bluuebunny/crossref_metadata_2025 huggingface dataset:
Ovine fetal renal development impacted by multiple fetuses and uterine space restriction
Authors: Meyer-Gesch K. M. , Sun M. Y. , Koch J. M. , Ramadoss J. , Blohowiak S. E. , Magness R. R. , Kling P. J.
Published: July 2013

Intrauterine growth restriction (IUGR) from uteroplacental dysfunction causes impaired nephrogenesis and ultimately hypertension, but it is unknown whether IUGR caused by insufficient space for placental development seen in uterine anomalies and/or multifetal gestation exerts the same effects. Fetal renal development and metabolism were studied in an ovine space-restriction model by combining unilateral horn surgical ligation and/or multifetal gestation. Reduced placental attachment sites and placental weight per fetus defined space-restricted (USR)v. control nonrestricted (NSR) fetuses. Space-restricted fetuses exhibited evidence for decreased plasma volume, with higher hematocrit and plasma albumin at gestational day (GD) 120, followed by lower blood pO2, and higher osmolarity and creatinine at GD130,P< 0.05 for all. By combining treatments, fetal kidney weight relative to fetal weight was inversely related to both fetal weight and plasma creatinine levels,P< 0.05 for both. At GD130, space-restricted fetal kidney weights, cortical depths and glomerular generations were decreased,P< 0.05 for all. Space-restricted kidneys underwent an adaptive response by prolonging active nephrogenesis and increasing maculae densa number,P< 0.05 for both. The major renal adaptations in space-restricted IUGR fetuses included immaturity in both development and endocrine function, with evidence for impaired renal excretory function.
Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight
Authors: Chow Cheryl-Emiliane T , Sachdeva Rohan , Cram Jacob A , Steele Joshua A , Needham David M , Patel Anand , Parada Alma E , Fuhrman Jed A
Published: July 2013

Time-series are critical to understanding long-term natural variability in the oceans. Bacterial communities in the euphotic zone were investigated for over a decade at the San Pedro Ocean Time-series station (SPOT) off southern California. Community composition was assessed by Automated Ribosomal Intergenic Spacer Analysis (ARISA) and coupled with measurements of oceanographic parameters for the surface ocean (0–5 m) and deep chlorophyll maximum (DCM, average depth ∼30 m). SAR11 and cyanobacterial ecotypes comprised typically more than one-third of the measured community; diversity within both was temporally variable, although a few operational taxonomic units (OTUs) were consistently more abundant. Persistent OTUs, mostly Alphaproteobacteria (SAR11 clade), Actinobacteria and Flavobacteria, tended to be abundant, in contrast to many rarer yet intermittent and ephemeral OTUs. Association networks revealed potential niches for key OTUs from SAR11, cyanobacteria, SAR86 and other common clades on the basis of robust correlations. Resilience was evident by the average communities drifting only slightly as years passed. Average Bray-Curtis similarity between any pair of dates was ∼40%, with a slight decrease over the decade and obvious near-surface seasonality; communities 8–10 years apart were slightly more different than those 1–4 years apart with the highest rate of change at 0–5 m between communities <4 years apart. The surface exhibited more pronounced seasonality than the DCM. Inter-depth Bray-Curtis similarities repeatedly decreased as the water column stratified each summer. Environmental factors were better predictors of shifts in community composition than months or elapsed time alone; yet, the best predictor was community composition at the other depth (that is, 0–5 m versus DCM).
F‐block Elements Recovery
Authors: Natrajan Louise S. , Langford Paden Madeleine H.
Published: July 2013

The rare‐earth elements (lanthanides) have become vital components in many areas of modern day life and fulfil an unparalleled role in many advanced ‘green‐technologies’ ranging from powerful magnets in wind turbines to energy efficient fluorescent lighting. Equally, the actinide element uranium is an extremely powerful commodity in nuclear power generation in low carbon energy production. The essential role of these elements in these technologies has resulted in an unprecedented increase in demand and price of raw material resources. However, all the f‐block elements are finite resources and concerns over exhaustion of raw materials, security of supply, the supply chain and in the case of the actinides, the build up of long‐lived radioactive wastes are now of immense global concern. Focus has recently turned to post consumer recovery and recycling strategies in order to address these issues and to circumvent the pressing matter of supply vulnerability by closing the mining/manufacturing processes and the nuclear fuel cycle. This chapter describes the many modern commercial uses of the f‐elements and outlines current and future recovery/recycling options in line with the transition to a more sustainable energy conscious society.
Histidine kinases from bacteria to humans
Authors: Attwood Paul V.
Published: July 2013

It is more than 50 years since protein histidine phosphorylation was first discovered in 1962 by Boyer and co-workers; however, histidine kinases are still much less well recognized than the serine/threonine and tyrosine kinases. The best-known histidine kinases are the two-component signalling kinases that occur in bacteria, fungi and plants. The mechanisms and functions of these kinases, their cognate response regulators and associated phosphorelay proteins are becoming increasingly well understood. When genomes of higher eukaryotes began to be sequenced, it did not appear that they contained two-component histidine kinase system homologues, apart from a couple of related mitochondrial enzymes that were later shown not to function as histidine kinases. However, as a result of the burgeoning sequencing of genomes from a wide variety of eukaryotic organisms, it is clear that there are proteins that correspond to components of the two-component histidine kinase systems in higher eukaryotes and that operational two-component kinase systems are likely to occur in these organisms. There is unequivocal direct evidence that protein histidine phosphorylation does occur in mammals. So far, only nucleoside diphosphate kinases have been shown to be involved in protein histidine phosphorylation, but their mechanisms of action are not well understood. It is clear that other, yet to be identified, histidine kinases also exist in mammals and that protein histidine phosphorylation may play important roles in higher eukaryotes.
Intron excision from precursor tRNA molecules in mammalian cells requires ATP hydrolysis and phosphorylation of tRNA-splicing endonuclease components
Authors: Mair Barbara , Popow Johannes , Mechtler Karl , Weitzer Stefan , Martinez Javier
Published: July 2013

The process of tRNA splicing entails removal of an intron by TSEN (tRNA–splicing endonuclease) and ligation of the resulting exon halves to generate functional tRNAs. In mammalian cells, the RNA kinase CLP1 (cleavage and polyadenylation factor I subunit) associates with TSEN and phosphorylates the 3′ exon at the 5′ end in vitro, suggesting a role for CLP1 in tRNA splicing. Interestingly, recent data suggest that the ATP-binding and/or hydrolysis capacity of CLP1 is required to enhance pre-tRNA cleavage. In vivo, the lack of CLP1 kinase activity leads to progressive motor neuron loss and accumulation of novel 5′ leader–5′ exon tRNA fragments. We have extended the investigation of the biochemical requirements in pre-tRNA splicing and found that β–γ-hydrolysable ATP is crucial for the productive generation of exon halves. In addition, we provide evidence that phosphorylation of the TSEN complex components supports efficient pre-tRNA cleavage. Taken together, our data improve the mechanistic understanding of mammalian pre-tRNA processing and its regulation.
The kinase triad, AMPK, mTORC1 and ULK1, maintains energy and nutrient homoeostasis
Authors: Dunlop Elaine A. , Tee Andrew R.
Published: July 2013

In order for cells to divide in a proficient manner, they must first double their biomass, which is considered to be the main rate-limiting phase of cell proliferation. Cell growth requires an abundance of energy and biosynthetic precursors such as lipids and amino acids. Consequently, the energy and nutrient status of the cell is acutely monitored and carefully maintained. mTORC1 [mammalian (or mechanistic) target of rapamycin complex 1] is often considered to be the master regulator of cell growth that enhances cellular biomass through up-regulation of protein translation. In order for cells to control cellular homoeostasis during growth, there is close signalling interplay between mTORC1 and two other protein kinases, AMPK (AMP-activated protein kinase) and ULK1 (Unc-51-like kinase 1). This kinase triad collectively senses the energy and nutrient status of the cell and appropriately dictates whether the cell will actively favour energy- and amino-acid-consuming anabolic processes such as cellular growth, or energy- and amino-acid-generating catabolic processes such as autophagy. The present review discusses important feedback mechanisms between these three homoeostatic protein kinases that orchestrate cell growth and autophagy, with a particular focus on the mTORC1 component raptor (regulatory associated protein of mammalian target of rapamycin), as well as the autophagy-initiating kinase ULK1.
Role of PI3K, mTOR and Akt2 signalling in hepatic tumorigenesis via the control of PKM2 expression
Authors: Nemazanyy Ivan , Espeillac Catherine , Pende Mario , Panasyuk Ganna
Published: July 2013

To sustain increased growth, rapidly proliferating cells, such as tumour cells, undergo metabolic adaptations. In recent years, the mechanisms of glycolysis activation as a key metabolic adaptation in proliferating cells became the topic of intense research. Although this phenomenon was described more than 50 years ago by Otto Warburg, the molecular mechanisms remained elusive. Only recently, it was demonstrated that the expression of specific glycolytic enzymes, namely PKM2 (pyruvate kinase M2) and HK2 (hexokinase 2), occurs simultaneously with the glycolytic addiction of cancer cells. The PI3K (phosphoinositide 3-kinase)/mTOR [mammalian (or mechanistic) target of rapamycin] signalling pathway is a central signalling hub co-ordinating the growth in response to growth factor signalling and nutrient availability. Not surprisingly, it is found to be activated in the majority of the tumour cells. In the present article, we discuss the requirement of different PI3K/mTOR downstream effectors for the metabolic adaptation in liver cancer cells driven by this signalling pathway. We provide evidence for a selective involvement of the mTOR target Akt2 in tumoral growth. In addition, PTEN (phosphatase and tensin homologue deleted on chromosome 10)-negative human hepatocellular carcinoma cell lines display an up-regulation of PKM2 expression in an Akt2-dependent manner, providing an advantage for cell proliferation and anchorage-independent growth. Our data have implications on the link between the metabolic action of insulin signal transduction and tumorigenesis, identifying Akt2 as a potential therapeutical target in liver malignancies depending on cancer genotype.
WIPI β-propellers in autophagy-related diseases and longevity
Authors: Bakula Daniela , Takacs Zsuzsanna , Proikas-Cezanne Tassula
Published: July 2013

Autophagy is a catabolic pathway in which the cell sequesters cytoplasmic material, including long-lived proteins, lipids and organelles, in specialized double-membrane vesicles, called autophagosomes. Subsequently, autophagosomes communicate with the lysosomal compartment and acquire acidic hydrolases for final cargo degradation. This process of partial self-eating secures the survival of eukaryotic cells during starvation periods and is critically regulated by mTORC1 (mammalian target of rapamycin complex 1). Under nutrient-poor conditions, inhibited mTORC1 permits localized PtdIns(3)P production at particular membranes that contribute to autophagosome formation. Members of the human WIPI (WD-repeat protein interacting with phosphoinositides) family fulfil an essential role as PtdIns(3)P effectors at the initiation step of autophagosome formation. In the present article, we discuss the role of human WIPIs in autophagy, and the identification of evolutionarily conserved amino acids of WIPI-1 that confer PtdIns(3)P binding downstream of mTORC1 inhibition. We also discuss the PtdIns(3)P effector function of WIPIs in the context of longevity and autophagy-related human diseases, such as cancer and neurodegeneration.
Argonaute and GW182 proteins: an effective alliance in gene silencing
Authors: Pfaff Janina , Meister Gunter
Published: July 2013

Argonaute proteins interact with small RNAs and facilitate small RNA-guided gene-silencing processes. Small RNAs guide Argonaute proteins to distinct target sites on mRNAs where Argonaute proteins interact with members of the GW182 protein family (also known as GW proteins). In subsequent steps, GW182 proteins mediate the downstream steps of gene silencing. The present mini-review summarizes and discusses our current knowledge of the molecular basis of Argonaute–GW182 protein interactions.
Nuclear receptor-binding protein 1: a novel tumour suppressor and pseudokinase
Authors: Kerr Jason S. , Wilson Catherine H.
Published: July 2013

Pseudokinases are a class of kinases which are structurally designated as lacking kinase activity. Despite the lack of kinase domain sequence conservation, there is increasing evidence that a number of pseudokinases retain kinase activity and/or have critical cellular functions, casting aside previous notions that pseudokinases simply exist as redundant kinases. Moreover, a number of recent studies have implicated pseudokinases as critical components in cancer formation and progression. The present review discusses the interactions and potential functions that nuclear receptor-binding protein 1, a pseudokinase recently described to have a tumour-suppressive role in cancer, may play in cellular homoeostasis and protein regulation. The recent findings highlighted in the present review emphasize the requirement to fully determine the function of pseudokinases in vitro and in vivo, the understanding of which may ultimately uncover new directions for drug discovery.
Attempting to rewrite History: challenges with the analysis of histidine-phosphorylated peptides
Authors: Gonzalez-Sanchez Maria-Belen , Lanucara Francesco , Helm Matthew , Eyers Claire E.
Published: July 2013

A significant number of proteins in both eukaryotes and prokaryotes are known to be post-translationally modified by the addition of phosphate, serving as a means of rapidly regulating protein function. Phosphorylation of the amino acids serine, threonine and tyrosine are the focus of the vast majority of studies aimed at elucidating the extent and roles of such modification, yet other amino acids, including histidine and aspartate, are also phosphorylated. Although histidine phosphorylation is known to play extensive roles in signalling in eukaryotes, plants and fungi, roles for phosphohistidine are poorly defined in higher eukaryotes. Characterization of histidine phosphorylation aimed at elucidating such information is problematic due to the acid-labile nature of the phosphoramidate bond, essential for many of its biological functions. Although MS-based strategies have proven extremely useful in the analysis of other types of phosphorylated peptides, the chromatographic procedures essential for such approaches promote rapid hydrolysis of phosphohistidine-containing peptides. Phosphate transfer to non-biologically relevant aspartate residues during MS analysis further complicates the scenario.
Pseudokinase drug intervention: a potentially poisoned chalice
Authors: Claus Jeroen , Cameron Angus J.M. , Parker Peter J.
Published: July 2013

Pseudokinases, the catalytically impaired component of the kinome, have recently been found to share more properties with active kinases than previously thought. In many pseudokinases, ATP binding and even some activity is preserved, highlighting these proteins as potential drug targets. In both active kinases and pseudokinases, binding of ATP or drugs in the nucleotide-binding pocket can stabilize specific conformations required for activity and protein–protein interactions. We discuss the implications of locking particular conformations in a selection of (pseudo)kinases and the dual potential impact on the druggability of these proteins.
Mechanistic and functional diversity in the mechanosensory kinases of the titin-like family
Authors: Mayans Olga , Benian Guy M. , Simkovic Felix , Rigden Daniel J.
Published: July 2013

The giant cytoskeletal kinases of the titin-like family are emerging as key mediators of stretch-sensing in muscle. It is thought that their elastic conformational deformation during muscle function regulates both their catalysis and the recruitment of regulatory proteins to signalosomes that assemble in their vicinity. In the present article, we discuss the speciation of mechanosensory mechanisms in titin-like kinases, their scaffolding properties and the kinase/pseudokinase domain variations that define a rich functional diversity across the family.
On mTOR nomenclature
Authors: Hall Michael N.
Published: July 2013

In the present article, I discuss recent developments in the naming of the TOR (target of rapamycin) protein. In particular, I address the issue of mammalian target of rapamycin (mTOR) versus the newer mechanistic target of rapamycin (MTOR). mTOR is the name given by the TOR community almost two decades ago and widely used ever since. MTOR is a name recently imposed on the TOR community by database curators and used mainly by newcomers. I argue that MTOR is causing needless confusion in the field, and conclude that one should use the name mTOR.
Structural characterization of the cyclin-dependent protein kinase family
Authors: Endicott Jane A. , Noble Martin E.M.
Published: July 2013

Structural studies of members of the CDK (cyclin-dependent protein kinase) family have made a significant contribution to our understanding of the regulation of protein kinases. The structure of monomeric unphosphorylated CDK2 was the first of an inactive protein kinase to be determined and, since then, structures of other members of the CDK family, alone, in complex with regulatory proteins and in differing phosphorylation states, have enhanced our understanding of the molecular mechanisms regulating protein kinase activity. Recently, our knowledge of the structural biology of the CDK family has been extended by determination of structures for members of the transcriptional CDK and CDK-like kinase branches of the extended family. We include these recent structures in the present review and consider them in the light of current models for CDK activation and regulation.
Development of a precision nanoindentation platform
Authors: Nowakowski B. K. , Smith D. T. , Smith S. T. , Correa L. F. , Cook R. F.
Published: July 2013

The design, construction, and performance of a surface-referenced nanoindentation instrument, termed a precision nanoindentation platform (PNP), are presented. The PNP is a symmetrically designed instrument with a centrally located indenter tip attached to a force cell for measuring the forces between the tip and a specimen. Penetration of the indenter tip into the specimen surface is measured using two proximity sensors placed symmetrically about the indenter. Each proximity sensor is attached to a piezoelectric actuator that is servo controlled to maintain the sensor and the reference frame to which it is attached at a constant height relative to the specimen surface. As the indenter tip penetrates the specimen surface, the movement of the tip relative to the two surface reference frames is measured using capacitance gauges and the average of these displacements is used as a measure of penetration depth. The current indenter is capable of applying indentation forces of up to 150 mN with a noise floor below 2 μN rms for a sampling rate of 1 kHz, and measuring displacement with 0.4 nm rms noise for the same sampling rate. The proximity sensors are capable of maintaining surface height variations of less than 1.0 nm with penetration depths of up to 10 μm. Long-term stability tests indicate a total uncertainty in indentation depth less than 10 nm for periods as long as 12 h. To demonstrate instrument accuracy, repeated indention cycles were performed on a fused silica specimen using incrementally increasing indention force. From this test, an average value of 72 GPa ± 1.5 GPa for the Young's modulus was obtained from the elastic unloading curves for 10 measurements ranging in maximum force from 5 mN to 50 mN. To demonstrate longer-term instrument stability, a poly(methyl methacrylate) specimen was subjected to a fixed 5 mN indentation force for 4 h; two distinct creep-like mechanisms were observed.
A guiding potential method for evaluating the bending rigidity of tensionless lipid membranes from molecular simulation
Authors: Kawamoto Shuhei , Nakamura Takenobu , Nielsen Steven O. , Shinoda Wataru
Published: July 2013

A new method is proposed to estimate the bending rigidity of lipid membranes from molecular dynamics simulations. An external cylindrical guiding potential is used to impose a sinusoidal deformation to a planar membrane. The bending rigidity is obtained from the mean force acting on the cylinder by calibrating against a discretized Helfrich model that accounts for thermal fluctuations of the membrane surface. The method has been successfully applied to a dimyristoyl phosphatidylcholine bilayer simulated with a coarse-grained model. A well-converged bending rigidity was obtained for the tension-free membrane and showed reasonable agreement with that obtained from the height fluctuation spectrum.
Report on the IUTAM Symposium on Mobile Particulate Systems: Kinematics, Rheology, and Complex Phenomena, Bangalore, India, 2012
Authors: Nott P. R. , Davis R. H. , Reeks M. , Saintillan D. , Sundaresan S.
Published: July 2013

This report summarizes the presentations and discussions conducted during the symposium, which was held under the aegis of the International Union of Theoretical and Applied Mechanics during 23–27 January 2012 in Bangalore, India.
Pair-particle dynamics and microstructure in sheared colloidal suspensions:Simulation and Smoluchowski theory
Authors: Nazockdast Ehssan , Morris Jeffrey F.
Published: July 2013

The Smoluchowski equation (SE) approach reduced to pair level provides an accepted method for analysis of the pair microstructure, i.e., the pair distribution functiong(r), in sheared colloidal suspensions. Under dilute conditions, the resulting problem is well-defined, but for concentrated suspensions the coefficients of the pair SE are unclear. This work outlines a recently developed theoretical approach for analytical and numerical study of the pair SE for concentrated colloidal suspensions of spheres in shear flow, and then focuses upon evaluation of coefficients and related properties of the problem from Stokesian Dynamics simulation, over a wide range of particle volume fraction, ϕ, and Péclet number (ratio of shear to Brownian motion). The pair distribution functiondetermined from the SE theory is in generally good agreement with Stokesian Dynamics, as are the computed viscosity and normal stresses of the material. The primary focus of the work is to consider the pair relative velocity predicted by the theoryin comparison to Stokesian Dynamics simulations, as well as to evaluate quantities related to the hydrodynamic dispersion needed in the theoretical approach. The pair dynamics for moderate particle volume fraction, 0.20 ⩽ ϕ ⩽ 0.35, are found to be remarkably different from the form for an isolated pair of spheres, and at ϕ ⩾ 0.40 a qualitative change is again seen. Agreement of the theory and simulation on the primary features of the particle motion and structure is good, and discrepancies are clearly delineated.
The effect of base roughness on the development of a dense granular flow down an inclined plane
Authors: Kumaran V. , Bharathraj S.
Published: July 2013

The development of the flow of a granular material down an inclined plane starting from rest is studied as a function of the base roughness. In the simulations, the particles are rough frictional spheres interacting via the Hertz contact law. The rough base is made of a random configuration of fixed spheres with diameter different from the flowing particles, and the base roughness is decreased by decreasing the diameter of the base particles. The transition from an ordered to a disordered flowing state at a critical value of the base particle diameter, first reported by Kumaran and Maheshwari [Phys. Fluids 24, 053302 (2012)]10.1063/1.4710543 for particles with the linear contact model, is observed for the Hertzian contact model as well. The flow development for the ordered and disordered flows is very different. During the development of the disordered flow for the rougher base, there is shearing throughout the height. During the development of the ordered flow for the smoother base, there is a shear layer at the bottom and a plug region with no internal shearing above. In the shear layer, the particles are layered and hexagonally ordered in the plane parallel to the base, and the velocity profile is well approximated by Bagnold law. The flow develops in two phases. In the first phase, the thickness of the shear layer and the maximum velocity increase linearly in time till the shear front reaches the top. In the second phase, after the shear layer encompasses the entire flow, there is a much slower increase in the maximum velocity until the steady state is reached.
Coarse-grained local and objective continuum description of three-dimensional granular flows down an inclined surface
Authors: Weinhart Thomas , Hartkamp Remco , Thornton Anthony R. , Luding Stefan
Published: July 2013

Dry, frictional, steady-state granular flows down an inclined, rough surface are studied with discrete particle simulations. From this exemplary flow situation, macroscopic fields, consistent with the conservation laws of continuum theory, are obtained from microscopic data by time-averaging and spatial smoothing (coarse-graining). Two distinct coarse-graining length scale ranges are identified, where the fields are almost independent of the smoothing length w. The smaller, sub-particle length scale, w ≪ d, resolves layers in the flow near the base boundary that cause oscillations in the macroscopic fields. The larger, particle length scale, w ≈ d, leads to smooth stress and density fields, but the kinetic stress becomes scale-dependent; however, this scale-dependence can be quantified and removed. The macroscopic fields involve density, velocity, granular temperature, as well as strain-rate, stress, and fabric (structure) tensors. Due to the plane strain flow, each tensor can be expressed in an inherently anisotropic form with only four objective, coordinate frame invariant variables. For example, the stress is decomposed as: (i) the isotropic pressure, (ii) the “anisotropy” of the deviatoric stress, i.e., the ratio of deviatoric stress (norm) and pressure, (iii) the anisotropic stress distribution between the principal directions, and (iv) the orientation of its eigensystem. The strain rate tensor sets the reference system, and each objective stress (and fabric) variable can then be related, via discrete particle simulations, to the inertial number, I. This represents the plane strain special case of a general, local, and objective constitutive model. The resulting model is compared to existing theories and clearly displays small, but significant deviations from more simplified theories in all variables – on both the different length scales.
Following the relaxation dynamics of photoexcited aniline in the 273-266 nm region using time-resolved photoelectron imaging
Authors: Thompson James O. F. , Livingstone Ruth A. , Townsend Dave
Published: July 2013

Time-resolved photoelectron imaging was used to investigate the relaxation dynamics of electronically excited aniline in the gas-phase following ultraviolet irradiation in the 273-266 nm region. We find that at all wavelengths studied, excitation is predominantly to the long-lived (>1 ns) S1(ππ*) state, which exhibits ultrafast intramolecular vibrational redistribution on a <1 ps timescale. At excitation wavelengths centred on resonant transitions in the aniline absorption spectrum that have previously been assigned to the higher lying S2(3s/πσ*) state, we also see clear evidence of this state playing a role in the dynamics. However, we see no indication of any non-adiabatic coupling between the S1(ππ*) and S2(3s/πσ*) states over the range of excitation wavelengths studied.
Controlling adsorption of semiflexible polymers on planar and curved substrates
Authors: Kampmann Tobias A. , Boltz Horst-Holger , Kierfeld Jan
Published: July 2013

We study the adsorption of semiflexible polymers such as polyelectrolytes or DNA on planar and curved substrates, e.g., spheres or washboard substrates via short-range potentials using extensive Monte Carlo simulations, scaling arguments, and analytical transfer matrix techniques. We show that the adsorption threshold of stiff or semiflexible polymers on a planar substrate can be controlled by polymer stiffness: adsorption requires the highest potential strength if the persistence length of the polymer matches the range of the adsorption potential. On curved substrates, i.e., an adsorbing sphere or an adsorbing washboard surface, the adsorption can be additionally controlled by the curvature of the surface structure. The additional bending energy in the adsorbed state leads to an increase of the critical adsorption strength, which depends on the curvature radii of the substrate structure. For an adsorbing sphere, this gives rise to an optimal polymer stiffness for adsorption, i.e., a local minimum in the critical potential strength for adsorption, which can be controlled by curvature. For two- and three-dimensional washboard substrates, we identify the range of persistence lengths and the mechanisms for an effective control of the adsorption threshold by the substrate curvature.
Accurate evaluation of the angular-dependent direct correlation function of water
Authors: Zhao Shuangliang , Liu Honglai , Ramirez Rosa , Borgis Daniel
Published: July 2013

The direct correlation function (DCF) plays a pivotal role in addressing the thermodynamic properties with non-mean-field statistical theories of liquid state. This work provides an accurate yet efficient calculation procedure for evaluating the angular-dependent DCF of bulk SPC/E water. The DCF here represented in a discrete angles basis is computed with two typical steps: the first step involves solving the molecular Ornstein-Zernike equation with the input of total correlation function extracted from simulation; the resultant DCF is then polished in second step at small wavelength for all orientations in order to match correct thermodynamic properties. This function is also discussed in terms of its rotational invariant components. In particular, we show that the component c112(r) that accounts for dipolar symmetry reaches already its long-range asymptotic behavior at a short distance of 4 Å. With the knowledge of DCF, the angular-dependent bridge function of bulk water is thereafter computed and discussed in comparison with referenced hard-sphere bridge functions. We conclude that, even though such hard-sphere bridge functions may be relevant to improve the calculation of Helmholtz free energies in integral equations or density functional theory, they are doomed to fail at a structural level.
Higher-order approximation of the phase transition in the Pb-based perovskite oxide solid-solutions
Authors: Li Lin , Kim Ilhwan , Jang Kumok , Ri Kwangson , Cha Jongchol
Published: July 2013

It is shown that the ferroelectric phase transitions in the mixture compounds PbZr1−xTixO3 (PZT), Pb(Mg1/3Nb2/3)1−xTixO3 (PMN-PT), and Pb(Zn1/3Nb2/3)1−xTixO3 (PZN-PT) are described by a twelfth-order expansion of the Landau potential in terms of the phenomenological order parameter. Classical Poincaré transformation is used in constructing the appropriate Landau potential. Our consideration requires two more basic monomials, a 10th-order invariant and a 12th-order one, to be present than the previous model. A phase diagram is calculated in phenomenological parameter space. T-x phase diagrams for the PZT and PZN-PT are estimated. The PbTiO3-concentration dependence of physical properties is calculated in the vicinity of the morphotropic phase boundary.
Interactions of S-peptide analogue in aqueous urea and trimethylamine-N-oxide solutions: A molecular dynamics simulation study
Authors: Sarma Rahul , Paul Sandip
Published: July 2013

The ability of the osmolyte, trimethylamine-N-oxide (TMAO), to protect proteins from deleterious effect of urea, another commonly available osmolyte, is well-established. However, the molecular mechanism of this counteraction is not understood yet. To provide a molecular level understanding of how TMAO protects proteins in highly concentrated urea solution, we report here molecular dynamics simulation results of a 15-residue model peptide in two different conformations: helix and extended. For both conformations, simulations are carried out in pure water as well as in binary and ternary aqueous solutions of urea and TMAO. Analysis of solvation characteristics reveals direct interactions of urea and TMAO with peptide residues. However, the number of TMAO molecules that enter in the first solvation shell of the peptide is significantly lower than that of urea, and, unlike water and urea, TMAO shows its inability to form hydrogen bond with backbone oxygen and negatively charged sidechains. Preferential accumulation of urea near the peptide surface and preferential exclusion of TMAO from the peptide surface are observed. Inclusion of osmolytes in the peptide solvation shell leads to dehydration of the peptide in binary and ternary solutions of urea and TMAO. Solvation of peptide residues are investigated more closely by calculating the number of hydrogen bonds between the peptide and solution species. It is found that number of hydrogen bonds formed by the peptide with solution species increases in binary urea solution (relative to pure water) and this relative enhancement in hydrogen bond number reduces upon addition of TMAO. Our simulation results also suggest that, in the ternary solution, the peptide solvation layer is better mixed in terms of water and urea as compared to binary urea solution. Implications of the results for counteraction mechanism of TMAO are discussed.
An improved treatment of empirical dispersion and a many-body energy decomposition scheme for the explicit polarization plus symmetry-adapted perturbation theory (XSAPT) method
Authors: Lao Ka Un , Herbert John M.
Published: July 2013

We recently introduced a low-cost quantum chemistry method for computing intermolecular interactions, combining a monomer-based self-consistent field calculation (the “explicit polarization” method, XPol) with pairwise-additive symmetry adapted perturbation theory (SAPT). The method uses Kohn-Sham (KS) orbitals in the SAPT formalism but replaces the SAPT dispersion and exchange-dispersion terms with empirical potentials (“+D”), and we called this method XPol+SAPT(KS)+D. Here, we report a second-generation version of this approach, XPol+SAPT(KS)+D2 or XSAPT(KS)+D2 for short, in which we have modified the form of the empirical atom–atom dispersion potentials. Accurate binding energies are obtained for benchmark databases of dimer binding energies, and potential energy curves are captured accurately for a variety of challenging systems. We suggest that using different asymptotic corrections for different monomers is necessary to get good binding energies in general, especially for hydrogen-bonded complexes. As compared to our original “+D” formulation, the second-generation “+D2” method accurately reproduces not only total binding energies but also the various components of the interaction energy, and on this basis we introduce an energy decomposition scheme that extends traditional SAPT energy decomposition to systems containing more than two monomers. For $\rm (H_2O)_6$(H2O)6, the many-body contribution to the interaction energy agrees well with that obtained from traditional Kitaura-Morokuma energy decomposition analysis in a large basis set.
A new six-dimensional potential energy surface for H2–N2O and its adiabatic-hindered-rotor treatment
Authors: Wang Lecheng , Xie Daiqian , Le Roy Robert J. , Roy Pierre-Nicholas
Published: July 2013

A six-dimensional ab initio potential energy surface (PES) for H2–N2O which explicitly includes the symmetric and asymmetric vibrational coordinates Q1 and Q3 of N2O is calculated at the coupled-cluster singles and doubles with noniterative inclusion of connected triple level using an augmented correlation-consistent polarized-valence quadruple-zeta basis set together with midpoint bond functions. Four-dimensional intermolecular PESs are then obtained by fitting the vibrationally averaged interactions energies for υ3(N2O) = 0 and 1 to the Morse/long-range analytical form. In the fits, fixing the long-range parameters at theoretical values smoothes over the numerical noise in the ab initio points in the long-range region of the potential. Using the adiabatic hindered-rotor approximation, two-dimensional PESs for hydrogen–N2O complexes with different isotopomers of hydrogen are generated by averaging the 4D PES over the rotation of the hydrogen molecule within the complex. The band-origin shifts for the hydrogen–N2O dimers calculated using both the 4D PESs and the angle-averaged 2D PESs are all in good agreement with each other and with the available experimental observations. The predicted infrared transition frequencies for para-H2–N2O and ortho-D2–N2O are also consistent with the observed spectra.
Local unitary transformation method toward practical electron correlation calculations with scalar relativistic effect in large-scale molecules
Authors: Seino Junji , Nakai Hiromi
Published: July 2013

In order to perform practical electron correlation calculations, the local unitary transformation (LUT) scheme at the spin-free infinite-order Douglas–Kroll–Hess (IODKH) level [J. Seino and H. Nakai, J. Chem. Phys. 136, 244102 (2012)10.1063/1.4729463; J. Seino and H. Nakai, J. Chem. Phys. 137, 144101 (2012)]10.1063/1.4757263, which is based on the locality of relativistic effects, has been combined with the linear-scaling divide-and-conquer (DC)-based Hartree–Fock (HF) and electron correlation methods, such as the second-order Møller–Plesset (MP2) and the coupled cluster theories with single and double excitations (CCSD). Numerical applications in hydrogen halide molecules, (HX)n (X = F, Cl, Br, and I), coinage metal chain systems, Mn (M = Cu and Ag), and platinum-terminated polyynediyl chain, trans,trans-{(p-CH3C6H4)3P}2(C6H5)Pt(C≡C)4Pt(C6H5){(p-CH3C6H4)3P}2, clarified that the present methods, namely DC-HF, MP2, and CCSD with the LUT-IODKH Hamiltonian, reproduce the results obtained using conventional methods with small computational costs. The combination of both LUT and DC techniques could be the first approach that achieves overall quasi-linear-scaling with a small prefactor for relativistic electron correlation calculations.
The influence of the interfacial heat release on nonlinear convective oscillations in two-layer systems
Authors: Simanovskii Ilya B.
Published: July 2013

Nonlinear convective regimes developed under the joint action of buoyant and thermocapillary effects in the silicone oil 2cSt-water system in the presence of an interfacial heat release are investigated. Transitions between the flows with different symmetry properties are studied. It is shown that the presence of the interfacial heat release can change the sequence of bifurcations and lead to the appearance of specific oscillatory regimes in the system.
The current-voltage characteristics of polymer/C60 diodes in the dark: A direct way to assess photovoltaic devices efficiency parameters
Authors: Koehler M. , Yamamoto N. A. D. , Macedo A. G. , Grodniski D. Z. , Roman L. S. , da Luz M. G. E.
Published: July 2013

A general description of dark transport properties in bi-layer organic photovoltaic devices formed by a heterojunction of a semiconducting co-polymer and fullerene (C60) is presented. The copolymers are composed of thiophene, phenylene, and fluorene units, where the thiophene content is kept constant while the fluorene/phenylene ratio is varied. Measurements show that the j × V characteristics display typical diode behavior (exponential increasing) at low and are space-charge limited at high voltages. Extending a theoretical analysis by Koehler et al. [J. Appl. Phys. 92, 5575 (2002)], a model which assumes a space-charge dependent inner series resistance—attributed to molecular and morphological aspects of the materials—is proposed. It turns out to be general and able to nicely fit the experimental curves for all the studied samples. Furthermore, the model quantifies relevant parameters (the effective mobility and the diode reverse saturation current j0) which will determine the systems efficiency. The framework hence allows to foremost the devices functioning under illumination from direct experiments of the active material in the dark.
Dielectric and magnetic properties of BiFe1-4x/3TixO3 ceramics with iron vacancies: Experimental and first-principles studies
Authors: Zou L. Y. , Yang R. P. , Lin Y. B. , Qin M. H. , Gao X. S. , Zeng M. , Liu J.-M.
Published: July 2013

BiFe1-4x/3TixO3 (x = 0-0.2) ceramics with Fe vacancies created by nonstioichiometric compositions were synthesized to study their crystal structures, dielectric, and ferromagnetic behaviors. X-ray diffraction and Raman spectroscopy analysis reveal a structure transition from rhombohedral to orthorhombic phases at x = 0.2. Dielectric measurement shows that the dielectric loss is significantly reduced in the Ti-doped BiFeO3 samples. With increasing x concentration, the remanent magnetization (Mr) first increases and then decreases. The maximal Mr of 0.13 emμ/g is obtained at x = 0.05. Furthermore, theoretical calculations based on the density-functional theory prove that the Ti-doping does enhance the lattice constants, band gap, and magnetization. These results show that the Ti-doped BiFeO3 with Fe vacancies could enhance resistivity and magnetism, implying a possible improvement in multiferroic behavior.
Doping controlled roughness and defined mesoporosity in chemically etched silicon nanowires with tunable conductivity
Authors: McSweeney W. , Lotty O. , Mogili N. V. V. , Glynn C. , Geaney H. , Tanner D. , Holmes J. D. , O'Dwyer C.
Published: July 2013

By using Si(100) with different dopant type (n++-type (As) or p-type (B)), we show how metal-assisted chemically etched (MACE) nanowires (NWs) can form with rough outer surfaces around a solid NW core for p-type NWs, and a unique, defined mesoporous structure for highly doped n-type NWs. We used high resolution electron microscopy techniques to define the characteristic roughening and mesoporous structure within the NWs and how such structures can form due to a judicious choice of carrier concentration and dopant type. The n-type NWs have a mesoporosity that is defined by equidistant pores in all directions, and the inter-pore distance is correlated to the effective depletion region width at the reduction potential of the catalyst at the silicon surface in a HF electrolyte. Clumping in n-type MACE Si NWs is also shown to be characteristic of mesoporous NWs when etched as high density NW layers, due to low rigidity (high porosity). Electrical transport investigations show that the etched nanowires exhibit tunable conductance changes, where the largest resistance increase is found for highly mesoporous n-type Si NWs, in spite of their very high electronic carrier concentration. This understanding can be adapted to any low-dimensional semiconducting system capable of selective etching through electroless, and possibly electrochemical, means. The process points to a method of multiscale nanostructuring NWs, from surface roughening of NWs with controllable lengths to defined mesoporosity formation, and may be applicable to applications where high surface area, electrical connectivity, tunable surface structure, and internal porosity are required.
Structural, optical, vibrational, and magnetic properties of sol-gel derived Ni doped ZnO nanoparticles
Authors: Srinet Gunjan , Kumar Ravindra , Sajal Vivek
Published: July 2013

With a view to study structural, optical, vibrational, and magnetic properties of solgel derived Zn1−xNixO (x = 0.02, 0.04, and 0.06) nanoparticles, systematic investigations have been carried out. The Rietveld refinement of X-ray powder diffraction data revealed a single hexagonal phase with space group P63mc. The secondary phase of NiO appeared only in 6% Ni doped sample. Phonon modes in Ni doped ZnO nanoparticles were studied through Fourier transform infrared measurements. Furthermore, the enhancement in optical band gap with Ni doping from 3.29 to 3.32 eV has been observed through UV-visible spectroscopic analysis. Photoluminescence spectra of Zn1−xNixO show the UV-emission peak showing the blue shift with increase in doping concentration followed by broad visible (blue) emission corresponding to the defect emission whose intensity decreased with increasing Ni concentration. A clear room temperature ferromagnetism is observed in all samples but saturation magnetization decreased with increasing Ni content. The suitability of bound magnetic polarons (BMP) model is checked and numbers of BMPs are found to be of the order 1015 per cm3, which is very small for the percolation in ZnO. In the present case, oxygen rich stoichiometry with enhanced Zn-O bonding favours the indirect Ni-O-Ni ferromagnetic exchange coupling and reduction of oxygen vacancies leading to strong hybridization of Ni in ZnO host matrix responsible for room temperature ferromagnetism.
Near-field mapping of dipole nano-antenna-coupled bolometers
Authors: Tucker Eric , Archangel Jeffrey D' , Raschke Markus , Briones Edgar , Javier González Francisco , Boreman Glenn
Published: July 2013

The near-field characteristics of single, double, and arrays of connected dipole nano-antennas coupled to bolometers were studied by infrared scattering scanning near-field optical microscopy (s-SNOM) and analyzed by numerical simulations. Results were consistent with classical antenna theory showing the expected π phase difference across the terminals of the dipoles. However, according to the observed differences between the measurements and simulations, the symmetry of the amplitude signal appeared to be sensitive with respect to the position of the bolometric element relative to the dipoles. The effect of the position of the bolometer on the associated near-field distribution suggests an influence on the coupling and efficiency of energy transfer into these detectors, which could be important for determining tolerances in the fabrication of such devices. These results show how near-field measurements in general can provide critical information to guide the design of nano-antennas, nano-antenna-phased arrays, and integrated photonic devices.