Always make sure your beam is traveling in a straight line down the table; make sure it doesn't travel slightly to the left or right because at far distances little mistakes are amplified

When aligning a pinhole, first align the pinhole by adjusting the height and horizontal placement of the pinhole close to the element before it. Once it is aligned, measure the distance from the edge of the table to the pinhole. Then move the pinhole back to the desired distance from the prior optical element, making sure the pinhole is the same distance from the edge of the table, and then adjust the prior optical element until the beam travels through the pinhole

Steps for aligning a collimating lens:

1. Move the collimating lens back one focal length from the last optical element

2. Line up the lens so that the laser hits at approximately the center of the lens

3. There will be a reflection from the front and the back of teh lens, which will appear as a small and large dot. When these two dots are aligned with the incoming laser beam, the lens will be aligned. To get the dots at the same height, you adjust the height of the lens; to get the dots at the same place horizontally, you move the mirror to the left and right.

set up for sending the laser through the slide with arrangements of A

Once we got the set-up aligned, we shined the laser beam through the different arrangements of A's and observed the diffraction patterns. At first, I was suprised by the patterns we were getting, but as we went on it became more evident how they were formed. When we moved the paper close to the slide (about a foot away), we observed an x pattern for every arrangement of A's. When we moved further from the slide, different diffraction patterns arose that were related to the way the A's were arranged. For example, the row of A's produced bands of intensity similar to if there had been multiple slits. Dr. Noé' thought this was because at that the shorter distance we were in the far-field for the A, which caused the x diffraction pattern, but were not yet in the far-field for the overall pattern.

diffraction pattern from rectangular lattice of A's 1m and 2m from the slide

diffraction pattern from hexaganol lattice of A's 1m and 2m from the slide

diffraction pattern from random arrangement of A's 1m and 2m from the slide

diffraction pattern from a single row of A's 1m and 2m from the slide

After searching around for a bit, I discovered that these slides were designed by Ronald Bergesten for the American Association of Physics Teachers apparatus contest to demonstrate Laue diffraction. It sounds like both Laue diffraction and Bragg's law would be good things to learn more about.

---

July 10th, 2013

Today was Samantha's first day in the lab. She gave a really nice presentation on her research finding misclassified blue stars in the Sloan Digital Sky Survey, SDSS. After her presentation was finished, we had our weekly group meeting.

Dr. Noé told to us about his meeting with Kiko Galvez on Sunday. They talked about a number of topics; I was most interested by their conversation on spatial light modulators, SLMs. At this point, Dr. Noé is thinking of buying a Hamamatsu and a Cambridge Correlator SLM. The Hamamatsu is high-quality and will be reserved for special research projects, while the Cambridge Correlator is lower quality and will be good for exploration. Dr. Noé said that MATLAB is often used to control the SLMs, so I am going to try and learn as much as I can about MATLAB before the SLMs arrive. I found a tutorial produced by the company that created MATLAB that looks pretty useful.

I talked to Dr. Noé about my project; he encouraged me to stray away from the bacteria aspect of my proposed project and maybe focus on something like modelling scatter patterns using molded plastic or something else. Talking to him more, we came up with some more ideas, such as printing something out on a transparency sheet and observing its diffraction pattern and recreating objects using their diffraction patterns, also known as lensless imaging. Dr. Noé encouraged me to look further into diffraction by a 'whole lot of little things', identifying things with diffraction, and diffraction around soft edges. He suggested Euiwon Bae, John Sokolov, and Jenny Magnus might be good people to contact about my project.

---

July 9th, 2013

Optical Tractor Beams

Reading an issue of OPN, I stumbled across an article on optical tractor beams. An optical tractor beams is a beam of light that can pull an object toward the source of illumination. They are different from laser tweezers, which trap a particle, but do not move objects 'up' the laser beam.

At first glance optical tractor beams seem impossible; when the photons in a laser beam hit a particle, momentum is conserved and the particle travels forward away from the light source. If you think of the laser beam as a stream and the particle as a rock, it becomes obvious why it is counterintuitive that a particle should move up the laser beam. Just as rocks don't move upstream, it seems neither should particles move towards the source of a laser beam. Researchers, such as David Grier and Pavel Zemánek, have been able to experimentally realize optical tractor beams though and an even greater number of research groups have showed that there exists a theoretical basis for optical tractor beams.

set-up for the tractor beam created by the University of St Andrews and the Institute of Scientific Instruments

In an ordinary beam, each photon moves in the direction of the beam, so when a photon encounters an object it bounces directly back from the object and imparts the greatest possible forward force on the particle. For optical tractor beams though, a beam is used where the photons travel at an angle relative to the light source, so when the photons encounter an object, it imparts a reduced forward force. [One experiment used pseudo-Bessel beams, which were created by overlapping light waves at an angle relative to the desired direction of flow.] When the photons interact with the object, they polarize the material electrically and magnetically. The now polarized object then radiates and redirects the light. By adjusting the material properties of the object and the polarization and synchronization of the individual light waves in the beam, the object can radiate more light away from the light source than towards it. This pushes the particle towards the light source by overcoming the reduced push forward from the photons. So far the optical tractor beam has been used to move particles less than 500nm in size up to 30 μm. Optical tractor beams could have applications in cell sorting. Sadly, we don't have a laser with enough power to create one in the LTC.

net force on object from laser when photons approach object at an angle to the light source

I also read about solenoid beams, which were created by David Grier using a Hamamatsu spatial light modulator. I would be very interested in studying them once we get our SLM.

---

July 8th, 2013

I've been thinking a lot lately about how to turn my project concept, imaging bacterial colony scatter patterns, into a research project.

  What's the next step? What concepts do I have to understand before I start this project? What do   I need for the set up? What controls do I need to establish and what are the variables? How       many trials should I run?

These are just some of the many questions I've been mulling over in the back of my head for weeks. I've looked into the cameras that other studies used and we have comparable, although our CCD camera has a slightly larger pixel size and lower resolution. We also have lasers that operate at the same wavelength, 632 nm, as past studies used. The main thing holding me back from getting my project started today is culturing and growing the bacteria. In order to go from a bacterial sample to colonies, I would need to culture the bacteria, make and inoculate the plates, and incubate the sample.

Below are some of the kinks in my project that I will have to work out before my project becomes a reality and my tentative solutions:

SBU would have a fit if we grew bacteria in the LTC: I thought I had read a paper about imaging the scatter patterns of yeast colonies. Trying to relocate the paper for this entry though, I realized the paper I had discussed imaging the scatter patterns of single yeast cells, not colonies. Yeast colonies should still be capable of creating unique distinctive scatter patterns, but I would have no pictures to compare the images of the scatter pattern I captured to. I will have to talk to Dr. Noé about how to address this issue.

How to culture the bacteria: E. Bae et. al. reported culturing their bacteria in brain-heart infusion broth, BHI broth. They grew the culture for 15-18 hours at 37 ^o C, about 98.6 ^o F or the internal temperature of humans.

What dilution to use: When growing a culture, it is impossible to know the exact cell concentration. Instead of trying to do the possible, conventional practice is to use serial dilution, the stepwise dilution of a solution, to innoculate plates with successively less concentrated solutions. The ideal concentration to be able to image distinct colonies, while having the largest sample size is about 30-50 colonies per plate, E. Bae et. al.

How to plate the bacteria: E. Bae et. al. reported growing their bacteria on agar plates composed of 40 mg trypticase soy agar and 1 L Millipore water (just purified water). They boiled the mixture for 1 minute and then poured the plates, about 25 ml in a 88 mm round plate. After the plates dried, they reported inoculating the plates with 25 µl of bacterial culture. They inoculated the plate using the spread method.

How to grow the bacteria: E. Hirleman et. al. incubated the plates for 18-36 hours or until the diameter of the colony reached 1.2-1.5 mm at 37 ^o C.

How to get the materials I need: All of the materials I would need are fairly common place in a biology lab, minus possibly the specific brand of trypticase [different brands can affect colony growth]. We are not a biology lab though. It would take about two to three days to make the plates, cultures, and grow the colonies. I found out one of my friends is working in an oncology lab in the HSC, maybe his lab would have the resources I would need.

On a side note, I also found a paper that used Fresnel patterns to identify bacteria type, which could be another possible project, and Kevin also emailed me the photos of the diffraction patterns from Friday, so here they are:

triangular and square aperture diffraction pattern

July 5th, 2013

Fourier Optics

I've heard the name Fourier tossed around quite a lot in the pass year: in relation to Angela's project, mentioned by Abby Flowers, and most recently in reference to scatter patterns. So what is Fourier optics? Fourier optics is the study of classical optics using Fourier transforms, a method of describing functions in terms of sinusoids, which is reversible.

Fourier optics is used in optical information processing [spatial filtering, optical correlation, computer generated holograms], interferometry, optical tweezers, atoms, quantum computing, and in determining the phase of light intensity in a spatial frequency plane. It can also be used to describe Fraunhofer diffraction patterns, which are the Fourier transform of the diffracting object, like the ones Melia and I made [July 3rd entry]. Fourier optics also play an important role in the formation of scatter patterns in that scatter patterns are the Fourier transforms of the diffracting colonies. Fourier transforms describe an object in terms of the individual spatial frequencies that make it up. One website I found compared Fourier transforms to finding the recipe for a smoothie:

 "What does the Fourier Transform do? Given a smoothie, it finds the recipe.
 How? Run the smoothie through filters to extract each ingredient.
 Why? Recipes are easier to analyze, compare, and modify than the smoothie itself.
 How do we get the smoothie back? Blend the ingredients."

In not smoothie terms, the Fourier transform is breaks a function into its symmetrical, sinusoidal components. The 'goal' of Fourier transforms are to find the sources of an observed outcome. The smoothie-analogy might seem silly, but the article presents Fourier transforms in a very relatable way and I would recommend it to anyone trying to grasp what Fourier transforms are.

Melia and I created diffraction patterns for the square and triangle aperture again, but this time Kevin took photos of them on his nice camera, so hopefully I will be able to put those up soon. I also added betterexplained.com to my links page. Betterexplained.com is a website that tries to explain math in the least 'mathematical way' possible, pulling in lots of examples and diagrams, the website makes it really easy to understand the concepts behind the equations and terms.

July 3rd, 2013

Today was awesome! To start off the day, Melia and I shined a laser through different apertures and observed the diffraction patterns. We tried it with a circular, triangular, and square aperture. I haven't had a chance to work with lasers yet and I found it rewarding to plan out the path of the laser and then align the mirrors, lens, and apertures, so that the laser beam traveled straight through.

original setup for sending the laser through different apertures

The circular and triangular aperture diffraction patterns we made matched the patterns I have seen online. The square one did not look match the diffraction patterns I had seen online as well and looked more like a cluster of squares in the middle with some squares extending vertically and horizontally than a single bright square with dimmer squares extending horizontally and vertically. The circular aperture produced an Airy ring pattern; the triangular aperture created a distorted curved edge triangle pattern; and the square aperture created a central square cluster pattern with vertical and horizontal squares extending outwards. We dimmed all the lights in the LTC and were able to observe the diffraction pattern about 13.7 meters from the light source. [I apologize for the quality of my photos. I only had my cell phone camera on me at the time. Kevin said that he will bring his nice camera on Friday, so hopefully we will be able to capture better photos of the diffraction patterns then.]

diffraction pattern from: circular, triangular, and square aperture

After lunch, Marty visited. I talked to him some about my project: an earlier more simplified set-up I had found and the properties of agar. Melia and I then talked to him about the diffraction patterns we had made in the morning. After talking to him, we realized that we had set up the beam expander incorrectly. Marty showed us how to how to properly set it up. The problem with our original beam expander was the light rays weren't parallel to one another; this was fixed in our second attempt.

set up with corrected beam expander

After we fixed the set up, we reobserved the diffraction patterns. The circle and triangle looked pretty similar to the original patterns we had created. The diffraction pattern from the square aperture however looked more like the patterns I had seen online. [We were able to create a cleaner diffraction pattern than the one pictured below by adjusting the lenses in the beam expander, however I do not have a picture of the cleaned up pattern.]

diffraction pattern from the square aperture with corrected beam expander

Marty then worked with me and Melia to calculate where the second intensity peak should occur and how far away from the aperture is considered the far-field when using the square aperture. We calculated that the second intensity peak should occur about 8.8mm away from the center of the central intensity peak. We measured the distance to actually be about 9.5 mm, fairly close to our predicted value. We also calculated that over 0.775m from the aperture is considered the far-field.

       

---

July 2nd, 2013

Inspired by the directory at the top of Melia's An Introduction to Spatial Light Modulators, I decided to reformat my Beginner's Guide to Linux. The top directory should make it easier to maneuver the page and give a head's up as to what content is covered by the page. [As an added bonus, if students wan't to learn how to create a directory themselves, they can just look at the page's source code.] After that the formatting bug bit me, so I reformatted my links page and my research journal. [I'm not sure yet if I like the new format; I might change it back.]

I also found a paper which specifies the best type of agar to use as well as the optimal drying time of agar plates to capture unique scatter patterns for E. coli. I was surprised by the results of the paper (mainly how short the drying time was- 10 to 20 minutes). I'm glad I came across it because I hadn't thought about how drying time would affect the scatter patterns.

Fraunhofer Diffraction

I keep coming across the term Fraunhofer diffraction in my readings on bacterial scatter patterns. Dr. Noé has also mentioned the term to me once and brought up that sending a laser beam through different shaped apertures (circular, triangular, etc) and observing the diffraction patterns in the far-field should help me better understand the optics at work in forming scatter patterns and is a good supplement to my project.

Starting with the basics, when a beam of light is partly obstructed by an object, some of the light will bend around the object; this phenomenon is called diffraction. Fraunhofer diffraction occurs when both the light source and viewing plane are effectively infinitely far away from the obstruction. To be exact, it occurs when the distance between the object and the plane in which the pattern is observed is large enough that the phase difference between the light from the extremes of the aperture is much less than a wavelength, so that the individual contributions can be treated as if they are parallel (parallel ray approximation) or when w²/Lλ<<1. Fraunhofer diffraction takes place in either the far field or the focal plane of a positive lens. Ironically enough, Fraunhofer diffraction was named after Joseph von Fraunhofer, although he was not directly involved in the development of the theory.

In Fraunhofer diffraction, the wavefronts are planar. In the case of an aperture, the incident light being a plane wave makes it so that the phase of the light at every point in the aperture is identical. With lenses, all the rays have the same phase at the point of focus, which is equivalent to viewing the plane wave at infinity. The diffracted light after passing through a lens and aperture is a set of plane waves of varying orientation; this is because each plane wave was brought to focus at a different point in the focal plane with the point of focus being proportional to the x- and y- direction cosines, so that the positional variation in intensity is a map to the variation in intensity as a function of direction. These properties make adding up the contributions of the individual wavelets simpler. The diffraction pattern's shape and intensity are constant and independent of distance to the aperture or lens.

Rectangular aperture diffraction pattern: diffraction pattern in each direction is similar to that of a single-slit (rectangular peak with a series of horizontal and vertical fringes); the dimensions and spacing of the bands are related to the dimensions of the slit

Circular aperture diffraction pattern: Airy ring diffraction pattern (bright central circular disk surrounded by concentric dark and light rings)

Grating diffraction pattern: first off grating is any arrangement which imposes on incident waves a periodic variation of amplitude and/or phase; spectrum

July 1st, 2013

The first day of July, hooray! Today, I am going to focus on the optical phenomenon at play in creating scatter patterns. One study found the scattering patterns of three Listeria species to be composed of Airy ring patterns, secondary bright rings in the middle of the diffraction patterns, random speckle effects, and radial spokes. All of these features can be explained using optics.

Airy ring patterns

Airy ring patterns are made of a central bright circular region with a series of concentric dark and bright rings around it. Airy beams were named after George Biddel Airy; while he was not the first to observe the beams; he was the first to formulate a complete theoretical explanation of the beams. Airy beams are typically formed by uniformly illuminating a circular aperture; they can also be formed however by obstructing the middle of a beam with a circular object. This explains why Airy ring patterns were found in the scatter patterns formed by the Listeria species because the diameter of the Gaussian beam exceeds that of the colony, so that the colony acts as a circular obstruction. The portion of the beam that passes through the colony is attenuated (the intensity of the beam lessens), while the portion that does not pass through the colony is transmitted. This causes a phase- and amplitude- aperture effect producing an Airy ring pattern.

Knife-edge effect/Edge effect

When radiation hits a well-defined object, a portion of the incident radiation is redirected as a result of diffraction. This phenomenon is referred to as the knife-edge effect, or edge effect. The behavior of the redirected light can be explained using the Huygens-Fresnel principle, which says a well-defined object that obstructs an electromagnetic wave will act as a secondary source and create a new wavefront. This phenomenon is responsible for the bright ring in the center of the Listeria scatter patterns. In Listeria colonies, the "knife-edge" is created by the difference between the transmission coefficients at the center and edges of the colony. At the center of the colony, transmission is influenced by the thickness [read a greater number of bacteria to absorb and/or scatter light] and the fact that the bacteria nearest to the agar surface are the oldest and have excreted the greatest amount of extracellular matter meaning there is a higher mass density. At the edges, transmission is greater because there are fewer and younger bacteria.

Speckle patterns

Speckle patterns are intensity patterns produced by the mutual interference waves. They result when many waves with the same frequency, but varying phase and amplitude interfere creating a wave with randomly varying amplitude [intensity]. Researchers found circular spots in Listeria ivanovii's scatter patterns which mirrored the speckle effect. The spots in the scatter pattern were caused by numerous circular spots in the center part of the colony (observed via microscopy) that acted as random phase modulations causing the speckling.

Phase modulation

Phase modulation is a change in the phase of a wave. One of the many ways, the phase of a wave can be modulated is by traveling through a medium with internal density fluctuations. The radial spokes that appear in the scatter patterns of Listeria monocytogenes are believed to be caused by internal density fluctuations within the colony related to the multiplication and growth properties of the bacteria.

***I was able to find an earlier old paper [2006 vs 2007] by the same research group that had different optical reasoning about why certain patterns formed. I believe that the explanation I have above is a more accurate and correct optical description of why features within the scatter patterns formed, but I think it is important to know and understand different theories. They believe the Airy ring pattern was formed because the colony acted as a circular aperture [above version is much more plausible]; the dimmer rings were formed by the overall circular shape of the colony; the bright ring in the center was caused by two different effective focal lengths, result of radii of curvature and refractive index; and the radial spokes were sinc function intensity modulation in the azuthimal direction because of internal structures which were positioned in this direction (similar to the diffraction pattern from a plane wave on a rectangular aperture).***

Spatial light modulators, SLMs, are objects that modulate a beam in a spatially varying manner. Bacterial colonies, like SLMs, also vary the phase and amplitude of incident wavefronts sort of making bacterial colonies 'biological spatial light modulators'. The similarities between spatial light modulators and bacterial colonies have helped researchers gain an understanding of the way in which bacterial colonies modulate incoming light's phase and amplitude.

Spatial light modulators use techniques like varying the refractive indices, thickness, and alignment of molecules to selectively modulate light; variations in many of the same properties are at play when bacterial colonies modulate light. Understanding the effect of changing certain properties in a spatial light modulator on the far-field diffraction pattern can help us understand what properties are causing the formation of certain features in bacterial colonies' scatter pattern.

June 28th, 2013

We started out the day talking about the double slit experiment. I have been working on understanding the Huygens-Fresnel equations, so Dr. Noé helped clarify some of the concepts. Dr. Noé had us create an equation for the amplitude and intensity of circular waves. Below, the first equation is for the amplitude of a planar wave and the second, a spherical wave.

We talked some about binomial expansions and Euler's formula and some other useful equations and then Dr. Noé asked us to formulate an equation for the amplitude and intensity of a wave at a point P on a plane in the far-field. We found the amplitude and intensity to be equal to

Dr. Noé then told us about how laser beams generally have a divergence of 1 milliradian, which is very close to λ /d. The talk was helpful and helped clarify the physics behind waves for me. After the "lesson" ended, I talked to the Simons/LTC scholars about LaTex.

Modeling bacterial scatter patterns using scalar diffraction theory

Since bacteria colonies are large in comparison to compared the wavelength of the light and the scattered/diffracted fields are observed in the far field, scalar diffraction theory is sufficient to model bacterial scatter patterns. [For a more rigorous model, Maxwell's equations and vector diffraction theory can be used] Scalar diffraction theory encompasses a set of theories, such as Huygens' Principle, the Rayleigh-Sommerfield theory, the Kirchoff formulation, and the angular spectrum of plane waves that are used to create diffraction models.

June 27th, 2013

Slowly, but surely I am making progress understanding the optics behind scatter patterns. I discovered that complex amplitude is a complex number, of the form , where the amplitude, A, represents the magnitude and the phase, φ, represents the angle. The magnetic and electric fields in a light wave are harmonic oscillators, therefore their motion can be described by . Using Euler's formula, you can prove that sinusoids are mathematically equivalent to the sum of two complex-valued functions or the real part of one of the solutions to the equation, meaning:

[A proof of the second term can be found here.]

Focusing on the third term, you can see where Huygen's equation for the primary wavefront's complex amplitude, , came from. The U_o is the initial complex amplitude of the wave, which represents the Ae^(iθ) term; the 1/r_o arises from the intensity of light decreasing as it moves away from light source by a factor of 1/r, and the e^ikr_o term is equivalent to the e^iwt term.

I am now trying to understand the wave equation for the complex amplitude of the secondary waves, which involves the Fresnel-Kirchoff diffraction formula. Dr. Noé told me that the analytical proof for the complex amplitude of the secondary waves is overly complicated and that nowadays it can be proven pretty easily numerically [meaning I don't have to memorize the proof]. I did discover that the 1+cosx in the equation is a directionality constant, which was added to account for the fact that the wavelets only move forward and not backwards.

***On a side note, I found a "diary" of sorts after Dr. Noé mentioned to me about a graduate student's interactions with Hans Bethe and Gerry Brown that is very good so far.***

June 26th, 2013

Our presentations are today. I am nervous, but also excited because I'm really interested in identifying bacteria by their elastic light scattering patterns and I also think that many of the people attending the presentations won't know much about the topic, so I will have the opportunity to introduce it to them. After talking to Dr. Noé, I decided to include a bit about the algorithms utilized by the systems. My presentation is finished, so all that's left now is to present it. I found a nice article about how to give a good presentation. I also found a quote about giving presentations, "The amateur worries about what he is going to put in his speech; the expert worries about what he is going to leave out." I am still an amateur.

The presentations went pretty well. I learned something from every one. After the presentations, Dave Battin came in and showed us a projector he owns, which was about the size of an iPhone. It was amazing to see; the colors were very vivid and whatever the image stayed in focus regardless of the distance to the imaging plane. He was able to buy the projector for only $50 on eBay.

The type of projector he was using is known as a pico projector. They are handheld projectors, which are companion devices for products such as cameras, cell phones, and tablets. The projectors are able to conveniently and quickly project the content of their companion devices on to any surface. They usually utilize either an LED or laser light source.

Moving forward my goal is to understand the optics behind bacterial scatter patterns as completely as possible.

Huygen's Fresnel Principle

The Huygen's-Fresnel principle is a method for solving wave propagation problems. The original OPN article I read said that the Huygen's-Fresnel property can be used to model forward scatterometry. It is a modification of the Huygens' principle which explains that the amplitude of the secondary waves fall off by a factor of cos(θ), where θ is the angle between the normals to the original and secondary waves, and the secondary waves interfere with one another according to the superposition principle. The complex amplitude of the primary wave is given by:

where k is the wavenumber, 2π/λ, and r_o is the distance from the primary wave to the point source. The 1/r_o arises from the intensity of light dropping off by a factor of 1/r and the kr_o is equal to the phase changes. I believe that e^ikr_o represents the phase modulation that the wave undergoes and U_o is the initial complex amplitude.

The complex amplitude of the secondary wave is given by the equation:

where s is the distance between Q and P, -i/λ is a constant, S represents the surface of the sphere, and K(X) is an inclination factor equal to 1/2(1+cosx). I do not yet understand this equation.

June 25th, 2013

We started off today with Dr. Noé talking about the difference between interference and diffraction in relation to interference vs. diffraction patterns; terminology usage is inconsistent. After doing some research, I think I understand both terms better now. An interference pattern is the pattern that forms when two or more waves interact producing regions of constructive and destructive interfernce. A diffraction pattern is the interference pattern that is formed when two or more waves undergo diffraction. These definitions could account for the incosistent terminology usage because by these definitions, a difraction pattern is an interference pattern, but an interference pattern isn't automatically a diffraction pattern. The relationship is a lot like that of a rectangle and a square.

Our presentations are tomorrow, so I spent the majority of today putting together my powerpoint presentation (which I will upload to my website tomorrow). I am giving a presentation on Identifying bacteria by their light scattering patterns. I am pretty confident; I know all the material and have a lot of good graphics. I really hope the presentations go well!!! I also forwarded the paper on the mathematics behind scatter patterns to Dr. Noé, so hopefully he will be able to help me make sense out of it.

June 24th, 2013

Today was the high school students' first day in the lab. It was nice meeting them. We started the day with a breakfast for all the Simons scholars in the SAC. We then showed the students and their families the LTC. William's younger siblings came and they LOVED the optics demonstrations. It was exciting to see these young kids get excited about optics and learning. The little sister even said, "Learning is fun." It was very heart-warming to hear.

For lunch, we went to the Simons Center Cafe with Marty. After which, we talked to the students about their Wednesday presentations, lab notebooks, and webpages. We crafted titles for all of the student's presentations. I decided that the title of my presentation is going to be Identifying Bacteria by Their Light Scattering Patterns. Melia talked to the students about how to use their lab notebooks and I talked to them about their webpage. It went well. I am very excited for this summer. I edited my Beginner's Guide to Linux so that it now includes a link to the DoIT page where you can download an SSH client from Stony Brook.

On a side note, after talking to a friend, I gained a little more insight into the math behind elastic light scattering, but I still have a long way to go before I truly understand it.

June 21st, 2013

I'm on the search for an image processing software, which will be able to capture the scatter patterns from bacteria. When I was trying to find information on the CCD camera we have yesterday, I stumbled across an old LTC student's project. This student mentions using Scion for their project. I checked and this image processing software is still free. The newest version is compatible with Windows 7/8/Vista. Scion Image can be used to capture, display, analyze, enhance, measure, annotate, and output images. From what I've learned so far I think it would fit my purposes. I also found a program called ImageJ, which looks like it could be useful for finding colonies and alo determing the shape of them.

I am trying to understand the math behind modelling scatter patterns right now. It is extremely complicated, but I am confident that if I go home and think about it over the weekend I will be able to make some progress.

I made a diagram of the experimental set up described in a 2009 E. Bae et. al. paper.

Papers to read: Modeling light propagation through bacterial colonies and its correlation with forward scattering patterns ; Analysis of time-resolved scattering from macroscale bacterial colonies; Label-free detection of multiple bacterial pathogens using light-scattering sensor; Automated classification of bacterial particles in flow by multiangle scatter measurement and support vector machine classifier; System Automation for a Bacterial Colony Detection and Identifcation Instrument via Forward Scattering

June 20th, 2013

Portable Bacterial Identification System Based on Elastic Light Scatter Patterns

This paper outlines the specifications of a low-cost, environmentally-friendly, portable, and speedy microbial-identification system that relies on forward-scatterometry. The final system includes a nine pound 12" x 6" x 10.5" machine, which utilizes elastic light scattering to capture bacterial colony characteristics and delivers the colonies' classifications via wireless access. The device comprises of 2 CCD cameras, a rotational and translational stage, and a 635-nm laser diode. The system employs software algorithms, such as the Hough transform, 2D geometric moments, and the traveling salesman problem to count the number of colonies and calculate their circularity, to center the colonies, and to minimize the travel time between colonies. An "in-the-field" test was conducted by using the system to identify four different types of bacteria on both pure and mixed plates in a number of locations and was found to be between 95 and 100 percent accurate. The device has possible applications in biosecurity, food safety, and monitoring and preventing nosocomial infections, hospital-acquired infections.

The Rundown

Function: counts colonies and captures the colonies' forward scattering patterns to identify them

Physics behind it: incoming wavefront interacts with microscopic features of colonies and propagate to imaging plate, providing a unique scatter pattern

1. Cameras

   1. Used 2 PixeLINK PL-B741U cameras with 1280 x 1024 resolution and a 6.9 µm pixel size

      1. Imaging lens Tauron M118FM08 with f=8mm and 34 x 25.6^o viewing angle so that camera can view whole area of plate

   2. We have an Electrim EDC1000N with 658 X 496 resolution and 7.4 µm pixel size

2. Forward scatterometer

   1. Circular laser beam module λ=635 nm P=0.95mW

   2. 45 mirror

   3. Monochrome camera

      1. Natural-density filter to prevent saturation

3. Motorized stage that rotates in θ and R direction

   1. 2 stepper motors

   2. Step motor driver

   3. Electroluminescent screen placed under petri dish to provide back illumination

4. Computer

   1. Used a PC with a Pentium 4 processor, CPU 2.80 GHz, and 1 GB of RAM

      1. Images sent to custom built analysis software coded in visual C#, which centers the stage and initializes the system, counting, and locating bacterial colonies

There are three basic steps to correctly identify microbes:

1. Sample acquisition/preparation

2. Microbe detection

3. Microbe identification

The first scatterometers required manual positioning of beam and motion control to record forward-scattering signature. This would require less programming and materials and would be easier to execute for a research project.

Light Pollution

I've heard the term light pollution a number of times throughout the years, usually in reference to how you couldn't see the stars any longer. I wasn't really too concerned because I thought it only affected astronomers. I realize now that light pollution has been getting progressively worse and has a wide range of adverse effects on not only astronomy, but also animal and human health.

Astronomy

Light pollution is making it harder for astronomers to observe the stars. Having to contend with "sky glow", the increased brightness in the background sky caused by light pollution, Astronomers often have to observe celestial bodies for longer periods of time to reduce the noise-to-signal ratio or increasingly, travel to remote locations, like Antarctica, in order to view the celestial bodies they are studying.

Animals

I hadn't thought about how light pollution would affect living organisms; light pollution has been shown to disrupt a number of animal behaviors though, often at the expense of the animals life. Loggerhead turtles for example have evolutionarily adapted to head towards the brightest light source after hatching. Traditionally, this has been the moon and stars reflecting off the water; nowadays, it is often hotels or parking lots. The loggerhead babies journey towards the hotels and parking lots only to meet their maker in the form of a car or dehydration. Bugs also often fly into lights killing themselves in the process. This can have a negative effect on an ecosystem by disrupting the food chain. Birds have also lost their way while migrating tricked by the lights and songbirds have been known to crash into brightly lit buildings killing themselves.

Human health

Light suppresses the secretion of melatonin in humans. Melatonin has been linked to inhibiting cancer growth and inducing sleep. Light pollution also poses a hazard to drivers and also causes a higher risk of malaria because mosquitoes are attracted to the light.

***On a side note, I've noticed it has been taking longer for my journal to load, so I moved all of my spring journal entries into the spring 2013 section of my webpage. ***

June 19th, 2013

The Parallax Effect

Parallax is the difference in the apparent position of an object as viewed by the right and left eye. The parallax effect can be exploited to see 3D object. In the diagram below, the far left figure illustrates the path of light from an object directly in front of you into your eyes. While the diagram in the middle, shows how your eyes perceive two pictures of an object transposed on a projection plane the same as if the object were directly in front of you; the light paths between the center crossing points and the eyes are the same as they would have been if the ball were directly in front of you. Your eye does not distinguish a difference between these two objects. To achieve a 3D image though, each eye must only see one picture of the ball meaning that the dashed lines must be blocked, while the crisscrossing paths are allowed to pass [Situation illustrated in the far right figure]. This can be achieved by blocking the dashed lines with one's hands or by wearing horse blinder glasses.

The article I was reading went on to suggest four experiments one could perform to better understand the physics behind the parallax effect.

Experiment 1: What Controls How Far the Image Pops-Out?

1. Make two dots of the same size in Paint or Adobe Photoshop and place them about 10 cm apart from one another

2. Make a pair of horse blinder glasses[A template can be found in the article]

3. Open the flaps on the horse blinder glasses to about 30 degrees

4. Adjust your distance from the computer screen until the a dot appears 'out' of the screen

5. Gradually increase the distance of separation between the two dots; you should observe the image of the dot moving towards you until a point where the effect ceases

Looking at the diagram below, it is apparent that the farther apart the two dots are, the closer to you eyes the point of intersection between the two light paths become, thereby making the image of the object appear closer.

Experiment 2: Creating a 3D Image from the Left & Right Views of an Object

In order to create a 3D effect, the right and left view of a scene must be transposed on top of one another.

1. Take a picture of a scene

2. Move 30cm to the left and take a picture of the same scene

3. Place the two pictures side by side in an image editing program

4. Put on horse blinder glasses and observe as the images become 3D. [As an alternative, you can cross your eyes until you see four images and then slowly uncross them until you only see three images, focus on the middle image and it should appear 3D.]

Experiment 3: Encryption

1. View encrypted image[like one below] with horse blinder glasses

2. One aspect of the picture should jump out at you [In the picture I provided, it's JFK's birthplace.]

Experiment 4: Converting Your Laptop Computer into a 3D Display

As always, the best was saved for last. In this experiment, you will create a 3D display using polarized light. In order to complete this experiment, you will need:

1. A source of polarized light, such as the liquid crystal display of a laptop computer [The light from liquid crystal displays are already linearly polarized]

2. Two polarizer sheets

3. Clear cellophane, 25-microns thick, such as the kind used to gift wrap baskets [Cellophane is birefringent]

4. A stereoscopic pair of images (left and right view of image)

In this experiment, the polarization direction of light is rotated 90^o away from the polarization direction of the other half of the screen. A crisscross between the paths of light can be created by wearing polarizer glasses with the polarization direction of each lens varying by 90^o.

1. First orient the polarizers so that their directions of polarization are perpendicular to one another [You will be able to tell because almost no light will be transmitted].

2. Insert the cellophane sheet between the two polarizers and rotate ONLY the cellophane sheet; observe the variations in the intensity of light transmitted [If the light intensity does not vary, try another brand of cellophane]

3. Find the orientation of the cellophane at which the transmitted light is minimized; mark a line on the polarizer so that you remember the protrusion direction

4. Determine the direction of the polarization of light from the liquid crystal display by holding one of the polarizers in front of the screen and rotating it until you find maximum transmission

5. Cover the right half of the screen with cellophane oriented so that the protrusion marker is at a 45^o angle to the direction of polarization of the screen

6. Make your own polarizer glasses by matching the polarizer for the left eye to the polarizer covering the right side of the screen and the polarizer for the right eye to the polarizer covering the left side of the screen.

7. Display the stereoscopic image on your computer screen and watch as the image becomes 3D

Interested in learning more? Check out the links below:

Creating the Parallax Effect: OPN Article

Full Parallax 3D TVs

A 3D Coffee Break

An Introduction to 3D Images

3D Holographic Displays

We had a really nice pizza lunch today: the LTC group, Marty, James, and Seth. It was interesting to hear a little about what people were working on or interested in. We talked about secondary education, college, grad school, and which field of physics to go into. It was helpful for me to hear about other people's journey's through college and it helped me get to know everyone a little better.

I found a nice quote by David Mermin today:

My complete answer to the late 19th century question "what is electrodynamics trying to tell us?" would simply be this: Fields in empty space have physical reality; the medium that supports them does not.

Having thus removed the mystery from electrodynamics, let me immediately do the same for quantum mechanics: Correlations have physical reality; that which they correlate, does not.

June 18th, 2013

I created A Beginner's Guide to Linux today. It isn't an all-encompassing guide, but it includes many of the commands that I use on a day-to-day basis and think will be useful to the high school students working in the LTC this summer.

Dr Noé suggested that I read an article in the June 2013 edition of Physics Today on water in the atmosphere. Although, water only makes up 0.25% of the atmosphere, it plays a big role in determining how the Sun's energy is distributed through the atmosphere and across Earth's surface and the character of large-scale circulations. Water is so influential because of its unique physical and radiative properties; it is effective at interacting with radiation throughout most of the IR spectrum, which makes water the most important absorber of solar radiation in the lower atmosphere and its radiative effects also power the hydrological cycle. These properties make understanding water fundamental to understanding the atmosphere and climate. The authors of the paper argued that given the known properties of water, previous studies have overestimated the warming Earth will experience as a result of atmospheric CO₂ doubling, the climate sensitivity. They believe that much of what we don't understand about the climate and the atmosphere is linked to what we don't yet understand about water. In a separate article by the same authors published in Science magazine, they argue that the climate community has not given water its due diligence. They believe that inaccuracies in climate models can be reduced by better understanding the role of water in the atmosphere in phenomena like cloud formation, moist convection, and mixing.

June 17th, 2013

I read a paper entitled LaTex for the Horrified by Paul Brna today. [I was unable to find the document online] From talking to upperclassmen, it seems like LaTex is a good program to know. They have used LaTex to write lab reports, theses, and other papers for school. Therefore, I have compiled a page about formatting in LaTex.

I was reading more about labeling fruits and vegetables using low powered lasers, when I stumbled across the website for a company called Best. Best is a Norwegian-based company that uses the latest and most advanced in optical technologies to sort different products and materials across a number of industries. They employ a number of technologies to find defective and foreign objects within a product, including: Advanced Forign Material Detection (AMFD), cameras, lasers (detox, fluo, and shortwave infrared [SWIR]), Rear Ejection System [RES], hyperspectral, Hyperion, and X-rays.

Advanced Foreign Material Detector (AMFD)- designed for the detection of defects and foreign material that are often difficult to find because of similar structure or color characteristics; currently used in raisin and nut industry currently; potential to be used in any food industry

Cameras- Best has developed a high resolution camera with adapted spectrum; works in the visible, infrared, ultra violet, and other spectrum; multiple cameras can be placed at different angles to scan the product from many sides; has shape recognition; can differentiate between water and non-water based products; used for food and non-food applications (French fries, shrimp, vegetable, snacks, raw cotton, and plastics)

Hyperspectral- recognizes the scattering pattern of each type of produce and will remove anything without the target scattering pattern; measures different spectra; removes discolored, deformed, or foreign items; mainly used in food industry

Lasers- Best's most effective technology for maintaining product quality; able to sort based on color, structure, size, shape, chlorophyll content, water content, and biological characteristics

1. Detox- able to detect Aflatoxin, a highly-toxic substance, in nuts and dried fruits and remove the toxin; relies on on aflatoxin's distinctive scattering pattern to identify and remove it

2. Fluo- provides better contrast to detect color and texture differences in products with fluorescence features; can sort products with chlorophyll (peas, green beans, spinach) from those without (wood, plastic, glass)

3. Shortwave Infrared (SWIR)- range of wavelength in infrared used to detect water content of objects; used for frozen fruits and vegetables

X-rays- able to detect defects based on density differences; used on packaged products (nuts, canned vegetables and fruits); can be used to detect pits in cherries and olives

The research Best is doing is similar to many of the possible research project ideas I have come up with, in that the both are looking to create optical technologies with the capabilities of catergorizing things (elastic light scattering to identify bacteria, laser labeling, cartenoid-level detectors). I find the work Best is doing to be both interesting and innovative and I would be very interested in applying for a job at TOMRA (Best's mother company) after I finish my schooling.

June 14th, 2013

References

1. Robinson, J.p., B.p. Rajwa, E. Bae, V. Patsekin, A.m. Roumani, A.k. Bhunia, J.e. Dietz, V.j. Davisson, M.m. Dundar, J. Thomas, and E.d. Hirleman. "Using Scattering to Identify Bacterial Pathogens." Optics and Photonics News 22.10 (2011): 20-27. Print.

2. McGrath, Jane. "10 Costly Food Recalls" 12 March 2009. HowStuffWorks.com. http://www.howstuffworks.com/10-food-recalls.htm 14 June 2013.

3. Bloggs, Bill. Baby Bugbuster Project. 2011. Video. YoutubeWeb. 14 Jun 2013. http://www.youtube.com/watch?v=kDgh2xoEWIw.

June 13th, 2013

Dr. Metcalf gave the second part of his talk on entanglement today. He started off the talk by showing us a speech given by Joseph Eberly entitled, "When Malus Tangles with Euclid Who Wins?". In the talk, Dr. Eberly used the Bell inequalities to showcase the differences between classical and quantum systems. In classical systems, the Bell inequalities hold; Dr. Eberly demonstrated this using the probability of a penny, dime, and nickle landing on heads or tails. The following equation is an example of a Bell inequality. [The uppercase letters represent a heads while the lowercase letters represent a tails.]

Dr. Eberly then proved that after a sufficient number of trials this inequality will always hold true as demonstrated in the equations below.

The probability of any of the three above situations occurring is equal to 1/8, therefore the Bell inequality will be satisfied after a sufficient number of trials because . Flipping coins represents a classical system and so the Bell inequalities hold.

Eberly then explained that the Bell inequality can be violated by quantum systems. He showed this using the example of a photon polarization experiment using a Clauser inferometer (pictured below).

When you write the Bell inequality for this example, you get . This equation can be simplified down using trigonometric relations and the situation to get . By plugging in π/8 into the inequality, () you can see that the inequality is violated. This violation of the Bell inequalities arises from the fact that the Bell inequality is defined for systems where there only exist specific states. In our example though, the polarization state does not exist if we do not observe it therefore our example contains superposition states, or limbo states, where the photons are in both polarization states.

After the video, Dr. Metcalf went on to explain entanglement to us. Entanglement seems to a relationship between seemingly unrelated variables. With entanglement, if you know the value for one entangled variable, you know the value for the other entangled variable. He showed us an example of entanglement involving an atom and circularly polarized light. In his example, there existed a connection between the motion of the atom and the atom's original internal state. By knowing the motion of the atom, you could deduce the polarization of the absorbed light and the original internal state of the atom. Hopefully this graphic will clarify what I cannot.

Laser Labels for Fruits and Vegetables

The current method for tracking and identifying tainted fruits and vegetables is to use stickers. Stickers pose a problem though because they can fall off and can leave a sticky residue on the outside of the produce. Lasers hold the answer. Physicists have created a system which labels produce using an infrared laser to label onto produce its variety, price code, and where it was grown. The whole process only takes about 25 milliseconds and has proven safe. Sunkist is one of the first companies to adopt this new technology, purchasing the rights to it for their citrus products.

Lasers That Can Tell If You've Been Eating Your Fruits and Vegetables

Up until this point measuring biomarkers has often relied on obtaining blood, urine, or skin samples. Obtaining these samples can be painful, costly, cumbersome, and can sometimes expose the body to pathogenic organisms. Scientists have created a device which measures the cartenoid levels in the blood by bouncing a blue laser light off of the skin and using resonance Raman spectroscopy, RRS, to analyze the data. RRS works by measuring the changes in the energy levels of electrons in molecules after they have been excited. Cartenoids are an ideal subject for RRS because the compounds resonate very strongly and uniquely at a certain wavelength of light, which is uncharacteristic of the other compounds found in skin. The whole process takes about one minute and is completely painless.

This technology is the brain child of a nutritional epidemiologist and a laser physicist [a good example of how the lines between different disciplines of sciences are becoming increasingly fuzzy]. It has been known for decades that people that eat a high vegetable diet tend to have a yellowish tint in their skin that is particularly pronounced in their palms due to the build up of cartenoids. The device they have created take advantage of this fact. The device consists of a flexible fiber optic probe connected to a boxlike central machine. Their data so far has corresponded very well with cartenoid levels measured by serum and skin biopsy and with data collected from dietary self-report. The next step is to determine the half-life of cartenoid in the body and discover how changes in the diet affect cartenoid levels.

June 12th, 2013

Today was really exciting; there was a talk organized by Eden, a tour of Eden's lab, and a pizza lunch followed by a talk given by Dr. Metcalf.

Eden's lab was quite impressive. I hadn't realized that his research deals with quantum computing. After reading his website, I now realize that he is the head of the Quantum Information Technology Group at Stony Brook. His lab hopes find the quantum equivalents of the computer elements (logic gates, bits) we have now, which obey the laws of classical physics. Their first goal is to find a way to collect the information and then find a way to store said information. Below is a graphic illustrating the differences between bits and qubits, their quantum equivalents.

Dr. Metcalf gave the "first half" of his talk on entanglement today. His talk mostly just set the stage and put us in the right mind set for his talk on entanglement tomorrow. He is also going to show us a movie on entanglement tomorrow. Dr. Metcalf explained that Schroedinger believed that entanglement is the heart of quantum mechanics; it is what distinguishes between a classical and quantum system. Dr. Metcalf explained that common sense is a set of information that we acquire from growing up in a classical world, therefore quantum mechanics fundamentally defies common sense. Superposition states violate intuition because there is no classical analog. Quantum mechanics is better viewed as a highly theoretical and mathematical concept.

[Dr. Metcalf mentioned David Mermin in passing today. David Mermin is a great writer and I would highly suggest perusing his Reference Frame column for Physics Today.]

Bruise Detection on Tomatoes Based on the Light Scattering Image

If you've ever eaten a bruised tomato, you know that the quality is significantly reduced when bruised. Detecting bruises on tomatoes can often be difficult though because the changes in coloration are often tiny. Reducing bruising in the fruit and vegetable industries could have annual paybacks in the billions of dollars; it would also increase food safety by reducing the potential for microbial infestation.

This paper elaborated how one research group analyzed light scattering images from tomatoes to detect bruised tomatoes from unbruised ones with a 90% success rate; they did find however that accuracy was affected by the age of the tomatoes. Because the optical properties of biological tissue are dependent on the morphology of the tissue, when cell walls and membranes are broken down in the bruising process this causes the scattering [light scattering is when a portion of the radiation incident on a object is scattered back to the surface of incident and leaves the object near the point of incidence] properties of the produce to change.

June 11th, 2013

I created an ideas page today to keep track of possible research topics. I also updated my journal and read a number of papers on elastic light scattering.

Scattering

Scattering is the interaction between radiation and localized non-uniformities that causes radiation (such as light) to deviate from its straight trajectory. [Interestingly, reflections that undergo scattering are called diffuse reflections and unscattered reflections are called specular.] If I were to shine a red laser on yeast, I believe it would undergo Thomson scattering. Thomson scattering occurs when light is elastically scattered by charged particles. Elastic scattering occurs when the incoming and outgoing wavelength are identical.

Bacteria Size Determination by Elastic Light Scattering

Light scattering offers an in-situ method for identifying bacteria that could identify bacteria based on their size and shape. This method is advantageous to past methods of bacteria identification because the specimen does not have to be isolated and grown before being tested. "'The characteristic of each distinct microorganism that scatters is an essentially unique scattering pattern' due to the distinct biochemical nature and structure of each microorganism." It has been proven that the Rayleigh-Gans theory agrees with experimental values for the angular distribution of scattered light from bacteria. Forward scattering from cell suspensions has also been used to correlate internal structures and scattering properties. The angular and wavelength distribution of scattered light from bacteria is heavily dependent on its size and shape. Light scattering could advance society's ability to monitor the environment for microbial contamination, rapidly respond to biological contamination, and prevent the spread of disease.

Investigation of the Presence of Rod-Shaped Bacteria on Food Surface via Elastic Light Scattering

Our food supply is highly suspceptible to contamination from pathogenic microorganisms due to the way it is grown and processed. Contamination poses a risk to public health and agricultural companies that could stand to lose in the millions of dollars from food recalls. Food and healthcare industries are searching for methods to rapidly detect and identify pathogenic bacteria. Some methods that are currently being employed are: real-time PCR, recirculating immunomagnetic separation coupled with real-time PCR, standard culture methods, piezoelectric-excited millimeter-size cantilever, light scattering, Fourier transformed infrared spectroscopy, and Raman spectroscopy. These methods still leave much to be desired though.

Light scattering has been used for feature detection and identification because of its speed and accuracy. This method utilizes lasers to generate transmission and differentiate reflection signals from the incoming beam depending on the shape, thickness, or color of the sample being tested. Angle-resolved backscattering has been used to identify microcolonies of bacteria in flow by matching their known surface textures. Light scattering signatures from colonies have been proven to be reproducible and differentiable without losing their uniqueness. Currently, most of the optics-based quality control produce undergoes tests the firmness or sugar content using a single wavelength.

This study sought to investigate the presence and noise-to-signal ratio of rod-shaped bacteria (E. coli) on the surface of produce (tomato) using elastic scattering. The researchers found that the light component parallel to the plane of incidence's polarization was less sensitive to the background noise as the incident angle increased; while the perpendicular portion of the light's polarization became more sensitive to background noise as the incident angle increased. They were able to use elastic scattering to detect the presence of rod-shaped bacteria.

Elastic Light Scattering from Single Cells: Orientational Dynamics in Optical Trap

A complex spatial pattern is formed by a cell, which is dependent on the cell's size, shape, index of refraction, density, and morphology. Elastic light scattering may offer us more information on a cell's morphology than incoherent techniques (ex. fluorescence spectroscopy). Studying the scattered light from a cell at a number of different angles can reveal information about the cell's morphology. The ability to differentiate between minute differences in morphology could be used in the future to differeniate between different cell states.

In this experiment, the researchers were able to record light scattering patterns from three different types of bacteria. Their setup was subject to currents in the medium they were using causing distortions in the wavefront, the orientation of the cell to change, and at great enough depths even made it impossible to trap a single cell. The authors suggest that a follow up experiment be conducted in which multiple lasers are used to illuminate the cell from different directions so that the orientational dependence is averaged out and the accuracy of the light-scattering measurements is increased.

I also learned a very useful command today for Linux ctrl+ins-copy; shift+ins-paste [To the best of my knowledge, this command only works on PCs]

June 10th, 2013

Today was our first day as a real group. I had the pleasure of meeting Melia today and it was nice to see Casey again. I spent the majority of the morning today updating my journal because my computer sadly broke on Sunday. For lunch, we joined Dr. Metcalf's research group and Marty Cohen. It was nice to meet some other students who will be working here over the summer.

After lunch, we attended a talk organized by Eden on creating elementary quantum networks out of single atoms in optical cavities. The goal of the researcher's lab was to build quantum networks. Ideally this network would be composed of many identical nodes, so that any node is capable of doing any job it is tasked with, connected by quantum links. Quantum networks could have applications in quantum communication, quantum cryptography, and quantum networks between quantum computers.

Melia and I had dinner with Dr. Noé at Mirabelle Tavern today and talked about the summer, physics, and life in general. It was a lot of fun!

June 7th, 2013

Today is the last day of our "spring cleaning". I learned a lot about the lab and the instruments in it during our cleaning. I'm excited to meet Melia and see the other undergrads again on Monday. I read an article in OPN today on using elastic light scattering to identify bacterial pathogens that really interested me. I would definitely be interested in doing a project involving using elastic light scattering to identify "bacteria" because it would marry my love of biology, microscopy, and physics.

The diagram above on the left shows how photon-colony interactions change the wavefront characteristics. The picture on the right shows the ELS pattern from 30 different Listeria innocua colonies.

June 6th, 2013

Today was very exciting because I got to take apart an old projector. I had never taken a machine apart before today and found it really interesting to see the insides of the projector. The projector we took apart was a Sharp Thin Film Transistor Active Matrix Liquid Crystal Projector XG-2000U. Below is a diagram of how I think the light traveled through the projector.

In order for the projector to work:

1. There would have to be three different paths the light follows (one for each of the primary colors: red, blue, and yellow)

2. Each path would travel through only one lcd and lens

3. The paths would have to obey the laws of reflection and transmission.

June 5th, 2013

Dr. Noé and I had a long late lunch-early dinner at Mario's today, in anticipation of a planned late afternoon power outage that never took place, which gave us time to discuss a number of different physics topics. The first topic we discussed was why the periodic table looks the way it does.

The Periodic Table from a Physicist's Standpoint

The first thing we discussed is principal quantum number, N, which can be any positive integer. We then discussed orbital quantum numbers, ℓ, which have the values of 0 through N-1. Next, we talked about magnetic quantum numbers, m, which is the set of integers from -ℓ to +ℓ with 2ℓ+1 possible values. For each magnetic quantum number, there are also two spin quantum numbers, which arise from there being both an up and down spin for electrons. No two electrons can have identical quantum numbers as dictated by the Pauli Exclusion Principle.

From the diagram, you can see that for N=1, there is a maximum of 2 possible electrons. Looking at the periodic table, you can see that in the first row there are two elements, which corresponds to the maximum number of electrons when N=1. As you progress down the periodic table, it is important to note that the number of elements in a row corresponds to the maximum number of electrons for a given principal quantum state. When l=1 that corresponds to the s(sharp) shell; when l=1, it corresponds to the p(principal) shell; when l=2, it corresponds to the d(diffuse shell; lastly, when l=3, it corresponds to the f(fundamental) shell.

Adaptive Optics

Adaptive optics is a technology which allows machines to correct for nonhomogenity in real-time. Adaptive optics works by measuring the distortions in a wavefront and then correcting for said distortions. Adaptive optics is used in astronomical telescopes to correct for distortions in the atmosphere, microscopy, optical fabrication, and retinal imaging.

We also talked about singular optics, which is the study of optical vortices (also known as phase singularities) and complex light. Dr. Noé also talked to me about Michael Berry, one of the "fathers of singular optics". Complex light is a newer area of study, which I still am a little unclear on. It seems like the term is semi-superficial at this point and there is no common thread running between the different research projects. Dr Noé also told me about a past LTC student, Maanit, who wrote a program to find the intensity peak caused by coherent back scattering. After talking to Dr. Noé, I have many more ideas for possible project ideas.

June 4th, 2013

I read another OPN today and came across some more idea for projects.

Bessel Beams

Ideally, a Bessel beam is a non-diffracting light beam with an infinite number of rings that covers an infinite distance and requires an infinite amount of power. In reality, scientists can only approximate Bessel beams. (Researchers can create quasi-Bessel beams which are very similar to the theoretical ideal.) Bessel beams are capable of self-healing meaning the beam can be partially obstructed at one point, but will reform at a point further down the beam axis. Bessel beams have been around since the late nineteen-eighties and have a number of applications, including optical tweezers and precision drills; researchers are looking into the possibility of using Bessel beams to transfer information.

Airy Beams

Airy beams are light beams that transversely accelerate as they travel. The intensity peaks of these beams follow parabolic trajectories, much like the ballistics of projectiles. Due to their shape-preserving character, Airy beams are "self-healing" like Bessel beams, which has useful applications in turbulent and turbid systems. Some applications of thee beams are: particle and cell micromanipulation, laser micromachining, light-induced curved plasma channels, self-bending electron beams, and accelerating plasmons.

Dr. Noé and I had gelato for dessert. After ordering, I asked Dr. Noé if he knew how gelato was made; he did not and challenged me to find out how gelato is made.

June 3rd, 2013

Today marks the beginning of my summer research in the Laser Teaching Center. Dr Noé was a couple minutes late arriving to the lab, which worked out well for me because it gave me a chance to browse an OPN magazine. An article on optical vortices and another on edible lasers stood out.

Optical Vortices

Optical vortices are points of zero intensity within an optical field. In an optical vortex, light twists around its axis of travel like a corkscrew; extinction occurs at the axis. The article mentioned the some applications of vortices: synthetic aperture radar, electron microscopy, adaptive optics, and phase unwrapping. I would be interested in looking further into the applications of optical vortices as a possible project topic.

Edible Lasers

The laser that was the inspiration for this article wasn't truly edible (The laser was made out of a clear, unflavored gelatin and sodium fluorescein dye, which the author describes as "almost non-toxic".). The author however does speculate on a number of ways edible lasers could be created.

-Dyed lasers-If the laser made use of a dye, the dye would have to be nontoxic, soluble, and lasable in ethanol, so that in principle they could be drank. Just a droplet of the alcohol containing dye would by itself constitute an ideal laser. The author suggests that if you were to try to create an edible laser in this way (although, he does not endorse eating the laser), sodium fluorescein, coumarin, and sulforhodamines would be good dyes to start with because they tend to be less toxic.

-Salty lasers-A laser could also be created using lasing defects in crystal lattices, such as potassium chloride or sodium chloride. The author also speculates that lasing defects or impurity centers may also be present in rock candy or crystallized protein, which could allow those mediums to become lasable.

-Liquid lasers-The author notes that lasers can be made out of ethyl and methyl alcohol. Lasers can be made out of vodka, gin, and rum, but only lase on one line and lase rather weakly when compared to methyl alcohol.

Further Reading:

-"Laser Action of Dyes in Gelatin"

-"Edible Lasers and Other Deligts of the 1970's"

I mentioned "bubblegrams" to Dr Noé and he suggested that finding a novel way to measure the size of the bubbles within the crystal as a possible project idea.