bluuebunny/crossref_metadata_2025 huggingface dataset:
All of this and he can cook, too…
Authors: Van Dalen Jan
Published: November 2012

Professor Cees van der Vleuten has been awarded the 2012 Karolinska Insitutet
Prize for Research in Medical Education for his research in evaluation and assessment of
medical competences.
Crossword puzzles: self-learning tool in pharmacology
Authors: Gaikwad Nitin , Tankhiwale Suresh
Published: November 2012

Students of the second professional MBBS course of the Indian medical curriculum
(II MBBS) perceive pharmacology as a ‘Volatile Subject’ because they often find it
difficult to remember and recall drug names. We evaluated the usefulness of crossword
puzzles as a self-learning tool to help pharmacology students to remember drug names. We
also measured the students’ satisfaction with this learning method. This was an
open-label randomized, two-arm intervention study, conducted with II MBBS students (n =
70), randomly selected and assigned to two groups A (n = 35) and B (n = 35). Two
self-learning modules containing crossword puzzles with antihypertensive and
antiepileptic drug terms were prepared and pre-validated. Hard copies of both crossword
puzzles were administered to Group A (Intervention group) on two different occasions.
One hour was allotted to solve a puzzle. Students were allowed to refer to their
textbooks. Group B (Control group) underwent the self-learning module without the
crossword puzzles. In both groups, pre- and post-test knowledge was assessed. Students’
perceptions of the crossword puzzles were assessed using a pre-validated 10-item
questionnaire. Responses to items 1–8 were recorded using a 5-point Likert scale.
Responses to item 9 were recorded on a 10-point rating scale while item 10 was an
open–ended question. The crossword completion index was 92.86 %.
AMDD: Antimicrobial Drug Database
Authors: Danishuddin Mohd , Kaushal Lalima , Hassan Baig Mohd , Khan Asad U.
Published: November 2012

Drug resistance is one of the major concerns for antimicrobial chemotherapy against any particular target. Knowledge of the primary structure of antimicrobial agents and their activities is essential for rational drug design. Thus, we developed a comprehensive database, anti microbial drug database (AMDD), of known synthetic antibacterial and antifungal compounds that were extracted from the available literature and other chemical databases, e.g., PubChem, PubChem BioAssay and ZINC, etc. The current version of AMDD contains ∼2900 antibacterial and ∼1200 antifungal compounds. The molecules are annotated with properties such as description, target, format, bioassay, molecular weight, hydrogen bond donor, hydrogen bond acceptor and rotatable bond. The availability of these antimicrobial agents on common platform not only provides useful information but also facilitate the virtual screening process, thus saving time and overcoming difficulties in selecting specific type of inhibitors for the specific targets. AMDD may provide a more effective and efficient way of accessing antimicrobial compounds based on their properties along with the links to their structure and bioassay. All the compounds are freely available at the advanced web-based search interface http://www.amddatabase.info.
Massed versus spaced visuospatial memory in cognitively healthy young and older adults
Authors: Jackson Colleen E. , Maruff Paul T. , Snyder Peter J.
Published: November 2012

Background

The present study examined the effect of massed versus spaced learning trials on 24‐hour delayed recall for a visuospatial learning task. To determine the utility of measuring the incremental benefit of spaced training as a cognitive assay that may be useful in early clinical trials, we used a within‐subject crossover design, with two small samples (typical sample sizes for phase I clinical trials).

Methods

Young adults and cognitively healthy older adults without significant physical, neurological, or psychiatric illness were trained on a visuospatial paired‐associate learning task under a massed condition (learning trials were presented in immediate succession) and a spaced condition (learning trials were presented with 15‐minute intertrial delays).

Results

Statistically significant differences between training conditions on the visuospatial task, such that young adult participants performed better on delayed recall after spaced training, were identified. Large effect sizes for young and older adults on this task suggest meaningful differences between training conditions, reflecting the expected “spacing effect.” The role of amyloid aggregation was also considered for a subset of participants; as amyloid levels increased, the benefit of spaced training decreased, suggesting that the effect of this training paradigm is modulated by disease burden.

Conclusions

The utility of this paradigm as a potential assay for phase I proof‐of‐concept trials, targeting molecular mechanisms that are central to the encoding and consolidation of new learning, is discussed.
Intersite variability of CSF Alzheimer's disease biomarkers in clinical setting
Authors: Dumurgier Julien , Vercruysse Olivier , Paquet Claire , Bombois Stéphanie , Chaulet Chloé , Laplanche Jean‐Louis , Peoc'h Katell , Schraen Susanna , Pasquier Florence , Touchon Jacques , Hugon Jacques , Lehmann Sylvain , Gabelle Audrey
Published: November 2012

Background

The assessment of total tau, phosphorylated tau (pTau‐181) and amyloid beta (Aβ 1–42) concentrations in the cerebrospinal fluid (CSF) of subjects has been validated for the diagnosis of Alzheimer's disease (AD). Although these measurements have shown some variability, little is known about their intersite variability in clinical settings.

Methods

A total of 880 subjects (AD, n = 515; non‐AD, n = 365) from three French memory centers were included. Receiver–operating characteristic analyses were performed to computerized area under curves (AUCs) and optimal thresholds for each biomarker in the three centers. A test–retest study was performed in a group of 32 CSF samples by repeated blind analysis of the three biomarkers using the same immunoassay batches in the three centers.

Results

In the three centers, tau (AUC, 0.82–0.88) and pTau‐181 (AUC, 0.83–0.89) outperformed Aβ 1–42 (AUC, 0.70 –0.73) to discriminate subjects with AD from those without AD. An intersite variation of mean levels and cutoffs was observed for the three biomarkers. This variation was higher for Aβ 1–42 (range of cutoff, 368–582 pg/mL) than for tau (range of cutoff, 289–353 pg/mL). In a test–retest study, the mean interlaboratory coefficients of variation were 12.2% for Aβ 1–42, 11.3% for tau, and 11.5% for pTau‐181.

Conclusion

Intercenter variability of CSF biomarkers has been confirmed in a multisite cohort of subjects and can be improved in clinical settings. Efforts on harmonization of procedures should be encouraged to optimize the accuracy of CSF biomarkers in AD.
Renin‐angiotensin system blockers affect cognitive decline and serum adipocytokines in Alzheimer's disease
Authors: Furiya Yoshiko , Ryo Miwa , Kawahara Makoto , Kiriyama Takao , Morikawa Masami , Ueno Satoshi
Published: November 2012

Background

Accumulating evidence indicates an association of Alzheimer's disease (AD) with the metabolic syndrome (MetS), characterized by visceral fat accumulation with insulin resistance and altered secretion of adipocytokines such as adiponectin and leptin. The renin‐angiotensin system (RAS) regulates blood pressure and insulin resistance. Recent studies suggest that the RAS plays crucial roles in cognitive functions and that adipocytokines exert neuroprotective activity in the brain. We investigated whether RAS blockers (RASB) affect adipocytokines and cognitive function in patients with AD.

Methods

We studied 78 patients with a diagnosis of probable AD according to the Diagnostic and Statistical Manual of Mental Disorders, 4th edition and 106 nondemented control subjects who visited our clinic with a main complaint of headache or dizziness. We examined retrospectively the effects of RASB on adipocytokines and cognitive decline in patients with AD who were divided into three groups: hypertension treated with RASB (HT‐RASB; n = 17), hypertension treated with other antihypertensive drugs (HT‐other; n = 34), and no hypertension (non‐HT; n = 27).

Results

The HT‐RASB group had a significantly higher serum leptin level and a relatively larger visceral fat area than the other groups, because of the bias toward patients with MetS in this group. The HT‐RASB group also had a significantly lower immunoreactive insulin level, a relatively low homeostasis model assessment as an index of insulin resistance, and a relatively high serum adiponectin level among the three groups. Cognitive decline, estimated on the basis of the mean annual decline using the Hasegawa Dementia Scale score was significantly low in the HT‐RASB group.

Conclusion

Treatment with RASB might modulate serum adipocytokines and glucose homeostasis, potentially slowing cognitive decline in patients with AD.
Optimized Bias Estimation Model for Mobile Radar Error Registration
Authors: Wang G. H. , Chen L. , Jia S. Y. , Progri I.
Published: November 2012

For mobile 3-D radar installed on a gyro-stabilized platform, its measurements are usually contaminated by the systematic biases which contain radar offset biases (i.e., range, azimuth and elevation biases) and attitude biases (i.e., yaw, pitch and roll biases) of the platform because of the errors in the Inertial Measurement Units (IMU). Systematic biases can NOT be removed by a single radar itself; however, fortunately, they can be estimated by using two different radar measurements of the same target. The process of estimating systematic biases and then compensating radar measurements is called error registration. In this paper, the registration models are established first, then, the equivalent radar measurement error expressions caused by the attitude biases are derived and the dependencies among attitude biases and offset biases are analysed by using the observable matrix criterion. Based on the analyses above, an Optimized Bias Estimation Model (OBEM) is proposed for registration. OBEM uses the subtraction of azimuth and yaw bias as one variable and omits roll and pitch biases in the state vector, which decreases the dimension of the state vector from fourteen of the All Augmented Model (AAM), (which uses all the systematic biases of both radars as state vector) to eight and has about 80% reduction in calculation costs. Also, OBEM can decrease the coupling influences of roll and pitch biases and improve the estimation performance of radar elevation bias. Monte Carlo experiments were made. Numerical results showed that the bias estimation accuracies and the rectified radar raw measurement accuracies can be improved.
Automatic Detection of Spherical Particles from Spot-Scan
Electron Microscopy Images
Authors: Thuman-Commike Pamela A. , Chiu Wah
Published: November 2012

In this article we present a method to identify and extract
spherical particle images from noisy spot-scan and flood beam
electron microscopy images. We use a template matching algorithm
with additional image preprocessing operations to allow consistent
particle selection in spot-scan and other highly spatially varying
images. In addition, this algorithm incorporates an automated
image-cutting and edge-sewing mechanism that allows efficient
particle selection despite the large size of electron microscopy
images. We have tested this template matching algorithm on various
spherical virus particle images with a large range of defocus
values and have found that the particles are consistently selected
in an accurately centered manner. In addition, this method is
able to extract spherical virus particles from 400-kV electron
microscopy images with defocus values of less than 1.0 μm
underfocus where the particles are not readily visible to the
human eye.
Characteristics of colored dissolved organic matter (CDOM) in the Arctic outflow in the Fram Strait: Assessing the changes and fate of terrigenous CDOM in the Arctic Ocean
Authors: Granskog Mats A. , Stedmon Colin A. , Dodd Paul A. , Amon Rainer M. W. , Pavlov Alexey K. , de Steur Laura , Hansen Edmond
Published: November 2012

Absorption coefficients of colored dissolved organic matter (CDOM) were measured together with salinity, δ18O, and inorganic nutrients across the Fram Strait. A pronounced CDOM absorption maximum between 30 and 120 m depth was associated with river and sea ice brine enriched water, characteristic of the Arctic mixed layer and upper halocline waters in the East Greenland Current (EGC). The lowest CDOM concentrations were found in the Atlantic inflow. We show that the salinity‐CDOM relationship is not suitable for evaluating conservative mixing of CDOM. The strong correlation between meteoric water and CDOM is indicative of the riverine/terrigenous origin of CDOM in the EGC. Based on CDOM absorption in Polar Water and comparison with an Arctic river discharge weighted mean, we estimate that a 49–59% integrated loss of CDOM absorption across 250–600 nm has occurred. A preferential removal of absorption at longer wavelengths reflects the loss of high molecular weight material. In contrast, CDOM fluxes through the Fram Strait using September velocity fields from a high‐resolution ocean–sea ice model indicate that the net southward transport of terrigenous CDOM through the Fram Strait equals up to 50% of the total riverine CDOM input; this suggests that the Fram Strait export is a major sink of CDOM. These contrasting results indicate that we have to constrain the (C)DOM budgets for the Arctic Ocean much better and examine uncertainties related to using tracers to assess conservative mixing in polar waters.
Statistical tests for a correlation between decadal variation in June precipitation in China and sunspot number
Authors: Wang Jing‐Song , Zhao Liang
Published: November 2012

Six different statistical methods (i.e., correlation, difference, prominent period, variance contribution, scale‐averaged spectrum, and cross spectrum) are used to test for regional differences in the relationship between the 11 year sunspot cycle and June precipitation in China during the 20th century. In the Huaihe River basin (HRB) of central China, located at the marginal region of the East Asian summer monsoon (EASM), there exists a reliable positive‐correlation relationship between the 11 year sunspot cycle and June precipitation; whereas, possible negative and very weak positive correlations in the south of the middle–lower Yangtze River Region and the HeTao Basin (HTB), located in the interior of the EASM and the westerlies, respectively. The reasons for these regional differences are investigated, revealing that the marginal region of EASM may be more sensitive to solar forcing than is its interior, which results in the HRB becoming the most susceptible (strongest correlation) region. That is to say, in June during the high sunspot number (SSN) years, the influence of the EASM is significantly greater and more to the north than that in June during the low SSN years, causing the HRB to be mainly influenced by the EASM (westerlies) in June during the high (low) SSN years. The northward expansion of the June EASM probably resulted from enhancement of the low‐level southwesterly monsoon flow over the northern tropical Indian Ocean, combined with an expansion of the western Pacific subtropical high at times of high SSN.
Investigating the origin of candidate lava channels on Mercury with MESSENGER data: Theory and observations
Authors: Hurwitz Debra M. , Head James W. , Byrne Paul K. , Xiao Zhiyong , Solomon Sean C. , Zuber Maria T. , Smith David E. , Neumann Gregory A.
Published: November 2012

Volcanic plains identified on Mercury are morphologically similar to lunar mare plains but lack constructional and erosional features that are prevalent on other terrestrial planetary bodies. We analyzed images acquired by the MESSENGER spacecraft to identify features on Mercury that may have formed by lava erosion. We used analytical models to estimate eruption flux, erosion rate, and eruption duration to characterize the formation of candidate erosional features, and we compared results with analyses of similar features observed on Earth, the Moon, and Mars. Results suggest that lava erupting at high effusion rates similar to those required to form the Teepee Butte Member of the Columbia River flood basalts (0.1–1.2 × 106 m3 s–1) would have been necessary to form wide valleys (>15 km wide) observed in Mercury's northern hemisphere, first by mechanical erosion to remove an upper regolith layer, then by thermal erosion once a lower rigid layer was encountered. Alternatively, results suggest that lava erupting at lower effusion rates similar to those predicted to have formed Rima Prinz on the Moon (4400 m3 s–1) would have been required to form, via thermal erosion, narrower channels (<7 km wide) observed on Mercury. Although these results indicate how erosion might have occurred on Mercury, the observed features may have formed by other processes, including lava flooding terrain sculpted during the formation of the Caloris basin in the case of the wide valleys, or impact melt carving channels into impact ejecta in the case of the narrower channels.
Magnesium‐rich crustal compositions on Mercury: Implications for magmatism from petrologic modeling
Authors: Stockstill‐Cahill Karen R. , McCoy Timothy J. , Nittler Larry R. , Weider Shoshana Z. , Hauck Steven A.
Published: November 2012

We have conducted petrologic modeling of MESSENGER‐derived compositions and analog compositions to gain a better understanding of the petrogenesis of the crust of Mercury. Analog compositions included a 1425°C partial melt of the Indarch (EH4) meteorite and a range of Mg‐rich terrestrial rocks (magnesian basalt, basaltic komatiite, and peridotitic komatiite). All models were held at the iron‐wüstite buffer to simulate the reducing conditions that likely existed during Mercury's formation. We then compared modeled mineral compositions and abundances, liquidus temperatures, and viscosities to better constrain the characteristics of the lavas that erupted on Mercury's surface. Our results show that the surface composition of Mercury is most similar to that of a terrestrial magnesian basalt (with lowered FeO), composed mainly of Mg‐rich orthopyroxene and plagioclase. Because the model magmas are Mg‐rich, their counterparts on Mercury would have erupted at high temperatures and displayed low viscosities. Producing melts of these compositions would have required high temperatures at the mantle source regions on Mercury. The inferred low‐viscosity lavas would have erupted as thin, laterally extensive flows (depending upon their effusion rate) and would be expected to display surficial flow features that might be preserved to the present.
The influence of land‐use composition on fecal contamination of riverine source water in southern British Columbia
Authors: St Laurent Jacques , Mazumder Asit
Published: November 2012

The potential for riverine drinking source water to become contaminated with pathogens is related to the production and transport of fecal waste from within the local catchment area. Identifying specific relationships between land‐use types and fecal contamination in riverine water provides an indication of the risk associated with land‐use change and helps to target mitigation measures toward land‐use types of concern. Fecal coliform (FC) data from 42 riverine sites across British Columbia (BC), Canada, were examined in relation to land‐use composition (including 16 land‐use types) in the local catchment area. FC concentration significantly increased in relation to anthropogenic land‐use impacts but was negatively associated with undisturbed and high‐elevation land types. Regression tree analysis identified that highest FC concentrations occurred in catchments characterized by more than 12.5% agricultural land and more than 1.6% urban land. Furthermore, the risk of violation of the BC partial treatment raw drinking water quality guideline for FC concentration (100 CFU 100 mL−1) increased in relation to agricultural impacts. Additional factors, such as sewage treatment discharge, low dilution in smaller streams, and higher temperatures, were associated with higher FC concentration among sites with similar levels of agricultural development. These results identify land‐use types that present the greatest threat to riverine contamination, namely agricultural and urban land, and indicate the proportion of such land use associated with high contamination. Land use should be managed and source water protection should be targeted in light of these results so as to minimize the risk of surface water exposure to fecal contaminants.
EGLN1 variants influence expression and SaO2 levels to associate with high-altitude pulmonary oedema and adaptation
Authors: Mishra Aastha , Mohammad Ghulam , Thinlas Tashi , Pasha M. A. Qadar
Published: November 2012

EGLN1 [encoding HIF (hypoxia-inducible factor)-prolyl hydroxylase 2] plays a pivotal role in the HIF pathway and has emerged as one of the most intriguing genes with respect to physiology at HA (high altitude). EGLN1, being an actual oxygen sensor, appears to have a potential role in the functional adaptation to the hypobaric hypoxic environment. In the present study, we screened 30 polymorphisms of EGLN1, evaluated its gene expression and performed association analyses. In addition, the role of allelic variants in altering TF (transcription factor)-binding sites and consequently the replacement of TFs at these loci was also investigated. The study was performed in 250 HAPE-p [HAPE (HA pulmonary oedema)-patients], 210 HAPE-f (HAPE-free controls) and 430 HLs (healthy Ladakhi highland natives). The genotypes of seven polymorphisms, rs1538664, rs479200, rs2486729, rs2790879, rs480902, rs2486736 and rs973252, differed significantly between HAPE-p and HAPE-f (P<0.008). The genotypes AA, TT, AA, GG, CC, AA and GG of rs1538664, rs479200, rs2486729, rs2790879, rs480902, rs2486736 and rs973252, prevalent in HAPE-p, were identified as risk genotypes and their counterpart homozygotes, prevalent in HLs, were identified as protective. EGLN1 expression was up-regulated 4.56-fold in HAPE-p (P=0.0084). The risk genotypes, their haplotypes and interacting genotypes were associated with up-regulated EGLN1 expression (P<0.05). Similarly, regression analysis showed that the risk alleles and susceptible haplotypes were associated with decreased SaO2 (arterial oxygen saturation) levels in the three groups. The significant inverse correlation of SaO2 levels with PASP (pulmonary artery systolic pressure) and EGLN1 expression and the association of these polymorphisms with SaO2 levels and EGLN1 expression contributed to uncovering the molecular mechanism underlying hypobaric hypoxic adaptation and maladaptation.
A triplectic bi-Darboux theorem and para-hypercomplex geometry
Authors: Batalin Igor A. , Bering Klaus
Published: November 2012

We provide necessary and sufficient conditions for a bi-Darboux theorem on triplectic manifolds. Here, triplectic manifolds are manifolds equipped with two compatible, jointly non-degenerate Poisson brackets with mutually involutive Casimirs, and with ranks equal to 2/3 of the manifold dimension. By definition bi-Darboux coordinates are common Darboux coordinates for two Poisson brackets. We discuss both the Grassmann-even and the Grassmann-odd Poisson bracket case. Odd triplectic manifolds are, e.g., relevant for Sp(2)-symmetric field-antifield formulation. We demonstrate a one-to-one correspondence between triplectic manifolds and para-hypercomplex manifolds. Existence of bi-Darboux coordinates on the triplectic side of the correspondence translates into a flat Obata connection on the para-hypercomplex side.
Dissipative properties of systems composed of high-loss and lossless components
Authors: Figotin Alexander , Welters Aaron
Published: November 2012

We study here dissipative properties of systems composed of two components one of which is highly lossy and the other is lossless. A principal result of our studies is that all the eigenmodes of such a system split into two distinct classes characterized as high-loss and low-loss. Interestingly, this splitting is more pronounced the higher the loss of the lossy component. In addition, the real frequencies of the high-loss eigenmodes can become very small and even can vanish entirely, which is the case of overdamping.
Understanding turbulent flow over ripple-shaped random roughness in a channel
Authors: Chau Long , Bhaganagar Kiran
Published: November 2012

Direct numerical simulation is used to understand the flow over ripple-shaped random rough elements. The random roughness has been generated using the model for sand ripples consisting of saltation, creep and suspension processes. A set of metrics based on both the geometrical and statistical properties of roughness was derived to characterize random roughness. The eight cases that have been studied with varied asymmetric distribution and “peakedness” as specified by the skewness and kurtosis of the height distribution varying from 0.28 to 0.7, and from 1.8 to 2.2, respectively. Analogous to λ/h for canonical (regular) roughness, λavg/hmax was selected as the geometrical parameter to characterize the surface, ranging from 4 to 26. The results have revealed that roughness significantly alters the mean velocity as well as turbulence in the inner layer. The outer layer is relatively unaffected due to the presence of roughness. The results further revealed that roughness distribution that is symmetric and which is well spread out has a stronger influence on the mean flow in the near-wall flow region. Altering the λavg/hmax affects the skewness and kurtosis of the height distribution, which are the important metrics to quantify the mean flow over a rough wall with random rough elements. The peak turbulence intensities increased with increasing λavg/hmax, however its effect on rms of the velocity fluctuations was confined to a region very close to the rough wall. Similar to mean flow, a symmetrical and a well-spread roughness distribution resulted in more energetic turbulent structures, stronger near-wall vortices, and increased turbulence activity. A similar trend was observed for the small scale features of the turbulent flow as seen from the vorticity fluctuations. To characterize turbulent flow over random rough surface of given maximum height, the geometrical parameter λavg/hmax as well as statistical parameters, the skewness and kurtosis are important metrics to be considered.
A shallow underground laboratory for low-background radiation measurements and materials development
Authors: Aalseth C. E. , Bonicalzi R. M. , Cantaloub M. G. , Day A. R. , Erikson L. E. , Fast J. , Forrester J. B. , Fuller E. S. , Glasgow B. D. , Greenwood L. R. , Hoppe E. W. , Hossbach T. W. , Hyronimus B. J. , Keillor M. E. , Mace E. K. , McIntyre J. I. , Merriman J. H. , Myers A. W. , Overman C. T. , Overman N. R. , Panisko M. E. , Seifert A. , Warren G. A. , Runkle R. C.
Published: November 2012

Pacific Northwest National Laboratory recently commissioned a new shallow underground laboratory, located at a depth of approximately 30 meters-water-equivalent. This new addition to the small class of radiation measurement laboratories located at modest underground depths houses the latest generation of custom-made, high-efficiency, low-background gamma-ray spectrometers and gas proportional counters. This paper describes the unique capabilities present in the shallow underground laboratory; these include large-scale ultra-pure materials production and a suite of radiation detection systems. Reported data characterize the degree of background reduction achieved through a combination of underground location, graded shielding, and rejection of cosmic-ray events. We conclude by presenting measurement targets and future opportunities.
Insights into the ultraviolet spectrum of liquid water from model calculations: The different roles of donor and acceptor hydrogen bonds in water pentamers
Authors: Cabral do Couto Paulo , Chipman Daniel M.
Published: November 2012

With a view toward a better understanding of changes in the peak position and shape of the first absorption band of water with condensation or temperature, results from electronic structure calculations using high level wavefunction based and time-dependent density functional methods are reported for water pentamers. Excitation energies, oscillator strengths, and redistributions of electron density are determined for the quasitetrahedral water pentamer in its C2v equilibrium geometry and for many pentamer configurations sampled from molecular simulation of liquid water. Excitations associated with surface molecules are removed in order to focus on those states associated with the central molecule, which are the most representative of the liquid environment. The effect of hydrogen bonding on the lowest excited state associated with the central molecule is studied by adding acceptor or donor hydrogen bonds to tetramer and trimer substructures of the C2v pentamer, and by sampling liquid-like configurations having increasing number of acceptor or donor hydrogen bonds of the central molecule. Our results provide clear evidence that the blueshift of excitation energies upon condensation is essentially determined by acceptor hydrogen bonds, and the magnitudes of these shifts are determined by the number of such, whereas donor hydrogen bonds do not induce significant shifts in excitation energies. This qualitatively different role of donor and acceptor hydrogen bonds is understood in terms of the different roles of the 1b1 monomer molecular orbitals, which establishes an intimate connection between the valence hole and excitation energy shifts. Since the valence hole of the lowest excitation associated with the central molecule is found to be well localized in all liquid-like hydrogen bonding environments, with an average radius of gyration of ∼1.6 Å that is much lower than the nearest neighbor O–O distance, a clear and unambiguous connection between hydrogen bonding environments and excitation energy shifts can be established. Based on these results, it is concluded that peak position of the first absorption band is mainly determined by the relative distribution of single and double acceptor hydrogen bonding environments, whereas the shape of the first absorption band is mainly determined by the relative distribution of acceptor and broken acceptor hydrogen bonding environments. The temperature dependence of the peak position and shape of the first absorption band can be readily understood in terms of changes to these relative populations.
Optimized boundary driven flows for dynamos in a sphere
Authors: Khalzov I. V. , Brown B. P. , Cooper C. M. , Weisberg D. B. , Forest C. B.
Published: November 2012

We perform numerical optimization of the axisymmetric flows in a sphere to minimize the critical magnetic Reynolds number Rmcr required for dynamo onset. The optimization is done for the class of laminar incompressible flows of von Kármán type satisfying the steady-state Navier-Stokes equation. Such flows are determined by equatorially antisymmetric profiles of driving azimuthal (toroidal) velocity specified at the spherical boundary. The model is relevant to the Madison plasma dynamo experiment, whose spherical boundary is capable of differential driving of plasma in the azimuthal direction. We show that the dynamo onset in this system depends strongly on details of the driving velocity profile and the fluid Reynolds number Re. It is found that the overall lowest Rmcr≈200 is achieved at Re≈240 for the flow, which is hydrodynamically marginally stable. We also show that the optimized flows can sustain dynamos only in the range Rmcr<Rm<Rmcr2, where Rmcr2 is the second critical magnetic Reynolds number, above which the dynamo is quenched. Samples of the optimized flows and the corresponding dynamo fields are presented.
Stochastic operator-splitting method for reaction-diffusion systems
Authors: Choi TaiJung , Maurya Mano Ram , Tartakovsky Daniel M. , Subramaniam Shankar
Published: November 2012

Many biochemical processes at the sub-cellular level involve a small number of molecules. The local numbers of these molecules vary in space and time, and exhibit random fluctuations that can only be captured with stochastic simulations. We present a novel stochastic operator-splitting algorithm to model such reaction-diffusion phenomena. The reaction and diffusion steps employ stochastic simulation algorithms and Brownian dynamics, respectively. Through theoretical analysis, we have developed an algorithm to identify if the system is reaction-controlled, diffusion-controlled or is in an intermediate regime. The time-step size is chosen accordingly at each step of the simulation. We have used three examples to demonstrate the accuracy and robustness of the proposed algorithm. The first example deals with diffusion of two chemical species undergoing an irreversible bimolecular reaction. It is used to validate our algorithm by comparing its results with the solution obtained from a corresponding deterministic partial differential equation at low and high number of molecules. In this example, we also compare the results from our method to those obtained using a Gillespie multi-particle (GMP) method. The second example, which models simplified RNA synthesis, is used to study the performance of our algorithm in reaction- and diffusion-controlled regimes and to investigate the effects of local inhomogeneity. The third example models reaction-diffusion of CheY molecules through the cytoplasm of Escherichia coli during chemotaxis. It is used to compare the algorithm's performance against the GMP method. Our analysis demonstrates that the proposed algorithm enables accurate simulation of the kinetics of complex and spatially heterogeneous systems. It is also computationally more efficient than commonly used alternatives, such as the GMP method.
Ultra-thin atomic-layer deposited alumina incorporating silica sol makes ultra-durable antireflection coatings
Authors: Li Jia , Lan Pinjun , Xu Hua , Zhang Xianpeng , Yang Ye , Tan Ruiqin , Jylhä Olli , Lu Yuehui
Published: November 2012

We propose a strategy to make soda-lime glass maintain both high transparency and long-term durability in stringent high temperature and humid environments. Experiments reveal that the double-layered coatings with 110-nm-thick SiO2 and ultra-thin 25-nm- or 50-nm-thick Al2O3 layers, prepared by sol-gel dip coating and atomic layer deposition (ALD), respectively, exhibit the improvement of 5.88–6.32% in Tave (the average transmittance from the wavelength of 400–700 nm), as compared with that of the bare glass. On the other hand, the highly accelerated temperature and humidity stress test (HAST) confirms that both samples can sustain the 180 h test without any proven transmittance degradation, while the normalized Tave of the bare glass drastically drops to 43.1% of the initial value after the 108 h HAST. It implies that the ultra-thin Al2O3 films prepared by ALD, followed by dip-coated low-index layers such as SiO2 or nanostructured layer, can achieve both higher average transmittance and better durability, which would be of significance for the applications of ALD and dip coating techniques in the fields of consumer electronics, architecture with glass facades, and photovoltaics.
Angular dependence of switching field distribution in (Co/Pd)n multilayer nanostructure arrays
Authors: Lau June W. , Liu Xiaoyong
Published: November 2012

The characterization of switching field and its angular dependence has been tremendously useful in understanding the switching mechanisms in magnetic thin-films and patterned structures. However, the study of the distribution in switching fields (SFD) in arrays and its angular dependence is less common. In this work, we investigate this dependency in arrays of (Co/Pd)n multilayer nanostructures. Results from arrays with different element sizes and periodicities (pitches) are presented, and we found that, like the switching field, the SFD varies with applied field angle in a Stoner-Wohlfarth-like fashion. Furthermore, when the SFD is represented as a dependent variable of the switching field, we consistently found a linear relationship between the two, and that the slope depends on both array element size and pitch. In general, the SFD in arrays with the largest structures and the smallest pitch tends to have the strongest dependence on the switching field. For arrays with nanostructures of a fixed size, however, we found that SFD values are virtually identical, regardless of pitch, if the reversal field is applied near 45° with respect to the surface normal. That the minimum SFD depends only on the size of the elements and not the pitch has significant implications for the practical design of densely-packed magnetic nanostructure arrays.
Surface plasmon polaritons in a semi-bounded degenerate plasma: Role of spatial dispersion and collisions
Authors: Tyshetskiy Yu. , Kompaneets R. , Vladimirov S. V.
Published: November 2012

Surface plasmon polaritons (SPPs) in a semi-bounded degenerate plasma (e.g., a metal) are studied using the quasiclassical mean-field kinetic model, taking into account the spatial dispersion of the plasma (due to quantum degeneracy of electrons) and electron-ion (electron-lattice, for metals) collisions. SPP dispersion and damping are obtained in both retarded (ω/kz∼c) and non-retarded (ω/kz≪c) regions, as well as in between. It is shown that the plasma spatial dispersion significantly affects the properties of SPPs, especially at short wavelengths (less than the collisionless skin depth, λ ≲ c/ωpe). Namely, the collisionless (Landau) damping of SPPs (due to spatial dispersion) is comparable to the purely collisional (Ohmic) damping (due to electron-lattice collisions) in a wide range of SPP wavelengths, e.g., from λ∼20 nm to λ∼0.8 nm for SPP in gold at T = 293 K and from λ∼400 nm to λ∼0.7 nm for SPPs in gold at T = 100 K. The spatial dispersion is also shown to affect, in a qualitative way, the dispersion of SPPs at short wavelengths λ ≲ c/ωpe.
Lattice Boltzmann simulations of pressure-driven flows in microchannels using Navier–Maxwell slip boundary conditions
Authors: Reis Tim , Dellar Paul J.
Published: November 2012

We present lattice Boltzmann simulations of rarefied flows driven by pressure drops along two-dimensional microchannels. Rarefied effects lead to non-zero cross-channel velocities, and nonlinear variations in the pressure along the channel. Both effects are absent in flows driven by uniform body forces. We obtain second-order accuracy for the two components of velocity and the pressure relative to asymptotic solutions of the compressible Navier–Stokes equations with slip boundary conditions. Since the common lattice Boltzmann formulations cannot capture Knudsen boundary layers, we replace the usual discrete analogs of the specular and diffuse reflection conditions from continuous kinetic theory with a moment-based implementation of the first-order Navier–Maxwell slip boundary conditions that relate the tangential velocity to the strain rate at the boundary. We use these conditions to solve for the unknown distribution functions that propagate into the domain across the boundary. We achieve second-order accuracy by reformulating these conditions for the second set of distribution functions that arise in the derivation of the lattice Boltzmann method by an integration along characteristics. Our moment formalism is also valuable for analysing the existing boundary conditions. It reveals the origin of numerical slip in the bounce-back and other common boundary conditions that impose conditions on the higher moments, not on the local tangential velocity itself.
Morphology and porosity of nanoporous Au thin films formed by dealloying of AuxSi1−x
Authors: Gupta G. , Thorp J. C. , Mara N. A. , Dattelbaum A. M. , Misra A. , Picraux S. T.
Published: November 2012

We have investigated the morphology, structure, and annealing response of nanoporous Au films synthesized via electrochemical dealloying of amorphous AuxSi1−x co-deposited films on Si substrates. The starting Au alloy film concentrations were varied from x = 0.09 to 0.41 and the resulting nanoscale porous films were characterized by electron microscopy and Rutherford backscattering techniques. Our observations provide a systematic description of the nanoporous Au film morphology, porosity, and degree of collapse as a function of starting AuxSi1−x alloy composition. The characteristic pore sizes increased from 10 to 45 nm and the porosity increased from 45% to 70% for the nanoporous Au films with decrease in the starting Au concentrations. The degree of film collapse due to dealloying also increased with decreasing Au concentration. The electrochemical dealloying process for nanoporous film formation was observed to change from a layer-by-layer dealloying process to a localized, percolation-dominated process as the Au concentration was decreased from 40 to 9 at. %. The thin film porous synthesis approach presented here enables the integration of “bottom up” dealloying self-assembly with “top down” microelectronics-based fabrication techniques, making it a useful new approach for Si-based microsystem applications.
Kinetics, mechanism, and pathway of reorientation of multi-variants in Ni-Mn-Ga shape memory alloys under continuous compressive stress: Phase-field simulation
Authors: Cui Y. G. , Wan J. F. , Zhang J. H. , Rong Y. H.
Published: November 2012

The kinetics and mechanism of reorientation of martensitic variants as well as the evolutional pathway under the continuous compressive stress along different directions in Ni-Mn-Ga alloys have been investigated by using phase-field method. The simulated results revealed that the final structures and the pathway of evolution were determined by the stress-applied direction: two variants, single variant and the complete parent corresponding to the [100], [110], and [111] directions, respectively. The related kinetics and the mechanism of the structural conversion and the phase transition will be proposed to explain the inner physical nature. The twinning or detwinning stress was calculated for different directions and also discussed from the effect of the interfacial dynamic factor and the shear modulus, which was close to the experimental measurements. The pseudo-elasticity related to the structural conversion as well as phase transition was also investigated. The reversibility of structural evolution between two variants and among three variants was observed and discussed.
Note: Mechanically and chemically stable colloidal probes from silica particles for atomic force microscopy
Authors: Kuznetsov V. , Papastavrou G.
Published: November 2012

In this note we present a novel approach to prepare colloidal probes for atomic force microscopy by sintering. A central element of this procedure is the introduction of an inorganic “fixation neck” between the cantilever and a micrometer-sized silica particle that is acting as probe. This procedure overcomes previous restrictions for the probe particles, which had to be low melting point materials, such as borosilicate glass or latex particles. The here-presented colloidal probes from silica can withstand large mechanical forces. Additionally, they have high chemical resistivity due to the absence of adhesives and the well-studied surface chemistry of colloidal silica.
Hybrid functional study rationalizes the simple cubic phase of calcium at high pressures
Authors: Liu Hanyu , Cui Wenwen , Ma Yanming
Published: November 2012

Simple cubic (SC) phase has been long experimentally determined as the high-pressure phase III of elemental calcium (Ca) since 1984. However, recent density functional calculations within semi-local approximation showed that this SC phase is structurally unstable by exhibiting severely imaginary phonons, and is energetically unstable with respect to a theoretical body-centered tetragonal I41/amd structure over the pressure range of phase III. These calculations generated extensive debates on the validity of SC phase. Here we have re-examined the SC structure by performing more precise density functional calculations within hybrid functionals of Heyd-Scuseria-Erhzerhof and PBE0. Our calculations were able to rationalize fundamentally the phase stability of SC structure over all other known phases by evidence of its actual energetic stability above 33 GPa and its intrinsically dynamical stability without showing any imaginary phonons in the entire pressure range studied. We further established that the long-thought theoretical I41/amd structure remains stable in a narrow pressure range before entering SC phase and is actually the structure of experimental Ca-III′ synthesized recently at low temperature 14 K as supported by the excellent agreement between our simulated x-ray diffraction patterns and the experimental data. Our results shed strong light on the crucial role played by the precise electron exchange energy in a proper description of the potential energy of Ca.
Separation of magnetic field lines
Authors: Boozer Allen H.
Published: November 2012

The field lines of magnetic fields that depend on three spatial coordinates are shown to have a fundamentally different behavior from those that depend on two coordinates. Unlike two-coordinate cases, a flux tube in a magnetic field that depends on all three spatial coordinates that has a circular cross section at one location along the tube characteristically has a highly distorted cross section at other locations. In an ideal evolution of a magnetic field, the current densities typically increase. Crudely stated, if the current densities increase by a factor σ, the ratio of the long to the short distance across a cross section of a flux tube characteristically increases by e2σ, and the ratio of the longer distance to the initial radius increases as eσ. Electron inertia prevents a plasma from isolating two magnetic field structures on a distance scale shorter than c/ωpe, which is about 10 cm in the solar corona, and reconnection must be triggered if σ becomes sufficiently large. The radius of the sun, R⊙=7×1010cm is about e23 times larger, so when σ≳23, two lines separated by c/ωpe at one location can be separated by the full scale of any magnetic structures in the corona at another. The conditions for achieving a large exponentiation, σ, are derived, and the importance of exponentiation is discussed.
Test particle simulation of direct laser acceleration in a density-modulated plasma waveguide
Authors: Lin M.-W. , Jovanovic I.
Published: November 2012

Direct laser acceleration (DLA) of electrons by the use of the intense axial electric field of an ultrafast radially polarized laser pulse is a promising technique for future compact accelerators. Density-modulated plasma waveguides can be implemented for guiding the propagation of the laser pulse to extend the acceleration distance and for the quasi-phase-matching between the accelerated electrons and the laser pulse. A test particle model is developed to study the optimal axial density modulation structure of plasma waveguides for laser pulses to efficiently accelerate co-propagating electrons. A simple analytical approach is also presented, which can be used to estimate the energy gain in DLA. The analytical model is validated by the test particle simulation. The effect of injection phase and acceleration of electrons injected at various radial positions are studied. The results indicate that a positively chirped density modulation of the waveguide structure is required to accelerate electron with low initial energies, and can be effectively optimized. A wider tolerance on the injection phase and radial distance from the waveguide axis exists for electrons injected with a higher initial energy.