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

Decision support system using near cloud for disaster and risk management: an interview with Dane Ancheta (BS APS-ACS 2017)

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“Design and development of decision support system using near cloud for disaster management and risk reduction” by E. D. Ancheta (right), J. A. Dela Cruz, and A. J. Domingo. Advisory committee: N. Libatique, PhD, G. Tangonan, PhD, D. Solpico, and D. Lagazo. Department of Electronics, Computer and Communications Engineering, Ateneo de Manila University.  Interlinks 13.0 was held last 5 May 2015, 1:00-5:00 p.m., at Convergent Technologies Center (CTC) Rm 413.

by Dane Ancheta and Quirino Sugon Jr

Dane Ancheta is a graduating student of BS Applied Physics and Applied Computer Systems (BS APS-ACS) of the Ateneo de Manila University and is one of the four last BS APS-ACS majors taking this course. After graduating High School from Ateneo de Zamboanga University in 2012, she went on to Ateneo de Manila University on a 100% financial aid scholarship, and a DOST merit scholarship. She worked at Manila Observatory (MO) for her physics thesis entitled “Temporal variability of localized rainfall events in metro manila over 2 years (2013-2014).” She also worked in Ateneo Innovations Center (AIC) for her Applied Computer Systems (ACS) thesis entitled “Design and development of decision support system using near cloud for disaster management and risk reduction.” Her co-workers are April Domingo (BS Computer Engineering) and Jane Dela Cruz (BS Electronics and Communications Engineering). They presented a poster of their work last 5 May 2017 at Interlinks 13.0, an annual research poster exhibition organized by the Ateneo Innovation Center for the School of Science and Engineering (SOSE) of Ateneo de Manila University. The abstract of their poster reads as follows:

In disaster scenarios, the lack of wireless internet or weak cellular network signal poses a very real threat to crucial information gathering and sharing. Using Near Cloud to store, load and upload information, this project has designed and developed decision support nodes that is able to to gather and distribute intelligent information before, during, and after disasters. These nodes are cached in with key information and data needed for disasters, i.e. maps, message reports, and images. The nodes serve as the command and control in early warning and disaster management systems. Key capabilities featured in for the decision support node include: broadcast mode that is broadcasting message via RF, mapping and visualization, data mining, near cloud, and the medical decision support system. A decision support node architecture is then developed and proposed as the main command and control as mobile kiosks. This mobile kiosk architecture is developed with a number of Raspberry Pi 3‘s, each of which are connected to perform and handle one application in a grid pattern.

Below is an interview with Dane Ancheta by Ateneo Physics News:

1. Why did you choose physics?

I could not imagine myself not taking physics.  I chose physics in all colleges that I applied. I don’t want to live my life wondering, “What if I had taken physics?”  

I love science. When I was a little girl, I would watch National Geographic. I’m naturally inquisitive. My teachers were great and supportive, but it was generally my curiosity that drove me to take physics.

2. Can you tell us about your your physics thesis?

I worked at the Manila Observatory for my thesis entitled “Temporal variability of localized rainfall events in metro manila over 2 years (2013-2014)”. My thesis adviser is Dr. James Simpas and Ma’am Genie Lorenzo. The data comes from the, at the time, newly installed dense network of weather stations around Metro Manila. For my thesis, I used at around 24 stations that are at a 5 km radius apart each. Basically, what I did was characterize localized rain events such as thunderstorms and precipitation; bigger events such as monsoons and typhoons are not included. We found out that the most amount of rainfall is experienced in Tayuman, Manila, though Makati City and Quezon City also experience high amounts of rainfall. The probability of rainfall is highest in middle and western Metro Manila, while it is lowest in southeastern Metro Manila. The study characterizes for the first time the areas of likelihood, rainfall and temporal correlation for the localized rain events in Metro Manila. It does not, however, explain such behavior, so we are still looking for an explanation  This work will definitely be continued or taken over.

For this thesis, all data were being sent to Manila Observatory. It is hard work to make sure that the data we are preparing are usable. We don’t get the data “clean”, that is why we have to check if they are healthy or anomalous. The data come from the weather stations that are exposed to the elements. But I did not have to go out as data from these stations were directly received by MO. I used QGIS and a little Python. I had learned many things working on this project.  This August 2017, we shall go to Singapore for the Asia Oceania Geoscience Society ( AOGS) conference. I shall present a poster of my physics thesis there. A good number from the research team is going because we have both the AQD-ITD (Air Quality DynamicsInstrumentation and Technology Development under Dr. Obiminda Cambaliza and Dr. James Simpas) and RCS (Regional Climate Systems under Dr. Narisma) researchers presenting.

3. Can you tell us about our Applied Computer Systems thesis?

In our 5th year, we start working on our ACS thesis under a thesis group with the ECCE (Electronics, Computer, and Communications Engineering) Department. I got involved in Ateneo Innovation Center where I became part of a big research team. On-going projects were laid out and discussed for us. The bigger research team is currently working on Multi-platform ICT Decision Support System UAVs , Vehicle Hubs, Ubiquitous Computing for Disaster Risk Reduction. We settled on the mission control end of the system. There are three of us in the thesis group- April Domingo is from CoE (Computer Engineering) and Jane Dela Cruz is from ECE (Electronics and Communications Engineering). Basically what we do is we receive all information from the responders and UAVs, and develop a system for this flow of information.

In the event of a disaster scenario, communication lines may be cut off due to damages to infrastructure, making information sharing difficult. Information that may be crucial for damage assessment and rescue operation would be lost or would not be transmitted effectively. In the research, we used the near cloud to store, load and upload information, this project has designed and developed decision support nodes that is able to gather and distribute intelligent information before, during, and after disasters.

We built upon the thesis of those who worked on near cloud before us. The previous team used Ionics plug computer, however, since this product was discontinued, we decided to make our own near cloud using Raspberry Pi 3 and terabyte hard drives. Our architecture is as follows: there is a raspberry pi node which serves as a serve/gateway. All other Raspberry Pi units with their corresponding applications are connected to this node. The architecture itself is an enabler: it enables all the applications to run in the same network.

The system also has near cloud capabilities. It acts as a cloud storage, but for a local network. This is done by configuring a Raspberry Pi for hotspot capabilities, while connecting the terabyte hard drive storage to it. Therefore, anyone can connect to the Raspberry Pi network and access all the files stored in the hard drive. Devices such as phones and laptops can access, download or upload (with permissions) files into the hard drive through this network as long as they are connected to the hotspot. The system also has drop box capabilities. This technology will be useful in evacuation centers. Given that communication lines could be cut off and there might not be enough power, it is hard to get information through. But the Raspberry Pi is low maintenance and low power, but powerful enough to make information available for access via the preloaded data in the hard drive. We tried to test this system by connecting about 10 devices, and it can work well in accessing files and streaming videos.

Another capability is our war room display with multiple screens where the interface is shown. This is how it works: responders and UAVs are on the ground send data to the mission control. The communication is done by radio frequency module at 900 MHz, which reach about 5km point to point without walls. If the messages from a responder is being sent, the message will be relayed to the different phones until it reaches mission control. For the responders sending a message to the mission control, the message and location of the responder will show up in the Google Maps API, so it will be easier to visualize where the responders are. This is how information will be received and instructions will be sent out from the mission control.

The most difficult part of the thesis are the times we have to learn the language then and there. We try to solve problems not encountered in class. We used a lot of different languages for different functions, such as C#, HTML, PHP and mySQL. We used Raspbian for the Raspberry pi the Windows 10 IoT (Internet of Things) core, Visual Studio for the interface, PHP for the chatroom, and Google API for the mapping. We have to learn using internet and the kindness of people.

4. Were you under a scholarship?

I am a Financial Aid scholar. Our kind benefactor is a BS APS-CE (Applied Physics / Computer Engineering) graduate and he gives scholarships to students who are pursuing the same course. I am lucky to have a benefactor like that who is passionate about supporting students interested in physics.

I am also a DOST scholar ever since sophomore year. So that makes three or four years. My failure in one class did not impact my scholarship that bad. It had to be put on hold for a time until I passed, but I did eventually get it back. The failure in that class is just a bump. I did study and did well in my other classes, so I did not feel like I was in danger. My QPI was 2.89 even with the failed class. I survived.

5. What are your plans for the future?

I am not sure yet if I want to take engineering or masters. I am thinking of going to China to do my masters, but I still have to consider the requirements, e.g. fixing papers and submissions. I am very nervous, since it is really an open field.  There is no one direct path to go to. There is so much freedom to choose from. So I have not decided yet on what to do.

6. Any parting words to our Physics majors?

The most difficult part of being a BS Physics/Computer Engineering major is the rigor that comes into the work. It is both a difficulty and a blessing. Not everybody undergoes that kind of rigor that is required of physics. We had to learn a lot: even failure is a learning process. I learned to shift focus from just getting good grades to learning something and growing in the course. I did fail one class: Electromagnetics. I try to look on the bright side and say it was not that bad because it pushed me to do better in my studies.

Physics and Computer systems go very well together. As a physicist, it is really important to work with computers and use them for your advantage. It was sad that the course had to be discontinued. We do learn to program using C++ in PS 130 Computational Physics; however I think it is not enough programming for physics. Even if the course does create excellent and competent students, after college they get into web develop or work in IT related fields. Now, there’s no ACS. It is a shame. Programming is so useful.  In today’s age, if you can program, you can hold the world on a string.

Stay curious. Be inquisitive. Never stop asking questions.

 

 

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.

Satellite systems and space development programs: a talk by Prof. Motoi Wada of Doshisha University

 

The Department of Physics of Ateneo de Manila University cordially invites you to

Art of Science and Engineering III: A Talk on Satellite Systems and Space Development Programs

by Prof. Motoi Wada (Applied Physics Laborary, Doshisha University)

  • Date: 16 January 2017
  • Time: 1:00-3:00 p.m.
  • Venue: SOM 211 (John Gokongwei School of Management)

Abstract: The previous talk covered a story of gravitational wave detection. It is a science supported by an advanced technology. We go out to interstellar space this time. There, sophisticated control systems determine trajectories of explorer satellites solving Newtonian mechanics problems that you learn in your classroom. Mathematical formulations visualize images of photon signals in invisible wavelength range from dark deep space. This talk will cover status of space development programs at both USA and Japan

Map:


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