bluuebunny/crossref_metadata_2025_split huggingface dataset:
PyADF — A scripting framework for multiscale quantum chemistry
Authors: Jacob Christoph R. , Beyhan S. Maya , Bulo Rosa E. , Gomes André Severo Pereira , Götz Andreas W. , Kiewisch Karin , Sikkema Jetze , Visscher Lucas 
Published: May 2011

AbstractApplications of quantum chemistry have evolved from single or a few calculations to more complicated workflows, in which a series of interrelated computational tasks is performed. In particular multiscale simulations, which combine different levels of accuracy, typically require a large number of individual calculations that depend on each other. Consequently, there is a need to automate such workflows. For this purpose we have developed PYADF, a scripting framework for quantum chemistry. PYADF handles all steps necessary in a typical workflow in quantum chemistry and is easily extensible due to its object‐oriented implementation in the Python programming language. We give an overview of the capabilities of PYADF and illustrate its usefulness in quantum‐chemical multiscale simulations with a number of examples taken from recent applications. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
SwissParam: A fast force field generation tool for small organic molecules
Authors: Zoete Vincent , Cuendet Michel A. , Grosdidier Aurélien , Michielin Olivier 
Published: May 2011

AbstractThe drug discovery process has been deeply transformed recently by the use of computational ligand‐based or structure‐based methods, helping the lead compounds identification and optimization, and finally the delivery of new drug candidates more quickly and at lower cost. Structure‐based computational methods for drug discovery mainly involve ligand‐protein docking and rapid binding free energy estimation, both of which require force field parameterization for many drug candidates. Here, we present a fast force field generation tool, called SwissParam, able to generate, for arbitrary small organic molecule, topologies, and parameters based on the Merck molecular force field, but in a functional form that is compatible with the CHARMM force field. Output files can be used with CHARMM or GROMACS. The topologies and parameters generated by SwissParam are used by the docking software EADock2 and EADock DSS to describe the small molecules to be docked, whereas the protein is described by the CHARMM force field, and allow them to reach success rates ranging from 56 to 78%. We have also developed a rapid binding free energy estimation approach, using SwissParam for ligands and CHARMM22/27 for proteins, which requires only a short minimization to reproduce the experimental binding free energy of 214 ligand‐protein complexes involving 62 different proteins, with a standard error of 2.0 kcal mol−1, and a correlation coefficient of 0.74. Together, these results demonstrate the relevance of using SwissParam topologies and parameters to describe small organic molecules in computer‐aided drug design applications, together with a CHARMM22/27 description of the target protein. SwissParam is available free of charge for academic users at www.swissparam.ch. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Conformational state‐specific free energy differences by one‐step perturbation: Protein secondary structure preferences of the GROMOS 43A1 and 53A6 force fields
Authors: Lin Zhixiong , Van Gunsteren Wilfred F. , Liu Haiyan 
Published: May 2011

AbstractThe one‐step free energy perturbation approach can be applied to obtain conformational state‐specific free energy differences (FEDs) associated with changes in force field parameters, and thus offers the possibility to consider conformational equilibria during force field parameterization. In this work, using the alanine decapeptide in explicit water solution as a model, the α‐helical and β‐hairpin state‐specific FEDs associated with force field changes between two widely used parameter sets of the GROMOS force field, namely, 43A1 and 53A6, were determined using one‐step perturbation. The results mostly deviated by only 1 kJ mol−1 in absolute or a few percent in relative values from thermodynamic integration results, suggesting that the convergence ranges of one‐step perturbation were large enough to cover the substantial changes in nonbonded parameters between the two parameter sets. It was also found that one‐step perturbation may give larger errors when the changes from the reference state include a large decrease in van der Waals radius, as indicated by the result for the β‐hairpin state‐specific free energy change going from 53A6 to 43A1. According to the free energy results, the α‐helical state of the alanine decapeptide is destabilized by 15 kJ mol−1, i.e., 1.5 kJ mol−1 per residue, relative to the β‐hairpin state when going from 43A1 to 53A6, in agreement with previous direct simulations in which native α‐helices were often found to be unstable in simulations using 53A6, despite that the 53A6 parameters better reproduce a range of thermodynamic properties of small molecular systems. By applying one‐step perturbation to analyze the effects of perturbing individual parameters, the differential stabilization of the two secondary structure states can be traced to the changes in van der Waals parameters, especially a van der Waals parameter involved in third‐neighbor interactions. This study provides an example of the efficiency of one‐step perturbation in force field development, reducing the computational cost by orders of magnitude. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Computational study of energetic nitrogen‐rich derivatives of 1,1′‐ and 5,5′‐bridged ditetrazoles
Authors: Zhu Weihua , Zhang Chenchen , Wei Tao , Xiao Heming 
Published: May 2011

AbstractDensity functional theory method was used to study the heats of formation (HOFs), electronic structure, energetic properties, and thermal stability for a series of bridged ditetrazole derivatives with different linkages and substituent groups. The results show that the N3 group and azo bridge (NN) play a very important role in increasing the HOF values of the ditetrazole derivatives. The effects of the substituents on the HOMO–LUMO gap are combined with those of the bridge groups. The calculated detonation velocities and detonation pressures indicate that the NO2, NF2, NN, or N(O)N group is an effective structural unit for enhancing the detonation performance for the derivatives. An analysis of the bond dissociation energies for several relatively weak bonds suggests that the NN bond in the ring or outside the ring is the weakest one and the NN cleavage is possible to happen in thermal decomposition. Overall, the CH2CH2 or NHNH group is an effective bridge for enhancing the thermal stability of the bridged ditetrazoles. Because of their desirable detonation performance and thermal stability, five compounds may be considered as the potential candidates of high‐energy density materials (HEDMs). These results provide basic information for the molecular design of novel HEDMs. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Syntheses of dual‐radioisotope‐labeled CP‐I, a GABAA receptor partial agonist
Authors: Zhang Yinsheng , Greenfield Laura , Hong Yang 
Published: May 2011

AbstractCP‐I is a potent subtype‐selective GABAA receptor partial agonist. Owing to its significant metabolic cleavage at C8 observed in preliminary biotransformation studies with non‐radiolabeled CP‐I, the syntheses of CP‐I labeled at the right or left hand side with 14C or labeled with 3H at the right hand side were required. The two compounds labeled with 14C at the left or right hand side were synthesized in 2 and 5 radio‐synthetic steps using [14C]2‐chloroacetyl chloride and [14C]NaCN as starting radiolabeled materials, respectively. CP‐I was labeled with tritium at the right hand side by a tritium de‐halogenation method. Batches of radiolabeled CP‐I were mixed to give dual‐radioisotope‐labeled CP‐I. An efficient approach to [14C]fluoropyridinyl imidazole was developed, and a short synthesis of iodo‐substituted fluoropyridinyl imidazole was also achieved. The details of these syntheses are discussed. Copyright © 2011 John Wiley & Sons, Ltd.
Functional morphology of the luminescence system of Siphamia versicolor (Perciformes: Apogonidae), a bacterially luminous coral reef fish
Authors: Dunlap Paul V. , Nakamura Masaru 
Published: May 2011

AbstractPrevious studies of the luminescence system of Siphamia versicolor (Perciformes: Apogonidae) identified a ventral light organ, reflector, lens, duct, and a ventral diffuser extending from the throat to the caudal peduncle. The control and function of luminescence in this and other species of Siphamia, however, have not been defined. Morphological examination of fresh and preserved specimens identified additional components of the luminescence system involved in control and ventral emission of luminescence, including a retractable shutter over the ventral face of the light organ, contiguity of the ventral diffuser from the caudal peduncle to near the chin, and transparency of the bones and other tissues of the lower jaw. The shutter halves retract laterally, allowing the ventral release of light, and relax medially, blocking ventral light emission; topical application of norepinephrine to the exposed light organ resulted in retraction of the shutter halves, which suggests that operation of the shutter is under neuromuscular control. The extension of the diffuser to near the chin and transparency of the lower jaw allow a uniform emission of luminescence over the entire ventrum of the fish. The live aquarium‐held fish were found to readily and consistently display ventral luminescence. At twilight, the fish left the protective association with their longspine sea urchin, Diadema setosum, and began to emit ventral luminescence and to feed on zooplankton. Ventral luminescence illuminated a zone below and around the fish, which typically swam close to the substrate. Shortly after complete darkness, the fish stopped feeding and emitting luminescence. These observations suggest that S. versicolor uses ventral luminescence to attract and feed on zooplankton from the reef benthos at twilight. Ventral luminescence may allow S. versicolor to exploit for feeding the gap at twilight in the presence of potential predators as the reef transitions from diurnally active to nocturnally active organisms. J. Morphol., 2011. © 2011 Wiley‐Liss, Inc
Topographic mapping of retinal neurons in the european anchovy by nuclear staining and immunohistochemistry
Authors: Koch Petra Christiane , Heß Martin 
Published: May 2011

AbstractThe anchovy retina is unique among vertebrates in being designed for polarization‐contrast vision and has a marked cone area in the ventrotemporal quadrant for acute vision in the frontal field of view. Whereas cone topography and fine structure have been well examined in the European anchovy, the morphological organization of its inner retina is poorly understood so far. Using fluorescence staining of cell nuclei in combination with antibody stainings, the 3D pattern of cell nuclei was recorded coevally in all three retinal cell layers by confocal laser scanning microscopy, and the topographies of several neuron types were mapped separately across the retina. Cell classification and quantification succeeded for rods, cones, three types of horizontal cells (H1–3), rod and cone bipolars, amacrines, ganglion cells, and displaced amacrines as well as Müller cells; moreover, the morphology of H1 horizontal cells (calretinin‐positive), rod bipolars (protein kinase C‐positive), and a subtype of cone bipolars (parvalbumin‐positive) is shown. Most cell types follow the cone topography, with a cell density maximum in the ventrotemporal quadrant (e.g., 730 cones, 2,800 cone bipolars, 230 GCL cells per 104 μm2), showing their affiliation to the photopic system, except rods and rod bipolars (showing a cell density minimum in the cone area). The correlation of density maps of different cell types provides insight into convergence and divergence patterns in cone and rod pathways. © 2011 Wiley‐Liss, Inc.
A theoretical investigation of super‐resolution CARS imaging via coherent and incoherent saturation of transitions
Authors: Beeker Willem P. , Lee Chris J. , Boller Klaus J. , Groß Petra , Cleff Carsten , Fallnich Carsten , Offerhaus Herman L. , Herek Jennifer L. 
Published: May 2011

AbstractWe review two approaches to achieving sub‐diffraction‐limited resolution coherent anti‐Stokes Raman scattering (CARS) microscopy (Beeker et al., Opt. Express, 2009, 17, 22632 and Beeker et al., J. Herek, Phys. Rev. A, 2010, 81, 012507). We performed a numerical investigation, based on the density matrix model, of the CARS emission process and identified two modified CARS experiments that lead to sub‐diffraction‐limited resolution images. At the heart of both processes is the spatial manipulation of the coherence between the ground state and the vibrational state being probed by the CARS process via a control state and a control laser that is resonant with the ground state to control state transition. We find two possible regimes of operation: in the first regime, the control and vibrational states are coupled via incoherent processes so that the populations of the two states reach equilibrium very quickly compared to the relevant coherence times. Under these conditions, pre‐populating the control state provides a saturable suppression of the coherence between the ground state and the vibrational state, suppressing CARS emission. By using a donut mode to pre‐populate the control state, CARS is suppressed everywhere but the central node, allowing sub‐diffraction‐limited resolution imaging. In the second regime, the control state has a rather long coherence lifetime, and the resonant laser drives Rabi oscillations that periodically deplete the ground state. As a result, the CARS emission process is amplitude‐modulated, which appear as sidebands on the CARS spectrum. By a process of spectral resolution and trilateration, sub‐diffraction‐limited resolution images can be obtained. Copyright © 2011 John Wiley & Sons, Ltd.
Timing for repair of mandible fractures
Authors: Barker Daniel A. , Oo Kenneth K. , Allak Amir , Park Stephen S. 
Published: May 2011

AbstractObjectives/Hypothesis:Timing for repair of mandible fractures is a significant factor with regard to the rate of complication.Study Design:Retrospective chart review of the previous 5 years (January 2005–January 2010).Methods:All patients undergoing mandible fracture fixation performed in the study period and having complete records were analyzed (n = 83). Patients were stratified by time to fixation following initial injury. Subjects were then separated by the presence or absence of any of the following complications: infection, malunion, and nonunion. Logistical regression was then performed.Results:Out of 83 patients there were 4 patients with six complications including malunion (n = 4) and infection (n = 2). There were no cases of nonunion. Delay in surgical intervention did not influence the complication rate.Conclusions:Complications from repair of mandible fractures are rare; it is difficult to detect significant variables that may impact outcomes. We found no relationship between complications and timing to repair.
Primary versus delayed tracheoesophageal puncture for laryngopharyngectomy with free flap reconstruction
Authors: Sinclair Catherine F. , Rosenthal Eben L. , McColloch Nancy L. , Magnuson J. Scott , Desmond Reneé A. , Peters Glenn E. , Carroll William R. 
Published: May 2011

AbstractObjectives:To determine whether postoperative complication rates and speech outcomes differ between patients undergoing primary versus secondary tracheoesophageal puncture following total laryngectomy with free flap reconstruction.Study Design:Retrospective clinical study in a tertiary academic center.Methods:Between November 2004 and June 2010, 137 patients underwent total laryngectomy or laryngopharyngectomy with pharyngeal free flap reconstruction for malignant disease. Data was collected on patient and operative demographics, early postoperative complications, speech outcomes, and predictive factors for tracheoesophageal puncture failure.Results:Thirty patients (22%) had a primary tracheoesophageal puncture performed at the time of laryngectomy, 27 patients (20%) received secondary punctures (>3 months postlaryngectomy), and 80 patients (58%) never received a puncture. Patient and operative demographics were similar between groups (P < .05), apart from proportionately more hypopharyngeal tumors in the “no puncture” group (P < .002). Similar numbers of patients in primary and secondary puncture groups achieved intelligible speech (67% vs. 71%, P = .82) and both groups reported good patient‐perceived voice‐related quality of life. Salvage surgery and nonpatch radial forearm free flap reconstruction both trended toward increased early postoperative complication rates (P = .09).Conclusions:There is no difference in the early postoperative complication rate for primary versus secondary tracheoesophageal puncture following total laryngectomy with concurrent free flap reconstruction. Radial forearm patch free flap reconstruction achieves good speech outcomes.
Multilevel and Multiscale Nanostructures of Polyaniline Doped With L‐Lysine
Authors: Wang Guang , Zhu Ying , Ding Chunmei , Wang Liang , Liu Hongying , Wan Meixiang , Jiang Lei 
Published: May 2011

AbstractNovel multiscale and multilevel nanostructures of polyaniline (PANI), such as brushlike micro/nanostructures, double hollow microspheres, and multicavity hollow microspheres, are fabricated for the first time with L‐lysine as the dopant and soft‐template. It is found that the morphology, crystallinity, and electrical properties of the micro/nanostructures strongly depend on the molar ratio of aniline to L‐lysine. At a 2.5:1 molar ratio of aniline to L‐lysine, brushlike micro/nanostructures are obtained. On the other hand, double hollow spheres and multicavity hollow spheres are observed at 1:2 and 1:3 molar ratios of aniline to L‐lysine, respectively. Since L‐lysine has one COOH group and two NH2 group, cooperation of L‐lysine micelles as the soft‐template of hollow spheres and aggregation between these hollow spheres results in the formation of the double hollow spheres or multicavity hollow spheres. On the other hand, cooperation of the aniline/L‐lysine salt micelle as the soft‐template and hydrogen band results in crosswire‐like micro/nanostructures as the cell unit to form novel brushlike micro/nanostructures via a self‐assembly process. magnified image
Evaluation of Coupling Agents in Poly(propylene)/Fly Ash Composites: Effect on Processing and Mechanical Properties
Authors: Iraola‐Arregui Itziar , Potgieter Herman , Liauw Christopher Mark 
Published: May 2011

AbstractComposites containing 50 wt.‐% fly ash in a PP homopolymer were prepared via batch mixing and compression moulding. The following coupling agents were evaluated: Lubrizol Solplus C800, N,N′‐(1,3‐phenylene)dimaleimide, γ‐methacryloxypropyltrimethoxysilane and maleic‐anhydride‐grafted PP. At the filler level investigated, C800 gave the best balance of composite strength and toughness. In the latter case filler‐matrix adhesion appeared weaker relative to γ‐MPS, BMI and m‐PP, all of which gave excessively strong filler‐matrix adhesion leading to a reduction in composite toughness. The unexpected weakness of the C800/fly ash interaction may be related to removal of surface calcium ions from the fly ash via reaction of a single calcium ion with two C800 molecules. magnified image
Electropatterning of Binary Polymer Brushes by Surface‐initiated RAFT and ATRP
Authors: Tria Maria Celeste R. , Advincula Rigoberto C. 
Published: May 2011

AbstractA new, simple, and effective method for preparing binary patterned brushes by electrodeposition and self‐assembly is presented. The technique involves the use of electrochemistry to immobilize a chain transfer agent (CTA) on a patterned conducting substrate that mediate surface‐initiated polymerization (SIP) through a reversible addition–fragmentation chain transfer (RAFT) process. The non‐electropatterned surfaces were then backfilled with self‐assembly of an atom transfer radical polymerization (ATRP) silane initiator where the polymerization of the next brush was initiated. The use of techniques such as RAFT and ATRP is well known to give a controlled polymerization mechanism, which would be of great advantage in generating binary patterned brushes. FT‐IR imaging was used to analyze these films. magnified image
Core‐Shell Structured Monodisperse Poly(3,4‐Ethylenedioxythiophene)/Poly(Styrenesulfonic Acid) Coated Polystyrene Microspheres and Their Electrorheological Response
Authors: Liu Ying Dan , Kim Ji Eun , Choi Hyoung Jin 
Published: May 2011

AbstractWe report the successful synthesis of transparent thin film of conducting poly(3,4‐ethylenedioxythiophene)/poly(styrenesulfonic acid) (PEDOT/PSS) coated monodisperse polystyrene (PS) microspheres via a simple physical adsorption route in an aqueous media and their electrorheological (ER) application under an applied electric field. Due to the insulating PS core, the PEDOT/PSS wrapped PS (PEDOT/PSS/PS) particles possess a low volume conductivity appropriately applied as ER active materials. Tested by a rotational rheometer under an applied electric field, the PEDOT/PSS/PS based ER fluid dispersed in a silicone oil shows a typical Bingham‐fluid behavior with increased yield stresses according to the increase of electric field strength. magnified image
Is It Worth the Effort to Reinforce Polymers With Carbon Nanotubes?
Authors: Loos Marcio R. , Schulte Karl 
Published: May 2011

AbstractCarbon nanotubes (CNTs) show exceptional properties that render them attractive for incorporation in a new generation of high‐performance engineering composites with tailored properties. While a great deal of work has been done toward using CNTs as a reinforcing agent in polymer composites, the full potential of CNTs has yet to be reached. In this work, two case studies were proposed in order to analyze the effectiveness of CNTs and carbon fibers (CFs) as reinforcing agents. Micromechanics models for the stiffness and strength of hybrid composites, comprising CNTs and CFs are derived by considering the concept of effective fiber. In addition, the 2009 prices of commercially available CNTs are reviewed. The strongest, the stiffest, and the cheapest CFs commercially available are compared with single walled CNTs (SWCNTs) and multiwalled CNTs (MWCNTs). The simulated results from the micromechanics models show that the use of CFs makes the acquisition of composites with maximum tensile strengths of 4.18 GPa possible. Analysis of the cost versus property relation showed that CNTs are the most viable strengthening option for achieving composites with strengths of up to 11.61 GPa. It is also shown that CFs are the most viable stiffening option, making composites with Young's moduli of up to 383 GPa possible at the expense of the material's toughness. Moreover, it is shown that, in order to achieve CNT's true potential, several challenges have to be faced. CNTs have to be produced with higher purity, longer lengths, better integrity, in larger amounts, and at lower cost. Moreover, issues such as orientation of the CNTs, their concentration, interfacial adhesion, distribution, and dispersion have to be overcome. magnified image
On the road to get structural recycled concrete
Authors: El Dalati R. , Matar P. 
Published: May 2011

AbstractThis paper presents new recommendations for recycling and reuse of concrete. It shows the influencing parameters for decreasing and increasing the concrete strength under compression. These parameters are the percentage of recycled aggregates used in new compositions of concrete, the age and the state of the original concrete, the addition of cement and plasticizer, and the nature of the original aggregates. Fixing some parameters and with some additions, we could increase the recycled concrete strength and even obtain the original value of concrete strength. The paper shows a new way to get structural recycled concrete.