibioenergy.com/dakar-pilot/project-overview/
  
Whitecliffs (Australia) solar steam plant (historic). In this plant, solar steam drove a lister diesel engine converted into a bash-valve steam engine.: http://www.rossen.ch/solar/wcengine.html
  
Trash to steam power in Ethiopia: https://www.unenvironment.org/news-and-stories/story/ethiopias-waste-energy-plant-first-africa
  
University of Nottingham (UK) Score: http://www.score.uk.com/
  
Micronesian Center for Sustainable Transport (University of South Pacific, Fiji): https://www.mcst-rmiusp.org
  
Biogas: https://homebiogas.com/blog/what-is-biogas-a-beginners-guide/
  
Cleancookstoves.org: http://cleancookstoves.org/
  
Emisense, developing fine particulate filters (PM2.5) for (diesel etc) combustion.: http://emisense.com/
  
London Science Museum. A big stationary steam engine (700 hp, compound type, Corliss valves) running – well made video with notes.: https://www.youtube.com/watch?v=PIza2qnOgQY&t=316s
  
A biggish marine paddlewheel engine in operation. Compound, Joys valve gear, 700hp.: https://www.youtube.com/watch?v=Zl_W-Ywif1o
  
Another German maritime engine. This one a 2 cylinder ‘wobbler’.: https://www.youtube.com/watch?v=Pb8myoy7EJU
  
Dan Gelbart’s solenoid valve unaflow Engine
Greensteam E1 is inspired by this work.: https://www.youtube.com/watch?v=ccjTMQwKWNs
  
See also: http://www.kimmelsteam.com/gelbart-uniflow.html
  
An Edgar Westbury Cygnet Royal. A late triradial (1962) with novel radial valve: https://www.youtube.com/watch?v=E_UTqFTS-VM
  
A Stuart Sirius – Two Cylinder with Unusual Overhead Piston Valve.: https://www.youtube.com/watch?v=W1CNfOkDM0A
  
This one generating 10 amps: https://www.youtube.com/watch?v=Q_xe1l8ETN4
  
A model steam engine running - Netco swashplate piston valve two cylinder: https://www.youtube.com/watch?v=sL7PHYRIXpg
  
Phase3 Project: https://sites.google.com/site/phase3project/projects/steam-engine/valves
  
Tom Kimmel is a leading figure in steam car history and development in USA, and has an extensive website. Kimmel Steam Power: http://www.kimmelsteam.com/



 Project #8:  Investigating Interpersonal Comparisons of Utility
Faculty Mentors:  
Dr. Sergio Gago-MasagueBiomedical Engineering

Professor Louis NarensCognitive Sciences

Dr. Kimberly JamesonInstitute for Mathematical Behavioral Sciences

Description:  Additional Mentor: Lucila Arroyo

Historically, there has been a lack of consensus on the plausibility of interpersonal utility comparisons (i.e. the ability of individuals to comprehend and consider the value judgments of other individuals). However, these types of comparisons are common in everyday life, such as a group of friends deciding what restaurant to eat dinner at or a married couple deciding who will wash the dishes. In an effort to reconcile the inconsistency between the prevailing theories and observed behavior, Narens and Skryms (2017) have developed a mathematical formalization of this phenomenon, called accommodation dynamics, which provides a dynamic process with which agents can learn over time how others' utilities compare to their own. While their theory has been proved mathematically, it is not guaranteed to hold true when applied to people. Therefore, we want to create an experimental study to determine whether there is empirical evidence to support this theory of accommodation dynamics. The strength of correlation between the experimental data and the theory will aid in the evaluation of the feasibility of scientifically representing the dynamics of interpersonal utility comparison. If the data matches Narens and Skryms’ theory, then there will be empirical evidence for the robustness of their theory. If the data does not match the theory, then we can explore what the best fitting mathematical representation of these dynamics might be.

Students will be working with the co-mentors as well as two Mathematical Behavioral Sciences Ph.D students. They will be involved in the design of an internet-based experiment with several treatments. The experiment should be designed in such a way that it can be applied in different countries around the world, with the purpose of learning how different cultures shape the way to approach interpersonal utility comparisons. Students will be responsible of coding the experiment in Python or oTree. They will be working together with students and faculty at the University of Konstanz (Germany) as well as other universities. Students will get valuable training in experimental psychology and economics, as well as the opportunity to enhance their coding skills.
Students will learn:
• How to design psychological and economic experiments, and the main differences between both types
• Important considerations when coding a user-friendly interface for human-subject research
• To design social bots (algorithms) capable of mimicking different human behavioral patterns. Various bots will be designed,and each will incorporate specific personality traits. The bots will then become subjects themselves, carrying out the internet-based experiment previously designed.

Prerequisites: 
• Strong computer skills, preferably prior knowledge of Python, JavaScript and HTML.
• Interest in experimental design

Recommended Web sites and publications: 
  
Narens, Louis & Skyrms, Brian. (2017). Accommodation dynamics for comparing utilities with others. Philosophical Studies. 10.1007/s11098-017-0966-6.:



 Project #9:  Oman Humanitarian Desalination Challenge: Passive Solar Desalination Water Bottles
Faculty Mentors:  
Professor Chenyang Sunny JiangCivil & Environmental Engineering

Professor Shane ArdoChemistry

Professor Jaeho LeeMechanical & Aerospace Engineering

Description:  A major new initiative in water research, the ‘Oman Humanitarian Desalination Challenge’ has been announced recently (https://afrialliance.org/news/oman-humanitarian-desalination-challenge/). The challenge is a $700,000 prize that looks to deliver a hand-held, stand-alone, low-cost, desalination device suitable for short-term use and rapid deployment in the event of a humanitarian crisis. This challenge is to address the access to clean fresh drinking water following a disaster. Current relief response measures often rely on transporting massive quantities of bottled water into the affected population or distributing water purification devices or tablets that do not have the ability to rid water of salt. There is an urgent need for a desalination device that can be deployed quickly and affordably to people in need of drinking water in times of crises. Such a device would revolutionize humanitarian emergency response efforts in the aftermath of natural disasters.

This project is to develop a passive solar desalination water bottle that uses solar heat as the sole energy source to produce fresh drinking water from seawater. The key principle of the solar desalination bottle relies on the membrane distillation technology, where a microporous membrane with a hydrophobic surface is used to separate salty water from freshwater. Solar heating of saltwater transforms a portion of the water molecules from the liquid to the vapor phase, where they can then pass through the micro-pores to the other side of the membrane. Cooling of the water vapor on a cooler surface will result in condensation of the pure water inside the bottle.

This past summer, several students started to test the permeability and salt rejection of hydrophobic membranes. A black coating was used to increase the solar heat adsorption. The students demonstrated production of freshwater using direct solar heat. In the next phase of the project, we will design and optimize solar heat captivation in seawater and passive cooling for re-condensing water vapor.

Students’ Involvement and Expected Outcomes: Students will conduct experiments to test water permeability and production rate under different conditions. Students will design desalination bottles using design software for prototype production and testing. There is also the possibility of 3D printing of the bottles. Students participating in the project are required to contribute on average 10 hours per week of time. Bi-weekly meetings with faculty mentors are required to discuss the design plan and report design progress. The outcome of this project may be used as preliminary results for Oman Desalination Challenge.

Prerequisites: Students should have fundamental knowledge of chemistry, physics and college-level math. Backgrounds in heat transfer, materials science, and general thermodynamics are also desired. Students will learn the fundamentals of membrane desalination theory and relevant technologies. The program is open to all undergraduate and graduate students.

Recommended Web sites and publications: 
  
Website: https://afrialliance.org/news/oman-humanitarian-desalination-challenge/
  
Abdullah Alkhudhiri, Naif Darwish, Nidal Hilal. 2012. Membrane distillation: A comprehensive review. Desalination 287 (2012) 2–18:
  
Dongare et al. 2017. Nanophotonics-enabled solar membrane distillation for off-grid water purification. PNAS. 6936-6941. www.pnas.org/cgi/doi/10.1073/pnas.1701835114:



 Project #10:  Quantitative Evaluation of Visual Function Using Cone Contrast Thresholds in Patients with Different Cone Opsin Genotypes or Eye Disease
Faculty Mentors:  
Professor Andrew BrowneOphthalmology

Dr. Kimberly JamesonInstitute for Mathematical Behavioral Sciences

Professor Cristina KenneyOphthalmology

Description:  Age-related eye disease: We seek to learn more about visual color perception, and what is required so a person can sustain high quality vision. We are particularly interested in identifying what happens when a person gets older and their eye sight declines. Drs. Browne and Jameson will test the visual properties of younger and older individuals, including color perception. Dr. Kenney’s laboratory will perform genetic analyses of the mitochondrial (mt) DNA, opsin genes and some high risk nuclear genes for age-related macular degeneration (AMD) to determine if there is an association between poor vision and specific gene profiles.
Testing vision genotype and function: We will characterize the opsin genes that are responsible for how the eye sees color. Furthermore, we will analyze the color vision genes in older individuals and compared the findings to those of younger people. We will use advanced color vision testing tools and genotyping of the subject’s DNA that has been isolated from blood samples to characterize the relationship between color vision genes and color vision function.

Students’ Involvement and Expected Outcomes:
• Understand fundamental sciences to gain skills in vision science and biology: Color vision testing, Responsible research in human subjects, DNA sample collection and analysis, DNA extraction, genotyping, platelet isolation.
• Brainstorm and develop optimal color vision screening and detailed analysis methods using conventional tools.
• Create, implement and test novel approaches to color vision testing.

Expected outcomes:
• Evaluate visual function using color testing tools in subjects with and without age related eye diseases.
• Assist approved Research Personnel with DNA extraction procedures and analyze opsin genes for all subjects.
• Perform allelic discrimination analyses to identify the mtDNA haplogroups.
• Assist approved Research Personnel with Isolating platelets from all subject’s specimens to be used for cybrid formation in future studies.
• Use statistical analysis to correlate genotype with functional performance on color vision testing.

Prerequisites: Strong passion for applying engineering skills for biomedical applications. The team collectively should have background knowledge and skills in:
• Molecular and cellular biology
• Experience in computer programming
• Hands-on experience in biology and human subject research
• Enjoy creative projects and perception of the visual arts

Recommended Web sites and publications: 
  
Udar N, Atilano SR, Memarzadeh M, Boyer DS, ChwaM, Lu S, Maguen B, Langberg J, Coskun P, Wallace DC, Nesburn AB, Khatibi N, Hertzog D, Le K, Hwang D, Kenney MC. Mitochondrial DNA haplogroups associated with Age-related Macular Degeneration.Investigative Ophthalmology and Visual Sciences. Jun;50(6):2966-7:
  
Cocce et al. Visual Function Metrics in Early and Intermediate Dry Age-related Macular Degeneration for Use as Clinical Trial Endpoints, American Journal of Ophthalmology. 2018 May;189:127-138. doi: 10.1016/j.ajo.2018.02.012.:
  
Neitz, M., Kraft, T. W. and Neitz, J. (1998). Expression of L cone pigment gene subtypes in females. Vision Research. 1998 Nov;38(21):3221-5.:



 Project #11:  Robust, User-Friendly Optical Platform for Long-Term In Vivo Neuroimaging
Faculty Mentors:  
Professor Bernard ChoiBiomedical Engineering

Professor Yama AkbariNeurology

Description:  Many diseases of the brain are associated with changes in cerebral blood flow. A cranial window procedure allows for long-term visualization of the superficial blood vessels of the mouse brain, to monitor how the blood flow and vasculature of the brain may change during development of different neurodegenerative diseases. Ideally, we would like to be able to image the cranial window over the course of a few weeks to months in the exact location for each imaging session. To successfully achieve such long-term monitoring, it is imperative to develop a robust optical imaging platform that enables accurate, repeatable measurements. The design goal of this project is to design, build, and validate the imaging platform.

Students' Involvement and Expected Outcomes:

Student activities will involve iteration of the design-build-test cycle, with specific design criteria set for each cycle. Students will be expected to work in an independent manner, with meetings held with the co-mentors and other project stakeholders every 1-2 weeks. Students will also take the lead on learning and refining the in vivo cranial window surgical procedure. Students will initially utilize resources in the Choi lab, and then work on replacing eselect xpensive commercial lab supplies with parts that they will design and print. They also will work on computer-based instrumentation, most likely using LabVIEW and/or MATLAB. They will be expected to analyze and reduce collected data into meaningful charts and presentations and to perform basic statistical analysis.

Prerequisites: Students should have a background in computer programming and/or SOLIDWORKS. Prior animal research is desired (but not required), to perform cranial window procedures successfully.

Recommended Web sites and publications: 
  
“Intact Skull Chronic Windows for Mesoscopic Wide-Field Imaging in Awake Mice.”: www.sciencedirect.com/science/article/pii/S0165027016300644



 Project #12:  Seeing the World Through the Sewage Microbiome
Faculty Mentors:  
Professor Chenyang Sunny JiangCivil & Environmental Engineering

Professor Katrine WhitesonMolecular Biology & Biochemistry

Description:  Recently we have learned a lot about human gut microbiome. The microbial community in the human gut assembles in the first few years of life and influences health and illness throughout one’s lifetime. The composition of the microbiome determines how a person reacts to a growing number of conditions including allergic disease, auto-immune diseases, Type 1 diabetes, cancer, obesity, autism, vaccine efficacy, and infection susceptibility. Recent research has also demonstrated that the clinical outcomes of undernutrition in infants are associated with gut dysfunction as well as altered gut microbiota with reduced diversity. How environment influences the diversity of the microbial community in the human gut is not well understood. Yet, the microbes shed in human feces that are collected in sewage treatment plants may serve as a window to see the human gut microbiome in different communities and at different times. We hypothesize that sewage microbiomes from different regions of the country have distinct fingerprints. And analysis of the sewage microbiome can reflect the endemic human diseases and the use of antibiotics.

This project will examine sewage microbiome at two different wastewater treatment plants in Los Angeles and Orange County. Sewage samples from primary effluent will be collected in autumn, winter and spring. Bacteria will be concentrated and genomic DNA extracted. Samples will be analyzed using NextGen Sequencing. Bioinformatic software will be used to understand the signature of the sewage microbiome.

Students’ Involvement and Expected Outcomes: Students will design experimental approaches and laboratory operations for the project. Students will collect sewage samples from wastewater treatment plants and perform sample concentration and DNA extraction. Students will read literature and learn bioinformatics software for data analysis. Students participating in the project are required to contribute on average 10 hours per week of time. Bi-weekly meetings with faculty mentors are required to discuss the research plan and report research progress. The outcome of this project may lead to large research projects to better understand the sewage microbiome. The project will prepare the participating students to enter the new research world of understanding the connection between human and environment.

Prerequisites: Students should have fundamental knowledge of biology, chemistry, and computer programing. Backgrounds in computer language and programing are strongly desired. Students will learn the fundamentals of NextGen sequencing and wastewater treatment. The program is open to all undergraduate and graduate students.

Recommended Web sites and publications: 
  
Guo et al. 2017. Metagenomic analysis reveals wastewater treatment plants as hotspots of antibiotic resistance genes and mobile genetic elements. Water Research. 123: 468-478.:
  
Ryan et al. 2015. Sewage Reflects the Microbiomes of Human Populations mBio 6 (2) e02574-14.:
  
García-Aljaro et al. 2017 Determination of crAssphage in water samples and applicability for tracking human faecal pollution, Microbial Biotechnology 10(6), 1775–1780:



 Project #13:  Smart Multimedia Technology for Understanding and Guiding Human Behavior
Faculty Mentors:  
Professor G. P. LiElectrical Engineering & Computer Science

Professor Susan CharlesPsychology & Social Behavior

Dr. Mark BachmanElectrical Engineering & Computer Science

Description:  This project will explore the use of smart multimedia products (e.g., Amazon Alexa) that interact with human beings for use in understanding human behavior or guiding human behavior. Devices such as Amazon Echo and Spot are currently gaining popularity for use in delivering content (e.g., music, news, weather) or controlling devices (e.g., TV, house appliances).

There is opportunity to use smart multimedia products to engage people in their natural environments to solicit information about their behavior, feelings, and attitudes. In addition, such devices may collect data that people would not normally share with other humans (for example in a doctor’s office). Smart multimedia products may also be used as an effective way to modify human behavior, or to provide human training. For example, a smart device might guide a human subject through a complex protocol, may provide hints about performing a job or task properly, or may provide feedback about the quality of work performed. Smart devices can also provide warnings or context specific information for people working or requiring assistance. Such devices could provide screening for people prior to meeting with a specialist, for example asking a few questions to someone before they meet with a physician.

Applications of such devices, and their algorithms, need to be designed so that they can effectively accomplish their goals while simultaneously maintaining an environment that is pleasing and respectful to human beings. This project will explore these issues and develop demonstration systems using Amazon Alexa products (e.g., echo, spot, show, fire) that show the utility of smart multimedia products for interacting with human beings beyond simply controlling devices or delivering content.

Students’ Involvement and Expected Outcomes: Students will perform research to determine appropriate use cases of smart multimedia products for understanding and/or guiding human behavior. New applications for smart multimedia products will be determined and at least one demonstration system will be developed. This demonstration system will be used to perform initial studies on the use of this technology for the applications envisioned. It is hoped that this project will lead to new research in the labs of the faculty investigators to do more rigorous and deeper studies of how smart multimedia technology can be used for understanding and guiding human behavior.

Prerequisites: Students must have an interest in human-computer interaction (HCI) and use of technology for assisting people, especially older adults or people with disabilities or special needs. Some coding will be involved—students will be expected to write code in Javascript and/or Python. Students should be willing to learn basic coding skills if they don’t already have them. Must have strong work ethic and be able to think and work independently. Strong communication skills and “can do” attitude I also desired.

Recommended Web sites and publications: 
  
Recommended that students spend considerable time on Google and YouTube to become immersed in the technology of smart multimedia products. In particular, students should become familiar with the Amazon Alexa products and its technology ecosystem. Basic knowledge of Javascript and Python will be very beneficial (www.trinket.io). In addition, students should perform preliminary research on products and applications that are being released to the market today for the purpose of understanding and guiding human behavior.:



 Project #14:  VR Digital Audio Workstation (VirDAW)
Faculty Mentors:  
Professor Vincent OlivieriDrama

Professor Josh TanenbaumInformatics

Professor Karen TanenbaumInformatics

Description:  The VR Digital Audio Workstation (VirDAW) is an exploratory design project combining sound design and virtual reality software development. VirDAW will reimagine the functions of traditional sound design software environments within virtual reality by taking processes that are often abstract (filters, device-chains, sample manipulation, etc.) and transferring them into a virtual environment. By taking design practices that are metaphorical or abstract and rendering them as physical things to be manipulated, VirDAW creates new experiential tools for creative storytelling through sound. Using Unity with the Wwise audio engine, student researchers on this project will work with faculty experts to create modules for a VR experience that will reconceptualize many of the basic functions and capabilities of professional sound design software (such as ProTools and Logic).

Sound is a spatial and physical phenomenon: sound waves propagate through the air, reflect off of surfaces, scatter in different directions, and are absorbed into different materials. Existing sound design software, referred to collectively as Digital Audio Workstations (DAW), simulate these physical properties, allowing designers to apply effects like reverberation, delay, and equalization to audio waveforms (among many others). In a conventional DAW, the controls for these effects often take the form of sliders, knobs, and numerical fields where engineers and designers can specify physical properties such as room size, decay time, and other relevant variables via abstracted UI widgets. In VirDAW we propose to reproduce the physical qualities of sound within a simulated physical environment. Thus, to adjust the reverberation of a sound, one might enter into a simulated room and turn a large crank to adjust the size of the space, while experiencing the impact this has on the sonic properties of the waveform. Such a tool would change a designer’s relationship to the sounds they design and would be a valuable resource for teaching acoustical physics, sound engineering, and sound design.

VirDAW also aspires to be a tool for the creation of spatialized soundscapes, including applications for theater, theme park design, film, video games and music. It will be a virtual reality interface that operates in conjunction with professional tools for interactive audio design, allowing designers to manipulate sound within a simulated context that directly maps into the final experience that they are designing for. More conventional sound design tools are well suited to manipulating sound over time but struggle to successfully and intuitively manipulative audio in space. VirDAW introduces new tools for spatial design that will extend and revolutionize existing practices of sound designers, composers, and engineers.

Students’ Involvement and Expected Outcomes: We want to build a team of designers and developers to implement preliminary modules in Unity and Wwise for the HTC Vive in VR. Students will be expected to rapidly familiarize themselves with these tools and with the practices of sound designers, engineers, and composers using traditional sound design tools. By the end of the project, we hope to have several preliminary modules for sound sequencing, spatial mixing, reverberation, and/or equalization developed, along with a framework and infrastructure for bringing future modules online. Students will have an opportunity to gain experience developing in Virtual Reality, and experience in creating sound design for interactive experiences.

Prerequisites: Students applying for this project should be experienced in either sound design or software development using the Unity game engine. Additional experience with Wwise and with traditional Digital Audio Workstations is also highly desired. We are also looking for students with expertise in user experience design, previsualization, and 3D modeling and animation. Students should be self-directed and capable of working to internal deadlines, they must be excellent communicators, and they must be experienced with collaborative and creative group work. We will be generating prototypes quickly and experimentally, so we are looking for students who can rapidly acquire new skills and specializations and work collaboratively within an iterative design context.

Recommended Web sites and publications: 
  
Tanenbaum, Seif El-Nasr, Nixon (2014) Nonverbal Communication in Virtual Worlds:
  
Oculus Developers, Introduction to Best Practices: https://developer.oculus.com/design/latest/concepts/book-bp/
  
Introduction to Wwise: https://www.audiokinetic.com/courses/wwise101/