Matching Items (66)
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Description
Proteins continually and naturally incur evolutionary selection through mutagenesis that optimizes their fitness, which is primarily determined by their function. It is known that allosteric regulation alters a protein's conformational dynamics leading to functional changes. We have computationally introduced a mutation at a predicted regulatory site of a short, 46

Proteins continually and naturally incur evolutionary selection through mutagenesis that optimizes their fitness, which is primarily determined by their function. It is known that allosteric regulation alters a protein's conformational dynamics leading to functional changes. We have computationally introduced a mutation at a predicted regulatory site of a short, 46 residue-long, protein interaction module composed of a WW domain and corresponding polyproline ligand (PDB id: 1k9r). The dynamic flexibility index (DFI) was computed for the binding site of the wild type and mutant WW domains to quantify the mutations effect on the rigidity of the binding pocket. DFI is used as a metric to quantify the resilience of a given position to perturbation along the chain. Using steered molecular dynamics (SMD), we also measure the effect of the point mutation on allosteric regulation by approximating the binding free energy of the system calculated using Jarzynski's Equality. Calculation of the DFI shows that the overall flexibility of the protein complex increases as a result of the distal point mutation. Total change in DFI percentile of the binding site showed a 0.067 increase suggesting an allosteric, loss of function mutation. Furthermore, we see that the change in the binding free energy is greater for that of the mutated complex supporting the idea that an increase in flexibility is correlated to a decrease in proteinlig and binding affinity. We show that sequence mutation of an allosteric site affects the mechanical stability and functionality of the binding pocket.
ContributorsMarianchuk, Tegan (Author) / Ozkan, Sefika (Thesis director) / Ros, Robert (Committee member) / Barrett, The Honors College (Contributor) / Department of Physics (Contributor)
Created2018-05
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Description
Topological insulators with conducting surface states yet insulating bulk states have generated a lot of interest amongst the physics community due to their varied characteristics and possible applications. Doped topological insulators have presented newer physical states of matter where topological order co&ndashexists; with other physical properties (like magnetic order). The

Topological insulators with conducting surface states yet insulating bulk states have generated a lot of interest amongst the physics community due to their varied characteristics and possible applications. Doped topological insulators have presented newer physical states of matter where topological order co&ndashexists; with other physical properties (like magnetic order). The electronic states of these materials are very intriguing and pose problems and the possible solutions to understanding their unique behaviors. In this work, we use Electron Energy Loss Spectroscopy (EELS) – an analytical TEM tool to study both core&ndashlevel; and valence&ndashlevel; excitations in Bi2Se3 and Cu(doped)Bi2Se3 topological insulators. We use this technique to retrieve information on the valence, bonding nature, co-ordination and lattice site occupancy of the undoped and the doped systems. Using the reference materials Cu(I)Se and Cu(II)Se we try to compare and understand the nature of doping that copper assumes in the lattice. And lastly we utilize the state of the art monochromated Nion UltraSTEM 100 to study electronic/vibrational excitations at a record energy resolution from sub-nm regions in the sample.
ContributorsSubramanian, Ganesh (Author) / Spence, John (Thesis advisor) / Jiang, Nan (Committee member) / Chen, Tingyong (Committee member) / Chan, Candace (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Disordered many-body systems are ubiquitous in condensed matter physics, materials science and biological systems. Examples include amorphous and glassy states of matter, granular materials, and tissues composed of packings of cells in the extra-cellular matrix (ECM). Understanding the collective emergent properties in these systems is crucial to improving the capability

Disordered many-body systems are ubiquitous in condensed matter physics, materials science and biological systems. Examples include amorphous and glassy states of matter, granular materials, and tissues composed of packings of cells in the extra-cellular matrix (ECM). Understanding the collective emergent properties in these systems is crucial to improving the capability for controlling, engineering and optimizing their behaviors, yet it is extremely challenging due to their complexity and disordered nature. The main theme of the thesis is to address this challenge by characterizing and understanding a variety of disordered many-body systems via unique statistical geometrical and topological tools and the state-of-the-art simulation methods. Two major topics of the thesis are modeling ECM-mediated multicellular dynamics and understanding hyperuniformity in 2D material systems. Collective migration is an important mode of cell movement for several biological processes, and it has been the focus of a large number of studies over the past decades. Hyperuniform (HU) state is a critical state in a many-particle system, an exotic property of condensed matter discovered recently. The main focus of this thesis is to study the mechanisms underlying collective cell migration behaviors by developing theoretical/phenomenological models that capture the features of ECM-mediated mechanical communications in vitro and investigate general conditions that can be imposed on hyperuniformity-preserving and hyperuniformity-generating operations, as well as to understand how various novel transport physical properties arise from the unique hyperuniform long-range correlations.
ContributorsZheng, Yu (Author) / Jiao, Yang (Thesis advisor) / Zhuang, Houlong (Committee member) / Beckstein, Oliver (Committee member) / Ros, Robert (Committee member) / Arizona State University (Publisher)
Created2022
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Description
Adsorption of fibrinogen on various surfaces, including biomaterials, dramatically reduces the adhesion of platelets and leukocytes. The mechanism by which fibrinogen renders surfaces non-adhesive is its surface-induced self-assembly leading to the formation of a nanoscale multilayer matrix. Under the applied tensile force exerted by cellular integrins, the fibrinogen matrix extends

Adsorption of fibrinogen on various surfaces, including biomaterials, dramatically reduces the adhesion of platelets and leukocytes. The mechanism by which fibrinogen renders surfaces non-adhesive is its surface-induced self-assembly leading to the formation of a nanoscale multilayer matrix. Under the applied tensile force exerted by cellular integrins, the fibrinogen matrix extends as a result of the separation of layers which prevents the transduction of strong mechanical forces, resulting in weak intracellular signaling and feeble cell adhesion. Furthermore, upon detachment of adherent cells, a weak association between fibrinogen molecules in the superficial layers of the matrix allows integrins to pull fibrinogen molecules out of the matrix. Whether the latter mechanism contributes to the anti-adhesive mechanism under the flow is unclear. In the present study, using several experimental flow systems, it has been demonstrated that various blood cells as well as model HEK293 cells expressing the fibrinogen receptors, were able to remove fibrinogen molecules from the matrix in a time- and cell concentration-dependent manner. In contrast, insignificant fibrinogen dissociation occurred in a cell-free buffer, and crosslinking fibrinogen matrix significantly reduced cell-mediated dissociation of adsorbed fibrinogen. Surprisingly, cellular integrins contributed minimally to fibrinogen dissociation since function-blocking anti-integrin antibodies did not significantly inhibit this process. In addition, erythrocytes that are not known to express functional fibrinogen receptors and naked liposomes caused fibrinogen dissociation, suggesting that the removal of fibrinogen from the matrix may be caused by nonspecific low-affinity interactions of cells with the fibrinogen matrix. These results indicate that the peeling effect exerted by flowing cells upon their contact with the fibrinogen matrix is involved in the anti-adhesive mechanism.
ContributorsMursalimov, Aibek (Author) / Ugarova, Tatiana (Thesis advisor) / Chandler, Douglas (Committee member) / Podolnikova, Nataly (Committee member) / Ros, Robert (Committee member) / Arizona State University (Publisher)
Created2022
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Description
Secondary active transporters play significant roles in maintaining living cells' homeostasis by utilizing the electrochemical gradient in driving ions or protons as the source of free energy to transport substrate through biological membranes.A broadly recognized molecular framework, the alternating access model, describes the transport mechanism as the transporter undergoes conformational

Secondary active transporters play significant roles in maintaining living cells' homeostasis by utilizing the electrochemical gradient in driving ions or protons as the source of free energy to transport substrate through biological membranes.A broadly recognized molecular framework, the alternating access model, describes the transport mechanism as the transporter undergoes conformational changes between different conformations and alternatingly exposes its binding site to intracellular and extracellular sides and, thus, exchanges ion and substrate in a cyclical manner. Recent progress in structural biology brought the first-ever structural insights into the mammalian Cation-Proton Antiporters (CPA) family of proteins. However, the dynamic atomic-level information about the interactions between the newly discovered structures and the bound ion or the corresponding substrate remains unknown. With Molecular Dynamics (MD), multiple spontaneous ion binding events were observed in the equilibrium simulations, revealing the binding site topology of Horse Sodium-Proton Exchanger 9 (NHE9) and Bison Sodium-Proton Antiporter 2 (NHA2) in their preferred protonation state. Further investigation into more CPA homologs compared various aspects, including sequence identity, binding site topology, and energetic properties, and obtained general insights into the similarities shared by the binding process of CPA members. The putative binding site and other conserved residues in their actively ion-bound poses were identified for each model, and their similarities were compared. The energetic properties accessed by the three-dimensional free energy profile, initially found to be binding unfavorable for the experimental structures, were recalculated based on the simulation data. The updated results show consistency with the correct binding affinity as indicated by the experimental methods. This work provided a general picture of the structures and the ion-protein interaction of CPA proteins and serves as comprehensive guidance for any related future structural and computational work.
ContributorsZhang, Chenou (Author) / Beckstein, Oliver (Thesis advisor) / Ozkan, Banu (Committee member) / Ros, Robert (Committee member) / Singharoy, Abhishek (Committee member) / Arizona State University (Publisher)
Created2023
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Description
Seeking an upper limit of the Neutron Electric Dipole Moment (nEDM) is a test of charge-parity (CP) violation beyond the Standard Model. The present experimentally tested nEDM upper limit is 3x10^(26) e cm. An experiment to be performed at the Oak Ridge National Lab Spallation Neutron Source (SNS) facility seeks

Seeking an upper limit of the Neutron Electric Dipole Moment (nEDM) is a test of charge-parity (CP) violation beyond the Standard Model. The present experimentally tested nEDM upper limit is 3x10^(26) e cm. An experiment to be performed at the Oak Ridge National Lab Spallation Neutron Source (SNS) facility seeks to reach the 3x10^(28) e cm limit. The experiment is designed to probe for a dependence of the neutron's Larmor precession frequency on an applied electric eld. The experiment will use polarized helium-3

(3He) as a comagnetometer, polarization analyzer, and detector.

Systematic influences on the nEDM measurement investigated in this thesis include (a) room temperature measurements on polarized 3He in a measurement cell made from the same materials as the nEDM experiment, (b) research and development of the Superconducting QUantum Interference Devices (SQUID) which will be used in the nEDM experiment, (c) design contributions for an experiment with nearly all the same conditions as will be present in the nEDM experiment, and (d) scintillation studies in superfluid helium II generated from alpha particles which are fundamentally similar to the nEDM scintillation process. The result of this work are steps toward achievement of a new upper limit for the nEDM experiment at the SNS facility.
ContributorsDipert, Robert (Author) / Alarcon, Ricardo (Thesis advisor) / Chamberlin, Ralph (Committee member) / Golub, Robert (Committee member) / Chen, Tingyong (Committee member) / Schmidt, Kevin (Committee member) / Arizona State University (Publisher)
Created2019
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Description
In this dissertation I studied the anomalous Hall effect in MgO/Permalloy/Nonmagnetic Metal(NM) based structure, spin polarized current in YIG/Pt based thin films and the origin of the perpendicular magnetic anisotropy(PMA) in the Ru/Co/Ru based structures.

The anomalous Hall effect is the observation of a nonzero voltage difference across a magnetic

In this dissertation I studied the anomalous Hall effect in MgO/Permalloy/Nonmagnetic Metal(NM) based structure, spin polarized current in YIG/Pt based thin films and the origin of the perpendicular magnetic anisotropy(PMA) in the Ru/Co/Ru based structures.

The anomalous Hall effect is the observation of a nonzero voltage difference across a magnetic material transverse to the current that flows through the material and the external magnetic field. Unlike the ordinary Hall effect which is observed in nonmagnetic metals, the anomalous Hall effect is only observed in magnetic materials and is orders of magnitude larger than the ordinary Hall effect. Unlike quantum anomalous Hall effect which only works in low temperature and extremely large magnetic field, anomalous Hall effect can be measured at room temperature under a relatively small magnetic field. This allows the anomalous Hall effect to have great potential applications in spintronics and be a good characterization tool for ferromagnetic materials especially materials that have perpendicular magnetic anisotropy(PMA).

In my research, it is observed that a polarity change of the Hall resistance in the MgO/Permalloy/NM structure can be obtained when certain nonmagnetic metal is used as the capping layer while no polarity change is observed when some other metal is used as the capping layer. This allows us to tune the polarity of the anomalous Hall effect by changing the thickness of a component of the structure. My conclusion is that an intrinsic mechanism from Berry curvature plays an important role in the sign of anomalous Hall resistivity in the MgO/Py/HM structures. Surface and interfacial scattering also make substantial contribution to the measured Hall resistivity.

Spin polarization(P) is one of the key concepts in spintronics and is defined as the difference in the spin up and spin down electron population near the Fermi level of a conductor. It has great applications in the spintronics field such as the creation of spin transfer torques, magnetic tunnel junction(MTJ), spintronic logic devices.

In my research, spin polarization is measured on platinum layers grown on a YIG layer. Platinum is a nonmagnetic metal with strong spin orbit coupling which intrinsically has zero spin polarization. Nontrivial spin polarization measured by ARS is observed in the Pt layer when it is grown on YIG ferromagnetic insulator. This result is contrary to the zero spin polarization in the Pt layer when it is grown directly on SiO2 substrate. Magnetic proximity effect and spin current pumping from YIG into Pt is proposed as the reason of the nontrivial spin polarization induced in Pt. An even higher spin polarization in the Pt layer is observed when an ultrathin NiO layer or Cu layer is inserted between Pt and YIG which blocks the proximity effect. The spin polarization in the NiO inserted sample shows temperature dependence. This demonstrates that the spin current transmission is further enhanced in ultrathin NiO layers through magnon and spin fluctuations.

Perpendicular Magnetic Anisotropy(PMA) has important applications in spintronics and magnetic storage. In the last chapter, I study the origin of PMA in one of the structures that shows PMA: Ru/Co/Ru. By measuring the ARS curve while changing the magnetic field orientation, the origin of the PMA in this structure is determined to be the strain induced by lattice mismatch.
ContributorsLi, Bochao (Author) / Chen, Tingyong (Committee member) / Bennett, Peter (Committee member) / Nemanich, Robert (Committee member) / Qing, Quan (Committee member) / Arizona State University (Publisher)
Created2018
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Description
Bio-molecules and proteins are building blocks of life as is known, and understanding

their dynamics and functions are necessary to better understand life and improve its

quality. While ergodicity and fluctuation dissipation theorem (FDT) are fundamental

and crucial concepts regarding study of dynamics of systems in equilibrium, biological

function is not possible in equilibrium.

In

Bio-molecules and proteins are building blocks of life as is known, and understanding

their dynamics and functions are necessary to better understand life and improve its

quality. While ergodicity and fluctuation dissipation theorem (FDT) are fundamental

and crucial concepts regarding study of dynamics of systems in equilibrium, biological

function is not possible in equilibrium.

In this work, dynamical and orientational structural crossovers in low-temperature

glycerol are investigated. A sudden and notable increase in the orientational Kirk-

wood factor and the dielectric constant is observed, which appears in the same range

of temperatures that dynamic crossover of translational and rotational dynamics oc-

cur.

Theory and electrochemistry of cytochrome c is also investigated. The seeming

discrepancy in reorganization energies of protein electron transfer produced by atom-

istic simulations and those reported by protein electrochemistry (which are smaller)

is resolved. It is proposed in this thesis that ergodicity breaking results in an effective

reorganization energy (0.57 eV) consistent with experiment.

Ergodicity breaking also affects the iron displacement in heme proteins. A model

for dynamical transition of atomic displacements in proteins is provided. Different

temperatures for rotational and translational crossovers of water molecules are re-

ported, which all are ergodicity breaking transitions depending on the corresponding

observation windows. The comparison with Mössbauer spectroscopy is presented.

Biological function at low temperatures and its termination is also investigated in

this research. Here, it is proposed that ergodicity breaking gives rise to the violation

of the FDT, and this violation is maintained in the entire range of physiological

temperatures for cytochrome c. Below the crossover temperature, the protein returns

to the FDT, which leads to a sudden jump in the activation barrier for electron

itransfer.

Finally the interaction of charges in dielectric materials is discussed. It is shown

that the potential of mean force between ions in polar liquids becomes oscillatory at

short distances.
ContributorsSeyedi, seyed salman (Author) / Matyushov, Dmitry V (Thesis advisor) / Beckstein, Oliver (Committee member) / Vaiana, Sara M (Committee member) / Ros, Robert (Committee member) / Arizona State University (Publisher)
Created2018
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Description
Chemical Vapor Deposition (CVD) is the most widely used method to grow large-scale single layer graphene. However, a systematic experimental study of the relationship between growth parameters and graphene film morphology, especially in the industrially preferred cold wall CVD, has not been undertaken previously. This research endeavored to address this

Chemical Vapor Deposition (CVD) is the most widely used method to grow large-scale single layer graphene. However, a systematic experimental study of the relationship between growth parameters and graphene film morphology, especially in the industrially preferred cold wall CVD, has not been undertaken previously. This research endeavored to address this and provide comprehensive insight into the growth physics of graphene on supported solid and liquid Cu films using cold wall CVD.

A multi-chamber UHV system was customized and transformed into a cold wall CVD system to perform experiments. The versatile growth process was completely custom-automated by controlling the process parameters with LabVIEW. Graphene growth was explored on solid electrodeposited, recrystallized and thin sputter deposited Cu films as well as on liquid Cu supported on W/Mo refractory substrates under ambient pressure using Ar, H₂ and CH₄ mixtures.

The results indicate that graphene grown on Cu films using cold wall CVD follows a classical two-dimensional nucleation and growth mechanism. The nucleation density decreases and average size of graphene crystallites increases with increasing dilution of the CH₄/H₂ mixture by Ar, decrease in total flow rate and decrease in CH₄:H₂ ratio at a fixed substrate temperature and chamber pressure. Thus, the resulting morphological changes correspond with those that would be expected if the precursor deposition rate was varied at a fixed substrate temperature for physical deposition using thermal evaporation. The evolution of graphene crystallite boundary morphology with decreasing effective C deposition rate indicates the effect of edge diffusion of C atoms along the crystallite boundaries, in addition to H₂ etching, on graphene crystallite shape.

The roles of temperature gradient, chamber pressure and rapid thermal heating in C precursor-rich environment on graphene growth morphology on thin sputtered Cu films were explained. The growth mechanisms of graphene on substrates annealed under reducing and non-reducing environment were explained from the scaling functions of graphene island size distribution in the pre-coalescence regime. It is anticipated that applying the pre-coalescence size distribution method presented in this work to other 2D material systems may be useful for elucidating atomistic mechanisms of film growth that are otherwise difficult to obtain.
ContributorsDas, Shantanu, Ph.D (Author) / Drucker, Jeff (Thesis advisor) / Alford, Terry (Committee member) / Chen, Tingyong (Committee member) / Arizona State University (Publisher)
Created2018
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Description
Mechanical properties, in particular elasticity, of cancer cells and their microenvironment are important in governing cancer cell fate, for example function, mobility, adhesion, and invasion. Among all tools to measure the mechanical properties, the precision and ease of atomic force microscopy (AFM) to directly apply force—in the range of Pico

Mechanical properties, in particular elasticity, of cancer cells and their microenvironment are important in governing cancer cell fate, for example function, mobility, adhesion, and invasion. Among all tools to measure the mechanical properties, the precision and ease of atomic force microscopy (AFM) to directly apply force—in the range of Pico to micronewtons—onto samples—with length scales from nanometers to tens of micrometers—has made it a powerful tool to investigate the mechanics of materials. AFM is widely used to measure deformability and stiffness of soft biological samples. Principally, these samples are indented by the AFM probe and the forces and indentation depths are recorded. The generated force-indentation curves are fitted with an elastic contact model to quantify the elasticity (e.g. stiffness). AFM is a precise tool; however, the results are as accurate as the contact model used to analyze them. A new contact model was introduced to analyze force-indentation curves generated by spherical AFM probes for deep indentations. The experimental and finite element analysis results demonstrated that the new contact model provides more accurate mechanical properties throughout the indentation depth up to radius of the indenter, while the Hertz model underestimates the mechanical properties. In the classical contact models, it is assumed that the sample is vertically homogenous; however, many biological samples—for example cells—are heterogeneous. A novel two-layer model was utilized to probe Polydimethylsiloxane hydrogel (PDMS) layers on PDMS substrates with stiffness mismatch. In this experiment the stiffness of the substrate was deconvoluted from the AFM measurements to obtain the stiffness of the layer. AFM and confocal reflectance microscopy were utilized along with a novel 3D microengineered breast cancer tumor model to study the crosstalk between cancer tumor and the stromal cells (CAFs) and the ECM remodeling caused by their interplay. The results showed that as the cancer cells invade into the extracellular matrix (ECM), they release PDGF ligands which enable Cafes to remodel the ECM and this remodeling increased the invasion rate of the cancer cells. Next, the effect of the ECM remodeling on anti-cancer drug resistant was investigated within the 3D microengineered cancer model. It was demonstrated that the combinatory treatment by anti-cancer and-anti-fibrotic drugs enhance the efficiency of the cancer treatment. A novel DNA-based 3D hydrogel model with tunable stiffness was investigated by AFM. The results showed the hydrogel stiffness can be enhanced by adding DNA crosslinkers. In addition, the stiffness was reduced to the control sample level by introducing the displacement DNA. Biophysical quantifications along with the in vitro microengineered tumor models provide a unique frame work to study cancer in more detail.
ContributorsRahmani Eliato, Kiarash (Author) / Ros, Robert (Thesis advisor) / Nikkhah, Mehdi (Committee member) / Ozkan, Sefika (Committee member) / Lindsay, Stuart (Committee member) / Arizona State University (Publisher)
Created2019