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Articles 1 - 30 of 532

Full-Text Articles in Physics

Characteristics Of Sulfur Atoms Adsorbed On Ag(100), Ag(110), And Ag(111) As Probed With Scanning Tunneling Microscopy: Experiment And Theory, Peter M. Spurgeon, Da-Jiang Liu, Holly Walen, Junepyo Oh, Hyun Jin Yang, Yousoo Kim, Patricia A. Thiel May 2019

Characteristics Of Sulfur Atoms Adsorbed On Ag(100), Ag(110), And Ag(111) As Probed With Scanning Tunneling Microscopy: Experiment And Theory, Peter M. Spurgeon, Da-Jiang Liu, Holly Walen, Junepyo Oh, Hyun Jin Yang, Yousoo Kim, Patricia A. Thiel

Chemistry Publications

In this paper, we report that S atoms on Ag(100) and Ag(110) exhibit a distinctive range of appearances in scanning tunneling microscopy (STM) images, depending on the sample bias voltage, VS. Progressing from negative to positive VS, the atomic shape can be described as a round protrusion surrounded by a dark halo (sombrero) in which the central protrusion shrinks, leaving only a round depression. This progression resembles that reported previously for S atoms on Cu(100). We test whether DFT can reproduce these shapes and the transition between them, using a modified version of the Lang–Tersoff–Hamann ...


Magnetic Borophenes From An Evolutionary Search, Meng-Hong Zhu, Xiao-Ji Weng, Guoying Gao, Shuai Dong, Ling-Fang Lin, Wei-Hua Wang, Qiang Zhu, Artem R. Oganov, Xiao Dong, Yongjun Tian, Xiang-Feng Zhou, Hui-Tian Wang May 2019

Magnetic Borophenes From An Evolutionary Search, Meng-Hong Zhu, Xiao-Ji Weng, Guoying Gao, Shuai Dong, Ling-Fang Lin, Wei-Hua Wang, Qiang Zhu, Artem R. Oganov, Xiao Dong, Yongjun Tian, Xiang-Feng Zhou, Hui-Tian Wang

Physics & Astronomy Faculty Publications

A computational methodology based on ab initio evolutionary algorithms and spin-polarized density functional theory was developed to predict two-dimensional magnetic materials. Its application to a model system borophene reveals an unexpected rich magnetism and polymorphism. A metastable borophene with nonzero thickness is an antiferromagnetic semiconductor from first-principles calculations, and can be further tuned into a half-metal by finite electron doping. In this borophene, the buckling and coupling among three atomic layers are not only responsible for magnetism, but also result in an out-of-plane negative Poisson's ratio under uniaxial tension, making it the first elemental material possessing auxetic and magnetic ...


Seeing Eye To Eye: A Machine Learning Approach To Automated Saccade Analysis, Maigh Attre May 2019

Seeing Eye To Eye: A Machine Learning Approach To Automated Saccade Analysis, Maigh Attre

Honors Scholar Theses

Abnormal ocular motility is a common manifestation of many underlying pathologies particularly those that are neurological. Dynamics of saccades, when the eye rapidly changes its point of fixation, have been characterized for many neurological disorders including concussions, traumatic brain injuries (TBI), and Parkinson’s disease. However, widespread saccade analysis for diagnostic and research purposes requires the recognition of certain eye movement parameters. Key information such as velocity and duration must be determined from data based on a wide set of patients’ characteristics that may range in eye shapes and iris, hair and skin pigmentation [36]. Previous work on saccade analysis ...


Quantification Of Contrast-Enhanced Ultrasound, Joseph Pathoulas Apr 2019

Quantification Of Contrast-Enhanced Ultrasound, Joseph Pathoulas

All College Thesis Program, 2016-present

The aim of this experiment was to investigate the effect of manipulating ultrasound scanner settings on time-intensity curve parameters in a tube perfusion phantom system using contrast-enhanced ultrasound imaging. Imaging was performed using a Philips LOGIQ E9 ultrasound scanner equipped with a C1-6VN transducer and utilized two different microbubble contrast agents: Definity and Lumason. The ultrasound scanner settings manipulated included: gain, dynamic range, and frequency. Additionally, relative microbubble concentration, microbubble type, and perfusion flow rate were manipulated. Four time-intensity curve parameters (time to peak, area under curve, gradient, peak intensity) were measured from linearized pixel data. Time to peak was ...


Mg Assisted Flux Growth And Characterization Of Single Crystalline Sm2co17, Tej Nath Lamichhane, Qisheng Lin, Valentin Taufour, Andriy Palasyuk, Tribhuwan Pandey, David Parker, Sergey L. Bud’Ko, Paul C. Canfield Mar 2019

Mg Assisted Flux Growth And Characterization Of Single Crystalline Sm2co17, Tej Nath Lamichhane, Qisheng Lin, Valentin Taufour, Andriy Palasyuk, Tribhuwan Pandey, David Parker, Sergey L. Bud’Ko, Paul C. Canfield

Ames Laboratory Accepted Manuscripts

This paper presents details of Mg-assisted flux growth of Sm2Co17 single crystals in a Ta crucible well below the melting temperature of binary Sm2Co17. Both the crushed single crystalline powder x-ray diffraction (XRD) and single crystalline XRD data revealed the Th2Zn17 type rhombohedral(R-3m) crystal structure. Ta atom is found to be statistically replacing the Co-Co dumbbell with its position being at the center of the dumbbell. The Curie temperature of our lightly Mg and Ta doped Sm2Co17 sample is determined to be ∼1100 K using method of generalized Bloch law fitting of easy axis spontaneous magnetization data.


Three-Dimensional Time-Resolved Trajectories From Laboratory Insect Swarms, Michael Sinhuber, Kasper Van Der Vaart, Rui Ni, James G. Puckett, Douglas H. Kelley, Nicholas T. Ouellette Mar 2019

Three-Dimensional Time-Resolved Trajectories From Laboratory Insect Swarms, Michael Sinhuber, Kasper Van Der Vaart, Rui Ni, James G. Puckett, Douglas H. Kelley, Nicholas T. Ouellette

Physics and Astronomy Faculty Publications

Aggregations of animals display complex and dynamic behaviour, both at the individual level and on the level of the group as a whole. Often, this behaviour is collective, so that the group exhibits properties that are distinct from those of the individuals. In insect swarms, the motion of individuals is typically convoluted, and swarms display neither net polarization nor correlation. The swarms themselves, however, remain nearly stationary and maintain their cohesion even in noisy natural environments. This behaviour stands in contrast with other forms of collective animal behaviour, such as flocking, schooling, or herding, where the motion of individuals is ...


A Theoretical Model Of Underground Dipole Antennas For Communications In Internet Of Underground Things, Abdul Salam, Mehmet C. Vuran, Xin Dong, Christos Argyropoulos, Suat Irmak Feb 2019

A Theoretical Model Of Underground Dipole Antennas For Communications In Internet Of Underground Things, Abdul Salam, Mehmet C. Vuran, Xin Dong, Christos Argyropoulos, Suat Irmak

Faculty Publications

The realization of Internet of Underground Things (IOUT) relies on the establishment of reliable communication links, where the antenna becomes a major design component due to the significant impacts of soil. In this paper, a theoretical model is developed to capture the impacts of change of soil moisture on the return loss, resonant frequency, and bandwidth of a buried dipole antenna. Experiments are conducted in silty clay loam, sandy, and silt loam soil, to characterize the effects of soil, in an indoor testbed and field testbeds. It is shown that at subsurface burial depths (0.1-0.4m), change in soil ...


Fluorine Chemistry At Extreme Conditions: Possible Synthesis Of Hgf4, Michael G. Pravica, Sarah Schyck, Blake Harris, Petrika Cifligu, Eunja Kim, Brant Billinghurst Feb 2019

Fluorine Chemistry At Extreme Conditions: Possible Synthesis Of Hgf4, Michael G. Pravica, Sarah Schyck, Blake Harris, Petrika Cifligu, Eunja Kim, Brant Billinghurst

Physics & Astronomy Faculty Publications

By irradiating a pressurized mixture of a fluorine-bearing compound (XeF2XeF2) and HgF2HgF2 with synchrotron hard x-rays ... (See full text for complete abstract)


Fundamental Limits Of Measuring Single-Molecule Rotational Mobility, Oumeng Zhang, Matthew D. Lew Feb 2019

Fundamental Limits Of Measuring Single-Molecule Rotational Mobility, Oumeng Zhang, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Various methods exist for measuring molecular orientation, thereby providing insight into biochemical activities at nanoscale. Since fluorescence intensity and not electric field is detected, these methods are limited to measuring even-order moments of molecular orientation. However, any measurement noise, for example photon shot noise, will result in nonzero measurements of any of these even-order moments, thereby causing rotationally-free molecules to appear to be partially constrained. Here, we build a model to quantify measurement errors in rotational mobility. Our theoretical framework enables scientists to choose the optimal single-molecule orientation measurement technique for any desired measurement accuracy and photon budget.


Kinetics, Energetics, And Size Dependence Of The Transformation From Pt To Ordered Ptsn Intermetallic Nanoparticles, Minda Chen, Yong Han, Tian Wei Goh, Rong Sun, Raghu V. Maligal‐Ganesh, Yuchen Pei, Chia‐ Kuang Tsung, James W. Evans, Wenyu Huang Jan 2019

Kinetics, Energetics, And Size Dependence Of The Transformation From Pt To Ordered Ptsn Intermetallic Nanoparticles, Minda Chen, Yong Han, Tian Wei Goh, Rong Sun, Raghu V. Maligal‐Ganesh, Yuchen Pei, Chia‐ Kuang Tsung, James W. Evans, Wenyu Huang

Chemistry Publications

The outstanding catalytic activity and chemical selectivity of intermetallic compounds make them excellent candidates for heterogeneous catalysis. However, the kinetics of their formation at the nanoscale is poorly understood or characterized, and precise control of their size, shape as well as composition during synthesis remains challenging. Here, using well-defined Pt nanoparticles (5 nm and 14 nm) encapsulated in mesoporous silica, we study the transformation kinetics from monometallic Pt to intermetallic PtSn at different temperatures by a series of time-evolution X-ray diffraction studies. Observations indicate an initial transformation stage mediated by Pt surface-controlled intermixing kinetics, followed by a second stage with ...


Shedding Light On The Atomic-Scale Structure Of Amorphous Silica–Alumina And Its Brønsted Acid Sites, Frédéric A. Perras, Zichun Wang, Takeshi Kobayashi, Alfons Baiker, Jun Huang, Marek Pruski Jan 2019

Shedding Light On The Atomic-Scale Structure Of Amorphous Silica–Alumina And Its Brønsted Acid Sites, Frédéric A. Perras, Zichun Wang, Takeshi Kobayashi, Alfons Baiker, Jun Huang, Marek Pruski

Ames Laboratory Accepted Manuscripts

In spite of the widespread applications of amorphous silica–aluminas (ASAs) in many important industrial chemical processes, their high-resolution structures have remained largely elusive. Specifically, the lack of long-range ordering in ASA precludes the use of diffraction methods while NMR spectroscopy has been limited by low sensitivity. Here, we use conventional as well as DNP-enhanced 29Si–29Si, 27Al–27Al, and 29Si–27Al solid-state NMR experiments to shed light on the ordering of atoms in ASAs prepared by flame-spray-pyrolysis. These experiments, in conjunction with a novel Monte Carlo-based approach to simulating RESPDOR dephasing curves, revealed that ASA materials obey Loewenstein's ...


Kinetics Of The Γ–Δ Phase Transition In Energetic Nitramine-Octahydro-1,3,5,7-Tetranitro-1,3,5,7-Tetrazocine, P. Bowlan, B. F. Henson, L. Smilowitz, Valery I. Levitas, N. Suvorova, D. Oschwald Jan 2019

Kinetics Of The Γ–Δ Phase Transition In Energetic Nitramine-Octahydro-1,3,5,7-Tetranitro-1,3,5,7-Tetrazocine, P. Bowlan, B. F. Henson, L. Smilowitz, Valery I. Levitas, N. Suvorova, D. Oschwald

Aerospace Engineering Publications

The solid, secondary explosive nitramine-octahydro-1,3,5,7-tetranitro-1,3,5,7 or HMX has four different stable polymorphs which have different molecular conformations, crystalline structures, and densities, making structural phase transitions between these nontrivial. Previous studies of the kinetics of the βδ HMX structural transition found this to happen by a nucleation and growth mechanism, where growth was governed by the heat of fusion, or melting, even though the phase transition temperature is more than 100 K below the melting point. A theory known as virtual melting could easily justify this since the large volume difference in the two ...


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 Jan 2019

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 ...


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 Oct 2018

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 Oct 2018

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 ...


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 Sep 2018

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 ...


From Photon To Neuron Chapter 16: Tunneling Of Photons And Electrons, Philip C. Nelson Aug 2018

From Photon To Neuron Chapter 16: Tunneling Of Photons And Electrons, Philip C. Nelson

Department of Physics Papers

This chapter extends Part III of the book From Photon to Neuron (Princeton Univ Press 2017). This preliminary version is made freely available as-is in the hope that it will be useful.


E. Coli Elongation Factor Tu Bound To A Gtp Analogue Displays An Open Conformation Equivalent To The Gdp-Bound Form, Jesper S. Johansen, Darius Kavaliauskas, Shawn H. Pfeill, Mickael Blaise, Barry C. Cooperman, Yale E. Goldman, Søren S. Thirup, Charlotte R. Knudsen Aug 2018

E. Coli Elongation Factor Tu Bound To A Gtp Analogue Displays An Open Conformation Equivalent To The Gdp-Bound Form, Jesper S. Johansen, Darius Kavaliauskas, Shawn H. Pfeill, Mickael Blaise, Barry C. Cooperman, Yale E. Goldman, Søren S. Thirup, Charlotte R. Knudsen

Physics

According to the traditional view, GTPases act as molecular switches, which cycle between distinct ‘on’ and ‘off’ conformations bound to GTP and GDP, respectively. Translation elongation factor EF-Tu is a GTPase essential for prokaryotic protein synthesis. In its GTP-bound form, EF-Tu delivers aminoacylated tRNAs to the ribosome as a ternary complex. GTP hydrolysis is thought to cause the release of EF-Tu from aminoacyl-tRNA and the ribosome due to a dramatic conformational change following Pi release. Here, the crystal structure of Escherichia coli EF-Tu in complex with a non-hydrolysable GTP analogue (GDPNP) has been determined. Remarkably, the overall conformation of EF-Tu ...


Potential Of Mean Force For Two Nanocrystals: Core Geometry And Size, Hydrocarbon Unsaturation, And Universality With Respect To The Force Field, Curt Waltmann, Nathan Horst, Alex Travesset Jul 2018

Potential Of Mean Force For Two Nanocrystals: Core Geometry And Size, Hydrocarbon Unsaturation, And Universality With Respect To The Force Field, Curt Waltmann, Nathan Horst, Alex Travesset

Ames Laboratory Accepted Manuscripts

We present a detailed analysis of the interaction between two nanocrystals capped with ligands consisting of hydrocarbon chains by united atom molecular dynamics simulations. We analyze large cores (up to 10 nm in diameter) and ligands with unsaturated carbon bonds (oleic acid) and we investigate the accuracy of the computed potential of mean force by comparing different force fields. We also analyze the vortices that determine the bonding, including the case of asymmetric nanocrystals, and discuss effects related to the intrinsic anisotropy of the core. Overall our results are in agreement with the predictions of the recently proposed orbifold topological ...


Pore Diameter Dependence Of Catalytic Activity: P-Nitrobenzaldehyde Conversion To An Aldol Product In Amine-Functionalized Mesoporous Silica, Andres Garcia, Igor I. Slowing, James W. Evans Jul 2018

Pore Diameter Dependence Of Catalytic Activity: P-Nitrobenzaldehyde Conversion To An Aldol Product In Amine-Functionalized Mesoporous Silica, Andres Garcia, Igor I. Slowing, James W. Evans

Chemistry Publications

The reaction yield for conversion of p-nitrobenzaldehyde (PNB) to an aldol product in amine-functionalized mesoporous silica nanoparticles (MSN) exhibits a 20-fold enhancement for a modest increase in pore diameter, d. This enhanced catalytic activity is shown to reflect a strong increase in the “passing propensity,” 𝒫, of reactant and product species inside the pores. We find that 𝒫 ≈ 0, corresponding to single-file diffusion, applies for the smallest d which still significantly exceeds the linear dimensions of PNB and the aldol product. However, in this regime of narrow pores, these elongated species must align with each other and with the pore ...


Spatial–Temporal Spectroscopy Characterizations And Electronic Structure Of Methylammonium Perovskites, Zhaoyu Liu, K. C. Bhamu, Liang Luo, Satvik Shah, Joong-Mok Park, Di Cheng, Men Long, Rana Biswas, F. Fungara, Ruth Shinar, Joseph Shinar, Javier Vela, Jigang Wang Jul 2018

Spatial–Temporal Spectroscopy Characterizations And Electronic Structure Of Methylammonium Perovskites, Zhaoyu Liu, K. C. Bhamu, Liang Luo, Satvik Shah, Joong-Mok Park, Di Cheng, Men Long, Rana Biswas, F. Fungara, Ruth Shinar, Joseph Shinar, Javier Vela, Jigang Wang

Chemistry Publications

Using time-resolved laser-scanning confocal microscopy and ultrafast optical pump/THz probe spectroscopy, we measure photoluminescence and THz-conductivity in perovskite micro-crystals and films. Photoluminescence quenching and lifetime variations occur from local heterogeneity. Ultrafast THz-spectra measure sharp quantum transitions from excitonic Rydberg states, providing weakly bound excitons with a binding energy of ~13.5 meV at low temperatures. Ab-initio electronic structure calculations give a direct band gap of 1.64 eV, a dielectric constant ~18, heavy electrons, and light holes, resulting in weakly bound excitons, consistent with the binding energies from experiment. The complementary spectroscopy and simulations reveal fundamental insights into perovskite ...


Molecular Dynamics Simulation Of The Solid-Liquid Interface Migration In Terbium, Mikhail I. Mendelev, Feng Zhang, H. Song, Yang Sun, Cai-Zhuang Wang, Kai-Ming Ho Jun 2018

Molecular Dynamics Simulation Of The Solid-Liquid Interface Migration In Terbium, Mikhail I. Mendelev, Feng Zhang, H. Song, Yang Sun, Cai-Zhuang Wang, Kai-Ming Ho

Ames Laboratory Accepted Manuscripts

We developed a Tb embedded atom method potential which properly reproduces the liquid structure obtained from the ab initio molecular dynamics simulation, the hexagonal close packed (hcp)-body-centered cubic (bcc) phase transformation, and melting temperatures. At least three crystal phases [hcp, face-centered cubic (fcc), and bcc] described by this potential can coexist with the liquid phase. Thus, the developed potential provides an excellent test bed for studies of the completive phase nucleation and growth in a single component system. The molecular dynamics simulation showed that all crystal phases can grow from the liquid phase close to their melting temperatures. However ...


Advancing Raman Microspectroscopy For Cellular And Subcellular Analysis: Towards In Vitro High Content Spectralomic Analysis, Hugh Byrne, Franck Bonnier, Alan Casey, Marcus Maher, Jennifer Mcintyre, Esen Efeoglu, Zeineb Farhane Jun 2018

Advancing Raman Microspectroscopy For Cellular And Subcellular Analysis: Towards In Vitro High Content Spectralomic Analysis, Hugh Byrne, Franck Bonnier, Alan Casey, Marcus Maher, Jennifer Mcintyre, Esen Efeoglu, Zeineb Farhane

Articles

In the confocal mode, Raman microspectroscopy can profile the biochemical content of biological cells at a subcellular level, and any changes to it by exogenous agents, such as therapeutic drugs or toxicants. As an exploration of the potential of the technique as a high content, label free analysis technique, this report reviews work to monitor the spectroscopic signatures associated with the uptake and response pathways of commercial chemotherapeutic agents and polymeric nanoparticles by human lung cells. It is demonstrated that the signatures are reproducible and characteristic of the cellular event, and can be used, for example, to identify the mode ...


Multicomponent Analysis Using A Confocal Raman Microscope, Zhengyuan Tang, Sinead J. Barton, Thomas E. Ward, John P. Lowry, Michelle M. Doran, Hugh Byrne, Bryan M. Hennelly Jun 2018

Multicomponent Analysis Using A Confocal Raman Microscope, Zhengyuan Tang, Sinead J. Barton, Thomas E. Ward, John P. Lowry, Michelle M. Doran, Hugh Byrne, Bryan M. Hennelly

Articles

Measuring the concentration of multiple chemical components in a low volume aqueous mixture by Raman spectroscopy has received significant interest in the literature. All of the contributions to date focus on the design of optical systems that facilitate the recording of spectra with high signal-to-noise ratio, by collecting as many Raman scattered photons as possible. In this study, the confocal Raman microscope set-up is investigated for multicomponent analysis. Partial Least Squares Regression is used to quantify physiologically relevant aqueous mixtures of glucose, lactic acid, and urea. The predicted error is 17.81 mg/dL for glucose, 10.6 mg/dL ...


Theoretical Prediction Of Crystallization Kinetics Of A Supercooled Lennard-Jones Fluid, K. G. S. H. Gunawardana, Xueyu Song May 2018

Theoretical Prediction Of Crystallization Kinetics Of A Supercooled Lennard-Jones Fluid, K. G. S. H. Gunawardana, Xueyu Song

Chemistry Publications

The first order curvature correction to the crystal-liquid interfacial free energy is calculated using a theoretical model based on the interfacial excess thermodynamic properties. The correction parameter (δ), which is analogous to the Tolman length at a liquid-vapor interface, is found to be 0.48 ± 0.05 for a Lennard-Jones (LJ) fluid. We show that this curvature correction is crucial in predicting the nucleation barrier when the size of the crystal nucleus is small. The thermodynamic driving force (Δμ) corresponding to available simulated nucleation conditions is also calculated by combining the simulated data with a classical density functional theory ...


Spectroscopy And Formation Of Lanthanum-Hydrocarbon Radicals Formed By Association And Carbon-Carbon Bond Cleavage Of Isoprene, Wenjin Cao, Dilkrushi Hewage, Dong-Sheng Yang May 2018

Spectroscopy And Formation Of Lanthanum-Hydrocarbon Radicals Formed By Association And Carbon-Carbon Bond Cleavage Of Isoprene, Wenjin Cao, Dilkrushi Hewage, Dong-Sheng Yang

Chemistry Faculty Publications

La atom reaction with isoprene is carried out in a laser-vaporization molecular beam source. The reaction yields an adduct as the major product and C—C cleaved and dehydrogenated species as the minor ones. La(C5H8), La(C2H2), and La(C3H4) are characterized with mass-analyzed threshold ionization (MATI) spectroscopy and quantum chemical computations. The MATI spectra of all three species exhibit a strong origin band and several weak vibronic bands corresponding to La-ligand stretch and ligand-based bend excitations. La(C5H8) is a five-membered metallacycle, whereas La(C2 ...


Collective Gradient Sensing In Fish Schools, James G. Puckett, Aawaz R. Pokhrel, Julia A. Giannini May 2018

Collective Gradient Sensing In Fish Schools, James G. Puckett, Aawaz R. Pokhrel, Julia A. Giannini

Physics and Astronomy Faculty Publications

Throughout the animal kingdom, animals frequently benefit from living in groups. Models of collective behaviour show that simple local interactions are sufficient to generate group morphologies found in nature (swarms, flocks and mills). However, individuals also interact with the complex noisy environment in which they live. In this work, we experimentally investigate the group performance in navigating a noisy light gradient of two unrelated freshwater species: golden shiners (Notemigonuscrysoleucas) and rummy nose tetra (Hemigrammus bleheri). We find that tetras outperform shiners due to their innate individual ability to sense the environmental gradient. Using numerical simulations, we examine how group performance ...


Local Structure Orders And Glass Forming Ability Of Ni-Nb Liquids, T. Q. Wen, Y. Zhang, Cai-Zhuang Wang, N. Wang, Kai-Ming Ho, Matthew J. Kramer May 2018

Local Structure Orders And Glass Forming Ability Of Ni-Nb Liquids, T. Q. Wen, Y. Zhang, Cai-Zhuang Wang, N. Wang, Kai-Ming Ho, Matthew J. Kramer

Ames Laboratory Accepted Manuscripts

Ab initio molecular dynamics simulations were performed to study the atomistic structures of Ni48Nb52, Ni59.5Nb40.5 and Ni75Nb25 liquids near their melting temperatures. It is found that the total coordination number only changes slightly across the compositions. However, there is significant difference in the chemical ordering. The Cluster Alignment method was used to identify the dominant local structure motifs. It is found that distorted and perfect icosahedral clusters are the most popular motifs around Ni atoms, while Z14, Z15, and Z16 Frank-Kasper polyhedra are dominant around Nb atoms. Among the three compositions, the eutectic composition (Ni59.5Nb40.5) has ...


Computational Analysis Of Poliovirus Structural Dynamics Using A Coarse-Grained Model, Maneesh Koneru May 2018

Computational Analysis Of Poliovirus Structural Dynamics Using A Coarse-Grained Model, Maneesh Koneru

University Scholar Projects

Though eradicated in most of the world, poliovirus remains a common model virus for a family of mammalian viruses known as Picornaviruses. Despite the development of a vaccination, little is understood about the infection process, particularly the mechanism of cell entry. Experimental studies have attempted to elucidate the dynamics of this process and have proposed pathways focused on VP4, the smallest of the four peptides which makes up the viral capsid, and its interaction with the pentameric interfaces of the five fold axes. This study utilizes coarse-grained molecular dynamics to supplement these proposed mechanisms with simplified simulations which reduce the ...


Raman Spectral Analysis For Rapid Screening Of Dengue Infection, Tahir Mahmood, Haq Nawaz, A. Ditta, M.I. Majeed, M.A. Hanif, N. Rashid, H.N. Bhatti, H.F. Nargis, M. Saleem, Franck Bonnier, Hugh Byrne May 2018

Raman Spectral Analysis For Rapid Screening Of Dengue Infection, Tahir Mahmood, Haq Nawaz, A. Ditta, M.I. Majeed, M.A. Hanif, N. Rashid, H.N. Bhatti, H.F. Nargis, M. Saleem, Franck Bonnier, Hugh Byrne

Articles

Infection with the dengue virus is currently clinically detected according to different biomarkers in human blood plasma, commonly measured by enzyme linked immunosorbent assays, including non-structural proteins (Ns1), immunoglobulin M (IgM) and immunoglobulin G (IgG). However, there is little or no mutual correlation between the biomarkers, as demonstrated in this study by a comparison of their levels in samples from 17 patients. As an alternative, the label free, rapid screening technique, Raman spectroscopy has been used for the characterisation/diagnosis of healthy and dengue infected human blood plasma samples. In dengue positive samples, changes in specific Raman spectral bands associated ...