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You searched for +publisher:"Clemson University" +contributor:("Dr. Steve Stuart"). Showing records 1 – 3 of 3 total matches.

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Clemson University

1. Jia, Zhe. Molecular Mechanics Studies of Protein Signaling and Conformation Change.

Degree: PhD, Chemistry, 2016, Clemson University

Physiology signals can be passed by proteins. Many protein signaling starts from ligand binding and undergoes conformation change of the receptors. Many cellular surface receptor proteins contain a Von Willebrand factor (vWF), which is a large multimeric glycoprotein present in blood plasma. This dissertation employed molecular dynamics (MD) simulation to investigate the binding and signaling process of several vWF type A proteins. Chapter 2 discussed the potential errors modeling and MD sampling methods, and evaluated the accuracy and precision of free energy calculation. An optimized sampling strategy was established to obtain the best computational efficiency. The strategy can be applied to a wide range of protein binding research. The following chapters investigated the binding and signaling process of anthrax receptors and integrins, which are vWF type A proteins. Binding mechanism, possibility of conformational change, and the role of metal ion in binding process, were analyzed and compared for two structurally highly similar anthrax receptor proteins, tumor endothelial marker 8 (TEM8) and capillary morphogenesis gene 2 (CMG2). The two highly similar proteins are the drug target for distinct diseases. The differences in these two processes were found can guide the further development of drug specifically targeting one of the proteins. A conformation change between open and closed conformation is known to exist in most vWF type A proteins, but has not been experimentally observed in the anthrax receptors. Chapter 5 investigated the binding and conformation change process of integrins using targeted molecular dynamics simulation, and compared with anthrax receptors. The key residues and correlated motions in conformation change process were revealed, which can serve as a reference to the development in small molecule inhibitors of the signaling process. Results further confirmed the difficulties of observing conformation change in anthrax receptors. Advisors/Committee Members: Dr. Brian Dominy, Committee Chair, Dr. Steve Stuart, Dr. Emil Alexov, Dr. Julia Brumaghim.

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Jia, Z. (2016). Molecular Mechanics Studies of Protein Signaling and Conformation Change. (Doctoral Dissertation). Clemson University. Retrieved from https://tigerprints.clemson.edu/all_dissertations/1727

Chicago Manual of Style (16th Edition):

Jia, Zhe. “Molecular Mechanics Studies of Protein Signaling and Conformation Change.” 2016. Doctoral Dissertation, Clemson University. Accessed October 31, 2020. https://tigerprints.clemson.edu/all_dissertations/1727.

MLA Handbook (7th Edition):

Jia, Zhe. “Molecular Mechanics Studies of Protein Signaling and Conformation Change.” 2016. Web. 31 Oct 2020.

Vancouver:

Jia Z. Molecular Mechanics Studies of Protein Signaling and Conformation Change. [Internet] [Doctoral dissertation]. Clemson University; 2016. [cited 2020 Oct 31]. Available from: https://tigerprints.clemson.edu/all_dissertations/1727.

Council of Science Editors:

Jia Z. Molecular Mechanics Studies of Protein Signaling and Conformation Change. [Doctoral Dissertation]. Clemson University; 2016. Available from: https://tigerprints.clemson.edu/all_dissertations/1727


Clemson University

2. Kulkarni, Dhruva. Metrology and Transport of Multiply Charged Ions.

Degree: PhD, Physics, 2017, Clemson University

The transport and interaction of singly- and multiply-charged ions with matter has been studied. The experiments were performed in an ultra-high vacuum environment. The low- and hyperthermal-energy ion beamline was used as a source of singly charged ions, while the CUEBIT facility was used as a source of multiply charged ions. The kinetic energy of the ion beam obtained from the CUEBIT is offset from the nominal value expected from the applied electrostatic potentials. These offsets were studied by measuring the kinetic energy of the beam using a retarding field analyzer (RFA). The offset was attributed to the space charge of the electron beam that is used to create the multiply charged ions. The charge density of the electron beam was varied by changing operational parameters of the electron beam, namely the electron beam current and the energy of the electron beam. Ion beams of Ar4+ and Ar8+ were extracted from the source and the offsets observed in the kinetic energy were related to the variation in the space charge potential of the electron beam. Measurements of these offsets, ranging from 100 eV/Q to 300 eV/Q, are significant and important for experiments that aim to utilize the potential energy of slow multiply charged ions. The transport of ions using capillaries has been studied to investigate the viability of ion-guiding as a means for a novel ion delivery mechanism. Results on transport through large bore capillaries (macrocapillaries) that probe both the geometric and ionguided mechanisms are presented. The angle- and position-dependent transport properties were found to depend on the material of the capillary (specifically, whether metal or insulator) and the geometry of the capillary. Rb+ ions at a kinetic energy of 1 keV were transmitted through metal and glass capillaries that were a few centimeters in length and a few millimeters in diameter. Oscillations were observed in the capillaries made of glass which were absent in the metal capillaries. Calculations based on the geometry of the experimental setup and kinematics of the ions showed that these oscillations could be attributed to the charge patches formed on the capillary walls. Electronic excitations in solids due to energetic ions at low kinetic energy were measured by using Schottky diodes. Hot electron currents measured at the backside of an Ag/n-Si Schottky diode due to ion bombardment on the frontside were found to depend on the kinetic energy (500 eV to 1500 eV) and angle of incidence (+/-30o) of the ion (Rb+) beam. A sharp upturn in the energy dependent yield is consistent with a kinetic emission model for electronic excitations utilizing the device Schottky barrier as determined from current-voltage characteristics. Backside currents measured for ion incident angle are strongly peaked about normal incidence. Accounting for the increased transport distance for excited charges at non-normal incidence, the mean free path for electrons in silver was found to be 5:2 +/- 1:4 nm, which is consistent with… Advisors/Committee Members: Dr. Chad Sosolik, Committee Chair, Dr. W. Rod Harrell, Dr. Endre Takacs, Dr. Steve Stuart.

Subjects/Keywords: capillary; EBIT; hot electron; schottky; space charge; stopping power

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Kulkarni, D. (2017). Metrology and Transport of Multiply Charged Ions. (Doctoral Dissertation). Clemson University. Retrieved from https://tigerprints.clemson.edu/all_dissertations/1919

Chicago Manual of Style (16th Edition):

Kulkarni, Dhruva. “Metrology and Transport of Multiply Charged Ions.” 2017. Doctoral Dissertation, Clemson University. Accessed October 31, 2020. https://tigerprints.clemson.edu/all_dissertations/1919.

MLA Handbook (7th Edition):

Kulkarni, Dhruva. “Metrology and Transport of Multiply Charged Ions.” 2017. Web. 31 Oct 2020.

Vancouver:

Kulkarni D. Metrology and Transport of Multiply Charged Ions. [Internet] [Doctoral dissertation]. Clemson University; 2017. [cited 2020 Oct 31]. Available from: https://tigerprints.clemson.edu/all_dissertations/1919.

Council of Science Editors:

Kulkarni D. Metrology and Transport of Multiply Charged Ions. [Doctoral Dissertation]. Clemson University; 2017. Available from: https://tigerprints.clemson.edu/all_dissertations/1919


Clemson University

3. Glatz, Brittany. Role of Surface Factors on Heterogeneous Ice Nucleation.

Degree: PhD, Chemical and Biomolecular Engineering, 2017, Clemson University

Heterogeneous ice nucleation is the primary pathway for ice formation. However, the detailed molecular mechanisms by which surfaces promote or hinder ice nucleation are not well understood. We present results from extensive molecular dynamics and forward flux sampling (FFS) simulations of ice nucleation near modified surfaces. The surfaces are modified to investigate the effects of different surface factors on the rate and mechanism of ice nucleation. We find that the surface charge distribution has significant effects on ice nucleation. We also investigate the interplay of surface lattice and hydrogen bonding properties in affecting ice nucleation. We find that lattice matching and hydrogen bonding are necessary but not sufficient conditions for observing ice nucleation at these surfaces. We correlate this behavior to the orientations sampled by the metastable supercooled water in contact with the surfaces. We find that ice is observed in cases where water molecules not only sample orientations favorable for bilayer formation but also do not sample unfavorable orientations. This distribution depends on both surface-water and water-water interactions and can change with subtle modifications to the surface properties. Our results provide insights into the diverse behavior of ice nucleation observed at different surfaces and highlights the complexity in elucidating heterogeneous ice nucleation. We also find that while the classical reaction coordinate of largest cluster size is a good measure of the transition between liquid water to ice, the addition of the neighboring liquid structure of the ice gives a better picture. We also have discovered that the structure of the second hydration layer gives a good representation of the reaction coordinate also. Advisors/Committee Members: Dr. Sapna Sarupria, Committee Chair, Dr. David Bruce, Dr. Rachel Getman, Dr. Mark Roberts, Dr. Steve Stuart.

Subjects/Keywords: ice; interface; nucleation; simulation; Chemical Engineering

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Glatz, B. (2017). Role of Surface Factors on Heterogeneous Ice Nucleation. (Doctoral Dissertation). Clemson University. Retrieved from https://tigerprints.clemson.edu/all_dissertations/2400

Chicago Manual of Style (16th Edition):

Glatz, Brittany. “Role of Surface Factors on Heterogeneous Ice Nucleation.” 2017. Doctoral Dissertation, Clemson University. Accessed October 31, 2020. https://tigerprints.clemson.edu/all_dissertations/2400.

MLA Handbook (7th Edition):

Glatz, Brittany. “Role of Surface Factors on Heterogeneous Ice Nucleation.” 2017. Web. 31 Oct 2020.

Vancouver:

Glatz B. Role of Surface Factors on Heterogeneous Ice Nucleation. [Internet] [Doctoral dissertation]. Clemson University; 2017. [cited 2020 Oct 31]. Available from: https://tigerprints.clemson.edu/all_dissertations/2400.

Council of Science Editors:

Glatz B. Role of Surface Factors on Heterogeneous Ice Nucleation. [Doctoral Dissertation]. Clemson University; 2017. Available from: https://tigerprints.clemson.edu/all_dissertations/2400

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