Physical Sciences and Mathematics Commons^™

The Optical Manifestation Of Dispersive Field‐Aligned Bursts In Auroral Breakup Arcs, H. Dahlgren, J. L. Semeter, R. A. Marshall, M. Zettergren

Publications

High‐resolution optical observations of a substorm expansion show dynamic auroral rays with surges of luminosity traveling up the magnetic field lines. Observed in ground‐based imagers, this phenomenon has been termed auroral flames, whereas the rocket signatures of the corresponding energy dispersions are more commonly known as field‐aligned bursts. In this paper, observations of auroral flames obtained at 50 frames/s with a scientific‐grade Complementary Metal Oxide Semiconductor (CMOS) sensor (30° × 30° field of view, 30 m resolution at 120 km) are used to provide insight into the nature of the precipitating electrons similar to high‐resolution particle detectors. Thanks to the …

Field Localization And The Nambu-Jona-Lasinio Mass Generation Mechanism In An Alternative 5-Dimensional Brane Model, Preston Jones, Gerardo Muñoz, Douglas Singleton, Triyanta

Publications

We consider a five-dimensional brane world model with a single brane which is distinct from the well known Randall-Sundrum model. We discuss the similarities and differences between our brane model and the Randall-Sundrum brane model. In particular we focus on the localization of five-dimensional fields with different spins—spin 0, spin 1 / 2 , and spin 1—to the brane, and a self-consistent mass-generation mechanism. We find that the brane model studied here has different (and in some cases superior) localization properties for fields/particles with different spins to the brane, as compared to the original five-dimensional brane models. In addition this …

Effect Of Variable Dose Rate On Biologically Effective Dose, Vadim Y. Kuperman, Gregory S. Spradlin

Publications

Purpose: to investigate the effect of variable dose rate on biologically effective dose ( BED ).

Materials and methods: by using the linear-quadratic (LQ) model with bi-exponential repair, we analytically determine the time-dependent dose rate R ~ which minimizes the effective protraction factor ( eff G ) and BEDunder the condition of fixed fraction time and dose per fraction.  Because normal tissue complication probability ( NTCP) monotonically decreases with decreasingBED , the dose rate R ~ also minimizes NTCP.

Results: the dependences of Geff, BED, and NTCP on fraction time were determined for different radiobiological parameters and two different …

Magnetic Field Generation In A Jet-Sheath Plasma Via The Kinetic Kelvin-Helmholtz Instability, K.-I. Nishikawa, P. Hardee, B. Zhang, I. Dutan, M. Medvedev, E. J. Choi, K. W. Min, J. Niemiec, Y. Mizuno, A Nordlund, J T. Frederiksen, H Sol, M Pohl, Dieter H. Hartmann

Publications

We have investigated the generation of magnetic fields associated with velocity shear between an unmagne-tized relativistic jet and an unmagnetized sheath plasma. We have examined the strong magnetic fields generated by ki-netic shear (Kelvin–Helmholtz) instabilities. Compared to the previous studies using counter-streaming performed by Alves et al. (2012), the structure of the kinetic Kelvin– Helmholtz instability (KKHI) of our jet-sheath configura-tion is slightly different, even for the global evolution of the strong transverse magnetic field. In our simulations the major components of growing modes are the electric field Ez, perpendicular to the flow boundary, and the magnetic field By, transverse …

Measuring The Evolutionary Rate Of Cooling Of Zz Ceti, Anjum S. Mukadam, Ted Von Hippel, Et Al.

Publications

We have finally measured the evolutionary rate of cooling of the pulsating hydrogen atmosphere (DA) white dwarf ZZ Ceti (Ross 548), as reflected by the drift rate of the 213.13260694 s period. Using 41 yr of time-series photometry from 1970 November to 2012 January, we determine the rate of change of this period with time to be dP/dt = (5.2 ± 1.4) × 10–15 s s–1 employing the O – C method and (5.45 ± 0.79) × 10–15 s s–1 using a direct nonlinear least squares fit to the entire lightcurve. We adopt the dP/dt obtained …

A Spectroscopic Analysis Of The Eclipsing Short-Period Binary V505 Persei And The Origin Of The Lithium Dip, Patrick Baugh, Jeremy R. King, Constantine P. Deliyannis, Ann Merchant Boesgaard

Publications

As a test of rotationally-induced mixing causing the well-known Li dip in older mid-F dwarfs in the local Galactic disk, we utilize high-resolution and -S/N Keck/HIRES spectroscopy to measure the Li abundance in the components of the ∼1 Gyr, [Fe/H]= −0.15 eclipsing short-period binary V505 Per. We find A(Li) ∼ 2.7 ± 0.1 and 2.4 ± 0.2 in the Teff∼6500 and 6450K primary and sec-ondary components, respectively. Previous Teff determinations and uncertainties suggest that each component is located in the midst of the Li dip. If so, their A(Li) are ≥2–5 times larger than A(Li) detections and upper limits observed …

Continuous Development Of Schemes For Parallel Computing Of The Electrostatics In Biological Systems: Implementation In Delphi, Chuan Li, Marharyta Petukh, Lin Li, Emil Alexov

Publications

Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano-objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano-objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (J Comput Chem. 2012 Sep 15; 33(24):1960–6.) to include parallelization …

Cancer Missense Mutations Alter Binding Properties Of Proteins And Their Interaction Networks, Hafumi Nisha, Manoj Tyagi, Shaolei Teng, Benjamin A. Shoemaker, Kosuke Hashimoto, Emil Alexov, Stefan Wuchty, Anna R. Panchenko

Publications

Many studies have shown that missense mutations might play an important role in carcinogenesis. However, the extent to which cancer mutations might affect biomolecular interactions remains unclear. Here, we map glioblastoma missense mutations on the human protein interactome, model the structures of affected protein complexes and decipher the effect of mutations on protein-protein, protein-nucleic acid and protein-ion binding interfaces. Although some missense mutations over-stabilize protein complexes, we found that the overall effect of mutations is destabilizing, mostly affecting the electrostatic component of binding energy. We also showed that mutations on interfaces resulted in more drastic changes of amino acid physico-chemical …

Linear Model Estimation Of Nonlinear Systems Using Least-Squares Algorithm5, Alireza Rahrooh, Walter W. Buchanan, Remzi Seker

Publications

This paper presents utilizes Least-Squares Algorithm to obtain more accurate linear models of nonlinear systems using parameter estimation. This approach generates an optimal linear model which is valid over a wide range of trajectories and converges to the desired steady-state value with no errors unlike the existing techniques. The proposed technique is very efficient and does not require storing the data. Therefore, it can easily be used and implemented with limited resources for undergraduate curriculum especially in underdeveloped countries. Most available techniques for linearization of nonlinear system are only valid about the operating point; furthermore, the knowledge of the operating …

Tips From The Board Of Broadcast Meteorology For Gaining The Certified Broadcast Meteorologist (Cbm) Designation, Rob Eicher

Publications

These notes are intended to maximize the likelihood that you will pass the AMS CBM evaluation on your first attempt. Typically half of first-time applicants pass the evaluation.

70 Da White Dwarfs Identified In Lamost Pilot Survey, J. K. Zhao, A. L. Luo, Terry D. Oswalt, G. Zhao

Publications

We present a spectroscopically identified catalog of 70 DA white dwarfs (WDs) from the LAMOST pilot survey. Thirty-five are found to be new identifications after cross-correlation with the Eisenstein et al. and Villanova catalogs. The effective temperature and gravity of these WDs are estimated by Balmer lines fitting. Most of them are hot WDs. The cooling times and masses of these WDs are estimated by interpolation in theoretical evolution tracks. The peak of the mass distribution is found to be ∼0.6M, which is consistent with prior work in the literature. The distances of these WDs are estimated using the method …

Dispersive Waves In Microstructured Solids, A. Berezovski, J. Engelbrecht, A. Salupere, K. Tamm, T. Peets, Mihhail Berezovski

Publications

The wave motion in micromorphic microstructured solids is studied. The mathematical model is based on ideas of Mindlin and governing equations are derived by making use of the Euler–Lagrange formalism. The same result is obtained by means of the internal variables approach. Actually such a model describes internal fields in microstructured solids under external loading and the interaction of these fields results in various physical effects. The emphasis of the paper is on dispersion analysis and wave profiles generated by initial or boundary conditions in a one-dimensional case.

The Role Of Protonation States In Ligand-Receptor Recognition And Binding, Marharyta Petukh, Shannon Stefl, Emil Alexov

Publications

In this review we discuss the role of protonation states in receptor-ligand interactions, providing experimental evidences and computational predictions that complex formation may involve titratable groups with unusual pKa’s and that protonation states frequently change from unbound to bound states. These protonation changes result in proton uptake/release, which in turn causes the pHdependence of the binding. Indeed, experimental data strongly suggest that almost any binding is pH-dependent and to be correctly modeled, the protonation states must be properly assigned prior to and after the binding. One may accurately predict the protonation states when provided with the structures of the unbound …

Influence Of Microstructure On Thermoelastic Wave Propagation, Arkadi Berezovski, Mihhail Berezovski

Publications

Numerical simulations of the thermoelastic response of a microstructured material on a thermal loading are performed in the one-dimensional setting to examine the influence of temperature gradient effects at the microstructure level predicted by the thermoelastic description of microstructured solids (Berezovski et al. in J. Therm. Stress. 34:413–430, 2011). The system of equations consisting of a hyperbolic equation of motion, a parabolic macroscopic heat conduction equation, and a hyperbolic evolution equation for the microtemperature is solved by a finite-volume numerical scheme. Effects of microtemperature gradients exhibit themselves on the macrolevel due to the coupling of equations of the macromotion …

Tracers Of Chromospheric Structure. I. Ca Ii H&K Emission Distribution Of 13,000 F, G, And K Stars In Sdss Dr7 Spectroscopic Sample, J. K. Zhao, T. D. Oswalt, G. Zhao, Q. H. Lu, A. L. Luo, L. Y. Zhang

Publications

We present chromospheric activity index S_HK measurements for over 13,000 F, G, and K disk stars with high signal-to-noise ratio (>60) spectra in the Sloan Digital Sky Survey (SDSS) Data Release 7 (DR7) spectroscopic sample. A parameter δS is defined as the difference between S_HK and a “zero” emission line fitted by several of the most inactive stars. The S_HK indices of subgiant stars tend to be much lower than dwarfs, which provide a way to distinguish dwarfs and giants with relatively low-resolution spectra. Cooler stars are generally more active and display a larger scatter than …

Tracers Of Chromospheric Structure. I. Caii H&K Emission Distribution Of 13000 F, G And K Stars In Sdss Dr7 Spectroscopic Sample, J. K. Zhao, T. D. Oswalt, G. Zhao, Q. H. Lu, L. Y. Zhang

Publications

We present chromospheric activity index SHK measurements for over 13,000 F, G and K disk stars with high signal-to-noise ratio (> 60) spectra in the Sloan Digital Sky Survey (SDSS) Data Release 7 (DR7) spectroscopic sample. A parameter S is defined as the difference between SHK and a ‘zero’ emission line fitted by several of the most inactive stars. The SHK indices of subgiant stars tend to be much lower than dwarfs, which provide a way to distinguish dwarfs and giants with relatively low resolution spectra. Cooler stars are generally more active and display a larger scatter than hotter stars. …

X-Ray Source Variability Study Of The M31 Central Field Using Chandra Hrc-1, F. Hofmann, W. Pietsch, M. Henze, F. Haberl, R. Sturm, M. Della Valle, Dieter H. Hartmann, D. Hatzidimitriou

Publications

Context. The central field of the Andromeda galaxy (M 31) has been monitored, using the Chandra HRC-I detector (about 0.1-10 keV energy range) from 2006 to 2012 with the main aim to detect X-rays from optical novae. We present a systematic analysis of all X-ray sources found in the 41 nova monitoring observations, along with 23 M 31 central field HRC-I observations available from the Chandra data archive starting in December 1999. Aims. Based on these observations, we studied the X-ray long-term variability of the source population and especially of X-ray binaries in M 31. Methods. We created a catalogue …

Kelvin-Helmholtz Instability Of The Cme Reconnection Outflow Layer In The Low Corona, Claire Foullon, Erwin Verwichte, Katariina Nykyri, Markus J. Aschwanden, Iain G. Hannah

Publications

New capabilities for studying the Sun allow us to image for the first time the magnetic Kelvin–Helmholtz (KH) instability developing at the surface of a fast coronal mass ejecta (CME) less than 150 Mm above the solar surface. We conduct a detailed observational investigation of this phenomenon, observed off the east solar limb on 2010 November 3, in the EUV with SDO/AIA. In conjunction with STEREO-B/EUVI, we derive the CME source surface position. We ascertain the timing and early evolution of the CME outflow leading to the instability onset. We perform image and spectral analysis, exploring the CME plasma structuring …

Nanobiotechnology Can Boost Crop Production And Quality: First Evidence From Increased Plant Biomass, Fruit Yield And Phytomedicine Content In Bitter Melon (Momordica Charantia), Chittaranjan Kole, Phullara Kole, K Manoj Randunu, Poonam Choudhary, Ramakrishna Podila, Pu Chen Ke, Apparao M. Rao, Richard K. Marcus

Publications

BACKGROUND:

Recent research on nanoparticles in a number of crops has evidenced for enhanced germination and seedling growth, physiological activities including photosynthetic activity and nitrogen metabolism, mRNA expression and protein level, and also positive changes in gene expression indicating their potential use in crop improvement. We used a medicinally rich vegetable crop, bitter melon, as a model to evaluate the effects of seed treatment with a carbon-based nanoparticle, fullerol [C60(OH)20], on yield of plant biomass and fruit characters, and phytomedicine contents in fruits.

RESULTS:

We confirmed the uptake, translocation and accumulation of fullerol through bright field imaging and Fourier transform …

Nature Of The Gas And Dust Around 51 Oph, W F. Thi, F Menard, G Meeus, A Carmona, P Riviere-Marichalar, J C. Augereau, I Kamp, P Woitke, C Pinte, I Mendigutia, C Eiroa, B Montesinos, Sean D. Brittain, W Dent

Publications

Circumstellar disc evolution is paramount for the understanding of planet formation. The GASPS program aims at determining the circumstellar gas and solid mass around ~250 pre-main-sequence Herbig Ae and TTauri stars. We aim to understand the origin and nature of the circumstellar matter orbiting 51 Oph, a young (Myr) luminous B9.5 star. We obtained continuum and line observations with the PACS instrument on board the Herschel Space Observatory and continuum data at 1.2 mm with the IRAM 30m telescope. The SED and line fluxes were modelled using the physico-chemo radiative transfer code ProDiMo. We detected a strong emission by OI …

Precipitation Modulation By The Saint Lawrence River Valley In Association With Transitioning Tropical Cyclones, Shawn M. Milrad, Eyad H. Atallah, John R. Gyakum

Publications

The St. Lawrence River valley (SLRV) is an important orographic feature in eastern Canada that can affect surface wind patterns and contribute to locally higher amounts of precipitation. The impact of the SLRV on precipitation distributions associated with transitioning, or transitioned, tropical cyclones that approached the region is assessed. Such cases can result in heavy precipitation during the warm season, as during the transition of Hurricane Ike (2008). Thirty-eight tropical cyclones tracked within 500 km of the SLRV from 1979 to 2011. Utilizing the National Centers for Environmental Prediction (NCEP) North American Regional Reanalysis (NARR), 19 of the 38 cases …

Asymmetry Of Magnetosheath Flows And Magnetopause Shape During Low Alfvén Mach Number Solar Wind, B. Lavraud, E. Larroque, E. Budnik, V. Génot, J. E. Borovsky, M. W. Dunlop, K. Nykyri, Et Al.

Publications

Previous works have emphasized the significant influence of the solar wind Alfvén Mach number (MA) on magnetospheric dynamics. Here we report statistical, observational results that pertain to changes in the magnetosheath flow distribution and magnetopause shape as a function of solar wind MA and interplanetary magnetic field (IMF) clock angle orientation. We use all Cluster 1 data in the magnetosheath during the period 2001–2010, using an appropriate spatial superposition procedure, to produce magnetosheath flow distributions as a function of location in themagnetosheath relative to the IMF and other parameters. The results demonstrate that enhanced flows in the magnetosheath are expected …

Progress In Developing Poisson-Boltzmann Equation Solvers, Chuan Li, Marharyta Petukh, Emil Alexov

Publications

This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nano-objects, the last one referring to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules. The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task provided the specific definition of the system to be modeled and as a physical problem aiming to better capture the phenomena occurring in the real experiments. In addition, specific attention is paid to …

Modelling And Hazard Analysis For Contaminated Sediments Using Stamp Model And Stpa Tool, Karim Hardy, Franck Guarnieri

Publications

The goal of this article is dual: first, introducing a new model of accident named STAMP (systems-theoretic accident modeling and processes); then applying the model to an innovative process for the treatment of contaminated substances and the re-use of treated substances. This article is a demonstration for a need of a new tool to take into account hazards and safety within socio-technical systems.

A Rational Free Energy-Based Approach To Understanding And Targeting Disease-Causing Missense Mutations., Zhe Zhang, Shawn Witham, Marharita Petukh, Gautier Moroy, Maria Miteva, Yoshihiko Ikeguchi, Emil Alexov

Publications

BACKGROUND AND SIGNIFICANCE:

Intellectual disability is a condition characterized by significant limitations in cognitive abilities and social/behavioral adaptive skills and is an important reason for pediatric, neurologic, and genetic referrals. Approximately 10% of protein-encoding genes on the X chromosome are implicated in intellectual disability, and the corresponding intellectual disability is termed X-linked ID (XLID). Although few mutations and a small number of families have been identified and XLID is rare, collectively the impact of XLID is significant because patients usually are unable to fully participate in society.

OBJECTIVE:

To reveal the molecular mechanisms of various intellectual disabilities and to suggest …

Enhancing Human Spermine Synthase Activity By Engineered Mutations, Zhe Zhang, Yueli Zheng, Margo Petukh, Anthony Pegg, Yoshihiko Ikeguchi, Emil Alexov

Publications

Spermine synthase (SMS) is an enzyme which function is to convert spermidine into spermine. It was shown that gene defects resulting in amino acid changes of the wild type SMS cause Snyder-Robinson syndrome, which is a mild-to-moderate mental disability associated with osteoporosis, facial asymmetry, thin habitus, hypotonia, and a nonspecific movement disorder. These disease-causing missense mutations were demonstrated, both in silico and in vitro, to affect the wild type function of SMS by either destabilizing the SMS dimer/monomer or directly affecting the hydrogen bond network of the active site of SMS. In contrast to these studies, here we report an …

In Silico Investigation Of Ph-Dependence Of Prolactin And Human Growth Hormone Binding To Human Prolactin Receptor, Lin Wang, Shawn Witham, Zhe Zhang, Michael E. Hodsdon, Emil Alexov

Publications

Experimental data shows that the binding of human prolactin (hPRL) to human prolactin receptor (hPRLr-ECD) is strongly pH-dependent, while the binding of the same receptor to human growth hormone (hGH) is pH-independent. Here we carry in silico analysis of the molecular effects causing such a difference and reveal the role of individual amino acids. It is shown that the computational modeling correctly predicts experimentally determined pKa’s of histidine residues in an unbound state in the majority of the cases and the pH-dependence of the binding free energy. Structural analysis carried in conjunction with calculated pH-dependence of the binding revealed that …

Delphi Web Server: A Comprehensive Online Suite For Electrostatic Calculations Of Biological Macromolecules And Their Complexes., Subhra Sarkar, Shawn Witham, Jie Zhang, Maxim Zhenirovskyy, Walter Rocchia

Publications

Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output …

Using Delphi Capabilities To Mimic Protein's Conformational Reorganization With Amino Acid Specific Dielectric Constants, Lin Wang, Zhe Zhang, Walter Rocchia, Emil Alexov

Publications

Many molecular events are associated with small or large conformational changes occurring in the corresponding proteins. Modeling such changes is a challenge and requires significant amount of computing time. From point of view of electrostatics, these changes can be viewed as a reorganization of local charges and dipoles in response to the changes of the electrostatic field, if the cause is insertion or deletion of a charged amino acid. Here we report a large scale investigation of modeling the changes of the folding energy due to single mutations involving charged group. This allows the changes of the folding energy to …

Between Algorithm And Model: Different Molecular Surface Definitions For The Poisson-Boltzmann Based Electrostatic Characterization Of Biomolecules In Solution, Sergio Decherchi, José Colmenares, Chiara Eva Catalano, Michela Spagnuolo, Emil Alexov, Walter Rocchia

Publications

The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field. In this work, two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface: the blobby surface, an implicit Gaussian atom centered surface, and the skin surface. As figures of merit, we considered surface differentiability and surface area continuity with respect to atom positions, and the agreement with explicit solvent simulations. Geometric …