First Day of the Program
Front row: Haviland Forrister, Ginny Cochran, Kara Fant, Ryan Leon, Xenia Fave, Bakari Hassan, Kevin Barkett
Back row: Alex Anderson, Suzanne Carter, Steven Wilcox
Last Night of the Program
This summer I worked under Franck Delmotte at Institut d'Optique. Concerned with developing optical components that reflect light that is absorbed by conventional mirrors, Prof. Delmotte's group fabricates multilayer mirrors for a wide range of applications. In general, a mirror is characterized by two quantities that depend on wavelength: (1) the reflectivity, or the outgoing light intensity divided by the incoming light intensity and the phase delay, which can roughly be thought of as a delay when the light hits the mirror but does not get reflected immediately. When the group is fabricating these mirrors, it is important to be able to characterize both the reflectivity and phase for a range of frequencies of light. It turns out that the reflectivity is easy to measure for a wide range of frequencies of light, but it is much more difficult to measure the phase delay. While there are some techniques that the lab uses to measure phase, the lab would benefit from a more simple technique of measuring phase.
By the suggestion of Sébastien de Rossi, a member of the group, I investigated the Kramers-Kronig relations. This mathematical relationship lets one calculate the phase for a particular frequency of light given the knowledge of the reflectivity for all frequencies of light. While this method seemed attractive in that it takes an easily measured quantity and allows one to calculate a hard to measure quantity, the Kramers-Kronig relations rely on additional information that cannot be measured easily. As for what I did day to day, I worked with matlab in order to obtain simulated data for these mirrors and I wrote code that tested the effectiveness of the Kramers-Kronig relations. I enjoyed discussing ideas with other members in the lab and I frequently bounced ideas off of Charles Bourassin-Bouchet when I was stuck. When I was not working, I had a fantastic time marveling at France's plethora of tourist attractions and getting acquainted with French culture by using my growing knowledge of French language.
This summer, I worked under Dr. Pierre Chavel and Dr. Franck Delmotte at Insitut d'Optique. My objective was to design multilayer mirrors composed of carbon and cobalt that would reflect hard x-rays. There are many materials that reflect hard x-rays, but they only reflect a small fraction of the indecent light. This was very difficult to accomplish because very little work has been done in designing these types of mirrors, which made it difficult to find information online or in books.
In order to produce these designs, I had to teach myself and use rigorous optics theories. I then read a book on multilayer structures for soft x-rays. I used my understanding of both to develop several multilayer designs and used IMD (commercial optics software) simulations to optimize my designs. Once these designs were approved by Dr. Delmotte, Dr. Evgueni Meltchakov and I created several single-layer, thin-film mirrors composed of carbon and cobalt in an effort to determine the deposition characteristics and rates of each element. Following the testing and analysis of these mirrors, we created 2 versions of one of my designs. In simulations, the mirror produced a reflectivity value of 61%. The fabricated mirror #1 only produced 0.00002% reflectivity. This was due to high layer roughness values of about 1.09 nm and layer thickness errors. In order to achieve maximum reflectivity, more optimization must be completed to minimize roughness and layer thickness errors.
I really enjoyed my summer research. It was very challenging, but equally enjoyable. I was able to experience both the theoretical and experimental approaches to research (design, simulation, fabrication, testing). I also gained extensive clean room experience. Everyone in the laboratory was very nice and helpful. I loved my visit to France. I learned lots of French, met people from all over the world, and hope to return as soon as possible!
Imaging of Single Protein/DNA Interactions by TIRF Microscopy
Ensuring the genomic integrity within living organisms is a vital function. NucS is a reparation protein that is responsible for cleaving off free single strand DNA, known as “flaps”, which are generated when an error occurs during the replication process. Flaps may also develop from exposure to ultraviolet radiation or as the result of a genetic mutation. The behavior and mechanism by which NucS operates and interacts with DNA is not well understood and formed the focus of this project. Using Total Internal Reflectance Fluorescence Microscopy and single particle tracking, we endeavored to determine the characteristic time for interactions between single proteins and single strand DNA in vitro. TIRF Microscopy allowed us to limit our observations to only the first 100 nm of our solution and thus increase our signal to noise ratio. Significant time was spent optimizing the surface treatment, and buffers with various concentrations of salt were tested in order to determine the most favorable conditions.
We first established the best concentration and incubation interval for each layer of the surface treatment in order to create a basic protocol. Changes were then made to the protocol as the results of our extensive experiments were analyzed. These included using a lab manufactured blocking reagent called BSA, in place of biotinylating our own solution. Another modification to our initial procedure resulted from our experiments with different buffers. We dissolved various concentrations of NaCl within each. Then for each prepared buffer we determined not only the characteristic behavior with the full surface treatment but also the characteristic time for photobleaching. Photobleaching is the phenomenon wherein a fluorophore ceases to admit light after several absorption and emission cycles because of changes to its covalent structure. When we can no longer observe a fluorophore, we cannot immediately state whether an interaction has ceased or if the protein has simply photobleached. In order to account for this possibility, we compared the distributions of photobleaching times to those of interactions. We found that a buffer with a concentration of 100 mM NaCl gave us the longest characteristic time of 4.10 seconds before photobleaching. However, a concentration of 500 mM NaCl catalyzed a greater number of reactions to take place. No significant difference could be discerned between the characteristic times for interactions within the different buffers.
In studying our curves for the probability distribution of dwell times of the protein on the DNA, it became obvious that the behavior we were observing was not a single step binding and unbinding. Had this been the case we would have expected to see a purely exponential function. To fit our data we developed a diffusion controlled model which provided a qualitative agreement with the characteristics of our experimental data curves. Thus we propose that NucS after initially binding to a single strand of DNA, diffuses along the flap until meeting the junction and unbinding. Further tests have been proposed including investigating the effects of glycerol and MnCl2 within the buffer and repeating the experiments with flaps composed of a greater number of base pairs. Additionally, in order to observe the cleaving step we intend to perform experiments within a heated solution containing Magnesium which will provide the conditions necessary for us to study this integral part of the interaction.
My project focused on using terahertz radiation to study various Iron oxide pigments underneath plaster on clay and plaster substrates for an upcoming research trip the group is taking to Turkey. Along with exploring various programs and methods to analyze our data, we learned several measurement techniques which we applied to mapping the electric field of the beam. We also learned the theory behind THz generation and detection which gave us a broader view of the system we were using. Working with Dr. Bianca Jackson at the C2RMF (Center for Research and Restoration of the French Museums) was an amazing experience and gave me a great perspective on grad school and the life of a research scientist.
Designing Multilayer Mirrors for Attosecond Pulses:
Attosecond science focuses on using pulses of ultrashort pulses of light to make new discoveries in science. An attosecond is defined as 10-18 seconds; a short enough time span to track electron movement in real-time. Attosecond photons are x-rays. This presents a problem when trying to manipulate these light pulses with mirrors because all materials readily absorb x-rays. Thus, lenses and conventional mirrors absorb all of the incident photons instead of transmitting or reflecting them. However, since multilayer mirrors have been successfully proven to reflect ultraviolet and extreme ultraviolet light, we will attempt to use them to reflect x-rays.
A multilayer mirror is a stack of thin films. Designing these mirrors requires selecting the best materials and optimizing layer thicknesses to maximize reflectivity and bandwidth. Bandwidth is an energy range of photons which can be reflected by the mirror. The goal of this project was to develop a mirror that is 10% reflective over a 40 electron Volt (eV) energy range in the “Water Window” energy range (281-530 eV). The key design principle in selecting materials is to alternate layers of a high and low absorbing material. Analysis of the laboratory’s extensive absorbance of materials database allowed me to determine that Platinum (high absorbing) and Scandium ( low absorbing) were the most promising and feasible choices between 300-400 eV.
I spent my summer simulating and optimizing reflectivity and bandwidth using different softwares, including MATLAB. I discovered the maximum theoretical reflecivity was 20%, but only over 3 eV. Increasing bandwidth was challenging because a slight increase in bandwidth will significantly decrease reflectivity. Nonetheless, I began by designing and simulating several configurations using a periodic layer thickness approach. The results were inadequate, prompting aperiodic layer arrangements to be explored. The results were more promising; a mirror with 9% over 15 eV was successfully optimized. Future work should include designing mirrors at energy ranges above 400 eV, adding roughness to my simulations to obtain more realistic reflectivities and considering new deposition techniques for improving mirror fabrication.
My name is Steven Wilcox. During the summer of 2011, I interned at Laboratoire pour l'Utilisation des Lasers Intenses (LULI). There high intensity CPA lasers are studied and used as tools to conduct physics research. The project I was assigned to was three parts. After the first week in Michigan and a weekend in Paris, the other iREU student and I were put in contact with our advisers and taken to the facilities where we would work. For the first two weeks at the lab, I was charged with reading and understanding two physics articles. One was on a plasma physics topic and the other described a technique known as SPIRITED, which stands for Self-Referenced Spectral Phase Interferometry Resolved in Time Extra Dimensional. Time was also spent observing a plasma physics experiment being conducted at the LULI's ELFIE facility and being given an orientation of various LULI facilities and the LULI 2000 laboratory where I was to work. After this preliminary period, I was assigned to calibrate lab equipment and continue my reading for the next two weeks while I waited to be given an optics table to build the project. The remaining three and a half weeks were spent building the SPIRITED setup so that, in the future, research could be done to further the measurement technique. Significant progress was made in this regard. Finally, last few days of the REU were spent preparing for the final presentation and taking care of other obligatory details. Needless to say, I learned a lot about applied optics and diagnostic techniques for CPA lasers during the 2011 summer. Furthermore, I found the experience as a whole to be both challenging and refreshing. The cultural, language, and scenic differences left few dull moments. There was always something to learn if you were willing to pay attention. Finally, if you are a prospective student, there are a few last comments I would like to make. Cité Internationale Universitaire de Paris is a fascinating place to live. While I was there I had the opportunity to meet great people from backgrounds that were very diverse. In addition, I made a conscious effort to get to know the city of Paris. Along with diligent work on your project, these things provide a very enriching opportunity!
This summer I studied Terahertz spectroscopy under Dr. J. Bianca Jackson at the C2RMF. My research project involved fresco work and field measurements. We used the terahertz spectroscopy system (Picometrix) to analyze clay and plaster fresco samples. The fresco samples had a lot of variation, containing different pigments under the plaster along with having different surface features. The goal of the fresco sampling was to find a pattern to decipher between the pigments hidden by the plaster. Using several image calculations, we were able to make images using our data to locate the pigment under the plaster. Some pigments were transparent while others were very reflective. Along with fresco work, we observed the shape of the terahertz beam (distribution of transmitter) by electric field mapping. Because the terahertz beam propagates as a diffractively spreading beam, we took measurements at different positions along the beam, rotating the receiver around the transmitter. This information will be useful for describing the interaction effects of the terahertz beam with different samples. Working at the Louvre was a once in a lifetime experience and I enjoyed every minute of it. I am very thankful for this research opportunity - I learned a lot about the research process, and am looking forward to continuing research in the future.
This summer, I went with an international REU program run by the University of Michigan to Paris, France, to study and do research at the Laboratoire d'Optique Appliquee at Ecole Polytechnique. My research specifically focused on laser plasma wakefield acceleration regimes, electron beam acceleration and characterization, and the creation and characterization of intense x-rays. I assisted in shooting a 1.3 J, 30-fs pulse laser, amplified to 100 TW, to create relativistic electron beams. On my own, I measured distances between experiment components; learned about relativistic plasma physics, radiation, and non-lineaer acceleration mechanisms; debugged several Matlab scripts; and characterized the electron beams resulting from H and He at various supersonic gas jet pressures, finding which pressures and which gases provided the "best" electron beam. And that was just my day job! On the weekends, I spent time walking through Paris and visiting the sites (the Latin Quarter has to be my favorite hang-out); taking a train to Geneva, Switzerland, over the weekend to see CERN and go to gruyere and chocolate factories; visiting Omaha Beach in Normandy; seeing several chateaus in the Loire Valley; attending a wine tasting that taught me about all the different wine regions in France; and taking pictures of at least seventeen cathedrals. (Did you know that some cathedrals have Norse mythology allusions in the architecture on the top of the columns?) All in all, it was a great experience, one for the books, and definitely one to last a lifetime.
This summer I studied laser proton acceleration under the supervision of Victor Malka and Mina Veltcheva at LOA. My project involved two experiments - proton beam generation using solid foil targets, and proton beam energy calibration. These were both carried out using the salle jaune laser, a ultrashort femtosecond laser with a power in terawatts. The solid target experiment varied target thickness and delay time between pulses and examined their effects on generated proton beam energies using a mass-charge spectrometer and a CCD camera. The calibration experiment required calibration of intensity plots obtained from a previous experiment's CCD results using MATLAB code I wrote myself. These results will be useful in calibrating pulse intensity distributions for future experiments. Laser particle acceleration has many potentially useful applications, particularly in the areas of cancer treatment and radiography and in potentially partially replacing conventional accelerators. My work in this summer's experiment may help to make this technology's applications more viable. I learned a great deal about research environments and independent inquiry and instruction, as well about the different phenomena that govern laser-induced particle beams. I appreciated the opportunity to work in such an interesting field and to explore parts of Paris and of France I had always hoped to see.
Building a Clock for Measuring Attosecond Laser Pulses
During this past summer, I participated in the summer REU program “Optics in the City of Lights” to perform research in experimental optics in Paris, France. The project goal was to measure the profile characteristics of temporal and spatial profile of an attosecond (~10-18s) laser pulse. Ultra short laser pulses, going as far down as femtosecond timescales, have been used before in biology and chemistry among other fields to “watch” and map out various different molecular interactions. They have been valuable in deriving a deeper understanding for how many different processes work on that level. Because of the brevity of attosecond pulses, they only last for about the time it takes for an electron to cross the length of an atom. This means that attosecond pulses have the potential for analyzing electron and atomic interactions which happen on a much briefer time scale than molecular interactions. In order to perform any experiments of this type, a detailed understanding of attosecond pulses’ spectral, spatial and temporal profiles, will be needed to understand how it will interact with its target. Furthermore, attosecond pulses are created when a laser pulse is focused onto a glass target at an extremely high intensity of at least 1016W/cm2. At this point, the laser has enough energy focused into a small enough spot that the surface becomes ionized and forms an optically reflective plasma layer. It is nonlinear interactions with this layer that ultimately create the attosecond pulses. Understanding how attosecond pulses are created and what shapes they take on will give insight into the realms of high intensity and plasma physics.
My work on the experiment can be broken up into two different parts: lab work with the laser system and work on the target feedback system. Because of the complexity of the laser system required to create the attosecond pulses, daily maintenance was required to ensure everything was aligned correctly. So much of my time was spent working with other members of the lab in getting it ready for experiments. In addition to aligning the laser, we also focused the parabola used to create the attosecond pulses, changed the glass target face, added more detectors, and installed an interferometer. While performing the actual experiments, I typically helped with recording data and adjusting some of the variable parameters. The second part of my job was to improve the stability of the glass target face. Because of the complexity in the experiment to measure the temporal profile, it requires nanometer scale stability in the glass target face and they had to use a camera to watch the target face. The camera they had been using was too slow to accurately determine the stability of the target face. I worked with a new camera’s software to integrate it into the feedback system and optimize its speed. While I managed to successfully set up the system, I did not have time to make major improvements before the end of the program.