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Description
Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.
ContributorsEdlund, Petra (Author) / Takala, Heikki (Author) / Claesson, Elin (Author) / Henry, Leocadie (Author) / Dods, Robert (Author) / Lehtivuori, Heli (Author) / Panman, Matthijs (Author) / Pande, Kanupriya (Author) / White, Thomas (Author) / Nakane, Takanori (Author) / Berntsson, Oskar (Author) / Gustavsson, Emil (Author) / Bath, Petra (Author) / Modi, Vaibhav (Author) / Roy Chowdhury, Shatabdi (Author) / Zook, James (Author) / Berntsen, Peter (Author) / Pandey, Suraj (Author) / Poudyal, Ishwor (Author) / Tenboer, Jason (Author) / Kupitz, Christopher (Author) / Barty, Anton (Author) / Fromme, Petra (Author) / Koralek, Jake D. (Author) / Tanaka, Tomoyuki (Author) / Spence, John (Author) / Liang, Mengning (Author) / Hunter, Mark S. (Author) / Boutet, Sebastien (Author) / Nango, Eriko (Author) / Moffat, Keith (Author) / Groenhof, Gerrit (Author) / Ihalainen, Janne (Author) / Stojkovic, Emina A. (Author) / Schmidt, Marius (Author) / Westenhoff, Sebastian (Author) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2016-10-19
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Description
Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement.

Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.
ContributorsNogly, Przemyslaw (Author) / Panneels, Valerie (Author) / Nelson, Garrett (Author) / Gati, Cornelius (Author) / Kimura, Tetsunari (Author) / Milne, Christopher (Author) / Milathianaki, Despina (Author) / Kubo, Minoru (Author) / Wu, Wenting (Author) / Conrad, Chelsie (Author) / Coe, Jesse (Author) / Bean, Richard (Author) / Zhao, Yun (Author) / Bath, Petra (Author) / Dods, Robert (Author) / Harimoorthy, Rajiv (Author) / Beyerlein, Kenneth R. (Author) / Rheinberger, Jan (Author) / James, Daniel (Author) / Deponte, Daniel (Author) / Li, Chufeng (Author) / Sala, Leonardo (Author) / Williams, Garth J. (Author) / Hunter, Mark S. (Author) / Koglin, Jason E. (Author) / Berntsen, Peter (Author) / Nango, Eriko (Author) / Iwata, So (Author) / Chapman, Henry N. (Author) / Fromme, Petra (Author) / Frank, Matthias (Author) / Abela, Rafael (Author) / Boutet, Sebastien (Author) / Barty, Anton (Author) / White, Thomas A. (Author) / Weierstall, Uwe (Author) / Spence, John (Author) / Neutze, Richard (Author) / Schertler, Gebhard (Author) / Standfuss, Jorg (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor) / Department of Chemistry and Biochemistry (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / School of Molecular Sciences (Contributor)
Created2016-08-22
Description

Affective computing allows computers to monitor and influence people’s affects, in other words emotions. Currently, there is a lot of research exploring what can be done with this technology. There are many fields, such as education, healthcare, and marketing, that this technology can transform. However, it is important to question

Affective computing allows computers to monitor and influence people’s affects, in other words emotions. Currently, there is a lot of research exploring what can be done with this technology. There are many fields, such as education, healthcare, and marketing, that this technology can transform. However, it is important to question what should be done. There are unique ethical considerations in regards to affective computing that haven't been explored. The purpose of this study is to understand the user’s perspective of affective computing in regards to the Association of Computing Machinery (ACM) Code of Ethics, to ultimately start developing a better understanding of these ethical concerns. For this study, participants were required to watch three different videos and answer a questionnaire, all while wearing an Emotiv EPOC+ EEG headset that measures their emotions. Using the information gathered, the study explores the ethics of affective computing through the user’s perspective.

ContributorsInjejikian, Angelica (Author) / Gonzalez-Sanchez, Javier (Thesis director) / Chavez-Echeagaray, Maria Elena (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

Cryptojacking is a process in which a program utilizes a user’s CPU to mine cryptocurrencies unknown to the user. Since cryptojacking is a relatively new problem and its impact is still limited, very little has been done to combat it. Multiple studies have been conducted where a cryptojacking detection system

Cryptojacking is a process in which a program utilizes a user’s CPU to mine cryptocurrencies unknown to the user. Since cryptojacking is a relatively new problem and its impact is still limited, very little has been done to combat it. Multiple studies have been conducted where a cryptojacking detection system is implemented, but none of these systems have truly solved the problem. This thesis surveys existing studies and provides a classification and evaluation of each detection system with the aim of determining their pros and cons. The result of the evaluation indicates that it might be possible to bypass detection of existing systems by modifying the cryptojacking code. In addition to this classification, I developed an automatic code instrumentation program that replaces specific instructions with functionally similar sequences as a way to show how easy it is to implement simple obfuscation to bypass detection by existing systems.

ContributorsLarson, Kent Merle (Author) / Bazzi, Rida (Thesis director) / Shoshitaishvili, Yan (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

This paper is centered on the use of generative adversarial networks (GANs) to convert or generate RGB images from grayscale ones. The primary goal is to create sensible and colorful versions of a set of grayscale images by training a discriminator to recognize failed or generated images and training a

This paper is centered on the use of generative adversarial networks (GANs) to convert or generate RGB images from grayscale ones. The primary goal is to create sensible and colorful versions of a set of grayscale images by training a discriminator to recognize failed or generated images and training a generator to attempt to satisfy the discriminator. The network design is described in further detail below; however there are several potential issues that arise including the averaging of a color for certain images such that small details in an image are not assigned unique colors leading to a neutral blend. We attempt to mitigate this issue as much as possible.

ContributorsMarkabawi, Jah (Co-author) / Masud, Abdullah (Co-author) / Lobo, Ian (Co-author) / Koleber, Keith (Co-author) / Yang, Yingzhen (Thesis director) / Wang, Yancheng (Committee member) / Computer Science and Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

This paper is centered on the use of generative adversarial networks (GANs) to convert or generate RGB images from grayscale ones. The primary goal is to create sensible and colorful versions of a set of grayscale images by training a discriminator to recognize failed or generated images and training a

This paper is centered on the use of generative adversarial networks (GANs) to convert or generate RGB images from grayscale ones. The primary goal is to create sensible and colorful versions of a set of grayscale images by training a discriminator to recognize failed or generated images and training a generator to attempt to satisfy the discriminator. The network design is described in further detail below; however there are several potential issues that arise including the averaging of a color for certain images such that small details in an image are not assigned unique colors leading to a neutral blend. We attempt to mitigate this issue as much as possible.

ContributorsMasud, Abdullah Bin (Co-author) / Koleber, Keith (Co-author) / Lobo, Ian (Co-author) / Markabawi, Jah (Co-author) / Yang, Yingzhen (Thesis director) / Wang, Yancheng (Committee member) / Computer Science and Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

The NCAA is changing the current rules and regulations around a student-athlete’s name, image, and likeness. Previously, student-athletes were not allowed to participate in business activities or noninstitutional promotional activities. With the new rule changes, student-athletes will be able to engage in business activities related to their own name, image,

The NCAA is changing the current rules and regulations around a student-athlete’s name, image, and likeness. Previously, student-athletes were not allowed to participate in business activities or noninstitutional promotional activities. With the new rule changes, student-athletes will be able to engage in business activities related to their own name, image, and likeness. The goal of the team was to help “prepare athletes to understand and properly navigate the evolving restrictions and guidelines around athlete name, image, and likeness”. In order to accomplish this, the team had to understand the problems student-athletes face with these changing rules and regulations. The team conducted basic market research to identify the problem. The problem discovered was the lack of communication between student-athletes and businesses. In order to verify this problem, the team conducted several interviews with Arizona State University Athletic Department personnel. From the interviews, the team identified that the user is the student-athletes and the buyer is the brands and businesses. Once the problem was verified and the user and buyer were identified, a solution that would best fit the customers was formulated. The solution is a platform that assists student-athletes navigate the changing rules of the NCAA by providing access to a marketplace optimized to working with student-athletes and offering an ease of maintaining relationships between student-athletes and businesses. The solution was validated through meetings with interested brands. The team used the business model and market potential to pitch the business idea to the brands. Finally, the team gained traction by initiating company partnerships.

ContributorsSchulte, Brooke (Co-author) / Recato, Bella (Co-author) / Winston, Blake (Co-author) / Byrne, Jared (Thesis director) / Lee, Christopher (Committee member) / Kunowski, Jeffrey (Committee member) / Computer Science and Engineering Program (Contributor) / Dean, W.P. Carey School of Business (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

A project about developing software for learning turned into a project for learning about software development. The submission here only includes the journal. However, the journal has a link to the public GitHub repository containing the source code for the thesis. The source code implements a program to facilitate self-study

A project about developing software for learning turned into a project for learning about software development. The submission here only includes the journal. However, the journal has a link to the public GitHub repository containing the source code for the thesis. The source code implements a program to facilitate self-study by allowing the user to create quizzes. The journal contains my experience working on the project (both successes and failures).

ContributorsRoper, Branden Gerald (Author) / Miller, Phillip (Thesis director) / Zazkis, Dov (Committee member) / Computer Science and Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

Education has been at the forefront of many issues in Arizona over the past several years with concerns over lack of funding sparking the Red for Ed movement. However, despite the push for educational change, there remain many barriers to education including a lack of visibility for how Arizona schools

Education has been at the forefront of many issues in Arizona over the past several years with concerns over lack of funding sparking the Red for Ed movement. However, despite the push for educational change, there remain many barriers to education including a lack of visibility for how Arizona schools are performing at a legislative district level. While there are sources of information released at a school district level, many of these are limited and can become obscure to legislators when such school districts lie on the boundary between 2 different legislative districts. Moreover, much of this information is in the form of raw spreadsheets and is often fragmented between government websites and educational organizations. As such, a visualization dashboard that clearly identifies schools and their relative performance within each legislative district would be an extremely valuable tool to legislative bodies and the Arizona public. Although this dashboard and research are rough drafts of a larger concept, they would ideally increase transparency regarding public information about these districts and allow legislators to utilize the dashboard as a tool for greater understanding and more effective policymaking.

ContributorsColyar, Justin Dallas (Author) / Michael, Katina (Thesis director) / Maciejewski, Ross (Committee member) / Tate, Luke (Committee member) / Computer Science and Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

University Devils is a Founders Lab Thesis group looking to find a way for post-secondary institutions to increase the number of and diversity of incoming applications through the utilization of gaming and gaming approaches in the recruitment process while staying low-cost. This propelling question guided the group through their work.

University Devils is a Founders Lab Thesis group looking to find a way for post-secondary institutions to increase the number of and diversity of incoming applications through the utilization of gaming and gaming approaches in the recruitment process while staying low-cost. This propelling question guided the group through their work. The team’s work primarily focused on recruitment efforts at Arizona State University, but the concept can be modified and applied at other post-secondary institutions. The initial research showed that Arizona State University’s recruitment focused on visiting the high schools of prospective students and providing campus tours to interested students. A proposed alternative solution to aid in recruitment efforts through the utilization of gaming was to create an online multiplayer game that prospective students could play from their own homes. The basic premise of the game is that one player is selected to be “the Professor” while the other players are part of “the Students.” To complete the game, the Students must complete a set of tasks while the Professor applies various obstacles to prevent the Students from winning. When a Student completes their objectives, they win and the game ends. The game was created using Unity. The group has completed a proof-of-concept of the proposed game and worked to advertise and market the game to students via social media. The team’s efforts have gained traction, and the group continues to work to gain traction and bring the idea to more prospective students.

ContributorsDong, Edmund Engsun (Co-author) / Ouellette, Abigail (Co-author) / Cole, Tyler (Co-author) / Byrne, Jared (Thesis director) / Pierce, John (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05