Matching Items (659)
Description
As robots become more prevalent, the need is growing for efficient yet stable control systems for applications with humans in the loop. As such, it is a challenge for scientists and engineers to develop robust and agile systems that are capable of detecting instability in teleoperated systems. Despite how much

As robots become more prevalent, the need is growing for efficient yet stable control systems for applications with humans in the loop. As such, it is a challenge for scientists and engineers to develop robust and agile systems that are capable of detecting instability in teleoperated systems. Despite how much research has been done to characterize the spatiotemporal parameters of human arm motions for reaching and gasping, not much has been done to characterize the behavior of human arm motion in response to control errors in a system. The scope of this investigation is to investigate human corrective actions in response to error in an anthropomorphic teleoperated robot limb. Characterizing human corrective actions contributes to the development of control strategies that are capable of mitigating potential instabilities inherent in human-machine control interfaces. Characterization of human corrective actions requires the simulation of a teleoperated anthropomorphic armature and the comparison of a human subject's arm kinematics, in response to error, against the human arm kinematics without error. This was achieved using OpenGL software to simulate a teleoperated robot arm and an NDI motion tracking system to acquire the subject's arm position and orientation. Error was intermittently and programmatically introduced to the virtual robot's joints as the subject attempted to reach for several targets located around the arm. The comparison of error free human arm kinematics to error prone human arm kinematics revealed an addition of a bell shaped velocity peak into the human subject's tangential velocity profile. The size, extent, and location of the additional velocity peak depended on target location and join angle error. Some joint angle and target location combinations do not produce an additional peak but simply maintain the end effector velocity at a low value until the target is reached. Additional joint angle error parameters and degrees of freedom are needed to continue this investigation.
ContributorsBevilacqua, Vincent Frank (Author) / Artemiadis, Panagiotis (Thesis director) / Santello, Marco (Committee member) / Trimble, Steven (Committee member) / Barrett, The Honors College (Contributor) / Mechanical and Aerospace Engineering Program (Contributor)
Created2013-05
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Description
Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the

Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergent evolution.
ContributorsLi, Dianfan (Author) / Stansfeld, Phillip J. (Author) / Sansom, Mark S. P. (Author) / Keogh, Aaron (Author) / Vogeley, Lutz (Author) / Howe, Nicole (Author) / Lyons, Joseph A. (Author) / Aragao, David (Author) / Fromme, Petra (Author) / Fromme, Raimund (Author) / Basu, Shibom (Author) / Grotjohann, Ingo (Author) / Kupitz, Christopher (Author) / Rendek, Kimberley (Author) / Weierstall, Uwe (Author) / Zatsepin, Nadia (Author) / Cherezov, Vadim (Author) / Liu, Wei (Author) / Bandaru, Sateesh (Author) / English, Niall J. (Author) / Gati, Cornelius (Author) / Barty, Anton (Author) / Yefanov, Oleksandr (Author) / Chapman, Henry N. (Author) / Diederichs, Kay (Author) / Messerschmidt, Marc (Author) / Boutet, Sebastien (Author) / Williams, Garth J. (Author) / Seibert, M. Marvin (Author) / Caffrey, Martin (Author) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2015-12-17
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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
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Description

Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We

Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Moreover, the double flow-focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improved operation and characteristics of these devices.

ContributorsOberthuer, Dominik (Author) / Knoska, Juraj (Author) / Wiedorn, Max O. (Author) / Beyerlein, Kenneth R. (Author) / Bushnell, David A. (Author) / Kovaleva, Elena G. (Author) / Heymann, Michael (Author) / Gumprecht, Lars (Author) / Kirian, Richard (Author) / Barty, Anton (Author) / Mariani, Valerio (Author) / Tolstikova, Aleksandra (Author) / Adriano, Luigi (Author) / Awel, Salah (Author) / Barthelmess, Miriam (Author) / Dorner, Katerina (Author) / Xavier, P. Lourdu (Author) / Yefanov, Oleksandr (Author) / James, Daniel (Author) / Nelson, Garrett (Author) / Wang, Dingjie (Author) / Calvey, George (Author) / Chen, Yujie (Author) / Schmidt, Andrea (Author) / Szczepek, Michael (Author) / Frielingsdorf, Stefan (Author) / Lenz, Oliver (Author) / Snell, Edward (Author) / Robinson, Philip J. (Author) / Sarler, Bozidar (Author) / Belsak, Grega (Author) / Macek, Marjan (Author) / Wilde, Fabian (Author) / Aquila, Andrew (Author) / Boutet, Sebastien (Author) / Liang, Mengning (Author) / Hunter, Mark S. (Author) / Scheerer, Patrick (Author) / Lipscomb, John D. (Author) / Weierstall, Uwe (Author) / Kornberg, Roger D. (Author) / Spence, John (Author) / Pollack, Lois (Author) / Chapman, Henry N. (Author) / Bajt, Sasa (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2017-03-16
Description

Long distance travel around the globe can potentially be revolutionized with the use of an intercontinental rocket that uses low earth orbit as its medium. This transport system can increase growth in many new businesses like tourism travel between the continents. This research evaluates the technical and non-technical possibilities

Long distance travel around the globe can potentially be revolutionized with the use of an intercontinental rocket that uses low earth orbit as its medium. This transport system can increase growth in many new businesses like tourism travel between the continents. This research evaluates the technical and non-technical possibilities of using a double-stage reusable rocket, where the second stage is also a reusable, rocket-powered passenger vehicle using a low earth orbit space journey with a stabilized re-entry method that ensures passenger comfortability. A potential network of spaceports spanning the globe is postulated within a range of 4,000 km to 8,000 km(2,160 nm to 4,320 nm) of each other, and each located within an hour by any other means of ground transport to population hubs greater than four million. This will help further connect the world as the journey from one major city to another would take at most an hour, and no point on the habited continents would be more than 4,000 km(2,160 nm) from a spaceport. It is assumed that the costs of an international first class flight ticket are in the thousands of dollars range showing how there is a potential market for this type of travel network. The reasoning and analysis, through a literature review, for an intercontinental rocket vehicle is presented along with the various aspects of the possibility of this kind of travel network coming to fruition in the near future.

ContributorsRanganathan, Anirudh (Co-author) / Karthikeyan, Sayish (Co-author) / Takahashi, Timothy (Thesis director) / Niemczyk, Mary (Committee member) / Mechanical and Aerospace Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

Long distance travel around the globe can potentially be revolutionized with the use of an intercontinental rocket that uses low earth orbit as its medium. This transport system can increase growth in many new businesses like tourism travel between the continents. This research evaluates the technical and non-technical possibilities

Long distance travel around the globe can potentially be revolutionized with the use of an intercontinental rocket that uses low earth orbit as its medium. This transport system can increase growth in many new businesses like tourism travel between the continents. This research evaluates the technical and non-technical possibilities of using a double-stage reusable rocket, where the second stage is also a reusable, rocket-powered passenger vehicle using a low earth orbit space journey with a stabilized re-entry method that ensures passenger comfortability. A potential network of spaceports spanning the globe is postulated within a range of 4,000 km to 8,000 km(2,160 nm to 4,320 nm) of each other, and each located within an hour by any other means of ground transport to population hubs greater than four million. This will help further connect the world as the journey from one major city to another would take at most an hour, and no point on the habited continents would be more than 4,000 km(2,160 nm) from a spaceport. It is assumed that the costs of an international first class flight ticket are in the thousands of dollars range showing how there is a potential market for this type of travel network. The reasoning and analysis, through a literature review, for an intercontinental rocket vehicle is presented along with the various aspects of the possibility of this kind of travel network coming to fruition in the near future.

ContributorsKarthikeyan, Sayish Priya (Co-author) / Ranganathan, Anirudh (Co-author) / Takahashi, Timothy (Thesis director) / Niemczyk, Mary (Committee member) / Mechanical and Aerospace Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

This paper outlines the design and testing of a z-scan spectrometer capable of measuring the third order refraction index of liquids. The spectrometer underwent multiple redesigns, with each explored in this paper with their benefits and drawbacks discussed. The first design was capable of measuring the third order

This paper outlines the design and testing of a z-scan spectrometer capable of measuring the third order refraction index of liquids. The spectrometer underwent multiple redesigns, with each explored in this paper with their benefits and drawbacks discussed. The first design was capable of measuring the third order refraction index for glass, and found a value of 8.43 +- 0.392 x 10^(-16) cm^2/W for the glass sample, with the literature stating glass has a refraction index between 1-100 x 10^(-16) cm^2/W. The second design was capable of measuring the third order refraction index of liquids, and found values of 1.23 $\pm$ 0.121 $\e{-16}$ and 9.43 +- 1.00 x 10^(-17) cm^2/W for water and ethanol respectively, with literature values of 2.7 x 10^(-16) and 5.0 x 10^(-17) cm^2/W respectively. The third design gave inconclusive results due to extreme variability in testing, and and the fourth design outlined has not been tested yet due to time constraints.

ContributorsClark, Brian Vincent (Author) / Sayres, Scott (Thesis director) / Steimle, Timothy (Committee member) / Keeler, Cynthia (Committee member) / School of Molecular Sciences (Contributor) / Department of Physics (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

This research endeavor explores the 1964 reasoning of Irish physicist John Bell and how it pertains to the provoking Einstein-Podolsky-Rosen Paradox. It is necessary to establish the machinations of formalisms ranging from conservation laws to quantum mechanical principles. The notion that locality is unable to be reconciled with the quantum

This research endeavor explores the 1964 reasoning of Irish physicist John Bell and how it pertains to the provoking Einstein-Podolsky-Rosen Paradox. It is necessary to establish the machinations of formalisms ranging from conservation laws to quantum mechanical principles. The notion that locality is unable to be reconciled with the quantum paradigm is upheld through analysis and the subsequent Aspect experiments in the years 1980-1982. No matter the complexity, any local hidden variable theory is incompatible with the formulation of standard quantum mechanics. A number of strikingly ambiguous and abstract concepts are addressed in this pursuit to deduce quantum's validity, including separability and reality. `Elements of reality' characteristic of unique spaces are defined using basis terminology and logic from EPR. The discussion draws directly from Bell's succinct 1964 Physics 1 paper as well as numerous other useful sources. The fundamental principle and insight gleaned is that quantum physics is indeed nonlocal; the door into its metaphysical and philosophical implications has long since been opened. Yet the nexus of information pertaining to Bell's inequality and EPR logic does nothing but assert the impeccable success of quantum physics' ability to describe nature.

ContributorsRapp, Sean R (Author) / Foy, Joseph (Thesis director) / Martin, Thomas (Committee member) / School of Earth and Space Exploration (Contributor) / Department of Physics (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

Titanium has been and continues to be a popular metal across any form of manufacturing and production because of its extremely favorable properties. In important circumstances, it finds itself outclassing many metals by being lighter and less dense than comparably strong metals like steel. Relative to other metals it has

Titanium has been and continues to be a popular metal across any form of manufacturing and production because of its extremely favorable properties. In important circumstances, it finds itself outclassing many metals by being lighter and less dense than comparably strong metals like steel. Relative to other metals it has a noteworthy corrosion resistance as it is stable when it oxidizes, and due to the inert nature of the metal, it is famously hypoallergenic and as a result used in a great deal of aviation and medical fields, including being used to produce replacement joints, with the notable limitation of the material being its cost of manufacturing. Among the variants of the metal and alloys used, Ti6Al4V alloy is famous for being the most reliable and popular combination for electron beam manufacturing(EBM) as a method of additive manufacturing. <br/>Developed by the Swedish Arcam, AB, EBM is one of the more recent methods of additive manufacturing, and is notable for its lack of waste by combining most of the material into the intended product due to its precision. This method, much like the titanium it is used to print in this case, is limited mostly by time and value of production. <br/>For this thesis, nine different simulations of a dogbone model were generated and analyzed in Ansys APDL using finite element analysis at various temperature and print conditions to create a theoretical model based on experimentally produced values.

ContributorsKauffman, Jordan Michael (Author) / Ladani, Leila (Thesis director) / Razmi, Jafar (Committee member) / Mechanical and Aerospace Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05