bluuebunny/crossref_metadata_2025 huggingface dataset:
An integrated approach for inference and mechanistic modeling for advancing drug development
Authors: Aksenov Sergej V. , Church Bruce , Dhiman Anjali , Georgieva Anna , Sarangapani Ramesh , Helmlinger Gabriel , Khalil Iya G.
Published: February 2005

An important challenge facing researchers in drug development is how to translate multi‐omic measurements into biological insights that will help advance drugs through the clinic. Computational biology strategies are a promising approach for systematically capturing the effect of a given drug on complex molecular networks and on human physiology. This article discusses a two‐pronged strategy for inferring biological interactions from large‐scale multi‐omic measurements and accounting for known biology via mechanistic dynamical simulations of pathways, cells, and organ‐ and tissue level models. These approaches are already playing a role in driving drug development by providing a rational and systematic computational framework.
Identification of cancer genes by mutational profiling of tumor genomes
Authors: Benvenuti Silvia , Arena Sabrina , Bardelli Alberto
Published: February 2005

It is now widely accepted that cancer is a genetic disease and that alterations in the DNA sequence underlie the development of every neoplasm. The identification of mutated genes that are causally implicated in oncogenesis (‘cancer genes’) has been a major goal in medical sciences for the last two decades. The availability of the human genome sequence coupled to the introduction of high throughput sequencing technologies has created an unprecedented opportunity in this field. It is now possible to perform mutational studies of entire cancer genomes thus providing a complete description of mutations underlying human oncogenesis. The recent identification of high frequency mutations in the BRAF and PI3K genes suggests that many more cancer genes remain to be discovered. In this review, we consider how the systematic mutational analysis of gene families in individual neoplasms has led to the identification of a number of cancer genes and how this information is influencing the treatment of cancer.
EARLY MARRIAGE AND EARLY MOTHERHOOD IN NEPAL
Authors: KIM CHOE MINJA , THAPA SHYAM , MISHRA VINOD
Published: February 2005

This paper examines age patterns of first marriage and motherhood and covariates of early marriage, delayed consummation of marriage and early motherhood in Nepal using data from the 2000 Nepal Adolescent and Young Adult Survey (NAYA). Both unmarried and married male and female youths (age 14–22) were included in the survey. The analysis is based on 2800 urban youths and 5075 rural youths with complete information on the variables examined. Proportional hazard models are used to estimate covariates of early marriage and early motherhood, and logistic regression models are used to estimate covariates of delayed consummation of marriage. The results show that early marriage and early motherhood are quite common among Nepalese women, especially in rural areas. Early marriage is much less common among men. Delayed consummation of marriage is common among very young brides, especially in rural areas. The main covariates associated with early marriage and early motherhood are respondent’s education, region of residence and ethnicity. The main covariates of delayed consummation of marriage are age at first marriage, region of residence and ethnicity. The study highlights the need to focus on less educated female youths in the Terai region in order to reduce the reproductive and child health risks associated with early marriage and early childbearing.
FAMILY BACKGROUND, SCHOOLING AND CHILDLESSNESS IN AUSTRALIA
Authors: PARR NICHOLAS J.
Published: February 2005

Using data from Wave 1 of the Household Income and Labour Dynamics in Australia (HILDA) survey, this paper analyses the extent to which childlessness among Australian women aged 40–54 years varies according to the size and type of family in which they were brought up, and the level and type of schooling they had. Multilevel logistic analysis shows that having been educated in a non-government school, having stayed at school to year 12, having a small number of siblings, at age 14 having a father who was either dead or absent, at age 14 having a father who was employed in a professional occupation, or being a migrant from North or West Europe, North America, East Asia or South-East Asia, all are significantly associated with higher rates of childlessness among women in the 40–54 years age range. The effects of these early lifecourse variables on marital and socioeconomic status in later life, and hence on childlessness, are also considered. The implications of the findings for fertility trends and for Australia’s public debate are discussed.
MOTHER’S DEATH AND CHILD SURVIVAL: THE CASE OF EARLY QUEBEC
Authors: PAVARD SAMUEL , GAGNON ALAIN , DESJARDINS BERTRAND , HEYER EVELYNE
Published: February 2005

The aim of this paper is to account for the effect of mother's death on child survival in a historical population. Using comprehensive data on the early French Canadian population of Quebec, evidence is provided for a higher risk of dying for motherless children that remains significant over all childhood and long after the death of the mother. The specific effect of the loss of maternal care was estimated by comparing mortality before and after mother's death, furnishing a means to control for family heterogeneity. No differential in investment between genders was detected before age 3, but older girls suffered a three-fold higher susceptibility to mother's death than their male counterparts. This suggests that grown-up girls assuming the responsibilities of the missing mother had a lower chance of survival.
CULTURAL AND SOCIAL ASPECTS OF HIV/AIDS SEX EDUCATION IN SECONDARY SCHOOLS IN NIGERIA
Authors: OSHI DANIEL C. , NAKALEMA SARAH , OSHI LUKE L.
Published: February 2005

This is an exploratory study to examine the social and cultural determinants of the teaching of HIV/AIDS sex education among secondary school teachers in Eastern Nigeria. The research analyses how teachers perceive passing their knowledge of HIV/AIDS prevention measures to their students in the context of their cultural and social norms, which restrict open discussion of sex. This is a qualitative study based on in-depth interviews with 60 teachers drawn from secondary school teachers in Eastern Nigeria, supplemented with five focus group discussions, and content analysis of teachers’ lesson preparatory notes. The findings show a high level knowledge of HIV/AIDS preventive measures among teachers. However, teachers are not passing on this knowledge because of cultural and social inhibitions. In addition, teachers have not been receiving adequate training and motivation on information, education and communication for HIV/AIDS sex education. The situation calls for serious policy intervention.
Civil Society in Argentina: Opportunities and Challenges for National and Transnational Organisation
Authors: JACOBS JAMIE ELIZABETH , MALDONADO MARTÍN
Published: February 2005

Among the many consequences of globalisation is the creation of new political spaces. As these emerge, new or redefined power relationships accompany the process. In the course of creating transnational relationships, citizenship, representation and the role of the stakeholders may be redefined. This article focuses on the case of Argentina and on the role of civil society orgnisations (CSOs) in the process of political integration. The relationship between the state and civil society has sparked a debate about the core status of the political system as the third sector assumes roles traditionally belonging exclusively to the state. This raises issues regarding the difference between rights and services, the sources of legitimacy and efforts to enhance accountability, among others. The existing and potential channels of regional cooperation in the context of Mercosur illustrate the interplay between domestic, regional and global norms and institutions. This article emphasises the role of organised civil society in providing sense and meaning in the formation and awareness of supranational concerns, but is sceptical about its possibilities of providing and guaranteeing rights, tasks that still remain in the sphere of the state.
Politics or Economics? International Migration during the Nicaraguan Contra War
Authors: LUNDQUIST JENNIFER H. , MASSEY DOUGLAS S.
Published: February 2005

The issue of whether Central Americans in the United States are ‘political’ or ‘economic’ migrants has been widely debated, yet little empirical research has informed the controversy. Earlier studies have relied primarily on cross-sectional aggregate data. In order to overcome these limitations we draw on recent surveys conducted in five Nicaraguan communities by the Latin American Migration Project. Using retrospective data, we reconstruct a history of a family's migration to the United States and Costa Rica from the date of household formation to the survey date and link these data to national-level data on GDP and Contra War violence. While out migration to both Costa Rica and the United States is predicted by economic trends, US-bound migration was more strongly linked to the level of Contra War violence independent of economic motivations, especially in an interactive model that allows for a higher wartime effect of social networks. We conclude that elevated rates of Nicaraguan migration to the United States during the late 1980s and early 1990s were a direct result of the US-Contra intervention. The approach deployed here – which relates to the timing of migration decisions to macro-level country trends – enables us to address the issue of political versus economic motivations for migration with more precision than prior work.
God's goodness and God's evil
Authors: KELLENBERGER JAMES
Published: February 2005

Starting with Job's reaction to evil, I identify three elements of Job-like belief. They are: (1) the recognition of evil in the world; (2) the conviction that God and God's creation are good; and (3) the sense of beholding God's goodness in the world. The interconnection of these three elements is examined along with a possible way of understanding Job-like believers beholding and becoming experientially aware of God's goodness. It is brought out why, given that they are as they understand themselves to be, Job-like believers properly do not see evil as evidence against God's goodness. Finally, Job-like belief is related to the different reactions to evil by Ivan and Aloysha in The Brothers Karamazov.
Uncomfortable Questions: Cyprus, October 1973–August 1974
Authors: FOUSKAS VASSILIS K.
Published: February 2005

Scholarly research to date has analysed the Cyprus issue from the perspective of Greek–Turkish relations, suggesting that the United States was attempting to strike a balance between them in order to safeguard the cohesion of NATO's southern flank during the cold war. This article, without undermining the validity of previous historical findings on the issue, nevertheless constitutes an attempt to move towards a differing research agenda: it locates Cyprus in the Middle Eastern theatre and suggests that the Yom Kippur war of October 1973 may have more linkages to the Cyprus crisis of summer 1974 than one may at first sight discern.
A New Historian?
Authors: FINK CAROLE
Published: February 2005

-Your mother is a judge. It's her job to put a line through the past by passing sentence. I'm a historian. For me the past is a gold mine of surprises and possibilities.

-A gold mine?…A dunghill is more like it.

-Dunghills have their surprises too.

President Ion Iliescu [of Romania] has just announced the formation of an international expert commission charged with studying the history of the Holocaust in Romania between 1937 and 1951.

Historians are not judges. A historical commission is not a court of law.
Toward the assimilation of time‐averaged observations
Authors: Dirren Sébastien , Hakim Gregory J.
Published: February 2005

A novel algorithm is described for the assimilation of time‐averaged observations. A demonstration of this algorithm in an ideal model using an ensemble Kalman filter technique suggests the potential for resolving dynamical features that have a characteristic time‐scale longer than the averaging time of the observations. This technique may offer new perspectives in climate reconstruction and in the assimilation of integrated meteorological quantities such as accumulated precipitation.
Variations in droughts over China: 1951–2003
Authors: Zou Xukai , Zhai Panmao , Zhang Qiang
Published: February 2005

The Palmer Drought Severity Index (PDSI) was calculated by using monthly air temperature and precipitation in China during the period 1951 to 2003. For the country as a whole, there are no long‐term upward or downward trends in the percentage areas of droughts (defined as PDSI < −1.0). However, significant increases of drought areas are found in North China. Most northern China (except western Northwest China) has experienced severe and prolonged dry periods since the late 1990s, when in some of the areas the extreme drought situations were unprecedented during the period of study. Since these regions are relatively dry areas, frequent drought stress in recent decades has become more serious.
Paleogene calcite compensation depth in the eastern subtropical Pacific: Answers and questions
Authors: Rea David K. , Lyle Mitchell W.
Published: February 2005

Ocean Drilling Program Leg 199 drilled a north‐south transect across the Eocene paleoequator in the eastern Pacific, permitting reconstruction the calcite compensation depth (CCD) since earliest Eocene time. The CCD was relatively shallow near the early Eocene Pacific equator, 3200 m, and unlike modern latitudinal CCD gradients deepened to the north (to ∼3600 m; paleolatitude ∼10°N). At 41 Ma the CCD underwent a brief, sharp, transient deepening of 700 m, then remained shallow until the Eocene/Oligocene boundary. At the E/O boundary, the CCD deepened by 1200 m in less than 300 kyr. This rapid deepening served to more than double the area of seafloor subject to CaCO3 deposition. Sea level fall associated with ice volume buildup, and ensuing shelf‐basin fractionation, is unlikely to be the sole cause of the increased deep‐ocean CaCO3 burial; rather, a sudden, rapid increase in the amount of Ca entering the ocean appears necessary to explain the observations.
The cellular level of telomere dysfunction determines induction of senescence or apoptosisin vivo
Authors: Lechel André , Satyanarayana Ande , Ju Zhenyu , Plentz Ruben R , Schaetzlein Sonja , Rudolph Cornelia , Wilkens Ludwig , Wiemann Stephanie U , Saretzki Gabriele , Malek Nisar P , Manns Michael P , Buer Jan , Rudolph K Lenhard
Published: February 2005

Telomere dysfunction induces two types of cellular response: cellular senescence and apoptosis. We analysed the extent to which the cellular level of telomere dysfunction andp53gene status affect these cellular responses in mouse liver using the experimental system of TRF2 inhibition by a dominant‐negative version of the protein (TRF2ΔBΔM). We show that the level of telomere dysfunction correlates with the level of TRF2ΔBΔMprotein expression resulting in chromosomal fusions, aberrant mitotic figures and aneuploidy of liver cells. These alterations provokedp53‐independent apoptosis, but a strictlyp53‐dependent senescence response in distinct populations of mouse liver cells depending on the cellular level of TRF2ΔBΔMexpression. Apoptosis was associated with higher expression of TRF2ΔBΔM, whereas cellular senescence was associated with low levels of TRF2ΔBΔMexpression. Our data provide experimental evidence that induction of senescence or apoptosisin vivodepends on the cellular level of telomere dysfunction and differentially onp53gene function.
Application of RNA interference to study stem cell function: current status and future perspectives
Authors: Zou Gang‐Ming , Yoder Mervin C.
Published: February 2005

RNA interference is a mechanism displayed by most eukaryotic cells to rid themselves of foreign double‐stranded RNA molecules. In the six years since the initial report, RNA interference has now been demonstrated to function in mammalian cells to alter gene expression, and has been used as a means for genetic discovery as well as a possible strategy for genetic correction. An equally popular topic over the past six years has been the proposal to utilize embryonic stem cells or adult stem cells as cell‐based therapies for human diseases. The aim of this review is to provide a general overview of how RNA interference suppresses gene expression and to examine some published RNA interference approaches that have resulted in changes in stem cell function and suggest the possible clinical relevance of this work.
Sodium–lithium countertransport and the Gly460→Trp α-adducin polymorphism in essential hypertension
Authors: MEAD Paul A. , HARVEY John N. , RUTHERFORD Peter A. , LEITCH Helen , THOMAS Trevor H.
Published: February 2005

A polymorphism of the α-subunit of adducin, Gly460→Trp, may affect membrane ion transport and be associated with human EH (essential hypertension). The α-adducin Gly460→Trp polymorphism was determined in 242 NC (normal controls) and 73 patients with EH and was related to the membrane ion transport marker in EH, erythrocyte Na/LiCT (sodium–lithium countertransport), in a subgroup of these subjects. The Km for external sodium was lower in patients with EH than NC. The Km of the Trp allele was lower than with the Gly/Gly genotype [NC, 105±6 compared with 88±5 mmol Na/l respectively (P=0.05); patients with EH, 76±5 compared with 64±4 mmol Na/l respectively (P=0.06)]. The Km was lower in patients with EH than NC for any adducin genotype. Thiol alkylation with NEM (N-ethylmaleimide) caused a decrease in Km in NC, but not in patients with EH. With a Trp allele, NEM lowered Km less in NC (−20 compared with −35) and increased it in patients with EH (+24 compared with +3; P=0.007 for genotype effect). Thiol alkylation with NEM caused an increase in Vmax in patients with EH but not in NC. With a Trp allele, NEM increased Vmax substantially in patients with EH (+0.12 compared with +0.03) but did not cause a decrease in NC (+0.02 compared with −0.06; P=0.007 for genotype effect). In conclusion, the Gly460→Trp polymorphism of α-adducin modifies the kinetics of Na/LiCT. The effect of this genotype is different in patients with EH compared with NC and it does not explain the abnormal kinetics in patients with EH. The Trp allele was not associated with disease in the population studied. Several cytoskeletal proteins may interact with adducin in the overall phenotype of EH.
New insights into amino acid metabolism, β-cell function and diabetes
Authors: NEWSHOLME Philip , BRENNAN Lorraine , RUBI Blanca , MAECHLER Pierre
Published: February 2005

Specific amino acids are now known to acutely and chronically regulate insulin secretion from pancreatic β-cells in vivo and in vitro. Understanding the molecular mechanisms by which amino acids regulate insulin secretion may identify novel targets for future diabetes therapies. Mitochondrial metabolism is crucial for the coupling of amino acid and glucose recognition to the exocytosis of the insulin granules. This is illustrated by in vitro and in vivo observations discussed in the present review. Mitochondria generate ATP, which is the main coupling factor in insulin secretion; however, the subsequent Ca2+ signal in the cytosol is necessary, but not sufficient, for full development of sustained insulin secretion. Hence mitochondria generate ATP and other coupling factors serving as fuel sensors for the control of the exocytotic process. Numerous studies have sought to identify the factors that mediate the amplifying pathway over the Ca2+ signal in nutrient-stimulated insulin secretion. Predominantly, these factors are nucleotides (GTP, ATP, cAMP and NADPH), although metabolites have also been proposed, such as long-chain acyl-CoA derivatives and the key amino acid glutamate. This scenario highlights further the importance of the key enzymes or transporters, glutamate dehydrogenase, the aspartate and alanine aminotransferases and the malate/aspartate shuttle, in the control of insulin secretion. Therefore amino acids may play a direct or indirect (via generation of putative messengers of mitochondrial origin) role in insulin secretion.
New evidence of baroreflex dysfunction in congenital central hypoventilation syndrome
Authors: van de BORNE Philippe
Published: February 2005

In this issue of Clinical Science, Trang and co-workers report the results of short-term blood pressure and heart rate variability measurements in patients with congenital central hypoventilation syndrome (CCHS). The results reveal that these young patients disclose signs of vagal withdrawal and baroreflex failure. Baroreflex sensitivity was reduced by one third compared with the matched control subjects; however, patients have a relative preservation of the cardiac and vascular sympathetic function. These findings are clearly new and improve our understanding of CCHS physiopathology. Nevertheless, more research is needed to better delineate the respective contribution of cardiac vagal and sympathetic dysregulation, and the extent to which these abnormalities relate to genetic mutations as well as to clinical status.
Interactions between stably rolling leukocytes in vivo
Authors: King Michael R. , Ruscio Aimee D. , Kim Michael B. , Sarelius Ingrid H.
Published: February 2005

We have characterized the two-dimensional spatial dependence of the hydrodynamic interactions between two adhesively rolling leukocytes in a live venule in the mouse cremaster muscle. Two rolling leukocytes were observed to slow each other down when rolling together in close proximity due to mutual sheltering from the external blood flow in the vessel lumen. A previous study of leukocyte rolling interactions using carbohydrate-coated beads in a parallel-plate flow chamber and a detailed computer model of adhesion in a multicellular environment is in qualitative agreement with the current in vivo results.
Introducing ONETEP: Linear-scaling density functional simulations on parallel computers
Authors: Skylaris Chris-Kriton , Haynes Peter D. , Mostofi Arash A. , Payne Mike C.
Published: February 2005

We present ONETEP (order-N electronic total energy package), a density functional program for parallel computers whose computational cost scales linearly with the number of atoms and the number of processors. ONETEP is based on our reformulation of the plane wave pseudopotential method which exploits the electronic localization that is inherent in systems with a nonvanishing band gap. We summarize the theoretical developments that enable the direct optimization of strictly localized quantities expressed in terms of a delocalized plane wave basis. These same localized quantities lead us to a physical way of dividing the computational effort among many processors to allow calculations to be performed efficiently on parallel supercomputers. We show with examples that ONETEP achieves excellent speedups with increasing numbers of processors and confirm that the time taken by ONETEP as a function of increasing number of atoms for a given number of processors is indeed linear. What distinguishes our approach is that the localization is achieved in a controlled and mathematically consistent manner so that ONETEP obtains the same accuracy as conventional cubic-scaling plane wave approaches and offers fast and stable convergence. We expect that calculations with ONETEP have the potential to provide quantitative theoretical predictions for problems involving thousands of atoms such as those often encountered in nanoscience and biophysics.
Two interacting electrons in a uniform magnetic field and a parabolic potential: The general closed-form solution
Authors: Kandemir B. S.
Published: February 2005

We present an analytical analysis of the two-dimensional Schrödinger equation for two interacting electrons subjected to a homogeneous magnetic field and confined by a two-dimensional external parabolic potential. We have found the general closed-form expression for the eigenstates of the problem and its corresponding eigenenergies for particular values of magnetic field and spatial confinement length. The mathematical framework is just based on a rigorous solution of the three-term recursion relation among the coefficients that arises from the series solution of biconfluent Heun (BHE) equation, connected with the radial part of the Schrödinger equation for the internal motion. It is also shown that, by vanishing of Coulomb repulsion strength, the obtained explicit analytical solutions of BHE equation reduces to the well-known polynomials satisfying the associated Laguerre differential equation. Furthermore, in the presence of this interaction, the results are compared with those previously obtained in the literature for first few low-lying states, and are found to be in an exact agreement with them.
Hydration of Li+-ion in atom-bond electronegativity equalization method–7P water: A molecular dynamics simulation study
Authors: Li Xin , Yang Zhong-Zhi
Published: February 2005

We have carried out molecular dynamics simulations of a Li+ ion in water over a wide range of temperature (from 248 to 368K). The simulations make use of the atom-bond electronegativity equalization method–7P water model, a seven-site flexible model with fluctuating charges, which has accurately reproduced many bulk water properties. The recently constructed Li+-water interaction potential through fitting to the experimental and ab initio gas-phase binding energies and to the measured structures for Li+-water clusters is adopted in the simulations. ABEEM was proposed and developed in terms of partitioning the electron density into atom and bond regions and using the electronegativity equalization method (EEM) and the density functional theory (DFT). Based on a combination of the atom-bond electronegativity equalization method and molecular mechanics (ABEEM/MM), a new set of water-water and Li+-water potentials, successfully applied to ionic clusters Li+(H2O)n(n=1–6,8), are further investigated in an aqueous solution of Li+ in the present paper. Two points must be emphasized in the simulations: first, the model allows for the charges on the interacting sites fluctuating as a function of time; second, the ABEEM-7P model has applied the parameter klp,H(Rlp,H) to explicitly describe the short-range interaction of hydrogen bond in the hydrogen bond interaction region, and has a new description for the hydrogen bond. The static, dynamic, and thermodynamic properties have been studied in detail. In addition, at different temperatures, the structural properties such as radial distribution functions, and the dynamical properties such as diffusion coefficients and residence times of the water molecules in the first hydration shell of Li+, are also simulated well. These simulation results show that the ABEEM/MM-based water-water and Li+-water potentials appear to be robust giving the overall characteristic hydration properties in excellent agreement with experiments and other molecular dynamics simulations on similar system.
An ab initio study of the lowest electronic states of yttrium dicarbide, YC2
Authors: Puzzarini Cristina , Peterson Kirk A.
Published: February 2005

The low-lying electronic states of yttrium dicarbide have been calculated using highly correlated wave functions and systematic sequences of correlation consistent basis sets. For the A12 ground electronic state, the near-equilibrium potential energy surface (PES) has been calculated using the coupled cluster method in conjunction with basis sets ranging in size from double to quintuple ζ. The relativistic effects have been taken into account by using pseudopotentials for the Y atom. After extrapolation to the complete basis set limit, additional corrections due to core-valence correlation and spin-orbit effects have also been included. The same approach has been followed for the B12,B22, and A22 states but only the C2V PESs have been considered in these cases. For the two A12 electronic excited states and, for comparison purposes, for the ground state, the multireference configuration interaction (MRCI) approach has been used in conjunction with double-ζ and triple-ζ basis sets for the construction of the PES. The molecular and spectroscopic properties predicted for the ground and excited states investigated in this work compare well with the available experimental data, particularly for the ground electronic state. The 0 K dissociation enthalpy of YC2,ΔHY–C2(0K), and its atomization enthalpy, ΣD0, are predicted to be 148.4 and 291.5kcal∕mol, respectively.
H
1
to H2 uniform cross-polarization nuclear magnetic resonance using H2 Lee–Goldburg irradiation in static powders
Authors: Mizuno Takashi , Takegoshi K. , Terao Takehiko
Published: February 2005

Application of conventional cross polarization (CP) to H2 results in only a narrowband enhancement of the powder line shape due to the quadrupole interaction. We propose a CP scheme to uniformly enhance H2 spectra in static powders. In this method, a Hartmann–Hahn matched H2 rf field is applied on the Lee–Goldburg (LG) condition to remove the zeroth-order quadrupole interaction. In order to achieve a uniformly enhanced H2 powder line shape with a limited H2 rf intensity, the H1 rf amplitude in CP is stepwise altered during the contact time. We develop a spin-thermodynamic theory to describe polarization transfer due to CP with LG irradiation (LG-CP) under the influence of the quadrupole interaction, which can successfully reproduce the LG-CP line shapes observed under various experimental conditions. Experimental and simulated H2 powder spectra are reported for some compounds.
How many dimensions are required to approximate the potential energy landscape of a model protein?
Authors: Komatsuzaki Tamiki , Hoshino Kyoko , Matsunaga Yasuhiro , Rylance Gareth J. , Johnston Roy L. , Wales David J.
Published: February 2005

A scheme to approximate the multidimensional potential energy landscape in terms of a minimal number of degrees of freedom is proposed using a linear transformation of the original atomic Cartesian coordinates. For one particular off-lattice model protein the inherent frustration can only be reproduced satisfactorily when a relatively large number of coordinates are employed. However, when this frustration is removed in a Gō-type model, the number of coordinates required is significantly lower, especially around the global potential energy minimum. To aid our interpretation of the results we consider modified disconnectivity graphs where a measure of the structural diversity and a metric relation between the stationary points are incorporated.
Ideal magnetohydrodynamic interchanges in low density plasmas
Authors: Huang Yi-Min , Goel Deepak , Hassam A. B.
Published: February 2005

The ideal magnetohydrodynamic equations are usually derived under the assumption VA⪡c, where VA is the Alfvén speed and c is the speed of light. This system of equations is extended to low density plasmas wherein VA can be comparable to or greater than c. This involves relaxation of the usual charge quasineutrality assumption and the inclusion of electromagnetic momentum on par with plasma momentum. The extended system is applied to interchange instabilities in “line-tied” slab geometry as well as to centrifugally confined plasmas. It is found that interchange growth rates are reduced by a factor of 1+VA2∕c2, corresponding to a larger effective mass resulting from the extra electromagnetic momentum. Line tying is unaffected.
Limit theorems for statistics of combinatorial partitions with applications to mean field Bose gas
Authors: Benfatto Giuseppe , Cassandro Marzio , Merola I. , Presutti E.
Published: February 2005

In this paper we study the statistics of combinatorial partitions of the integers, which arise when studying the occupation numbers of loops in the mean field Bose gas. We review the results of Lewis and collaborators and get some more precise estimates on the behavior at the critical point (fluctuations of the condensate component, finite volume corrections to the pressure). We then prove limit shape theorems for the loops occupation numbers. In particular we prove that in a certain range of the parameters, a finite fraction of the total mass is, in the limit, supported by infinitely long loops. We also show that this mass is equal to the mass of the condensed state where all particles have zero momentum.
Aspects of three-dimensional magnetic reconnection
Authors: Borgogno D. , Grasso D. , Porcelli F. , Califano F. , Pegoraro F. , Farina D.
Published: February 2005

The nonlinear behavior of reconnecting modes in three spatial dimensions (3D) is investigated, on the basis of a collisionless fluid model in slab geometry, assuming a strong constant guide field in one direction. Unstable modes in the so-called large Δ′ regime are considered. Single helicity modes, i.e., modes with the same orientation with respect to the guide field, depending on all three spatial coordinates correspond to “oblique” modes with, in general, mixed parity around the corresponding resonant magnetic surface, giving rise to a nonlinear drift of the magnetic island X point. The nonlinear coupling of initial perturbations with different helicities introduces additional helicities that evolve in time in agreement with quasilinear estimates, as long as their amplitudes remain relatively small. Magnetic field lines become stochastic when islands with different helicities are present. Basic questions such as the proper definition of the reconnection rate in 3D are addressed.
The poloidal distribution of turbulent fluctuations in the Mega-Ampère Spherical Tokamak
Authors: Antar G. Y. , Counsell G. , Ahn J.-W. , Yang Y. , Price M. , Tabasso A. , Kirk A.
Published: February 2005

Recently, it was shown that intermittency observed in magnetic fusion devices is caused by large-scales events with high radial velocity reaching about 1∕10th of the sound speed (called avaloids or blobs) [G. Antar et al., Phys. Rev. Lett. 87 065001 (2001)]. In the present paper, the poloidal distribution of turbulence is investigated on the Mega-Ampère Spherical Tokamak [A. Sykes et al., Phys. Plasmas 8 2101 (2001)]. To achieve our goal, target probes that span the divertor strike points are used and one reciprocating probe at the midplane. Moreover, a fast imaging camera that can reach 10μs exposure time looks tangentially at the plasma allowing us to view a poloidal cut of the plasma. The two diagnostics allow us to have a rather accurate description of the particle transport in the poloidal plane for L-mode discharges. Turbulence properties at the low-field midplane scrape-off layer are discussed and compared to other poloidal positions. On the low-field target divertor plates, avaloids bursty signature is not detected but still intermittency is observed far from the strike point. This is a consequence of the field line expansion which transforms a structure localized in the poloidal plane into a structure which expands over several tens of centimeters at the divertor target plates. Around the X point and in the high-field side, however, different phenomena enter into play suppressing the onset of convective transport generation. No signs of intermittency are observed in these regions. Accordingly, like “normal” turbulence, the onset of convective transport is affected by the local magnetic curvature and shear.
Enhancement of p-type conductivity in nanocrystalline BaTiO3 ceramics
Authors: Guo Xin , Pithan Christian , Ohly Christian , Jia Chun-Lin , Dornseiffer Jügen , Haegel Franz-Hubert , Waser Rainer
Published: February 2005

Undoped BaTiO3 ceramic samples with an average grain size of ∼35nm were prepared and the electrical properties investigated. The defect structure is dominated by acceptor impurities; therefore, the conductivity of nanocrystalline BaTiO3 is of p-type. Comparing with microcrystalline BaTiO3, the conductivity of nanocrystalline BaTiO3 is about 1 to 2 orders of magnitude higher and the activation energy remarkably lower, which is ascribed to a greatly reduced oxidation enthalpy in nanocrystalline BaTiO3 (∼0.3 versus ∼0.92eV for microcrystalline BaTiO3).
High-precision time-resolved cyclotron resonance measurements at microwave frequencies
Authors: Porţeanu H. E.
Published: February 2005

This work is a theoretical and experimental study of the time-resolved microwave spectroscopy, close to the limit ΔωΔτ∼1, especially applied for the case of cyclotron resonance. A dynamic perturbation theory of a resonator is presented. While the amplitude of a transmitted signal in a standard measuring setup can be determined quickly and accurately, the phase relation requires much longer time for the same accuracy. The use of a resonant system enhances the sensitivity for determination of amplitude and phase, but reduces the time resolution, both by a factor Q. The nonlinear regime for conductivity in cyclotron resonance conditions is compensated by the use of constant energy density in the resonator, independent of frequency. Examples for classical semiconductors are presented. Compared with terahertz time-resolved spectroscopy, this method offers precise information in a different time scale and essentially in a different experimental regime of conductivity: pulsed, E∼1kV∕cm in the first case; cw, E∼1V∕cm in ours.
Formation of an interfacial Zr-silicate layer between ZrO2 and Si through in situ vacuum annealing
Authors: Seo Kang-ill , McIntyre Paul C. , Kim Hyoungsub , Saraswat Krishna C.
Published: February 2005

In this letter, we demonstrate that formation of a Zr-silicate interfacial layer between ZrO2 and Si substrate can be controlled by the solid state reaction between Zr and an underlying SiO2/Si substrate through in situ vacuum anneals and subsequent UV oxidation. By investigating the chemical shifts of Si2p, Zr3d, and O1s features using x-ray photoelectron spectroscopy, the formation of a Zr-silicide phase after in situ vacuum anneals of the Zr/chemical SiO2/Si gate stack at 200 °C was confirmed. The Zr-silicide was oxidized to form a Zr-silicate phase in the subsequent UV-ozone oxidation treatment. According to spectroscopic analyses, Zr-silicate bonding occurred in the interfacial layer for the in situ vacuum annealed samples. Vacuum annealed samples containing the silicate interface layer exhibited excellent dielectric characteristics, such as negligible capacitance–voltage hysteresis (∼10mV), lower fixed charge density, and reduced equivalent oxide thickness compared to unannealed samples.
Infrared furnace with a superconducting magnet for floating zone growth of oxide single crystals
Authors: Park JongKwan , Shimomura Takumi , Yamanaka Minako , Watauchi Satoshi , Tanaka Isao , Kishio Kohji
Published: February 2005

A new type of infrared-heated floating-zone (FZ) crystal apparatus was designed and fitted with a magnetic field generator utilizing a liquid-helium-free superconducting magnet to grow crystals under a high magnetic field. An ellipsoidal mirror and two different parabolic mirrors were combined to guide the heating light from a 5 kW xenon lamp to the growth stage placed inside a superconducting magnet. The distance between the heating lamp and the center of the magnet was set to 1.6 m to suppress the instability of the lamp caused by the leakage of the magnetic field. The approximate range of melting points achieved is from 900 to 1800 °C, as determined through the melting of various oxides. The effect of the magnetic field on crystal growth was experimentally investigated by growing Ca12Al14O33 crystals under several different magnetic conditions and focusing on the behavior of oxygen bubbles in the melt.
Simple method for absolute calibration of geophones, seismometers, and other inertial vibration sensors
Authors: van Kann Frank , Winterflood John
Published: February 2005

A simple but powerful method is presented for calibrating geophones, seismometers, and other inertial vibration sensors, including passive accelerometers. The method requires no cumbersome or expensive fixtures such as shaker platforms and can be performed using a standard instrument commonly available in the field. An absolute calibration is obtained using the reciprocity property of the device, based on the standard mathematical model for such inertial sensors. It requires only simple electrical measurement of the impedance of the sensor as a function of frequency to determine the parameters of the model and hence the sensitivity function. The method is particularly convenient if one of these parameters, namely the suspended mass is known. In this case, no additional mechanical apparatus is required and only a single set of impedance measurements yields the desired calibration function. Moreover, this measurement can be made with the device in situ. However, the novel and most powerful aspect of the method is its ability to accurately determine the effective suspended mass. For this, the impedance measurement is made with the device hanging from a simple spring or flexible cord (depending on the orientation of its sensitive axis). To complete the calibration, the device is weighed to determine its total mass. All the required calibration parameters, including the suspended mass, are then determined from a least-squares fit to the impedance as a function of frequency. A demonstration using both a 4.5 Hz geophone and a 1 Hz seismometer shows that the method can yield accurate absolute calibrations with an error of 0.1% or better, assuming no a priori knowledge of any parameters.
Surface charging and current collapse in an AlGaN∕GaN heterostructure field effect transistor
Authors: Sabuktagin S. , Doğan S. , Baski A. A. , Morkoç H.
Published: February 2005

This work investigates the correlation between surface charging and current collapse in an AlGaN∕GaN heterostructure field effect transistor. Surface charging due to applied biases was sensed by mapping the surface potential between the gate and drain using scanning Kelvin probe microscopy. Due to the bias, the surface band bending near the gate edge was observed to increase by as much as 1 eV. This increase of band bending is caused by an accumulation of excess charge near the surface during the applied bias. By varying the duration of the applied bias, we find that this accumulation of excess charge near the gate takes about 20 s to saturate. Continuous monitoring of the surface potential after switching off the bias shows that a complete relaxation of the excess band bending requires about 800 s. Drain current transient measurements show that the collapse and recovery of the drain current also occur on similar time scales. This correlation between time scales indicates that the accumulation of excess charge near the gate edge causes current collapse by depletion of the channel.
In situ resistance measurement of the p-type contact in InP–InGaAsP coolerless ridge waveguide lasers
Authors: Kuntze S. B. , Sargent E. H. , White J. K. , Hinzer K. , Dixon-Warren St. J. , Ban D.
Published: February 2005

Scanning voltage microscopy (SVM) is employed to measure the voltage division—and resulting contact resistance and power loss—at the p-In0.53Ga0.47As–p-InP heterojunction in a working InP–InGaAsP laser diode. This heterojunction is observed to dissipate ∼35% of the total power applied to the laser over the operating bias range. This in situ experimental study of the parasitic voltage division (and resulting power loss and series contact resistance) highlights the need for a good p-type contact strategy. SVM technique provides a direct, fast and in situ measurement of specific contact resistance, an important device parameter.
A continuum model for zigzag single-walled carbon nanotubes
Authors: Leung A. Y. T. , Guo X. , He X. Q. , Kitipornchai S.
Published: February 2005

An idea of “spatial periodic strain” is proposed and an equilibrium relationship is established for the mechanics of zigzag single-walled carbon nanotubes (SWCNTs). An efficient approach is presented to investigate mechanical properties of zigzag SWCNT, and its validity is demonstrated by comparing its calculation results with existing results.
Electron field emission from GaN nanorod films grown on Si substrates with native silicon oxides
Authors: Yamashita T. , Hasegawa S. , Nishida S. , Ishimaru M. , Hirotsu Y. , Asahi H.
Published: February 2005

GaN nanorod films have been grown on Si(001) substrates with native silicon oxides by radio-frequency plasma-enhanced molecular beam epitaxy. GaN nanorod films are made up of single-crystalline nanorods with a so-called (0001) fiber-like texture. Each nanorod is elongated along c axis in perpendicular to the substrate surface and has no preferential axis in film plane. Excellent electron field emission characteristics were observed for the fabricated GaN nanorod films with a field emission threshold as low as 1.25V∕μm at a current density of 0.1μA∕cm2 and a field emission current density as high as 2.5mA∕cm2 at an applied field of 2.5V∕μm. These excellent characteristics are attributed to the geometrical configuration of nanorods and their good crystalline quality as well as the low electron affinity of GaN.
Atomic layer deposition of ZnO on ultralow-density nanoporous silica aerogel monoliths
Authors: Kucheyev S. O. , Biener J. , Wang Y. M. , Baumann T. F. , Wu K. J. , van Buuren T. , Hamza A. V. , Satcher J. H. , Elam J. W. , Pellin M. J.
Published: February 2005

We report on atomic layer deposition of an ∼2-nm-thick ZnO layer on the inner surface of ultralow-density (∼0.5% of the full density) nanoporous silica aerogel monoliths with an extremely large effective aspect ratio of ∼105 (defined as the ratio of the monolith thickness to the average pore size). The resultant monoliths are formed by amorphous-SiO2 core/wurtzite-ZnO shell nanoparticles which are randomly oriented and interconnected into an open-cell network with an apparent density of ∼3% and a surface area of ∼100m2g−1. Secondary ion mass spectrometry and high-resolution transmission electron microscopy imaging reveal excellent uniformity and crystallinity of ZnO coating. Oxygen K-edge and Zn L3-edge soft x-ray absorption near-edge structure spectroscopy shows broadened O p- as well as Zn s- and d-projected densities of states in the conduction band.
Photochromism of vacancy-related defects in thermochemically reduced α-Al2O3:Mg single crystals
Authors: Ramírez R. , Tardío M. , González R. , Chen Y. , Kokta M. R.
Published: February 2005

Oxygen vacancies and their aggregates are produced much more readily in Mg-doped α-Al2O3 than in undoped α-Al2O3 single crystals during thermochemical reduction at high temperatures. A reversible photochromic effect was discovered in Mg-doped Al2O3 crystals containing large concentrations of oxygen divacancies. Alternate excitation with 5.0 and 3.69 eV light results in brown or yellowish–green coloration, respectively. The yellowish–green coloration can also be restored by thermal anneals at temperatures of about 750 K.
Distribution of blocking temperature in exchange-coupled Fe3O4–CrMnPt system
Authors: Soeya Susumu , Takahashi Hiromasa , Takahashi Yoshio
Published: February 2005

The distribution of local blocking temperatures (TBi) in an exchange-coupled half-metallic-Fe3O4–antiferromagnetic-Cr45.5Mn45.5Pt9 system (in atomic %) was investigated, with the aim of confirming thermal stability of unidirectional anisotropy induced in Fe3O4 film, which has hard magnetic properties. The distribution of TBi was mostly at or around 265°C. This distribution in the Fe3O4–CrMnPt system was equivalent or superior to that found in a previously studied soft magnetic-Ni81Fe19–antiferromagnetic-Pt50Mn50 system, where PtMn had been used in a giant magnetoresistance device as the standard antiferromagnetic material for the exchange-biased layer. These results make it reasonable to conclude that the exchange coupled Fe3O4–CrMnPt system has excellent thermal stability.