Brain-on-a-chip for understanding cortical circuit formation and function: a talk by Dr. Vincent Daria of Australian National University

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by Marienette Morales Vega

The Department of Physics would like to invite you to the talk “Brain-on-a-chip for understanding cortical circuit formation and function” by Dr. Vincent Daria, Group Leader of Neurophotonics Laboratory at the Eccles Institute of Neuroscience of Australian National University to be held on 17 July 2017, Monday, 11:00 a.m. at CTC 118.

Title: Brain-on-a-chip for understanding cortical circuit formation and function

Abstract:

We aim to understand the formation and function of brain circuits by growing neurons on nanostructured semiconductor devices (a.k.a. Brain-on-a-chip). We artificially grow brain cells on a semiconductor wafer patterned with nanowire scaffolds. From a fundamental perspective, we aim to investigate the structural significance of nanoscale topographies for guiding neurite outgrowth. To correlate the circuit function on the neurons grown on-a-chip with that of certain areas in the brain, we need to analyse the function of single neurons and population of neurons forming circuits in living mammalian brain slices and that of an intact rodent brain. To achieve this, we use novel photonic technologies not only to visualize these neurons but also to stimulate and record neuronal activity to understand the input/output transfer function of neurons and circuits. Understanding neuronal and circuit function is in itself a grand challenge and has attracted major research thrusts worldwide. Hence, correlating the input-output transfer function of neuronal of circuits from both living brain and that of neurons grown on-a-chip can lead to new insights on how the brain functions during learning, memory and information processing.

About the Speaker

Vincent Daria earned his PhD in Applied Physics from Osaka University, Japan. From 2001 to 2004 he pursued postdoctoral work at the Risoe National Laboratory (Denmark) where their group pioneered the use of dynamic multi-beam optical tweezers for manipulating arrays of microscopic objects and cells simultaneously. From 2004, he established a research group at the University of the Philippines to work on ultrafast lasers in combination with spatial light encoding for multi-beam optical tweezers combined with non-linear optical processes. Such technique was applied to fs-laser surgery and manipulation of cells and 3D holographic micro-fabrication via photopolymerization. In 2007, he joined the physics department at the Australian National University (ANU) where they initially designed a unique microscope capable of probing living cells and neurons in the brain. In 2010, Dr. Daria moved his laboratory to the John Curtin School of Medical Research to fully engage their collaboration with neuroscientists and apply their holographic two-photon microscope for simultaneous photostimulation of synapses and multi-site Ca2+ imaging of neuronal networks in living brain tissue. The success of this venture enabled the group’s expansion where they continuously received highly competitive funding from the Australian Research Council and the National Health and Medical Research Council. He is currently the group leader of the Neurophotonics Laboratory at the Eccles Institute of Neuroscience at ANU. He continues to teach optics and laser courses as well as maintain collaborations with researchers from the Research School of Physics and Engineering at ANU.


Marienette Morales Vega, Ph. D.
Assistant Professor, Physics Department
Materials Science Laboratory
Head, NanoSpectroscopy Group
Ateneo de Manila University
Faura Hall 318
Email: mvega@ateneo.edu

Delay tolerant network front-end application for disaster risk reduction by Jherrielloyd Yao and Carlex Jose (BS APS-ACS)

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Carlex Randolph Jose and Jherrielloyd Lourrenz Yao (BS APS-ACS) at Interlinks 13.0 last May 5, 2017. Their poster is entitled, “Design and implementation of a delay tolerant network front-end application for disaster risk reduction.”

by Ellice Dane Ancheta, Sunshine Indias, and Quirino Sugon Jr

Last 5 May 2017, BS Applied Physics / Applied Computer Systems students Jherrielloyd Lourrenz Yao and Carlex Randolph Jose presented a poster at Interlinks 13.0 on their research entitled, “Design and implementation of a delay tolerant network front-end application for disaster risk reduction,” which is one of the disaster-related projects of the Ateneo Innovation Center. In his Physics thesis last year, Yao worked on interpolation methods for rainfall data in Metro Manila under Dr. James Simpas, while Jose worked on volume holographic reconstruction of Bessel beams at multiple wavelengths under Dr. Raphael Guerrero.

Below is an interview with Jherrielloyd Yao and Carlex Jose by Ateneo Physics News.

1. How did you arrive in Ateneo?

Yao: I graduated from Philippine Science Central Visayas Campus in Cebu. I chose Ateneo because it is a top school. My choices were Ateneo and UP. I passed UPCAT but I had no course in UP. My chosen course there was Materials Engineering. My first choice of course in the Ateneo is also BS APS MSE (BS in Applied Physics / Material Science and Engineering). It was in second year that I chose ACS. So I shifted. I am more interested in programming and electronics. I felt that MSE is too heavy with Chemistry, which is not exactly my favorite.  I was inclined to take science courses. I had three choices, some of the major branches of science: biology, chemistry and physics. I chose physics because it is more general, with more applications. I think it offers more choices in the future in terms of jobs. Also there are more grad school courses I can pursue given a physics background.

Jose: I graduated from Philippine Science Eastern Visayas campus in Leyte. I took both the UP and Ateneo entrance exams. For both universities, I chose physics. I actually couldn’t decide confidently between UP and Ateneo. But Ateneo offered a 100% scholarship. So nothing against UP, but Ateneo is a better choice financially. That is why I am here. On physics, one of the factors is that the coolest people I look up to are our physics professors. So I had appreciation for physics already. Also, the topic seems more interesting by how rudimentary the whole thing is compared to the other sciences.

2. What was your physics thesis about?

Yao: My study was about interpolation methods for rainfall data in Metro Manila under Dr. James Simpas. The usual setup involves weather stations with rain gauges measuring rainfall in specific points on the map every five minutes. However, the dense network of weather station has a minimum radius of 5 km across stations, which leaves the points in between stations with no data. Interpolation methods aim to address the lack of data for a given study area by generating estimates at points with no weather station. Multiple studies have been conducted involving interpolation methods for other areas or countries with different conditions, climate, topography, etc. All of them conclude different results: no interpolation method will work well for all cases. I have assessed a few of the common interpolation methods for my thesis – Nearest Neighbor, Cubic, and Inverse Distance Weighting (IDW) – and I have evaluated the results through correlation and root mean squared errors. I have also developed an interpolation method which worked better than the ones mentioned earlier. It is a hybrid method combining IDW and Successive Over relaxation (SOR). SOR is an iterative approach commonly used to solve potentials in electromagnetics. With some modifications and integration with the IDW, it has been used to generate rainfall values on a map of Metro Manila.  

Jose: I worked with Bessel beams with the Photonics lab under Dr. Raphael Guerrero. My thesis is entitled “Volume Holographic Reconstruction of Bessel Beams at Multiple Wavelengths” Basically, what I did was I would store Bessel beams at  a specific wavelength in a Lithium Niobate Crystal. Lithium Niobate Crystal (LiNbO3:Fe) is a photorefractive crystal in nature. I have the holographic data stored using red light at 633 nm wavelength, while reconstruction was performed using three different wavelengths: 633, 612, and 604 nm. I have not published my paper yet. The big deal about Bessel beams is that it is an interesting topic. Bessel light beams have a property of being non-diffractive over a certain distance, unlike plane waves (which are also non-diffracting) and Gaussian waves that spread out. An ideal Bessel beam possesses a well-defined central spot surrounded by concentric ring. It should be non-diffractive over infinity, which means that the central core would remain the same, without expanding, over an infinite distance. A true Bessel beam is impossible to create, what we work instead with are beams that are Bessel-like, these beams possess Bessel properties over a distance. They are called Bessel-like beams because their central core barely widens over a particular distance. With that, they have a property of self-healing even with obstruction partially covering the beam. The beam has the capability restore itself. Using photorefractive crystals like LiNbO3 crystal is another way of storing memory. An advantage of using the LiNbO3 crystal is that it is capable of storing 100 bits/um^2. Unlike conventional optical and magnetic data where information is processed serially (bit by bit), holographic data is processed in parallel (by blocks of data) with the capability to cache and retrieve multiple information blocks simultaneously.

3. What was your Applied Computer Systems thesis?

For this project, we were operating under possible conditions of the aftermath of a disaster. There might be limited resources due to damaged infrastructure, cut power lines, and downtime of basic telecommunication services. Given this backdrop, what we did is to develop a system to enable responders to communicate effectively under these limitations of a disaster scenario (no 3G, internet, or signal). Our main goal is to enable efficient and reliable communication systems even without the infrastructures we usually rely on for this purpose. We want to make it possible for responders to have a communication system which can assist them in sending images, audio clips, text messages, among other features that speed up the process of sending necessary information they might need in responding to the situation. That is the gist of the problem.

What we developed is an application that would implement the DTN (Delay tolerant network) system. Basically, DTN is a bundle transmission system where you do not have to wait for a secure line to send the message across. There is no end-to-end communication that is required. This transmission is unlike phone calls, wherein the phone call actually starts only if both ends have to acknowledge that they are ready to take the call. For the DTN, you are just sending information out whenever you have a chance and hope it gets to its destination. This is good in disaster scenarios because responders are moving dynamically and conducting operations always. It could be messy. For example, 20 people moving independently from one another are contained in a zone as in a protocol during disaster. With each DTN, each one of those 20 people can take information or data from their phones, and contact other responders when needed. Information is gathered in each device and bumping will occur as two phones meet. The exchange of information happens by mere proximity, by using their adhoc wifi capability. Most smartphones have the capability to set up its own network or “hotspot”. If the phones are close enough, they share information they gathered. For example, information can go from my phone to your phone and on to other phones until it reaches the phone that collects all the data in the zone. The phone that collects all the data in the zone is called an aggregator. Over time, as enough information is collected, a passing data ferry (VHub or UAV) along the zone can take that information and transmit it further. Its eventual destination will be in mission control, where decisions and instructions can be sent out to responders.

The mission control is the backbone wherein all information is sent and processed to assess disaster management, the other team–Dane Ancheta’s team–is working on this. Our work is more focused on those responders in the field. The responders then will be working with an application for communication and information sharing without the use of internet, but using the adhoc wifi instead.

4. What programming languages did you use?

For this project we used Android Java. The Delay Tolerant Network (DTN) part is the starting point and the foundation of our work. We started with IBR-DTN (developed by Institut für Betriebssysteme und Rechnerverbund), an existing application which we used for this purpose. What we did is we started from this application and modified it to suit our needs. Originally, what the application can do was send audio messages. We added several capabilities and functions to this, such as image sending, text messages, and appending text information to the image in Exif (Exchangeable image file format) file. Metadata such as GPS and notes are stored in this Exif file. Local face detection was also added on the app. This local face detection lessens the delay and work of the mission control group. This is possible because images taken on the field is immediately processed by the face detection capability, therefore, it does not have to spend time being sent and processed by mission control. Other functions include GPS and radio frequency module capability because the data ferry (the UAV) would pass by the zone, and get the information from the aggregator node. The communication is done in the 760MHz bandwidth, however we are exploring using 915 MHz. The team also wants to explore using LoRa (long range) communication for this purpose because this allows for the transmission of information farther distance in the kilometers range. However the trade-off for reaching a farther distance is that it will have a weaker transmission rate.

5. How did you choose your topic?

This project was already initiated and worked upon before we came in the lab. There have been a lot of collaborations and planning with external groups outside Ateneo, such as Toyota InfoTech Japan and some sectors in the government, as far as we know. This thesis is a part of the bigger project of the Ateneo Innovations Center (AIC) which is the Multi-Platform ICT Decision Support System UAVs, Vehicle Hubs, Ubiquitous Computing for Disaster Risk Reduction. We are just contributing to this bigger project. While our team is working on communication for the field responders, Dane and her team are working on mission control, receiving and processing all the data aggregated to them. There is also another group working on data ferries, which makes use of the UAV (Unmanned Aerial Vehicle). It is easier to use UAV for disaster scenarios as it is easier for it to go from place to place. There is also another group that works on flight simulation for the UAV flights.  

6. How are projects done in Ateneo Innovation Center?

There are many small tasks for all of the researchers. Working in the lab, especially in big active labs such as the Ateneo Innovations Center (AIC), requires a lot of collaboration and contribution from each one. A lot of our work intersects with the other group. Some results are based on their findings and the other way around. In a way, we are one big group, but each of us have our own focus. Other than the actual project itself, there were little side quests or tasks that we had to do. Eventually these small tasks would add up and contribute a great deal to the project.

7. What were some of the difficulties you encountered while working on your thesis?

Yao: It was difficult to shift from physics to communications. We had to learn by doing. There were expected outputs, and we had to learn how to do it on the spot. For example, we had to learn Android for our thesis which we started working on for the first semester. However, Android programming is offered in the second semester. We had to do a lot of research and reading. We try to understand and study existing apps because we could use some of the information for our thesis. We are given a shorter time for the ACS subjects and even the thesis is done in 2 semesters–part of which is our integration to the lab.

Jose: To be honest, the bulk of the work is programming, like we have to design the concept and  use-cases. My work there is objective: it involves coming up with a plan of action on how to solve it. We are designing a system and we have the available technology. We know what devices or software we want to use. The objective there is to make everything work together or how to make everything function properly–that is the aspect which is more physics-related. After that you, sit down and code for hours or days or months. Every time that here is something the team wishes to add, you have to adjust everything again.

8. Where do you go from here?

Jose: For our research in the Ateneo Innovations Center (AIC), we are sure that there will be people in AIC who will continue it, considering that there is a long term vision for this work. As for myself, I am not sure yet whether I will continue studying such as taking up a Master’s degree or PhD. But I  have also been looking at employment offers. I feel both are equally interesting. It is difficult to separate physics from the IT stuff.  You can think of it (IT) as being deeply in the physics realm as well. Unless it is hardcore programming, but even then, it is fun for me or challenging enough for me. So far I had taken an exam and an interview for work. There is no transaction yet.

Yao: I am really not sure. Perhaps I will work for a while then study further. Regarding the study, I am interested in the Toyota Motor Philippines School of Technology (TMP Tech). They have a school and it is in house meaning you could live there. I find it interesting because I like to tinker with stuff. Although I have not explored cars, I actually don’t know anything about cars but I want to build stuff.  With that in mind, I am also interested in Aeronautics–if not, robotics, but it is heavy on engineering. I still lack the knowledge. Definitely I am sure I will do Masters.  I am not sure what course yet but it will have to be related to physics or ACS.

9. How do you feel about being the last ACS batch?*

Jose: I shifted from pure physics to applied physics with computer systems. The department should rethink freezing ACS and bring it back because there might be students, like me, who will want to shift into the course.

Yao: I think the ACS track is a good course. It is a good combination because it incorporates programming, engineering and communications to complement our background in physics. I don’t know why they removed it. We shifted to ACS from other courses in physics.

*(Note: Though the Physics Department has not offered the BS APS/ACS program for two years, it still exists in Registrar’s records. The Physics and Chemistry Departments may revive the ACS program soon. BS APS/ACS is a rebranding of the BS Physics with Computer Engineering (BS PS/CE) which started in 1985.)

10. Do you have any parting words or advice?

Jose: Well as for advice, I feel like it would be reckless if I speak and I invoke my 5th amendment right (“right to remain silent”). All I can say is, “You do you.” Do what you think is best. There is no one course of action in or after college. I have seen people prosper in doing things I would advice otherwise. I don’t doubt my decisions but I might take it back at some point. Well, let’s see. It is difficult to advice because you can’t really say if it is going to be a success story. It might be too early to speak.

Yao: Pursue your dreams. We are proud to have earned our degrees because it is a proof of what we have learned in college for the last five years. It means that we are out to start a new phase in life. 

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In a disaster area, the DTN responders are grouped by zones and are connected by the adhoc wifi network. For each zones (green areas) there are responders limited by proximity. The red circles are the data aggregators. The blue dots are the responders on the ground doing their task, linked to each other by the adhoc. Each zone will have a leader. The leader will make decisions on where to go and when to dispatch instructions to the team. In this context, the work assigned to the leader is to be the aggregator to collect information. The aggregator entails having the RF module connected to the android phone, which will collect information from phones and responders to pass it on to incoming data ferries (UAV). Through this process of receiving and sending information, there will be links to other DTN groups in other zones, and lastly the information on the group through the bumping of data, will eventually reach mission control.

PhD Physics Dissertation Defense: Fluid-enhanced tunable diffraction with elastomer grating by Caironesa Pada

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The Department of Physics of Ateneo de Manila University cordially invites you to a Physics Dissertation Defense:

  • Student name: Caironesa Pada
  • Dissertation title: FLUID-ENHANCED TUNABLE DIFFRACTION WITH AN ELASTOMER GRATING
  • Schedule and venue: 10 May 2017, 4 PM, F-106

DISSERTATION PANEL

  • Dr. Raphael A. Guerrero (Physics), Dissertation Adviser
  • Dr. Percival F. Almoro (UPD), Dissertation Examiner
  • Dr. James Bernard Simpas (Physics), Dissertation Examiner
  • Dr. Maria Obiminda Cambaliza (Physics), Dissertation Reader
  • Dr. Christian Lorenz Mahinay (Physics), Dissertation Reader

ABSTRACT

A tunable diffraction grating shows promise in applications from beam steering to spectroscopy due to the versatility of its design. A diffraction grating made of polydimethylsiloxane (PDMS) is replicated using simple soft lithography. Tunable diffraction is accomplished by modifying groove spacing through the application of strain on the elastomeric grating replica. The range of strain-variable diffraction angles is extended by adding a refracting liquid layer to the grating. The scanning of the 1st-order diffraction angles as the grating pitch is tuned is demonstrated when the grating operates in transmission and reflection mode. In transmission mode, using a water layer, the diffraction angle is tuned from 38o to 33.4o with an applied strain of 17.7%. With an equal amount of strain, adding a glycerol layer results in the diffraction angle varying from 38.8o to 34.4o. When the grating operates in reflection mode, with a water layer, effective diffraction angle is 24.85o with 8.86% strain. This is equivalent to the output at an applied mechanical strain of 12.8% of an unmodified grating. The addition of glycerol as a refracting element to the tunable grating yields 27.8o with an applied strain of 8.86%. Without glycerol, this angle can be achieved at a strain level of approximately 14.76%. The addition of liquid layer proves an efficient way to extend the range of the 1st-order diffraction output. The experimental results are accurately described by the combined effects of diffraction by a deformable grating and refraction by a fluid with a curved surface.

PhD Physics Dissertation Defense: Generation of Periodic Beams with a Volume Holographic Axicon by Alvie Asuncion

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The Department of Physics of Ateneo de Manila University cordially invites you to a dissertation defense:

  • Dissertation title: GENERATION OF PERIODIC BEAMS WITH A VOLUME HOLOGRAPHIC AXICON
  • PhD Physics Candidate: Alvie Asuncion
  • Schedule and venue: May 4, 4 PM, F106

Dissertation panel

  • Dr. Raphael A. Guerrero (Physics), Dissertation Adviser
  • Dr. Paul Leonard Atchong C. Hilario (UPD), Dissertation Examiner
  • Dr. Marienette Vega (Physics), Dissertation Examiner
  • Dr. Mikaela Irene D. Fudolig (Physics), Dissertation Reader
  • Dr. Joel T. Maquiling (Physics), Dissertation Reader

Abstract

Superimposed Bessel beams (SBBs), which exhibit periodic behavior along the propagation axis, have been found useful in optical micromanipulation, atom trapping, laser drilling and other applications. The oscillating core diameter of such beams gained attention due to a pre-defined longitudinal pattern, which can be modified by varying certain experimental parameters. In this study, photorefractive volume holography is employed to generate SBBs with tunable periodicity. This is performed by using an axicon-telescope (a-t) system to generate quasi-Bessel beams (QBBs) with different transverse profiles corresponding to different cone angles. The generated QBBs are recorded as a thick hologram in a LiNbO3 photorefractive crystal. Stored holograms were considered as equivalent to a volume holographic axicon that effectively transforms the profile of Gaussian readout beams into QBBs. Retrieved QBBs from the crystal are focused by the original axicon to produce SBBs. Results show that both the QBB profile and the SBB period can be tuned by simply varying the a-t distance d. SBB oscillation periods that range from 4.3 cm to 6.1 cm were obtained. The method presented in this study allows tunability of SBB period through a simple rearrangement of optical elements.

Volume holographic generation of optical Bessel Beams: a physics dissertation defense of Jonathan Manigo on 19 Apr 2016

 

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The Department of Physics of Ateneo de Manila University cordially invites you to a Physics Dissertation Defense:

Ph.D. in Physics student name: Jonathan Manigo

Dissertation title: VOLUME HOLOGRAPHIC GENERATION OF OPTICAL BOTTLE BEAMS Schedule and venue: April 19, 4 PM at SECB 201.

Dissertation Adviser:

  • Dr. Raphael A. Guerrero

Dissertation Panel:

  •  Dr. Nathaniel Hermosa II (NIP-UPD), Dissertation Examiner
  • Dr. Nathaniel Joseph Libatique (ECCE), Dissertation Examiner
  • Dr. Ma. Obiminda Cambaliza (Physics), Dissertation Reader
  • Dr. Quirino Sugon, Jr. (Physics), Dissertation Reader

Abstract

Abstract. Self-imaging beams consisting of three-dimensional intensity voids are generated via photorefractive volume holography. Reconstruction of a volume hologram recorded at 594 nm is performed with a Bessel read-out beam. The holographic output is similar in appearance to a Bessel beam, with the central spot oscillating between maximum and zero intensity over a propagation distance of 10 to 55 cm. The oscillation period for the on-axis intensity is 30 cm. The reconstruction is capable of self-healing, with a fully recovered central core after the beam propagates 40 cm. Dual-wavelength reconstruction at 632.8 nm produces an output beam with similar self-imaging and self-healing properties. A theoretical framework based on the interference of a plane wave and a Bessel beam simultaneously reconstructed from a volume hologram is able to describe our experimental results.

Note:

This dissertation is based on the following article: