bluuebunny/crossref_metadata_2025_split huggingface dataset:
Can molecular dynamics simulations provide high‐resolution refinement of protein structure?
Authors: Chen Jianhan , Brooks Charles L. 
Published: March 2007

AbstractRecent advances in efficient and accurate treatment of solvent with the generalized Born approximation (GB) have made it possible to substantially refine the protein structures generated by various prediction tools through detailed molecular dynamics simulations. As demonstrated in a recent CASPR experiment, improvement can be quite reliably achieved when the initial models are sufficiently close to the native basin (e.g., 3–4 Å Cα RMSD). A key element to effective refinement is to incorporate reliable structural information into the simulation protocol. Without intimate knowledge of the target and prediction protocol used to generate the initial structural models, it can be assumed that the regular secondary structure elements (helices and strands) and overall fold topology are largely correct to start with, such that the protocol limits itself to the scope of refinement and focuses the sampling in vicinity of the initial structure. The secondary structures can be enforced by dihedral restraints and the topology through structural contacts, implemented as either multiple pair‐wise Cα distance restraints or a single sidechain distance matrix restraint. The restraints are weakly imposed with flat‐bottom potentials to allow sufficient flexibility for structural rearrangement. Refinement is further facilitated by enhanced sampling of advanced techniques such as the replica exchange method (REX). In general, for single domain proteins of small to medium sizes, 3–5 nanoseconds of REX/GB refinement simulations appear to be sufficient for reasonable convergence. Clustering of the resulting structural ensembles can yield refined models over 1.0 Å closer to the native structure in Cα RMSD. Substantial improvement of sidechain contacts and rotamer states can also be achieved in most cases. Additional improvement is possible with longer sampling and knowledge of the robust structural features in the initial models for a given prediction protocol. Nevertheless, limitations still exist in sampling as well as force field accuracy, manifested as difficulty in refinement of long and flexible loops. Proteins 2007. © 2007 Wiley‐Liss, Inc.
ZRANK: Reranking protein docking predictions with an optimized energy function
Authors: Pierce Brian , Weng Zhiping 
Published: March 2007

AbstractProtein–protein docking requires fast and effective methods to quickly discriminate correct from incorrect predictions generated by initial‐stage docking. We have developed and tested a scoring function that utilizes detailed electrostatics, van der Waals, and desolvation to rescore initial‐stage docking predictions. Weights for the scoring terms were optimized for a set of test cases, and this optimized function was then tested on an independent set of nonredundant cases. This program, named ZRANK, is shown to significantly improve the success rate over the initial ZDOCK rankings across a large benchmark. The amount of test cases with No. 1 ranked hits increased from 2 to 11 and from 6 to 12 when predictions from two ZDOCK versions were considered. ZRANK can be applied either as a refinement protocol in itself or as a preprocessing stage to enrich the well‐ranked hits prior to further refinement. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Molecular adaptation strategies to high temperature and thermal denaturation mechanism of the D‐trehalose/D‐maltose‐binding protein from the hyperthermophilic archaeon Thermococcus litoralis
Authors: Fessas Dimitrios , Staiano Maria , Barbiroli Alberto , Marabotti Anna , Schiraldi Alberto , Varriale Antonio , Rossi Mose' , D'Auria Sabato 
Published: March 2007

AbstractThe D‐trehalose/D‐maltose‐binding protein (TMBP), a monomeric protein of 48 kDa, is one component of the trehalose and maltose uptake system. In the hyperthermophilic archaeon T. litoralis this is mediated by a protein‐dependent ATP‐binding cassette system transporter. The gene coding for a thermostable TMBP from the archaeon T. litoralis has been cloned, and the recombinant protein has been expressed in E. coli. The recombinant TMBP has been purified to homogeneity and characterized. It exhibits the same functional and structural properties as the native one. In fact, it is highly thermostable and binds both trehalose and maltose with high affinity. In this work we used differential scanning calorimetry studies together with a detailed analysis, at the molecular level, of the three‐dimensional protein structure to shed light on the basis of the high thermostability exhibited by the recombinant TMBP from the archaeon T. litoralis. The obtained data suggest that the presence of trehalose does not change the overall mechanism of the denaturation of this protein but it selectively modifies the stability of the TMBP structural domains. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Comparison between computational alanine scanning and per‐residue binding free energy decomposition for protein–protein association using MM‐GBSA: Application to the TCR‐p‐MHC complex
Authors: Zoete Vincent , Michielin Olivier 
Published: March 2007

AbstractRecognition by the T‐cell receptor (TCR) of immunogenic peptides (p) presented by Class I major histocompatibility complexes (MHC) is the key event in the immune response against virus‐infected cells or tumor cells. A study of the 2C TCR/SIYR/H‐2Kb system using a computational alanine scanning and a much faster binding free energy decomposition based on the Molecular Mechanics—Generalized Born Surface Area (MM‐GBSA) method is presented. The results show that the TCR‐p‐MHC binding free energy decomposition using this approach and including entropic terms provides a detailed and reliable description of the interactions between the molecules at an atomistic level. Comparison of the decomposition results with experimentally determined activity differences for alanine mutants yields a correlation of 0.67 when the entropy is neglected and 0.72 when the entropy is taken into account. Similarly, comparison of experimental activities with variations in binding free energies determined by computational alanine scanning yields correlations of 0.72 and 0.74 when the entropy is neglected or taken into account, respectively. Some key interactions for the TCR‐p‐MHC binding are analyzed and some possible side chains replacements are proposed in the context of TCR protein engineering. In addition, a comparison of the two theoretical approaches for estimating the role of each side chain in the complexation is given, and a new ad hoc approach to decompose the vibrational entropy term into atomic contributions, the linear decomposition of the vibrational entropy (LDVE), is introduced. The latter allows the rapid calculation of the entropic contribution of interesting side chains to the binding. This new method is based on the idea that the most important contributions to the vibrational entropy of a molecule originate from residues that contribute most to the vibrational amplitude of the normal modes. The LDVE approach is shown to provide results very similar to those of the exact but highly computationally demanding method. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Malaria vector control in the third millennium: progress and perspectives of molecular approaches
Authors: Catteruccia Flaminia 
Published: March 2007

AbstractRemarkable progress has been made towards a deeper understanding of mosquito biology since the completion of the Anopheles gambiae Giles genome project. Combined with the development of efficient transgenic technologies for genetic modification of major vector species and the availability of powerful molecular, genetic and bioinformatics tools, this is allowing the identification of genes involved in mosquito biological functions crucial to malaria transmission, ranging from host‐seeking behaviour and innate immunity to insecticide resistance. Moreover, population genetic studies are beginning to elucidate the complex structure of vector populations. Finally, novel methods for malaria control are emerging that are based on the use of genetically modified mosquitoes either to interrupt the journey of the Plasmodium parasite within its insect host or to suppress those mosquito species that function as vectors for parasite transmission. Copyright © 2007 Society of Chemical Industry
West Nile virus in North America: perspectives on epidemiology and intervention
Authors: Reisen William , Brault Aaron C 
Published: March 2007

AbstractWest Nile virus (WNV) invaded New York in 1999 and rapidly swept across the North American continent to the West Coast, north into southern Canada and south into Latin America, with minimal genetic change. Regional epidemics in equines and humans typically have included a year of viral introduction with minimal activity, successful overwintering, explosive amplification to epidemic levels the following year and then rapid subsidence. Overwintering possibly included long‐term mosquito or avian infections, continued low‐level transmission at southern latitudes and dispersal by south–north migrants. Explosive amplification has been associated with infections in several corvid species and other urban birds that produce elevated viremias capable of efficiently infecting even moderately susceptible mosquito species. Intervention has included mass vaccination of equines, and proactive and reactive mosquito control. Proactive mosquito control in areas with established infrastructure has been successful in reducing case incidence. Copyright © 2007 Society of Chemical Industry
Longitudinal‐electric‐field influence on Rochelle salt crystals
Authors: Moina A. P. , Slivka A. G. , Kedyulich V. M. 
Published: March 2007

AbstractThe influence of the longitudinal electric field on the static and dynamic dielectric, elastic, piezoelectric characteristics of Rochelle salt, as well as sound attenuation, is studied within the two‐sublattice Mitsui model taking into account the piezoelectric coupling. A satisfactory agreement with experimental data is obtained for the field effect on the static dielectric permittivity near the lower Curie temperature. At the upper Curie temperature an effective field should be used in calculations to describe the experiment. A possible role of space‐charge build‐up in screening of the external field at high temperatures is discussed. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Properties of nanoporous carbon with pores filled by Ni atoms
Authors: Shanina B. D. , Veynger A. , Danishevskii A. M. , Popov V. V. , Kyutt R. N. , Shuman V. B. , Kurdyukov D. A. , Gordeev S. K. 
Published: March 2007

AbstractUsing the electron spin resonance (ESR) method, conductance measurements, and small‐angle X‐ray scattering (SAXS), the properties of nanoporous carbon (NPC) containing atoms of Ni in the pores are studied in comparison with the nickel‐free NPC studied before. Although the amount of Ni introduced into the nanopores is small, the NPC properties change significantly. The ESR spectra show that, at low temperatures, the charge carriers are captured at the localized states. The bulk ferromagnetism is not observed at temperatures as low as 3.2 K. Magnetic properties are strongly temperature dependent and are not limited by the paramagnetism of free charge carriers. The temperature dependence of the ESR resonance field indicates the influence of ferromagnetic inclusions. The ferromagnetic shift of the resonance fields is observed up to a temperature of 80 K. The temperature dependence of the conductance reveals an exponential growth with the activation energy close to those obtained from the ESR measurements. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The on‐shell self‐energy of the uniform electron gas in its weak‐correlation limit
Authors: Ziesche P. 
Published: March 2007

AbstractThe ring‐diagram partial summation or random‐phase approximation (RPA) for the ground‐state energy of the uniform electron gas (with the density parameter rs) in its weak‐correlation limit rs → 0 is revisited. It is studied, which treatment of the self‐energy Σ (k, ω is in agreement with the Hugenholtz–van Hove (Luttinger–Ward) theorem μ – μ0 = Σ (kF, μ and which is not. As known from Macke (1950), Gell‐Mann/Brueckner (1957), Onsager/Mittag/Stephen (1966) and using the Seitz theorem (1940), the correlation part of the lhs has the RPA asymptotics rs + a ′ + O (rs) [in atomic units]. The use of renormalized RPA diagrams for the rhs yields the similar expression a ln rs + a ″ + O (rs with the sum rule a ′ = a ″ resulting from three sum rules for the components of a ′ and a ″. This includes in the second order of exchange the relation μ2x = Σ2x(kF, $ k^2_{\rm F}/2 $ [P. Ziesche, Ann. Phys. (Leipzig) 16(1), 45 (2007)]. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Spin lifetime from the Hanle effect and fine structure of excitonic levels in InAlAs/AlGaAs quantum dots
Authors: Sahli A. , Melliti A. , Maaref M. A. , Testelin C. , Lemaitre A. , Kuszelewicz R. , Voisin P. 
Published: March 2007

AbstractExcitation of electron–hole pairs by circularly polarized light yields an electron spin polarization in InAlAs self‐assembled quantum dots. This spin polarization causes circular polarization of the photoluminescence light, its degree decreasing in a magnetic field perpendicular to the initial spin vector of the electron–hole pair (Hanle effect). The scaled spin lifetime $ g^{\rm e} _\bot $Ts, where $ g^{\rm e} _\bot $ is the transverse electron Landé factor and Ts is the electron spin lifetime is deduced from the Hanle curves and is of the order of 100 ps. It is attributed to the polarized spin confined in quantum dots. With increasing energy detection the width of the Hanle curve is reduced. The corresponding scaled electron–hole spin lifetime increases with increasing energy detection. We have also performed photoluminescence study of excitons localized in InAlAs quantum dots, in a longitudinal magnetic field. The magnetic‐field dependence of the linear and circular polarization evidences the exciton fine structure and helps to determine the anisotropic part of the exciton exchange, which is of the order of 14 μeV. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Isostructural BaSi2, BaGe2 and SrGe2: electronic and optical properties
Authors: Migas D. B. , Shaposhnikov V. L. , Borisenko V. E. 
Published: March 2007

AbstractWe have performed a theoretical study of the electronic band structure, density of states, dielectric function and absorption coefficient of isostructural BaSi2, BaGe2 and SrGe2 compounds by means of different ab initio methods. All materials are found to be indirect band‐gap semiconductors displaying almost equal dispersion of bands close to the gap region. The energy gaps of 0.83, 0.57 and 0.44 eV are estimated for BaSi2, BaGe2 and SrGe2, respectively. Analysis of the absorption coefficient of BaSi2 in comparison with data for other semiconducting silicides indicates its prospects for a solar cell application. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Deposition and properties of CdTe nanowires prepared by template replication
Authors: Enculescu Ionut , Sima Marian , Enculescu Monica , Enache Mihaela , Ion Lucian , Antohe Stefan , Neumann Reinhard 
Published: March 2007

AbstractWe used the template method to prepare CdTe wires with diameters ranging from 80 nm to 1 μm. As templates we used polycarbonate and polyethilene terephtalate ion track membranes and as the method of filling the pores of such membranes we employed electrochemical deposition. The conditions (i.e. bath composition and deposition potential) necessary to obtain the stoichiometric composition of the semiconductor were found. Scanning and transmission electron microscopy were employed for morphological characterization of the nano and microwires. Energy dispersive X‐ray analysis was employed for determining the Cd/Te ratio. Selected area electron diffraction was employed for structural measurements. Reflection spectroscopy measurements were performed on nanowire arrays for determining the band gap of the deposited nanostructures. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Dephasing of free carriers and excitons in bulk CdTe
Authors: Sprinzl D. , Kunc J. , Ostatnický T. , Horodyský P. , Grill R. , Franc J. , Malý P. , Němec P. 
Published: March 2007

AbstractIn this paper we report on the measurements of the dephasing of free carriers and excitons using a self‐diffraction technique in thin platelets of CdTe with different concentration of preparation‐induced dislocations. We show that in a high‐quality sample at low temperature the characteristic dephasing time constant is 1 ps and 2 ps for free carriers and excitons, respectively. The increased concentration of preparation‐induced dislocations leads to much stronger acceleration of the dephasing for free carriers than for excitons. We also discuss the intensity and temperature dependence of the dephasing. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Study on defect states using deep level transient spectroscopy of ZnO grown by pulsed laser deposition
Authors: Kim Jae‐Hoon , Kim Eun Kyu 
Published: March 2007

AbstractThe pulsed laser deposition (PLD) was used for fabrication of ZnO films on a sapphire substrate. We modulated the parameters, temperature and gas pressure, for the growth condition. After the growth, X‐ray diffraction, photoluminescence (PL), and deep level transient spectroscopy (DLTS) measurements were performed. We had got PL spectra of high intensity from the ZnO film grown at low temperature. And the existence of the defect states was fewer, according to the result. But the crystalline quality was good for the film grown at high temperature. It seems to be that the relation between crystallization and defined electronic bandgap is weak. The DLTS measurements show some defects, but the signal is noisy. A Schottky contact by using Ti/Au and a high conductance seem to be the cause. We had simulated the DLTS spectra from assumed defects and matched to measurement results. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Microwave plasma synthesis of nano‐crystalline YSZ
Authors: Brossmann U. , Sagmeister M. , Pölt P. , Kothleitner G. , Letofsky‐Papst I. , Szabó D. V. , Würschum R. 
Published: March 2007

AbstractNanocrystalline yttria‐stabilized zirconia (YSZ) powder and compacts have been successfully synthesized by microwave plasma synthesis co‐evaporating Y and Zr precursors from a single source. Both liquid and solid mixtures of chemically homologous precursors were tested. Electron micrographs and X‐ray diffraction studies reveal small crystallites in the range 3–4 nm with a narrow size distribution. Crystallite sizes smaller than 25 nm are preserved even after subsequent annealing at temperatures up to 950 °C. A comparison with other gas‐phase synthesis routes of nanocrystalline YSZ is given. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A global Eta model on quasi‐uniform grids
Authors: Zhang Hai , Rančić Miodrag 
Published: March 2007

AbstractThe application of quasi‐uniform grids in global models of the atmosphere is an attempt to increase the computational efficiency by a more cost‐effective exploitation of the computing infrastructure. This paper describes the development of a global version of NCEP's regional, step‐coordinate, Eta model on two quasi‐uniform grids: cubic and octagonal. The governing equations are expressed in a general curvilinear form, so that the cubic and the octagonal versions of the model share the same code in spite of different mapping of the computational domain.The dynamical core of the derived global Eta model is successfully tested in the benchmark test of Held and Suarez. The model with the step‐wise formulation of the terrain and full physics is integrated in a series of tests with real data, and the results are compared both with the analysis and the results of the regional Eta model. Copyright © 2007 Royal Meteorological Society
Impact of the Indian Ocean on ENSO variability in a hybrid coupled model
Authors: Yeh Sang‐Wook , Wu Renguang , Kirtman Ben P. 
Published: March 2007

AbstractThis study examines the impact of the Indian Ocean on El Niño and the Southern Oscillation (ENSO) variability through a series of numerical experiments with a hybrid coupled model. In the control run, an atmospheric general circulation model (AGCM) is coupled to the Zebiak–Cane simple ocean model in the tropical Pacific. Outside the tropical Pacific climatological sea surface temperatures are prescribed in the control simulation. In the first experiment, sea surface temperature anomalies (SSTAs) in the Indian Ocean are statistically predicted based on the state of the Pacific, and used to force the atmosphere. In the second experiment, a slab thermodynamic mixed layer model is coupled to the AGCM in the Indian Ocean. The Indian Ocean modifies the ENSO frequency via interactions with the Indian monsoon, but only when air–sea interactions in the Indian Ocean are included in the experimental design (i.e. the second experiment). The inclusion of the Indian Ocean, however, has little impact on the ENSO amplitude, which is at variance with other coupled simulations, suggesting that some missing dynamics or physics (i.e. Indian Ocean dynamics, Indonesian Throughflow, etc.) may play an important role. The Indian summer monsoon is more tightly coupled to ENSO in the second experiment than in the control run and the first experiment. The power spectrum of the Indian monsoon rainfall has a significant biennial time‐scale of around 20–30 months in the second experiment, which may enhance the biennial time‐scale of ENSO variability through a shift of the horizontal structure of zonal wind stress variability in the central equatorial Pacific. Copyright © 2007 Royal Meteorological Society
A modelling study of aerosol impacts on cloud microphysics and radiative properties
Authors: Cheng Chao‐Tzuen , Wang Wei‐Chyung , Chen Jen‐Ping 
Published: March 2007

AbstractA warm cloud microphysical parameterization was incorporated into a regional model to study the sensitivity to aerosols of cloud‐radiative properties and precipitation. Assuming a trimodal lognormal aerosol size distribution, the aerosol numbers were explicitly calculated from prognostic aerosol masses, considering advection, diffusion, and cloud and raindrop activation/deactivation processes. Clean continental, average continental and urban aerosols, each with different modal parameters, were used to serve as condensation nuclei (CCN) of cloud‐ and raindrops, whose activations depended on supersaturation and aerosol composition.Consistent with other studies, simulations conducted for a warm cloud system indicate that more aerosols result in more cloud water and more, but smaller, cloud drops, yielding increases in cloud albedo and decreases in surface precipitation. For example, the cloud drop effective radius decreased from ∼9 µm for clean continental aerosols to ∼5 and ∼2 µm, respectively, for average continental and urban aerosols, resulting in an increase in the respective cloud water path by ∼10% and ∼35% and cloud albedo by ∼6% and ∼12%. On the other hand, the accumulated precipitation decreased from 2.2 mm for clean continental aerosols to 1.9 and 1.2 mm, respectively, for average continental and urban aerosols. The presence of giant nuclei increased both the cloud drop effective radius and the precipitation, while the use of volumetric cloud drop radius tended to result in larger estimated cloud solar radiative forcing than the use of effective cloud drop radius. Copyright © 2007 Royal Meteorological Society