Open Access. Powered by Scholars. Published by Universities.®

Biological and Chemical Physics Commons

Open Access. Powered by Scholars. Published by Universities.®

960 Full-Text Articles 2,062 Authors 244,666 Downloads 115 Institutions

All Articles in Biological and Chemical Physics

Faceted Search

960 full-text articles. Page 6 of 33.

Sulfur Adsorption On Coinage Metal (100) Surfaces: Propensity For Metal-Sulfur Complex Formation Relative To (111) Surfaces, Da-Jiang Liu, Peter M. Spurgeon, Jiyoung Lee, Theresa L. Windus, Patricia A. Thiel, James W. Evans 2019 Ames Laboratory

Sulfur Adsorption On Coinage Metal (100) Surfaces: Propensity For Metal-Sulfur Complex Formation Relative To (111) Surfaces, Da-Jiang Liu, Peter M. Spurgeon, Jiyoung Lee, Theresa L. Windus, Patricia A. Thiel, James W. Evans

Chemistry Publications

Experimental data from low-temperature Scanning Tunneling Microscopy (LTSTM) studies on coinage metal surfaces with very low coverages of S is providing new insights into metal–S interactions. A previous LTSTM study for Cu(100), and a new analysis reported here for Ag(100), both indicate no metal–sulfur complex formation, but an Au4S5 complex was observed previously on Au(100). In marked contrast, various complexes have been proposed and/or observed on Ag(111) and Cu(111), but not on Au(111). Also, exposure to trace amounts of S appears to enhance mass transport far more dramatically on (111) than ...


Silicon Quantum Dots Conjunctive With Stable Radicals: Potential Application In Non-Invasive Cancer Diagnostics, Daylan R. Post 2019 Georgia Southern University

Silicon Quantum Dots Conjunctive With Stable Radicals: Potential Application In Non-Invasive Cancer Diagnostics, Daylan R. Post

Honors College Theses

Quantum Dots, and nanomaterials in general, are one of the most promising areas of current physical study, especially their potential medical uses. In this study we introduced Nitroxide free radicals into a Silicon Quantum Dot (SiQD) solution and conducted experiments on the modified SiQDs in order to characterize their physical properties. We gathered emission, excitation, absorption and electron spin resonance (ESR) spectra of both modified and unmodified SiQDs. Previous studies have shown the possibility of using proteins as markers for cancer detection. Our measurements show the potential of using the interaction between these protein markers and SiQDs as a form ...


The Structural Information Filtered Features Potential For Machine Learning Calculations Of Energies And Forces Of Atomic Systems., Jorge Arturo Hernandez Zeledon 2019 West Virginia University

The Structural Information Filtered Features Potential For Machine Learning Calculations Of Energies And Forces Of Atomic Systems., Jorge Arturo Hernandez Zeledon

Graduate Theses, Dissertations, and Problem Reports

In the last ten years, machine learning potentials have been successfully applied to the study of crystals, and molecules. However, more complex materials like clusters, macro-molecules, and glasses are out reach of current methods. The input of any machine learning system is a tensor of features (the most universal type are rank 1 tensors or vectors of features), the quality of any machine learning system is directly related to how well the feature space describes the original physical system. So far, the feature engineering process for machine learning potentials can not describe complex material. The current methods are highly inefficient ...


Effect Of (Poly)Electrolytes On The Interfacial Assembly Of Peg Functionalized Gold Nanoparticles, Srikanth Nayak, Max Fieg, Wenjie Wang, Wei Bu, Surya Mallapragada, David Vaknin 2019 Iowa State University and Ames Laboratory

Effect Of (Poly)Electrolytes On The Interfacial Assembly Of Peg Functionalized Gold Nanoparticles, Srikanth Nayak, Max Fieg, Wenjie Wang, Wei Bu, Surya Mallapragada, David Vaknin

Chemical and Biological Engineering Publications

We report on the effect of interpolymer complexes (IPCs) of poly(acrylic acid) (PAA) with poly(ethylene glycol) functionalized Au nanoparticles (PEG-AuNPs) as they assemble at the vapor-liquid interface, using surface sensitive synchrotron X-ray scattering techniques. Depending on the suspension pH, PAA functions both as a weak polyelectrolyte and a hydrogen bond donor, and these two roles affect the interfacial assembly of PEG-AuNPs differently. Above its isoelectric point, we find that PAA leads to the formation of a PEG-AuNPs monolayer at the interface with hexagonal structure. In the presence of high concentration of HCl (i.e., below the isoelectric point ...


Call For Abstracts - Resrb 2019, July 8-9, Wrocław, Poland, Wojciech M. Budzianowski 2018 Wojciech Budzianowski Consulting Services

Call For Abstracts - Resrb 2019, July 8-9, Wrocław, Poland, Wojciech M. Budzianowski

Wojciech Budzianowski

No abstract provided.


Molecular Dynamics Simulation Of Phase Competition In Terbium, H. Song, Mikhail I. Mendelev 2018 Ames Laboratory

Molecular Dynamics Simulation Of Phase Competition In Terbium, H. Song, Mikhail I. Mendelev

Ames Laboratory Accepted Manuscripts

The competition among multiple solid phases determines the final microstructures of a material. Such competition can originate at the very beginning of the solidification process. We report the results of molecular dynamics simulation of the phase competition between the hexagonal close-packed (hcp), face-centered cubic (fcc), and body-centered cubic (bcc) phases during the solidification of pure Tb. We found that the liquid supercooled below the hcp melting temperature has both bcc and hcp/fcc nuclei, but only the bcc nuclei grow such that the liquid always solidifies into the bcc phase, even at temperatures where the hcp phase is more stable ...


Evaluation Of Presage® As A 3d Dose Verification Tool In Proton Beams, Mitchell Carroll 2018 The University of Texas M D Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences

Evaluation Of Presage® As A 3d Dose Verification Tool In Proton Beams, Mitchell Carroll

The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)

Radiotherapy techniques have advanced and radiation dose plans have become much more complex over the last decade. This is especially true in proton therapy, which involves extremely steep dose gradients as a result of positioning the Bragg peak to cover the volumes to be treated. The Bragg peak can be shifted significantly in the patient as a result of nonuniformities in the tissue composition in its path, which can result in treatment complications. Some traditional dose verification tools used in proton beam commissioning and treatment plan verification are film, TLD, and ionization chambers. Such 0D and 2D dosimeters are incapable ...


Plasmonic Enhancement Of Photoluminescence And Photobrightening In Cdse Quantum Dots, David Alan French 2018 University of Arkansas, Fayetteville

Plasmonic Enhancement Of Photoluminescence And Photobrightening In Cdse Quantum Dots, David Alan French

Theses and Dissertations

Quantum dots are gaining recognition not just in the physics and chemistry community, but in the public eye as well. Quantum dot technologies are now being used in sensors, detectors, and even television displays. By exciting quantum dots with light or electricity, they can be made to emit light, and by altering the quantum dot characteristics the wavelength can be finely tuned. The light emitted can be also be made more intense by an increase in the excitation energy. The excitation light can be increased via plasmonic enhancement, leading to increased luminescence. Aside from the relatively steady-state response, quantum dots ...


Nonlinear Sliding Mode Observer Applied To Microalgae Growth, Rebecca J. Griffith 2018 Embry-Riddle Aeronautical University

Nonlinear Sliding Mode Observer Applied To Microalgae Growth, Rebecca J. Griffith

PhD Dissertations and Master's Theses

Modeling biological processes, such as algae growth, is an area of ongoing research. The ability to understand the multitude of parameters that influence this system provides a platform for better understanding the dynamics of microalgae growth. Empirical modeling efforts look to understand sources of driving nutrients that influence harmful algal blooms (HABs). These harmful algal blooms are dense aggregates that have an increasingly negative impact on local economics, marine and freshwater systems, and public health. They result from a high influx of nitrogen and nutrients that drive the algae biomass to exponentially grow. This growth blocks out the sun, potentially ...


Innate Immunity, The Hepatic Extracellular Matrix, And Liver Injury: Mathematical Modeling Of Metastatic Potential And Tumor Development In Alcoholic Liver Disease., Shanice V. Hudson 2018 University of Louisville

Innate Immunity, The Hepatic Extracellular Matrix, And Liver Injury: Mathematical Modeling Of Metastatic Potential And Tumor Development In Alcoholic Liver Disease., Shanice V. Hudson

Electronic Theses and Dissertations

The overarching goals of the current work are to fill key gaps in the current understanding of alcohol consumption and the risk of metastasis to the liver. Considering the evidence this research group has compiled confirming that the hepatic matrisome responds dynamically to injury, an altered extracellular matrix (ECM) profile appears to be a key feature of pre-fibrotic inflammatory injury in the liver. This group has demonstrated that the hepatic ECM responds dynamically to alcohol exposure, in particular, sensitizing the liver to LPS-induced inflammatory damage. Although the study of alcohol in its role as a contributing factor to oncogenesis and ...


The Role Of Anderson’S Rule In Determining Electronic, Optical And Transport Properties Of Transition Metal Dichalcogenide Heterostructures, Ke Xu, Yuanfeng Xu, Bo Peng, Hezhu Shao, Gang Ni, Jing Li, Mingyuan Yao, Hongliang Lu, Heyuan Zhu, Costas M. Soukoulis 2018 Fudan University

The Role Of Anderson’S Rule In Determining Electronic, Optical And Transport Properties Of Transition Metal Dichalcogenide Heterostructures, Ke Xu, Yuanfeng Xu, Bo Peng, Hezhu Shao, Gang Ni, Jing Li, Mingyuan Yao, Hongliang Lu, Heyuan Zhu, Costas M. Soukoulis

Ames Laboratory Accepted Manuscripts

Two-dimensional (2D) transition metal dichalcogenides (TMDs) MX2 (M = Mo, W; X = S, Se, Te) possess unique properties and novel applications in optoelectronics, valleytronics and quantum computation. In this work, we performed first-principles calculations to investigate the electronic, optical and transport properties of the van der Waals (vdW) stacked MX2 heterostructures formed by two individual MX2 monolayers. We found that the so-called Anderson's rule can effectively classify the band structures of heterostructures into three types: straddling, staggered and broken gap. The broken gap is gapless, while the other two types possess direct (straddling, staggered) or indirect (staggered) band gaps. The ...


Combined High-Speed Single Particle Tracking Of Membrane Proteins And Super-Resolution Of Membrane-Associated Structures, Hanieh Mazloom Farsibaf, Keith A. Lidke 2018 University of New Mexico

Combined High-Speed Single Particle Tracking Of Membrane Proteins And Super-Resolution Of Membrane-Associated Structures, Hanieh Mazloom Farsibaf, Keith A. Lidke

Shared Knowledge Conference

Many experiments have shown that the diffusive motion of lipids and membrane proteins are slower on the cell surface than those in artificial lipid bilayers or blebs. One hypothesis that may partially explain this mystery is the effect of the cytoskeleton structures on the protein dynamics. A model proposed by Kusumi [1] is the Fence-Picket Model which describes the cell membrane as a set of compartment regions, each ~ 10 to 200 nm in size, created by direct or indirect interaction of lipids and proteins with actin filaments just below the membrane. To test this hypothesis, we have assembled a high-speed ...


Temperature Dependence Of The Solid-Liquid Interface Free Energy Of Ni And Al From Molecular Dynamics Simulation Of Nucleation, Yang Sun, Feng Zhang, Huajing Song, Mikhail I. Mendelev, Cai-Zhuang Wang, Kai-Ming Ho 2018 Ames Laboratory

Temperature Dependence Of The Solid-Liquid Interface Free Energy Of Ni And Al From Molecular Dynamics Simulation Of Nucleation, Yang Sun, Feng Zhang, Huajing Song, Mikhail I. Mendelev, Cai-Zhuang Wang, Kai-Ming Ho

Ames Laboratory Accepted Manuscripts

The temperature dependence of the solid-liquid interfacial free energy, γ, is investigated for Al and Ni at the undercooled temperature regime based on a recently developed persistent-embryo method. The atomistic description of the nucleus shape is obtained from molecular dynamics simulations. The computed γ shows a linear dependence on the temperature. The values of γ extrapolated to the melting temperature agree well with previous data obtained by the capillary fluctuation method. Using the temperature dependence of γ, we estimate the nucleation free energy barrier in a wide temperature range from the classical nucleation theory. The obtained data agree very well ...


Model For Coordination Of Microtubule And Actin Dynamics In Growth Cone Turning, Erin M. Craig 2018 Central Washington University

Model For Coordination Of Microtubule And Actin Dynamics In Growth Cone Turning, Erin M. Craig

All Faculty Scholarship for the College of the Sciences

In the developing nervous system, axons are guided to their synaptic targets by motile structures at the axon tip called growth cones, which reorganize their cytoskeleton in order to steer in response to chemotactic cues. Growth cone motility is mediated by an actin-adhesion “clutch” mechanism, in which mechanical attachment to a substrate, coupled with polarized actin growth, produces leading-edge protrusion. Several studies suggest that dynamic microtubules (MTs) in the growth cone periphery play an essential role in growth cone steering. It is not yet well-understood how the MT cytoskeleton and the dynamic actin-adhesion clutch system are coordinated to promote growth ...


Equilibrium Partitioning Of Binary Polymer Mixtures Into Biological Nanopores, Mehmet Alphan Aksoyoglu 2018 University of Massachusetts Amherst

Equilibrium Partitioning Of Binary Polymer Mixtures Into Biological Nanopores, Mehmet Alphan Aksoyoglu

Doctoral Dissertations

The cell interior, enclosed by membrane barriers, is a condensed solution of inorganic ions, polymers, carbohydrates, polynucleotides, and a large number of other organic molecules. Within cells, transport of metabolites and biopolymers, such as polynucleotides and proteins, occurs partly through specific transmembrane pores (mesoscopic ion channels) spanning cellular compartments. Examples of such functions are translocation of matrix RNA molecules from cell nucleus through nuclear pore complexes, ejection of viral genome from bacterial virus capsids into host bacterial cells, and translocation of protein factors across toxin channels in biological membranes. All these processes, that occur in the cellular milieu, are mediated ...


Raman Spectroscopy Detects Biochemical Changes Due To Different Cell Culture Environments In Live Cells In Vitro, Mahmoud Gargotti, Esen Efeoglu, Hugh J Byrne, Alan Casey 2018 Technological University Dublin

Raman Spectroscopy Detects Biochemical Changes Due To Different Cell Culture Environments In Live Cells In Vitro, Mahmoud Gargotti, Esen Efeoglu, Hugh J Byrne, Alan Casey

Articles

The in vitro cell culture environment can impact on cell biochemistry and cell cycle. The manifestation of such substrate-induced changes in cell cycle in the Raman microspectroscopic profiles of cell cultures is investigated at the level of nucleolus, nucleus and cytoplasm. HeLa immortalised human cervical cells and HaCaT dermal cells were cultured on three different substrates, conventional polystyrene cell culture dishes, CaF2 slides as a commonly used Raman substrate, and glass slides coated with Collagen Rat Tail, as a mimic of the extra cellular matrix (ECM) environment. A cell cycle study, based on percentage DNA content, as determined using Propidium ...


Large-Scale Ab Initio Simulations Of Mas Dnp Enhancements Using A Monte Carlo Optimization Strategy, Frederic A. Perras, Marek Pruski 2018 Ames Laboratory

Large-Scale Ab Initio Simulations Of Mas Dnp Enhancements Using A Monte Carlo Optimization Strategy, Frederic A. Perras, Marek Pruski

Ames Laboratory Accepted Manuscripts

Magic-angle-spinning (MAS) dynamic nuclear polarization (DNP) has recently emerged as a powerful technology enabling otherwise unrealistic solid-state NMR experiments. The simulation of DNP processes which might, for example, aid in refining the experimental conditions or the design of better performing polarizing agents, is, however, plagued with significant challenges, often limiting the system size to only 3 spins. Here, we present the first approach to fully ab initio large-scale simulations of MAS DNP enhancements. The Landau-Zener equation is used to treat all interactions concerning electron spins, and the low-order correlations in the Liouville space method is used to accurately treat the ...


Structural And Wetting Properties Of Nature's Finest Silks (Order Embioptera), Grace Y. Stokes, Evangelea N. DiCicco, Trevor J. Moore, Vivian C. Cheng, Kira Y. Wheeler, John Soghigian, Richard P. Barber Jr., Janice Edgerly-Rooks 2018 Santa Clara University

Structural And Wetting Properties Of Nature's Finest Silks (Order Embioptera), Grace Y. Stokes, Evangelea N. Dicicco, Trevor J. Moore, Vivian C. Cheng, Kira Y. Wheeler, John Soghigian, Richard P. Barber Jr., Janice Edgerly-Rooks

Physics

Insects from the order Embioptera (webspinners) spin silk fibres which are less than 200 nm in diameter. In this work, we characterized and compared the diameters of single silk fibres from nine species—Antipaluria urichi, Pararhagadochir trinitatis, Saussurembia calypso, Diradius vandykei, Aposthonia ceylonica, Haploembia solieri, H. tarsalis, Oligotoma nigra and O. saundersii. Silk from seven of these species have not been previously quantified. Our studies cover five of the 10 named taxonomic families and represent about one third of the known taxonomic family-level diversity in the order Embioptera. Naturally spun silk varied in diameter from 43.6 ± 1.7 nm ...


Estimating And Correcting Interference Fringes In Infrared Spectra In Infrared Hyperspectral Imaging, Ghazal Azarfar, Ebrahim Aboualizadeh, Nicholas Walter,, Simona Ratti, Camilla Olivieri, Alessandra Alessandra, Michael Nasse, Achim Kohler, Mario Giordano, Carol Hirschmugl 2018 University of Wisconsin Milwaukee

Estimating And Correcting Interference Fringes In Infrared Spectra In Infrared Hyperspectral Imaging, Ghazal Azarfar, Ebrahim Aboualizadeh, Nicholas Walter,, Simona Ratti, Camilla Olivieri, Alessandra Alessandra, Michael Nasse, Achim Kohler, Mario Giordano, Carol Hirschmugl

Physics Faculty Articles

Short-term acclimation response of individual cells of Thalassiosira weissflogii was monitored by Synchrotron FTIR imaging over the span of 75 minutes. The cells, collected from batch cultures, were maintained in a constant flow of medium, at an irradiance of 120 μmol m−2 s−1 and at 20 °C. Multiple internal reflections due to the micro fluidic channel were modeled, and showed that fringes are additive sinusoids to the pure absorption of the other components of the system. Preprocessing of the hyperspectral cube (x, y, Abs(λ)) included removing spectral fringe using an EMSC approach. Principal component analysis of the ...


Supercharged Models Of Intrinsically Disordered Proteins And Their Utility In Sensing, Peter J. Schnatz 2018 The Graduate Center, City University of New York

Supercharged Models Of Intrinsically Disordered Proteins And Their Utility In Sensing, Peter J. Schnatz

Dissertations, Theses, and Capstone Projects

In this thesis I show that greatly increasing the magnitude of a protein’s net charge using surface supercharging transforms that protein into a ligand-gated or counterion-gated conformational molecular switch. To demonstrate this I first modified the designed helical bundle hemoprotein H4 using simple molecular modeling, creating a highly charged protein which both unfolds reversibly at low ionic strength and undergoes the ligand-induced folding transition commonly observed in signal transduction by intrinsically disordered proteins in biology. Due to the high surface charge density, ligand binding to this protein is allosterically activated by low concentrations of divalent cations and the polyamine ...


Digital Commons powered by bepress