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Articles 1 - 25 of 25

Full-Text Articles in Biological and Chemical Physics

Regulation Of Cytoplasmic Dynein By Lis1 And Adenomatous Polyposis Coli, Timothy Joshua Hines Jan 2018

Regulation Of Cytoplasmic Dynein By Lis1 And Adenomatous Polyposis Coli, Timothy Joshua Hines

Theses and Dissertations

Cytoplasmic dynein 1 (dynein) is a microtubule motor that plays a role in mitosis, cell migration, and minus-end directed microtubule-based transport. The lissencephaly protein, Lis1, and its binding partner, Ndel1, are critical regulators of cytoplasmic dynein (Niethammer et al., 2000). In humans, haploinsufficiency of Lis1 leads to lissencephaly, a devastating developmental neurological disorder characterized by severe brain malformation, leading to cognitive and motor defects, and progressively worsening seizures (Dobyns et al., 1993). While Lis1 is known to play a role in regulating dynein-dependent functions such as neuronal migration and mitotic spindle orientation during development, the protein is still highly expressed …

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Ecology And Virulence Capabilities Of Vibrios Isolated From The Pristine North Inlet Estuary, Savannah Leigh Klein Jan 2018

Ecology And Virulence Capabilities Of Vibrios Isolated From The Pristine North Inlet Estuary, Savannah Leigh Klein

Theses and Dissertations

Vibrio bacteria are Gram negative, motile organisms that occur naturally in most coastal and estuarine ecosystems. Some vibrios are important human pathogens, including Vibrio parahaemolyticus and Vibrio vulnificus. The CDC estimates that vibrios cause 80,000 cases of disease each year in the United States alone. Most cases are caused by V. parahaemolyticus, which infects humans after the consumption of contaminated raw or undercooked seafood, primarily oysters. V. parahaemolyticus causes mild gastroenteritis that is self-limiting unless the patient is immunocompromised. V. vulnificus has a much lower incidence of disease (100 cases in the USA yr-1); however, this organism causes much more …

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Investigation Of Iron Oxide Nanocolloidal Suspension Diffusion Using A Direct Imaging Method, Ashley E. Rice, Ana Oprisan Nov 2017

Investigation Of Iron Oxide Nanocolloidal Suspension Diffusion Using A Direct Imaging Method, Ashley E. Rice, Ana Oprisan

Journal of the South Carolina Academy of Science

We performed a set of experiments using a direct imaging method to investigate the diffusion process of iron oxide, Fe2O3, nanoparticles. We studied concentration fluctuations that move against the concentration gradient and induce disturbances in the interface between the iron oxide suspension and water in the sample cell. Using this imaging method in combination with the differential dynamic algorithm for image processing, we are able to extract information about the power, size, and lifetime of the fluctuations. We performed this experiment both in the presence and in the absence of a 4.2 mT magnetic field. We …

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Enhanced Nucleate Boiling On Horizontal Hydrophobic-Hydrophilic Carbon Nanotube Coatings, Xianming Dai, Xinyu Huang, Fanghao Yang, Xiaodong Li, Joshua Sightler, Yingchao Yang, Chen Li Apr 2013

Enhanced Nucleate Boiling On Horizontal Hydrophobic-Hydrophilic Carbon Nanotube Coatings, Xianming Dai, Xinyu Huang, Fanghao Yang, Xiaodong Li, Joshua Sightler, Yingchao Yang, Chen Li

Faculty Publications

Ideal hydrophobic-hydrophilic composite cavities are highly desired to enhance nucleate boiling. However, it is challenging and costly to fabricate these types of cavities by conventional micro/nano fabrication techniques. In this study, a type of hydrophobic-hydrophilic composite interfaces were synthesized from functionalized multiwall carbon nanotubes by introducing hydrophilic functional groups on the pristine multiwall carbon nanotubes. This type of carbon nanotube enabled hydrophobic-hydrophilic composite interfaces were systematically characterized. Ideal cavities created by the interfaces were experimentally demonstrated to be the primary reason to substantially enhance nucleate boiling

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The Schrödinger Equation With Friction From The Quantum Trajectory Perspective, Sophya V. Garashchuk, Vaibhav Dixit, Bing Gu, James Mazzuca Feb 2013

The Schrödinger Equation With Friction From The Quantum Trajectory Perspective, Sophya V. Garashchuk, Vaibhav Dixit, Bing Gu, James Mazzuca

Faculty Publications

Similarity of equations of motion for the classical and quantum trajectories is used to introduce afriction term dependent on the wavefunction phase into the time-dependent Schrödingerequation. The term describes irreversible energy loss by the quantum system. The force offriction is proportional to the velocity of a quantum trajectory. The resulting Schrödinger equationis nonlinear, conserves wavefunction normalization, and evolves an arbitrary wavefunction into the ground state of the system (of appropriate symmetry if applicable). Decrease in energy is proportional to the average kinetic energy of the quantum trajectory ensemble. Dynamics in the high friction regime is suitable for simple models of …

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Systematic Approach To Electrostatically Induced 2d Crystallization Of Nanoparticles At Liquid Interfaces, Sumit Kewalramani, Suntao Wang, Yuan Lin, Huong Giang Nguyen, Qian Wang, Masafumi Fukuto, Lin Yang Nov 2010

Systematic Approach To Electrostatically Induced 2d Crystallization Of Nanoparticles At Liquid Interfaces, Sumit Kewalramani, Suntao Wang, Yuan Lin, Huong Giang Nguyen, Qian Wang, Masafumi Fukuto, Lin Yang

Faculty Publications

We report an experimental demonstration of a strategy for inducing two-dimensional (2D)crystallization of charged nanoparticles on oppositely charged fluid interfaces. This strategy aims to maximize the interfacial adsorption of nanoparticles, and hence their lateral packing density, by utilizing a combination of weakly charged particles and a high surface charge density on the planar interface. In order to test this approach, we investigated the assembly of cowpea mosaic virus (CPMV) on positively charged lipid monolayers at the aqueous solution surface, by means of in situX-ray scattering measurements at the liquid–vapor interface. Theassembly was studied as a function of the solution …

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Modeling The Noble Metal/Tio2 (110) Interface With Hybrid Dft Functionals: A Periodic Electrostatic Embedded Cluster Model Study, Salai Cheettu Ammal, Andreas Heyden Jan 2010

Modeling The Noble Metal/Tio2 (110) Interface With Hybrid Dft Functionals: A Periodic Electrostatic Embedded Cluster Model Study, Salai Cheettu Ammal, Andreas Heyden

Faculty Publications

The interaction of Aun and Ptn (n=2,3) clusters with the stoichiometric and partially reduced rutile TiO2 (110) surfaces has been investigated using periodic slab and periodic electrostatic embedded cluster models. Compared to Au clusters, Pt clusters interact strongly with both stoichiometric and reduced TiO2 (110) surfaces and are able to enhance the reducibility of the TiO2 (110) surface, i.e., reduce the oxygen vacancy formation energy. The focus of this study is the effect of Hartree–Fock exchange on the description of the strength of chemical bonds at the interface of Au/Pt clusters and the TiO2 (110) surface. Hartree–Fock exchange helps describing …

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Dynamic Path Bifurcation For The Beckmann Reaction: Observation And Implication, H. Yamataka, M. Sato, H. Hasegawa, Salai Cheettu Ammal Jan 2010

Dynamic Path Bifurcation For The Beckmann Reaction: Observation And Implication, H. Yamataka, M. Sato, H. Hasegawa, Salai Cheettu Ammal

Faculty Publications

The reaction of oximes to amides, known as the Beckmann rearrangement, may undergo fragmentation to form carbocations + nitriles instead of amides when the cations have reasonable stability. The reactions of oxime derivatives of 1-substituted-phenyl-2-propanones and 3-substituted-phenyl-2-butanones in aqueous solvents gave both rearrangement and fragmentation products, the ratio of which was dependent on substituents. Transition state (TS) optimizations and intrinsic reaction coordinate (IRC) calculations for the reaction of 1-phenyl-2-propanone oximes showed that there is a single TS for each substituted compound. The IRC path from the TS either led to a rearrangement product or a fragmentation product depending on the …

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Growth And Transport Properties Of Complementary Germanium Nanowire Field Effect Transistors, Andrew B. Greytak, Lincoln J. Lauhon, Mark S. Gudiksen, Charles M. Lieber May 2004

Growth And Transport Properties Of Complementary Germanium Nanowire Field Effect Transistors, Andrew B. Greytak, Lincoln J. Lauhon, Mark S. Gudiksen, Charles M. Lieber

Faculty Publications

n- and p-type Ge nanowires were synthesized by a multistep process in which axial elongation, via vapor–liquid–solid (VLS) growth, and doping were accomplished in separate chemical vapor deposition steps. Intrinsic, single-crystal, Ge nanowires prepared by Au nanocluster-mediated VLS growth were surface-doped in situ using diborane or phosphine, and then radial growth of an epitaxial Ge shell was used to cap the dopant layer. Field-effect transistors prepared from these Ge nanowires exhibited on currents and transconductances up to 850 µA/µm and 4.9 µA/V, respectively, with device yields of >85%.

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Bohmian Dynamics On Subspaces Using Linearized Quantum Force, V. A. Rassolov, Sophya V. Garashchuk Jan 2004

Bohmian Dynamics On Subspaces Using Linearized Quantum Force, V. A. Rassolov, Sophya V. Garashchuk

Faculty Publications

In the de Broglie–Bohm formulation of quantum mechanics the time-dependent Schrödinger equation is solved in terms of quantum trajectories evolving under the influence of quantum and classical potentials. For a practical implementation that scales favorably with system size and is accurate for semiclassical systems, we use approximate quantum potentials. Recently, we have shown that optimization of the nonclassical component of the momentum operator in terms of fitting functions leads to the energy-conserving approximate quantum potential. In particular, linear fitting functions give the exact time evolution of a Gaussian wave packet in a locally quadratic potential and can describe the dominant …

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Geminal Model Chemistry Ii. Perturbative Corrections, V. A. Rassolov, F. Xu, Sophya V. Garashchuk Jan 2004

Geminal Model Chemistry Ii. Perturbative Corrections, V. A. Rassolov, F. Xu, Sophya V. Garashchuk

Faculty Publications

We introduce and investigate a chemical model based on perturbative corrections to the product of singlet-type strongly orthogonal geminals wave function. Two specific points are addressed (i) Overall chemical accuracy of such a model with perturbative corrections at a leading order; (ii) Quality of strong orthogonality approximation of geminals in diverse chemical systems. We use the Epstein–Nesbet form of perturbation theory and show that its known shortcomings disappear when it is used with the reference Hamiltonian based on strongly orthogonal geminals. Application of this model to various chemical systems reveals that strongly orthogonal geminals are well suited for chemical models, …

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Semiclassical Dynamics With Quantum Trajectories: Formulation And Comparison With The Semiclassical Initial Value Representation Propagator, Sophya V. Garashchuk, V. A. Rassolov Jan 2003

Semiclassical Dynamics With Quantum Trajectories: Formulation And Comparison With The Semiclassical Initial Value Representation Propagator, Sophya V. Garashchuk, V. A. Rassolov

Faculty Publications

We present a time-dependent semiclassical method based on quantum trajectories. Quantum-mechanical effects are described via the quantum potential computed from the wave function density approximated as a linear combination of Gaussian fitting functions. The number of the fitting functions determines the accuracy of the approximate quantum potential (AQP). One Gaussian fit reproduces time-evolution of a Gaussian wave packet in a parabolic potential. The limit of the large number of fitting Gaussians and trajectories gives the full quantum-mechanical result. The method is systematically improvable from classical to fully quantum. The fitting procedure is implemented as a gradient minimization. We also compare …

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Shape Imprinting Due To Variable Disulfide Bonds In Polyacrylamide Gels, Andrew B. Greytak, Alexander Y. Grosberg, Toyoichi Tanaka Jun 2001

Shape Imprinting Due To Variable Disulfide Bonds In Polyacrylamide Gels, Andrew B. Greytak, Alexander Y. Grosberg, Toyoichi Tanaka

Faculty Publications

Through the use of variable disulfide crosslinkers, we have created polyacrylamide gels whose shape can be altered after polymerization. N,N'-bisacryloylcystamine is incorporated as a crosslinker, along with a smaller amount of a permanent crosslinker. After polymerization, the disulfide bonds are cleaved into thiols through reduction. By reoxidizing the thiols with the gel held in a new macroscopic shape, a new set of disulfide bonds is formed, and the gel is forced to adopt the new shape. Retension of the new shape improves with greater distortion from the original shape, as well as with increased concentration of variable …

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Semiclassical Application Of The Mo/Ller Operators In Reactive Scattering, Sophya V. Garashchuk, J. C. Light Jan 2001

Semiclassical Application Of The Mo/Ller Operators In Reactive Scattering, Sophya V. Garashchuk, J. C. Light

Faculty Publications

Mo/ller operators in the formulation of reaction probabilities in terms of wave packet correlation functions allow us to define the wave packets in the interaction region rather than in the asymptotic region of the potential surface. We combine Mo/ller operators with the semiclassical propagator of Herman and Kluk. This does not involve further approximations and can be used with any initial value representation (IVR) semiclassical propagator. Time propagation in asymptotic regions of the potential due to Mo/ller operators reduces the oscillations of the propagator integrand and improves convergence of the results with respect to the number of trajectories. The effectiveness …

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Quasirandom Distributed Gaussian Bases For Bound Problems, Sophya V. Garashchuk, J. C. Light Jan 2001

Quasirandom Distributed Gaussian Bases For Bound Problems, Sophya V. Garashchuk, J. C. Light

Faculty Publications

We introduce quasirandom distributed Gaussian bases (QDGB) that are well suited for bound problems. The positions of the basis functions are chosen quasirandomly while their widths and density are functions of the potential. The basis function overlap and kinetic energy matrix elements are analytical. The potential energy matrix elements are accurately evaluated using few-point quadratures, since the Gaussian basis functions are localized. The resulting QDGB can be easily constructed and is shown to be accurate and efficient for eigenvalue calculation for several multidimensional model vibrational problems. As more demanding examples, we used a 2D QDGB-DVR basis to calculate the lowest …

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Simplified Calculation Of The Stability Matrix For Semiclassical Propagation, Sophya V. Garashchuk, J. C. Light Jan 2000

Simplified Calculation Of The Stability Matrix For Semiclassical Propagation, Sophya V. Garashchuk, J. C. Light

Faculty Publications

We present a simple method of calculation of the stability (monodromy) matrix that enters the widely used semiclassical propagator of Herman and Kluk and almost all other semiclassical propagators. The method is based on the unitarity of classical propagation and does not involve any approximations. The number of auxiliary differential equations per trajectory scales linearly rather than quadratically with the system size. Just the first derivatives of the potential surface are needed. The method is illustrated on the collinear H3 system.

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Cumulative Reaction Probability In Terms Of Reactant-Product Wave Packet Correlation Functions, Sophya V. Garashchuk, D. J. Tannor Jan 1999

Cumulative Reaction Probability In Terms Of Reactant-Product Wave Packet Correlation Functions, Sophya V. Garashchuk, D. J. Tannor

Faculty Publications

We present new expressions for the cumulative reaction probability (N(E)), cast in terms of time-correlation functions of reactant and product wave packets. The derivation begins with a standard trace expression for the cumulative reaction probability, expressed in terms of the reactive scattering matrix elements in an asymptotic internal basis. By combining the property of invariance of the trace with a wave packet correlation function formulation of reactive scattering, we obtain an expression for N(E) in terms of the correlation matrices of incoming and outgoing wave packets which are arbitrary in the internal coordinates. This formulation, like other recent formulations of …

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Semiclassical Calculation Of Cumulative Reaction Probabilities, Sophya V. Garashchuk, D. J. Tannor Jan 1999

Semiclassical Calculation Of Cumulative Reaction Probabilities, Sophya V. Garashchuk, D. J. Tannor

Faculty Publications

Calculation of chemical reaction rates lies at the very core of theoretical chemistry. The essential dynamical quantity which determines the reaction rate is the energy-dependent cumulative reaction probability, N(E), whose Boltzmann average gives the thermal rate constant, k(T). Converged quantum mechanical calculations of N(E) remain a challenge even for three- and four-atom systems, and a longstanding goal of theoreticians has been to calculate N(E) accurately and efficiently using semiclassical methods. In this article we present a variety of methods for achieving this goal, by combining semiclassical initial value …

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Chemical Signals From Submarine Fluid Advection Onto The Continental Shelf, W. S. Moore, Timothy J. Shaw Sep 1998

Chemical Signals From Submarine Fluid Advection Onto The Continental Shelf, W. S. Moore, Timothy J. Shaw

Faculty Publications

No abstract provided.

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Correlation Function Formulation For The State Selected Total Reaction Probability, Sophya V. Garashchuk, D. J. Tannor Jan 1998

Correlation Function Formulation For The State Selected Total Reaction Probability, Sophya V. Garashchuk, D. J. Tannor

Faculty Publications

A correlation function formulation for the state-selected total reaction probability, Nα(E), is suggested. A wave packet, correlating with a specific set of internal reactant quantum numbers, α, is propagated forward in time until bifurcation is complete at which time the nonreactive portion of the amplitude is discarded. The autocorrelation function of the remaining amplitude is then computed and Fourier transformed to obtain a reactivity spectrum. Dividing by the corresponding spectrum of the original, unfiltered, wave packet normalizes the reactivity spectrum, yielding the total reaction probability from the internal state, α. The procedure requires negligible storage and just one time-energy Fourier …

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Π-Systems As Lithium/Hydrogen Bond Acceptors: Some Theoretical Observations, Salai Cheettu Ammal, P. Venuvanalingam Jan 1998

Π-Systems As Lithium/Hydrogen Bond Acceptors: Some Theoretical Observations, Salai Cheettu Ammal, P. Venuvanalingam

Faculty Publications

Ab initio calculations at the Hartree–Fock and correlated levels and density functional theory calculations have been performed with 6-31++G(d,p) and 6-311++G(d,p)basis sets on LiF and HF complexes of benzene, ethylene, and acetylene. Complex binding energies have been corrected for basis set superposition error, and zero point energy corrections have been done on Hartree–Fock binding energies. Computed results indicate that the complexes exist in different conformations and among them those with π-lithium and π-hydrogen bonds are the most stable. π-lithium bonds are stronger than π-hydrogen bonds. The computed binding energies and geometry of HF complexes correlate well with the available experimental …

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Ab Initio Study Of Formazan And 3-Nitroformazan, G. Buemi, F. Zuccarello, P. Venuvanalingam, M. Ramalingam, Salai Cheettu Ammal Jan 1998

Ab Initio Study Of Formazan And 3-Nitroformazan, G. Buemi, F. Zuccarello, P. Venuvanalingam, M. Ramalingam, Salai Cheettu Ammal

Faculty Publications

Formazan and 3-nitroformazan have been investigated at abinitio level (MP2/6-31G** and B3LYP/6-31G**) in all their possible conformations, for studying the various possibilities of intramolecular hydrogen bonding formation. The trans-syn-s-cis (TSSC), known also asyellowform, has been found to be the most stable conformer (at least in the gas phase) in both compounds. This particular structure is strongly stabilized by a N–H···N hydrogen bridge, which gives rise to a hexatomic chelate ring, with the possibility of a proton transfer process.This closely resembles that of malondialdehyde, previously studied, in the evolution of the …

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Ab Initio And Dft Investigations Of Lithium/Hydrogen Bonded Complexes Of Trimethylamine, Dimethyl Ether And Dimethyl Sulfide, Salai Cheettu Ammal, P. Venuvanalingam Jan 1998

Ab Initio And Dft Investigations Of Lithium/Hydrogen Bonded Complexes Of Trimethylamine, Dimethyl Ether And Dimethyl Sulfide, Salai Cheettu Ammal, P. Venuvanalingam

Faculty Publications

Ab initio and DFT computations have been carried out on LiF and HF complexes of a set of n-donors viz. trimethylamine, dimethyl ether and dimethyl sulfide with a 6-31++G(d,p) basis set. The effect of correlation has been included with MP2, MP4 and DFT calculations. NBO analyses of the wavefunctions have been performed to examine the intermolecular interaction at the orbital level. Calculations reveal that these donors form strong n→σ* complexes and computed binding energies of the (CH3)2O···HF complex agree very well with the experimental binding energies from IR spectroscopy. LiF forms stronger complexes than HF, …

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Semiclassical Approach To The Hydrogen-Exchange Reaction Reactive And Transition-State Dynamics, Sophya V. Garashchuk, F. Grossmann, D. Tannor Jan 1997

Semiclassical Approach To The Hydrogen-Exchange Reaction Reactive And Transition-State Dynamics, Sophya V. Garashchuk, F. Grossmann, D. Tannor

Faculty Publications

Scattering matrix elements and symmetric transition-state resonances for the collinear H 2 + H → H + H 2 reaction are obtained using a time-dependent approach. The correlation function between reactant channel wavepackets and product channel wavepackets is used to determine the S-matrix elements. In a similar fashion, autocorrelation functions are used to extract the positions and widths of transition-state resonances. The time propagation of the wavepackets is performed by the improved semiclassical frozen Gaussian method of Herman and Kluk, which is an initial value, uniformly converged method. The agreement between the quantum and semiclassical results is far better …

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Lithium Bonding Interaction In H2Cy⋯Lif (Y=O,S) Complexes: A Theoretical Probe, Salai Cheettu Ammal, P. Venuvanalingam, S. Pal Jan 1997

Lithium Bonding Interaction In H2Cy⋯Lif (Y=O,S) Complexes: A Theoretical Probe, Salai Cheettu Ammal, P. Venuvanalingam, S. Pal

Faculty Publications

Ab initio calculations at 6-31++G(d,p) level have been done on H2CY⋯LiF (Y=O,S) complexes choosing ten possible orientations in each complex. The effect of correlation on complex binding energies has been studied via single point MP2 (full) calculations done on 6-31++G(d,p) geometry. Binding energies have been corrected for basis set superposition error. Frequency calculations confirm that H2CO⋯LiF and H2CS⋯LiF complexes have three and two stable forms, respectively. The most stable form in each complex has been found to have a strong lithium bonding interaction and a secondary hydrogen bondinginteraction. NBO analysis has revealed that in this form oxygen donates nσ lone …

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