Physical Sciences and Mathematics Commons^™

Progress In The Prediction Of Pka Values In Proteins, Emil Alexov, Ernest L. Mehler, Nathan Baker, Antonio Baptista, Yong Huang, Francesca Milletti, Jens Erik Nielsen, Damien Farrell, Tommy Carstensen, Mats H.M. Olsson, Jana K. Shen, Jim Warwicker, Sarah Williams, J Michael Word

Publications

The pK_a-cooperative aims to provide a forum for experimental and theoretical researchers interested in protein pK_a values and protein electrostatics in general. The first round of the pK_a-cooperative, which challenged computational labs to carry out blind predictions against pK_as experimentally determined in the laboratory of Bertrand Garcia-Moreno, was completed and results discussed at the Telluride meeting (July 6–10, 2009). This article serves as an introduction to the reports submitted by the blind prediction participants that will be published in a special issue of PROTEINS: Structure, Function and Bioinformatics. …

Developing Hybrid Approaches To Predict Pka Values Of Ionizable Groups, Shawn Witham, Kemper Talley, Lin Wang, Zhe Zhang, Daquan Gao, Wei Yang, Emil Alexov

Publications

Accurate predictions of pKa values of titratable groups require taking into account all relevant processes associated with the ionization/deionization. Frequently, however, the ionization does not involve significant structural changes and the dominating effects are purely electrostatic in origin allowing accurate predictions to be made based on the electrostatic energy difference between ionized and neutral forms alone using a static structure. On another hand, if the change of the charge state is accompanied by a structural reorganization of the target protein, then the relevant conformational changes have to be taken into account in the pKa calculations. Here we report a hybrid …

Lithium In The Upper Centaurus Lupus And Lower Centaurus Crux Subgroups Of Scorpius-Centaurus, Eric J. Bubar, Marc Schaeuble, Jeremy R. King, Eric E. Mamajek, John R. Stauffer

Publications

We utilize spectroscopically derived model atmosphere parameters and the Li i λ6104 subordinate line and the λ6708 doublet to derive lithium abundances for 12 members of the Upper Centaurus Lupus and Lower Centaurus Crux subgroups of the Scorpius–Centaurus OB Association. The results indicate any intrinsic Li scatter in our 0.9–1.4 M stars is limited to ∼0.15 dex, consistent with the lack of dispersion in 1.0 M stars in the 100 Myr Pleiades and 30–50 Myr IC 2391 and 2602 clusters. Both ab initio uncertainty estimates and the derived abundances themselves indicate that the λ6104 line yields abundances with equivalent or …

Electronic Charge And Spin Density Distribution In A Quantum Ring With Spin-Orbit And Coulomb Interactions, Csaba Daday, Andrei Manolescu, D C. Marinescu, Vidar Gudmundsson

Publications

Charge and spin density distributions are studied within a nanoring structure endowed with Rashba and Dresselhaus spin-orbit interactions (SOIs). For a small number of electrons, in the presence of an external magnetic field and of the Coulomb interaction, the energy spectrum of the system is calculated through an exact numerical diagonalization procedure. The eigenstates thus determined are used to estimate the charge and spin densities around the ring. We find that when more than two electrons are considered, the charge density deformations induced by SOIs are dramatically flattened by the Coulomb repulsion, while the spin density deformations are amplified.

Detailed Abundances Of The Solar Twins 16 Cygni And B Cygni: Constraining Planet Formation Models, Simon C. Schuler, Katia Cunha, Verne V. Smith, Luan Ghezzi, Jeremy R. King, Constantine P. Deliyannis, Ann Merchant Boesgaard

Publications

Results of a detailed abundance analysis of the solar twins 16 Cyg A and 16 Cyg B based on high-resolution, high signal-to-noise ratio echelle spectroscopy are presented. 16 Cyg B is known to host a giant planet while no planets have yet been detected around 16 Cyg A. Stellar parameters are derived directly from our high-quality spectra, and the stars are found to be physically similar, with ΔTeff = +43 K, Δ log g =−0.02 dex, and Δξ = +0.10 km s−1 (in the sense of A − B), consistent with previous findings. Abundances of 15 elements are derived and …

X-Ray Monitoring Of Classical Novae In The Central Region Of M 31 Iii. Autumn And Winter 2007/2008 And 2008/2009, M. Henze, W. Pietsch, F. Haberl, M. Hernanz, G. Sala, D. Hartzidimitriou, M. Della Velle, A. Rau, Dieter H. Hartmann, V. Burwitz

Publications

Context. Classical novae (CNe) represent the major class of supersoft X-ray sources (SSSs) in the central region of the galaxy M 31. Aims. We performed a dedicated monitoring of the M 31 central region with XMM-Newton and Chandra between Nov. 2007 and Feb. 2008 and between Nov. 2008 and Feb. 2009, respectively, to find SSS counterparts of CNe, determine the duration of their SSS phase, and derive physical outburst parameters. Methods. We systematically searched our data for X-ray counterparts of CNe, determined their X-ray light curves and characterised their spectra using blackbody fits and white dwarf (WD) atmosphere models. Additionally, …

A Missense Mutation In Clic2 Associated With Intellectual Disability Is Predicted By In Silico Modeling To Affect Protein Stability And Dynamics, Shawn Witham, Kyoko Takano, Charles Schwartz, Emil Alexov

Publications

Large-scale next generation resequencing of X chromosome genes identified a missense mutation in the CLIC2 gene on Xq28 in a male with X-linked intellectual disability (XLID) and not found in healthy individuals. At the same time, numerous nsSNPs (nonsynonomous SNP) have been reported in the CLIC2 gene in healthy individuals indicating that the CLIC2 protein can tolerate amino acid substitutions and be fully functional. To test the possibility that p.H101Q is a disease-causing mutation, we performed in silico simulations to calculate the effects of the p.H101Q mutation on CLIC2 stability, dynamics, and ionization states while comparing the effects obtained for …

Helical Antiferromagnetic Ordering In The Lowest Landau Level Of A Semiconductor Superlattice, Liqiu Zheng, D C. Marinescu

Publications

When subjected to a tilted magnetic field, the ground state of a semiconductor superlattice (SL) with two identical quantum wells per unit cell is shown to exhibit different magnetic configurations that are dependent on the strength and direction of the field and the SL characteristics. Intra- and interunit cell tunneling between the wells, assumed to be infinitely attractive, generate an energy miniband structure of the lowest Landau level that, in cooperation with the Zeeman splitting, creates, at certain points in the momentum space, an energy difference between opposite-spin single-particle states that can be overcome by the Coulomb interaction. Within the …

Nova M31n 2007-12b: Supersoft X-Rays Reveal An Intermediate Polar?, W. Pietsch, M. Henze, F. Haberl, M. Hernanz, G. Sala, Dieter H. Hartmann, M. Della Valle

Publications

Context. In the central part of M 31, a high number of optical novae can be targeted within the field of view of the XMM-Newton EPIC and Chandra HRC-I X-ray detectors. A special monitoring program of the area has allowed us to investigate supersoft emission of individual novae in detail and perform a statistical analysis of the sample. Aims. For the He/N nova M31N 2007-12b, we aimed to constrain the time of appearance of a supersoft source (SSS) and the duration of the SSS state as well as determine the spectral and time variability while the source was bright. Methods. …

Thermal Conductance Of A Two-Channel Kondo Model, C P. Moca, A Roman, D C. Marinescu

Publications

A theory of thermal transport in a two-channel Kondo system, such as the one formed by a small quantum dot coupled to two leads and to a larger dot, is formulated. The interplay of the two screening constants allow an exploration of the Fermi liquid and non-Fermi liquid regimes. By using analytical, as well as numerical, renormalization group methods, we study the temperature dependence of the thermal conductance and the Lorentz number. We find that in the low-temperature limit, the Lorentz number attains its universal value, irrespective of the nature of the ground state.

On The Role Of Electrostatics In Protein–Protein Interactions, Zhe Zhang, Shawn Witham, Emil Alexov

Publications

The role of electrostatics in protein–protein interactions and binding is reviewed in this paper. A brief outline of the computational modeling, in the framework of continuum electrostatics, is presented and the basic electrostatic effects occurring upon the formation of the complex are discussed. The effect of the salt concentration and pH of the water phase on protein–protein binding free energy is demonstrated which indicates that the increase of the salt concentration tends to weaken the binding, an observation that is attributed to the optimization of the charge–charge interactions across the interface. It is pointed out that the pH-optimum (pH of …

Order Independence In Asynchronous Cellular Automata, Matthew Macauley, Jon Mccammond, Henning S. Mortveit

Publications

A sequential dynamical system, or SDS, consists of an undirected graph Y, a vertex-indexed list of local functions F_Y, and a permutation pi of the vertex set (or more generally, a word w over the vertex set) that describes the order in which these local functions are to be applied. In this article we investigate the special case where Y is a circular graph with n vertices and all of the local functions are identical. The 256 possible local functions are known as Wolfram rules and the resulting sequential dynamical systems are called finite asynchronous elementary cellular automata, or ACAs, …

Ro-Vibrational Co Detected In The Β Pictoris Circumstellar Disk, Matthew R. Troutman, Kenneth H. Hinkle, Joan R. Najita, Terrence W. Rettig, Sean D. Brittain

Publications

We present high-resolution near-infrared spectra of β Pictoris—a nearby young star with a debris disk. Fundamental low-J CO absorption lines are detected and strict upper limits are placed on the flux of v = 2–1 low-J CO emission lines. The limit on the UV fluorescent emission flux in the v = 2–1 lines is used to place a tight constraint on the inner extent of the CO gas. Assuming Hi is the primary collision partner, the sub-thermal population of the low-J v = 0 rotational levels constrains the density of the gas in the disk to nH = (2.5+7.1 −1.2)×105 …

Grips - Gamma-Ray Imaging, Polarimetry And Spectroscopy, Jochen Greiner, Karl Mannheim, Felix Aharonian, Marco Ajello, Lajos G. Balaz, Guido Barbiellini, Ronaldo Bellazzini, Shawn Bishop, Gennady S. Bisnoyatij-Kogan, Steven Boggs, Andrej Bykov, Guido Dicocco, Roland Diehl, Dominik Elsasser, Suzanne Foley, Claes Fransson, Neil Gehrels, Lorraine Hanlon, Dieter H. Hartmann

Publications

We propose to perform a continuously scanning all-sky survey from 200 keV to 80 MeV achieving a sensitivity which is better by a factor of 40 or more compared to the previous missions in this energy range (COMPTEL, INTEGRAL; see Fig. 1). The Gamma-Ray Imaging, Polarimetry and Spectroscopy (“GRIPS”) mission addresses fundamental questions in ESA’s Cosmic Vision plan. Among the major themes of the strategic plan, GRIPS has its focus on the evolving, vio-lent Universe, exploring a unique energy window. We propose to investigate γ-ray bursts and blazars, the mechanisms behind supernova explosions, nucleosynthesis and spallation, the enigmatic origin of …

Simulation Of Relativistic Jets And Associated Self-Consistent Radiation, K.-I. Nishikawa, E. J. Choi, K. Min, P. Hardee, Y. Mizuno, C. Zhang, J. Niemiec, M. Medvedev, A. Norlund, J Frederiksen, M Pohl, H Sol, Dieter H. Hartmann, G J. Fishman

Publications

Plasma instabilities excited in collisionless shocks are responsible for particle acceleration. We have investigated the particle acceleration and shock structure associated with an unmagnetized relativistic electron-positron jet propagating into an unmagnetized electron-positron plasma. Cold jet electrons are thermalized and slowed while the ambient electrons are swept up to create a par-tially developed hydrodynamic-like shock structure. In the leading shock, electron density increases by a factor of about 3.5 in the simulation frame. Strong electromagnetic fields are generated in the trailing shock and provide an emission site. These magnetic fields contribute to the electrons transverse deflection behind the shock. Our initial …

Abundances Of Stars With Planets: Trends With Condensation Temperature, Simon C. Schuler, Davin Flateau, Katia Cunha, Jeremy R. King, Luan Ghezzi, Verne V. Smith

Publications

Precise abundances of 18 elements have been derived for 10 stars known to host giant planets from high signal-to-noise ratio, high-resolution echelle spectroscopy. Internal uncertainties in the derived abundances are typically 0.05 dex. The stars in our sample have all been previously shown to have abundances that correlate with the condensation temperature (Tc) of the elements in the sense of increasing abundances with increasing Tc; these trends have been interpreted as evidence that the stars may have accreted H-depleted planetary material. Our newly derived abundances also correlate positively with Tc, although slopes of linear least-square fits to the [m/H]–Tc relations …

In Silico And In Vitro Investigations Of The Mutability Of Disease-Causing Missense Mutation Sites In Spermine Synthase, Zhe Zhang, Joy Norris, Charles Schwartz, Emil Alexov

Publications

Background

Spermine synthase (SMS) is a key enzyme controlling the concentration of spermidine and spermine in the cell. The importance of SMS is manifested by the fact that single missense mutations were found to cause Snyder-Robinson Syndrome (SRS). At the same time, currently there are no non-synonymous single nucleoside polymorphisms, nsSNPs (harmless mutations), found in SMS, which may imply that the SMS does not tolerate amino acid substitutions, i.e. is not mutable.

Methodology/Principal Findings

To investigate the mutability of the SMS, we carried out in silico analysis and in vitro experiments of the effects of amino acid substitutions at the …

Nonadiabatic Generation Of A Pure Spin Current In A One-Dimensional Quantum Ring With Spin-Orbit Interaction, Marian Nita, D C. Marinescu, Andrei Manolescu, Vidar Gudmundsson

Publications

We demonstrate the theoretical possibility of obtaining a pure spin current in a 1D ring with spin-orbit interaction by irradiation with a nonadiabatic, two-component terahertz laser pulse, whose spatial asymmetry is reflected by an internal phase difference φ. The solutions of the equation of motion for the density operator are obtained for a spin-orbit coupling linear in the electron momentum (Rashba) and they are used to calculate the time-dependent charge and spin currents. We find that there are critical values of φ at which the charge current disappears, while the spin current reaches a maximum or a minimum value.

Detection Of Ch+ Emission From The Disc Around Hd 100546, W F. Thi, F Menard, G Meeus, C. Martin-Zaidi, P Woitke, E Tatulli, M Benisty, I Kamp, I Pascucci, C Pinte, C A. Grady, Sean D. Brittain, G J. White, C D. Howard, G Sandell, C Eiroa

Publications

Despite its importance in the thermal balance of the gas and in the determination of primeval planetary atmospheres, the chemistry in protoplanetary discs remains poorly constrained with only a handful of detected species. We observed the emission from the disc around the Herbig Be star HD 100546 with the PACS instrument in the spectroscopic mode on board the Herschel Space Telescope as part of the GAS in Protoplanetary Systems (GASPS) programme and used archival data from the DIGIT programme to search for the rotational emission of CH+. We detected in both datasets an emission line centred at 72.16 μm that …

Water Depletion In The Disk Atmosphere Of Herbig Aebe Stars, D Fedele, I Pascucci, Sean D. Brittain, I Kamp, P Woitke, J P. Williams, W.R.F. Dent, W F. Thi

Publications

We present high-resolution (R ∼ 100,000) L-band spectroscopy of 11 Herbig AeBe stars with circumstellar disks. The observations were obtained with the VLT/CRIRES to detect hot water and hydroxyl radical emission linespreviously detected in disks around T Tauri stars. OH emission lines are detected toward four disks. The OH 2Π3/2 P4.5 (1+,1−) doublet is spectrally resolved as well as the velocity profile of each component of the doublet. Its characteristic double-peak profile demonstrates that the gas is in Keplerian rotation and points to an emitting region extending out to ∼15–30 AU. The OH emission correlates with disk geometry as it …

The Unusual Protoplanetary Disk Around The T Tauri Star Et Chamaeleontis, P Woitke, B Riaz, G Duchene, I Pascucci, A Ran Lyo, W.R.F. Dent, N Phillips, W F. Thi, F Menard, G J. Herczeg, E Bergin, A Brown, A Mora, I Kamp, G Aresu, Sean D. Brittain, I De Gregorio-Monsalvo, G Sandell

Publications

We present new continuum and line observations, along with modelling, of the faint (6−8) Myr old T Tauri star ETCha belonging to the η Chamaeleontis cluster. We have acquired Herschel/PACS photometric fluxes at 70 μm and 160 μm, as well as a detection of the [OI] 63 μm fine-structure line in emission, and derived upper limits for some other far-IR OI, CII, CO and o-H2O lines. These observations were carried out in the frame of the open time key programme GASPS, where ETCha was selected as one of the science demonstration phase targets. The Herschel data is complemented by new …

The Nature Of "Dark" Gamma-Ray Bursts, J. Greiner, T. Krühler, S. Klose, P. Afonso, C. Clemens, R. Filgas, Dieter H. Hartmann, A. Küpcü Yoldas, M. Nardini, F. Olivares E., A Rau, A Rossi, P Schady, A Updike

Publications

Context. Thirteen years after the discovery of the first afterglows, the nature of dark gamma-ray bursts (GRB) still eludes explanation: while each long-duration GRB typically has an X-ray afterglow, optical/NIR emission is only seen for 40-60% of them. Aims. Here we use the afterglow detection statistics of the systematic follow-up observations performed with GROND since mid-2007 in order to derive the fraction of “dark bursts” according to different methods, and to distinguish between various scenarios for “dark bursts”. Methods. Observations were performed with the 7-channel “Gamma-Ray Optical and Near-infrared Detector” (GROND) at the 2.2m MPI/ESO telescope. We used the afterglow …

The Swift/Fermi Grb 080928 From 1 Ev To 150 Kev, A. Rossi, S. Schulze, S. Klose, D. A. Kann, A. Rau, H. A. Krimm, G. Jóhannesson, A. Panaitescu, F. Yuan, P Ferrero, T Krühler, J Greiner, P Schady, S B. Pandey, L Amati, P.M.F. Afonso, C W. Akerlof, L A. Arnold, C Clemens, R Filgas, Dieter H. Hartmann

Publications

We present the results of a comprehensive study of the gamma-ray burst 080928 and of its afterglow. GRB 080928 was a long burst detected by Swift/BAT and Fermi/GBM. It is one of the exceptional cases where optical emission had already been detected when the GRB itself was still radiating in the gamma-ray band. For nearly 100 s simultaneous optical, X-ray and gamma-ray data provide a coverage of the spectral energy distribution of the transient source from about 1 eV to 150 keV. In particular, we show that the SED during the main prompt emission phase agrees with synchrotron radiation. We …

Origin: Metal Creation And Evolution From The Cosmic Dawn, J. W. Den Herder, L. Piro, T. Ohashi, C. Kouveliotou, Dieter H. Hartmann, J. Kaastra, L. Amati, M. I. Andersen, M. Arnaud, J.-L. Attéia

Publications

ORIGIN is a proposal for the M3 mission call of ESA aimed at the study of metal creation from the epoch of cosmic dawn. Using high-spectral resolution in the soft X-ray band, ORIGIN will be able to identify the physical conditions of all abundant elements between C and Ni to red-shifts of z=10, and beyond. The mission will answer questions such as: When were the first metals created? How does the cosmic metal content evolve? Where do most of the metals reside in the Universe? What is the role of metals in structure formation and evolution? To reach out to …