bluuebunny/crossref_metadata_2025 huggingface dataset:
A breakthrough curve analysis of unstable density‐driven flow and transport in homogeneous porous media
Authors: Wood M. , Simmons C. T. , Hutson J. L.
Published: March 2004

In certain hydrogeological situations, density variations occur because of changes in solute concentration, temperature, and pressure of the fluid. These include seawater intrusion, high‐level radioactive waste disposal, groundwater contamination, and geothermal energy production. Under certain conditions, when the density of the invading fluid is greater than that of the ambient one, gravitational instabilities or fingers may lead to transport over larger spatial scales and significantly shorter timescales than compared with diffusion alone. This study has two key objectives: (1) to explore how the nature of a breakthrough curve changes as the density of the invading fluid changes and there is a subsequent transition from stable to unstable behavior and (2) to examine the feasibility of using 1‐D advection‐dispersion fitting models to fit the experimental data as the density of the invading fluid increases. Thirty‐six breakthrough curve experiments were carried out in fully saturated, homogeneous sand columns. Results show that an increase in the density of the source solutions leads to breakthrough curves with lower peak concentrations at breakthrough, earlier peak breakthrough pore volume and time, and an increase in positive skewness of the breakthrough curve. Visual experiments conducted in transparent columns confirm that a transition from stable to unstable behavior occurs as the density of the injectant increases and that backward convective reflux in the high‐density cases leads to dilution of the trailing edge of the pulse as evidenced by positively skewed breakthrough curves. These mixed convective systems (controlled by both forced and free convection) are characterized by a mixed convective ratio. Parameter estimation using a 1‐D advection‐dispersion fitting model suggests that unstable plume migration can be fitted with an apparent pore flow velocity and dispersivity at low‐density gradients. However, as the density of the injectant increases, it becomes progressively difficult to estimate parameters that fit the experimental curves with a model that does not explicitly account for density effects. Significantly poorer matches are obtained when the invading solution concentration is equal to, or exceeds, the solution concentration denoted by ML (the medium‐ to low‐density solution), i.e., invading solutions greater than approximately 13,000 mg/L in this study. Care must therefore be taken in applying standard advection‐dispersion models to breakthrough curve analyses where even modest density differences are encountered.
Pore‐scale processes that control dispersion of colloids in saturated porous media
Authors: Auset Maria , Keller Arturo A.
Published: March 2004

Colloidal dispersion in porous media is a consequence of the different paths and velocities experienced by the colloids. We examined at the pore scale the effect of particle and pore size on colloid dispersion using water‐saturated micromodels. The micromodels were produced with polydimethylsiloxane (PDMS), using a soft photolithography technique that allows creating transparent patterns that have dimensions in the range of those existing at the pore space. Four sizes of colloids were transported at several total pressure differences, and image analysis was used to determine particle trajectories, residence times, and dispersion coefficients through the micromodels. The magnitude of the dispersion at any given flow rate was found to be controlled by the pore‐space geometry and the relative size of colloids with regards to pore channels. Dispersion coefficient and dispersivity decrease with increasing colloid size. Dispersivity is thus not just a function of pore geometry but depends on colloid characteristics. Because of their size, larger colloids travel in the center streamlines, leading to faster velocities, less detours, and thus lower range of transit times. These findings emphasize the role of particle and pore size on colloidal dispersion and have significant implications for predicting the movement of colloids through saturated porous media.
Premier Forecasting Center Avoids Ax
Authors: Simpson Sarah
Published: March 2004

Last fall, the U.S. Senate proposed eliminating all 2004 funding for NOAA's Space Environment Center (SEC), but fortunately for the world's premier space weather forecasting center and its myriad customers, the Senate did not get its way. When the full Congress passed the final budget on 22 January, the Center's budget for the year was restored—at least partially.
Evaluation of the Rackwitz‐Fiessler Uncertainty Analysis Method for environmental fate and transport models
Authors: Schanz Robert W. , Salhotra Atul
Published: March 2004

The use of contaminant transport modeling has become an integral component of the regulatory and decision process for the disposal and cleanup of hazardous wastes. Because many of the input parameters to these models are uncertain, analysis of this uncertainty and its impact on the decision process has become increasingly important. Many contaminant transport models are computationally intensive and require run times that make traditional Monte Carlo analysis impractical. This paper therefore evaluates and tests an approximate technique, the Rackwitz‐Fiessler method, that can be used when computation time prohibits the use of Monte Carlo simulation. The accuracy and efficiency of the method is assessed and compared to Monté Carlo simulation for three contaminant transport models.
A method for delineating and estimating rainfall fields
Authors: Barancourt C. , Creutin J. D. , Rivoirard J.
Published: March 2004

A geostatistical model has been defined to deal with intermittent rainfall fields. The intermittency is represented by a binary random function, while, inside the rainy areas, the rainfall variability is rendered by an intrinsic random function. A rain gage data set from the Cevennes region (France) is used to infer the model. The inner variability is independent of the intermittency, thereby allowing a simple estimation relying on the separate kriging of these two components. Comparison of the rainfall assessments made by a classic global kriging and the proposed method shows its clear superiority for delineating and estimating rainfall fields.
Block hydraulic conductivity of cross‐bedded fluvial sediments
Authors: Bierkens Marc F. P. , Weerts Henk J. T.
Published: March 2004

This paper concerns the three‐dimensional block hydraulic conductivity of blocks of limited size in cross‐bedded sediments of meandering rivers. Based on a simplified sedimentological model of a single point bar, a stochastic model is proposed to simulate the spatial distribution of core scale conductivities within point bar deposits. The required parameters for these simulations are obtained from actual hydraulic conductivity measurements and sedimentological field data. The simulations are then used to calculate the three‐dimensional block conductivity tensor with a numerical upscaling procedure. The stochastic simulation model is used to investigate the influence of slope and aspect angle of the cross‐beds and the core scale anisotropy ratio on the block hydraulic conductivity. It is expected that the off‐diagonal elements of the block conductivity tensor generally cannot be neglected. The core scale anisotropy ratio, which reflects the small scale layering within the cross‐beds, can potentially have a significant impact on the elements of the block conductivity tensor.
Can One Gauge the Shape of a Basin?
Authors: Rinaldo Andrea , Vogel Gregor K. , Rigon Riccardo , Rodriguez‐Iturbe Ignacio
Published: March 2004

This paper investigates the effects of geometrical factors characterizing the shape of a river basin on the features of its hydrologic response. In particular, we wonder if by measuring the hydrologic response (i.e., gauging) the salient geomorphic features of the basin can be recovered. We argue that the basic structure of the channel network tends, in ideal conditions, to yield some universal characters of the width function W(x) defining the relative proportion of a contributing area at a distance x from the outlet.W(x) exhibits low‐frequency features, which are geometry‐dominated, and high‐frequency features determined by recurrent aggregation patterns. It is suggested that given the shape of the basin one can indeed forecast in a rational manner the main characters of the hydrologic response which are imprinted in reproducible width functions. However, the inverse problem (i.e., the determination of the shape from the measure of the hydrologic response) is less solidly defined because of the possible loss of irretrievable information induced by the dynamics of runoff processes. Therefore the question posed in the title cannot be solved in general, although many elements for a general theory are seemingly established.
The modeling of reactive solute transport with sorption to mobile and immobile sorbents: 1. Experimental evidence and model development
Authors: Knabner P. , Totsche K. U. , Kögel‐Knabner I.
Published: March 2004

Modeling carrier‐influenced transport needs to take into account the reactivity of the carrier itself. This paper presents a mathematical model of reactive solute transport with sorption to mobile and immobile sorbents. The mobile sorbent is also considered to be reactive. To justify the assumptions and generality of our modeling approach, experimental findings are reviewed and analyzed. A transformation of the model in terms of total concentrations of solute and mobile sorbents is presented which simplifies the mathematical formulations. Breakthrough data on dissolved organic carbon are presented to exemplify the need to take into account the reactivity of the mobile sorbent. Data on hexachlorobiphenyl and cadmium are presented to demonstrate carrier‐introduced increased mobility, whereas data on anthracene and pyrene are presented to demonstrate carrier‐introduced reduced mobility. The experimental conditions leading to the different findings are pointed out. The sorption processes considered in the model are both equilibrium and nonequilibrium processes, allowing for different sorption sites and nonlinear isotherms and rate functions. Effective isotherms, which describe the sorption to the immobile sorbent in the presence of a mobile sorbent and rate functions, are introduced and their properties are discussed.
Convection in groundwater below an evaporating Salt Lake: 1. Onset of instability
Authors: Wooding R. A. , Tyler Scott W. , White Ian
Published: March 2004

Convective groundwater motion can be generated in aquifers beneath and adjacent to saline lakes. Such motions strongly control the subsurface distribution of salts, the formation of saline minerals, and the distribution of contaminants that may be disposed of in the saline lake. In particular, schemes to use saline lakes as evaporation basins for irrigation waste waters must consider the groundwater dynamics associated with convection. The convection is driven by the evaporative concentration of salts at the land surface, leading to an unstable distribution of density. However, the evaporative groundwater discharge can dynamically stabilize this saline boundary layer and inhibit convection. In this work we investigate the nature and onset of convection for a range of boundary conditions typically found in saline lakes. Processes involved in the accumulation of salt at the surface of a groundwater discharge zone and in the gravitational instability of the near‐surface groundwater are considered. Results of theoretical stability analysis are applied through laboratory and numerical experimentation to the more complex geometries typically found in the field. These comparisons indicate that for large saline lakes, the stability of the saline boundary layer can be parameterized by traditional Rayleigh criteria, in which the aquifer permeability and the evaporation rate from the lake bed are principal controlling factors. For typical saline lake environments, convection will dominate in sediments whose permeability exceeds approximately 10−14 m2. Below this threshold permeability, the boundary layer should be stabilized by the evaporative flux, resulting in the accumulation of salts and evaporites at the land surface. These results provide insight into the predictive behavior of groundwater dynamics and solute distributions in many natural systems.
Average steady nonuniform flow in stratified formations
Authors: Indelman Peter , Zlotnik Vitaly
Published: March 2004

A mathematical model of average nonuniform flow in heterogeneous stratified media is developed. The averaged Darcy's law is obtained by deriving the analytical expression of the effective conductivity tensor for media with small heterogeneities. The fundamental solution of the average flow equation (mean Green function) corresponding to the flow toward a single point source of deterministic discharge is derived. The mean head distribution is calculated for a fully penetrating well, for a finite length well in an infinite domain, and for a dipole well. The concept of equivalent conductivity is defined for use in identifying the formation conductivity properties. The procedure for identifying the mean conductivity, log conductivity variance, and vertical integral scale is suggested for the case of dipole flow.
A Dose‐Finding Study of in utero and Lactational Exposure to Diethylstilboestrol and Flutamide in 129/Sv Mice
Authors: Kledal Thuri J. S. , Rajpert‐De Meyts Ewa , Skakkebæk Niels E. , Jørgensen Karin Damm
Published: March 2004

The purpose of the study was to test the experimental conditions and find the appropriate dose range for further investigations of the disruptive effects of oestrogens and antiandrogens on the development of testis. Groups of four 129/Sv mice were exposed from day 6 after mating until weaning to 1, 10 or 100 μg/kg/day of the non‐steroidal oestrogen diethylstilboestrol and to 0.1, 1 or 10 mg/kg/day of the non‐steroidal antiandrogen flutamide. The number of implantation sites, the litter size and reproductive parameters were examined and nipple development, anogenital distance and testicular morphology were investigated in the offspring. Dose‐related post‐implantation loss was seen in both diethylstilboestrol‐ and flutamide‐treated dams and the mean litter size was smaller in the groups given the high dosages of diethylstilboestrol and flutamide. Disturbance of testicular development was seen in males exposed to diethylstilboestrol. Because of the small data material, no statistical analyses were performed. Our findings indicate that very high doses of both diethylstilboestrol and flutamide given at early stages of gestation result in a high post‐implantation loss and should be avoided in further experiments using this strain which is known to have a poor reproductive performance. Exposure of the dams before mating may better reflect human exposure, but will presumably require even lower dose levels.
Beneficial Effects of Aluminum on the Progression of Lead‐Induced Nephropathy in Rats
Authors: Shakoor Abdul , Gupta Pawan Kumar , Singh Yash Pal , Kataria Meena
Published: March 2004

We studied the effect of aluminum on lead‐induced nephropathy in male albino rats. Five groups of male albino rats were given either water only or lead acetate (125 mg/kg body weight) and/or aluminum chloride (50 mg/kg body weight or 100 mg/kg body weight) for a period of 90 days. Aluminum was found to prevent the lead‐induced increase in the relative organ (kidney) weight in a dose‐dependent manner. Aluminum also prevented lead‐induced increase in plasma creatinine levels of the treated animals. Estimation of lead concentration in kidneys of different treatment groups revealed that the net deposition of lead was lower in animals which were given both lead acetate and aluminum chloride simultaneously. The results showed that aluminum offers some protection against lead‐induced nephrotoxicity in a time‐ and dose‐dependent manner.
Chronic Clorgyline Induces Selective Down‐Regulation of α2‐Adrenoceptor Agonist Binding Sites in Rat Brain
Authors: Miralles Antonio , Ribas Catalina , Escribá Pablo V. , García‐Sevilla Jesús A.
Published: March 2004

Inactivation of α2‐adrenoceptors by N‐ethoxycarbonyl‐2‐ethoxy‐1,2‐dihydroquinoline (EEDQ) has been shown to induce an increase in brain regulatory Gαi1/2 proteins, which was related to biphasic recovery of agonist binding sites. To investigate further the nature of this phenomenon, the chronic effects of clorgyline (a monoamine oxidase inhibitor antidepressant) on the recovery of α2‐adrenoceptors after EEDQ and on EEDQ‐induced up‐regulation of Gαi1/2 proteins were assessed in rat brain. Clorgyline (1 mg kg−1 for 7–35 days) induced a time‐dependent down‐regulation (20% to 55%) of the density of cortical α2‐adrenoceptor agonist sites ([3H]UK 14304/bromoxidine binding) but not of antagonist sites ([3H]RX 821002/2‐methoxy idazoxan binding). However, chronic clorgyline did not alter the immunoreactive levels of Gαi1/2, Gαi3, and Gαo proteins in cortex. In clorgyline‐treated rats, the turnover functions for agonist and antagonist binding sites (receptor recovery after EEDQ) were different and indicated that the reduced density of α2‐adrenoceptor agonist sites induced by clorgyline was due to a greater rate of receptor disappearance. The recovery of [3H]UK 14304 binding in clorgyline‐treated rats did not fit a biphasic recovery model and the turnover parameters were very similar to those obtained for the second phase of recovery (biphasic model) of agonist binding sites in naive rats. This suggested that clorgyline down‐regulated only the α2‐adrenoceptors of rapid turnover which is associated with the increases in the expression of Gαi1/2 proteins induced by EEDQ. In this context, clorgyline (1 mg kg−1 for 7 days) fully prevented the up‐regulation (50%) of brain Gαi1/2 proteins induced by EEDQ. The results indicate that one relevant mechanism involved in the in vivo desensitization of brain α2‐adrenoceptors is an effective impairment of receptor‐G protein coupling.
Distribution of Zinc‐Binding Metallothionein in Cirrhotic Liver of Rats Administered Zinc
Authors: Sato Shin , Shimizu Motohiro , Hosokawa Toshiyuki , Saito Takeshi , Okabe Masashi , Niioka Tadashi , Kurasaki Masaaki
Published: March 2004

This study was undertaken in order to investigate the effect of zinc (Zn) administration on induction of Zn‐binding metallothionein in rat liver with thioacetamide‐induced cirrhosis, and the localization of metallothionein in the liver. Normal and cirrhotic rats received intraperitoneal injections with or without Zn. Subsequently, metal analyses, purification of metallothionein by gel filtration and immunohistochemical assessments of metallothionein were carried out. Although in Zn‐injected cirrhotic rats, the Zn contents in the liver and plasma increased significantly depending upon the dose of Zn, the Zn contents in the liver and plasma of the cirrhotic rats were lower than those of normal rats after the same dose of Zn. The results of gel filtration also showed that the levels of Zn‐metallothionein in the cirrhotic liver were reduced in comparison with those of the normal liver. By the immunohistochemical method, the presence of metallothionein in the parenchymal areas but not in the fibrotic areas of the cirrhotic liver was confirmed. These results suggested that the induced metallothionein was only located in the parenchymal areas. The metallothionein induced in the parenchymal areas was considered to play a role in protecting the parenchymal cells against the progression of fibrosis, because metallothionein has been thought to be involved in the cellular defense against oxidative stress.
The human near‐term myometrial β3‐adrenoceptor but not the β2‐adrenoceptor is resistant to desensitisation after sustained agonist stimulation
Authors: Rouget C , Breuiller‐Fouché M , Mercier F J , Leroy M J , Loustalot C , Naline E , Frydman R , Croci T , Morcillo E J , Advenier C , Bardou M
Published: March 2004

In order to compare the β2‐ and β3‐adrenoceptor (β‐AR) desensitisation process in human near‐term myometrium, we examined the influence of a pretreatment of myometrial strips with either a β2‐ or a β3‐AR agonist (salbutamol or SR 59119A, respectively, both at 10 μM, for 5 and 15 h) on the relaxation and the cyclic adenosine monophosphate (cAMP) production induced by these agonists.

To assess some of the mechanisms potentially implicated in the β‐AR desensitisation process, we studied the influence of such treatment on the number of β2‐ and β3‐AR binding sites, the β2‐ and β3‐AR transcripts expression and the phosphodiesterase 4 (PDE4) activity.

Salbutamol, but not SR 59119A, concentration–response curve (CRC) was shifted by a 15 h salbutamol preincubation, with a significant difference in −log EC20 values (6.31±0.13 vs 5.58±0.24, for control and 15 h salbutamol pretreatment, respectively, P<0.05). Neither salbutamol nor SR 59119A CRCs were modified after a 15 h preincubation with SR 59119A.

A 15 h exposure of myometrial strips to salbutamol significantly reduced the salbutamol‐induced (0.60±0.26 vs 1.54±0.24 pmol mg−1 protein, P<0.05), but not the SR 59119A‐induced, cAMP production. No decrease in cAMP production was observed after a 15 h SR 59119A exposure.

A 15 h salbutamol exposure of myometrial strips significantly reduced the β2‐ but not the β3‐AR binding site density, whereas no decrease in the number of β2‐ and β3‐AR binding sites was observed after a 15 h SR 59119A treatment.

Neither PDE4 activity nor the β2‐ and β3‐AR mRNA expression levels were affected by salbutamol or SR 59119A treatments.

Our results indicate that β3‐AR, but not β2‐AR, are resistant to the agonist‐induced desensitisation. In our model, β2‐AR desensitisation is mediated by a decreased number of β2‐AR that was not explained by transcriptional regulation of the receptor.

British Journal of Pharmacology (2004) 141, 831–841. doi:10.1038/sj.bjp.0705616
The endocannabinoid system: a general view and latest additions
Authors: Petrocellis Luciano De , Cascio Maria Grazia , Marzo Vincenzo Di
Published: March 2004

After the discovery, in the early 1990s, of specific G‐protein‐coupled receptors for marijuana's psychoactive principle Δ9‐tetrahydrocannabinol, the cannabinoid receptors, and of their endogenous agonists, the endocannabinoids, a decade of investigations has greatly enlarged our understanding of this altogether new signalling system. Yet, while the finding of the endocannabinoids resulted in a new effort to reveal the mechanisms regulating their levels in the brain and peripheral organs under physiological and pathological conditions, more endogenous substances with a similar action, and more molecular targets for the previously discovered endogenous ligands, anandamide and 2‐arachidonoylglycerol, or for some of their metabolites, were being proposed. As the scenario becomes subsequently more complicated, and the experimental tasks to be accomplished correspondingly more numerous, we briefly review in this article the latest ‘additions’ to the endocannabinoid system together with earlier breakthroughs that have contributed to our present knowledge of the biochemistry and pharmacology of the endocannabinoids.

British Journal of Pharmacology (2004) 141, 765–774. doi:10.1038/sj.bjp.0705666
The role of bradykinin, AT2 and angiotensin 1–7 receptors in the EDRF‐dependent vasodilator effect of angiotensin II on the isolated mesenteric vascular bed of the rat
Authors: De Moura R Soares , Resende A C , Emiliano A F , Tano T , Mendes‐Ribeiro A C , Correia M L G , De Carvalho L C R Marins
Published: March 2004

The mechanisms involved in the vasodilator actions of angiotensin II (Ang II) have not yet been completely elucidated. We investigated the potential mechanisms that seem to be involved in the Ang II vasodilator effect using rat isolated mesenteric vascular bed (MVB).

Under basal conditions, Ang II does not affect the perfusion pressure of MVB. However, in vessels precontracted with norepinephrine, Ang II induces vasodilation followed by vasoconstriction. Vasoconstrictor, but not the vasodilation of Ang II, is inhibited by AT1 antagonist (losartan). The vasodilator effect of Ang II was not inhibited by AT2, angiotensin IV and angiotensin 1–7 receptor antagonists alone (PD 123319, divalinal, A 779, respectively).

The vasodilator effect of Ang II is significantly reduced by endothelial removal (deoxycholic acid), but not by indomethacin. Inhibition of NO‐synthase by NG‐nitro‐L‐arginine methyl ester (L‐NAME) and guanylyl cyclase by 1H‐[1,2,3] oxadiazolo [4,4‐a] quinoxalin‐1‐one (ODQ) reduces the vasodilator effect of Ang II. This effect is also reduced by tetraethylammonium (TEA) or L‐NAME, and a combination of L‐NAME plus TEA increases the inhibitory effect of the antagonists alone. However, indomethacin does not change the residual vasodilator effect observed in vessels pretreated with L‐NAME plus TEA.

In vessels precontracted with norepinephrine and depolarized with KCl 25 mM or treated with Ca2+‐dependent K+ channel blockers (charybdotoxin plus apamin), the effect of Ang II was significantly reduced. However, this effect is not affected by ATP and voltage‐dependent K+ channel blockers (glybenclamide and 4‐aminopyridine).

Inhibition of kininase II with captopril significantly potentiates the vasodilator effect of bradykinin (BK) and Ang II in the rat MVB. The inhibitory effect of the B2 receptor antagonist HOE 140 on the vasodilator effect of Ang II is further enhanced by PD 123319 and/or A 779.

The present findings suggest that BK plays an important role in the endothelium‐dependent vasodilator effect of Ang II. Probably, the link between Ang II and BK release is modulated by receptors that bind PD 123319 and A 779.

British Journal of Pharmacology (2004) 141, 860–866. doi:10.1038/sj.bjp.0705669
Robustness issues in multilevel regression analysis
Authors: Maas Cora J. M. , Hox Joop J.
Published: March 2004

A multilevel problem concerns a population with a hierarchical structure. A sample from such a population can be described as a multistage sample. First, a sample of higher level units is drawn (e.g. schools or organizations), and next a sample of the sub‐units from the available units (e.g. pupils in schools or employees in organizations). In such samples, the individual observations are in general not completely independent. Multilevel analysis software accounts for this dependence and in recent years these programs have been widely accepted. Two problems that occur in the practice of multilevel modeling will be discussed. The first problem is the choice of the sample sizes at the different levels. What are sufficient sample sizes for accurate estimation? The second problem is the normality assumption of the level‐2 error distribution. When one wants to conduct tests of significance, the errors need to be normally distributed. What happens when this is not the case? In this paper, simulation studies are used to answer both questions. With respect to the first question, the results show that a small sample size at level two (meaning a sample of 50 or less) leads to biased estimates of the second‐level standard errors. The answer to the second question is that only the standard errors for the random effects at the second level are highly inaccurate if the distributional assumptions concerning the level‐2 errors are not fulfilled. Robust standard errors turn out to be more reliable than the asymptotic standard errors based on maximum likelihood.
Modelling response error in school effectiveness research
Authors: Fox Jean‐Paul
Published: March 2004

Statistical modelling of school effectiveness in educational research is considered. Variance component models are generally accepted for the analysis of such studies. A shortcoming is that outcome variables are still treated as measured without an error. Unreliable variables produce biases in the estimates of the other model parameters. The variability of the relationships across schools and the effects of schools on students’ outcomes differ substantially when taking the measurement error in the dependent variables of the variance component models into account. The random effects model can be extended to handle measurement error using a response model, leading to a random effects item response theory model. This extended random effects model is in particular suitable when subjects are measured repeatedly on the same outcome at several points in time.
Performance of empirical Bayes estimators of random coefficients in multilevel analysis: Some results for the random intercept‐only model
Authors: Candel Math J. J. M.
Published: March 2004

For a multilevel model with two levels and only a random intercept, the quality of different estimators of the random intercept is examined. Analytical results are given for the marginal model interpretation where negative estimates of the variance components are allowed for. Except for four or five level‐2 units, the Empirical Bayes Estimator (EBE) has a lower average Bayes risk than the Ordinary Least Squares Estimator (OLSE). The EBEs based on restricted maximum likelihood (REML) estimators of the variance components have a lower Bayes risk than the EBEs based on maximum likelihood (ML) estimators. For the hierarchical model interpretation, where estimates of the variance components are restricted being positive, Monte Carlo simulations were done. In this case the EBE has a lower average Bayes risk than the OLSE, also for four or five level‐2 units. For large numbers of level‐1 (30) or level‐2 units (100), the performances of REML‐based and ML‐based EBEs are comparable. For small numbers of level‐1 (10) and level‐2 units (25), the REML‐based EBEs have a lower Bayes risk than ML‐based EBEs only for high intraclass correlations (0.5).
p2: a random effects model with covariates for directed graphs
Authors: van Duijn Marijtje A. J. , Snijders Tom A. B. , Zijlstra Bonne J. H.
Published: March 2004

A random effects model is proposed for the analysis of binary dyadic data that represent a social network or directed graph, using nodal and/or dyadic attributes as covariates. The network structure is reflected by modeling the dependence between the relations to and from the same actor or node. Parameter estimates are proposed that are based on an iterated generalized least‐squares procedure. An application is presented to a data set on friendship relations between American lawyers.
Multireference spin-adapted variant of density functional theory
Authors: Khait Yuriy G. , Hoffmann Mark R.
Published: March 2004

A new Kohn–Sham formalism is developed for studying the lowest molecular electronic states of given space and spin symmetry whose densities are represented by weighted sums of several reference configurations. Unlike standard spin-density functional theory, the new formalism uses total spin conserving spin-density operators and spin-invariant density matrices so that the method is fully spin-adapted and solves the so-called spin-symmetry dilemma. The formalism permits the use of an arbitrary set of reference (noninteracting) configurations with any number of open shells. It is shown that the requirement of degeneracy of the total noninteracting energies of the reference configurations (or configuration state functions) is equivalent to the stationary condition of the exact energy relative to the weights of the configurations (or configuration state functions). Consequently, at any molecular geometry, the weights can be determined by minimization of the energy, and, for given reference weights, the Kohn–Sham orbitals can be determined. From this viewpoint, the developed theory can be interpreted as an analog of the multiconfiguration self-consistent field approach within density functional theory.
An ab initio study of the competing reaction channels in the reaction of HOCO radicals with NO and O2
Authors: Poggi Gabriella , Francisco Joseph S.
Published: March 2004

The reaction between HOCO and NO, and that between HOCO and O2, have been examined using the quadratic configuration interaction method to locate and optimize the critical points on the potential energy surfaces. Analysis of the critical points provides new insight into new intermediates and pathways by which these reactions occur and help explain recent experimental results. In the HOCO+O2 reaction, the symmetry-allowed products, CO2+HO2, can be obtained both via direct hydrogen abstraction by O2 on the HCO radicals, as well as through an adduct, HOC(O)O2, which can proceed to give the same products. The less-than-unity yield of CO2 observed in the experimental studies of the HOCO+NO reaction, as well as the lack of CO, can be explained by the formation of a stable HOC(O)NO adduct.
Block-correlated coupled cluster theory: The general formulation and its application to the antiferromagnetic Heisenberg model
Authors: Li Shuhua
Published: March 2004

The general formalism of the block-correlated coupled cluster (BCCC) method, an alternative multireference coupled cluster method for calculating the ground-state electronic structures of molecular systems, has been presented. The BCCC theory is constructed in terms of a complete set of many-electron states of individual blocks, assumed that the whole system could be partitioned into a set of blocks. The reference state in the BCCC is selected as a tensor product of the most important many-electron state of each system block. By truncating the cluster operator to a certain n-block correlation level, an approximate but size-extensive BCCC method, denoted as BCCCn, is defined. For reducing the computational effort but without much loss of accuracy, the reduced density matrix is introduced to generate an optimal subset of many-electron states for each block. I have implemented the BCCCn (n=2,3) methods within the S=1/2 Heisenberg Hamiltonian, and applied them to calculate the ground-state energies of one-dimensional spin chains and quasi-one-dimensional two-leg spin ladders. The calculated results show that with the appropriate partition of the studied systems the BCCC3 method can yield quite satisfactory ground-state energies for these spin systems.
Isometric graphing and multidimensional scaling for reaction-diffusion modeling on regular and fractal surfaces with spatiotemporal pattern recognition
Authors: Kuriakose Jainy , Ghosh Anandamohan , Ravi Kumar V. , Kulkarni B. D.
Published: March 2004

Heterogeneous surface reactions exhibiting complex spatiotemporal dynamics and patterns can be studied as processes involving reaction-diffusion mechanisms. In many realistic situations, the surface has fractal characteristics. This situation is studied by isometric graphing and multidimensional scaling (IGMDS) of fractal surfaces for extracting geodesic distances (i.e., shortest scaled distances that obtain edges of neighboring surface nodes and their interconnections) and the results obtained used to model effects of surface diffusion with nonlinear reactions. Further analysis of evolved spatiotemporal patterns may be carried out by IGMDS because high-dimensional snapshot data can be efficiently projected to a transformed subspace with reduced dimensions. Validation of the IGMDS methodology is carried out by comparing results with reduction capabilities of conventional principal component analysis for simple situations of reaction and diffusion on surfaces. The usefulness of the IGMDS methodology is shown for analysis of complex patterns formed on both regular and fractal surfaces, and using generic nonlinear reaction-diffusion systems following FitzHugh Nagumo and cubic reaction kinetics. The studies of these systems with nonlinear kinetics and noise show that effects of surface disorder due to fractality can become very relevant. The relevance is shown by studying properties of dynamical invariants in IGMDS component space, viz., the Lyapunov exponents and the KS entropy for interesting situations of spiral formation and turbulent patterns.
Poisson–Boltzmann theory of the charge-induced adsorption of semi-flexible polyelectrolytes
Authors: Ubbink Job , Khokhlov Alexei R.
Published: March 2004

A model is suggested for the structure of an adsorbed layer of a highly charged semi-flexible polyelectrolyte on a weakly charged surface of opposite charge sign. The adsorbed phase is thin, owing to the effective reversal of the charge sign of the surface upon adsorption, and ordered, owing to the high surface density of polyelectrolyte strands caused by the generally strong binding between polyelectrolyte and surface. The Poisson–Boltzmann equation for the electrostatic interaction between the array of adsorbed polyelectrolytes and the charged surface is solved for a cylindrical geometry, both numerically, using a finite element method, and analytically within the weak curvature limit under the assumption of excess monovalent salt. For small separations, repulsive surface polarization and counterion osmotic pressure effects dominate over the electrostatic attraction and the resulting electrostatic interaction curve shows a minimum at nonzero separations on the Ångstrom scale. The equilibrium density of the adsorbed phase is obtained by minimizing the total free energy under the condition of equality of chemical potential and osmotic pressure of the polyelectrolyte in solution and in the adsorbed phase. For a wide range of ionic conditions and charge densities of the charged surface, the interstrand separation as predicted by the Poisson–Boltzmann model and the analytical theory closely agree. For low to moderate charge densities of the adsorbing surface, the interstrand spacing decreases as a function of the charge density of the charged surface. Above about 0.1 M excess monovalent salt, it is only weakly dependent on the ionic strength. At high charge densities of the adsorbing surface, the interstrand spacing increases with increasing ionic strength, in line with the experiments by Fang and Yang [J. Phys. Chem. B 101, 441 (1997)].
Effects of carbon on the stability and chemical performance of transition metal carbides: A density functional study
Authors: Liu Ping , Rodriguez José A.
Published: March 2004

Density functional theory was employed to study the stabilities and chemical activities of transition metal carbides. Here we take the well-known Mo carbides and Ti carbides as an example. Different kinds of structures including the bulk surfaces [Mo2C(001), MoC(001), and TiC(001)] and metcars [Mo8C12 and Ti8C12] are taken into consideration. Systematic studies show that by raising the C coordination number of the metal atoms in the carbides, in general the stability of the carbides increases (metcars are an exception since they include both high-coordinated and low-coordinated metal atoms.); at the same time, the chemical activities of the carbides decrease due to a downshift of the metal d-band center (ligand effect). Considering the better catalysts those that combine high stability and moderate chemical activity, our results suggest that the catalytic potential of Mo carbide systems should decrease in the following sequence: Mo8C12>Mo2C(001) or MoC(001)>pure Mo(110). In spite of having the largest C/Mo ratio, the metcar appears as the most attractive system. Our studies also indicate that the “magic” behavior of metcars is not unique for Mo carbides. Similar behavior is also observed for Ti carbides. This implies that nanoparticles like metcar species could exhibit better performances than the corresponding bulk metal carbides as catalysts.
Photophysics of protoporphyrin ions in vacuo: Triplet-state lifetimes and quantum yields
Authors: Calvo M. Reyes , Andersen Jens Ulrik , Hvelplund Preben , Nielsen Steen Brøndsted , Pedersen Ulrik V. , Rangama Jimmy , Tomita Shigeo , Forster James S.
Published: March 2004

Lifetimes of triplet-state molecules and triplet quantum yields are important parameters in photobiology as they determine the generation of singlet-oxygen upon irradiation with visible light. Here we report lifetimes of protoporphyrin IX (pp) in vacuo measured in an ion storage ring. We find that after 532 nm photon absorption, pp− (free base and negatively charged carboxylate) and pp+ (single protonation of ring nitrogen) have triplet-state lifetimes of 12 and 6 ms, respectively. After 415 or 390 nm absorption the lifetime of the anion is shorter (1.5 and 0.6 ms) as expected from the increase in temperature. Triplet quantum yields of pp− and pp+ are similar, 0.6–0.7, close to values reported for the free base and monocation in solution. The other channel, direct decay to the electronic ground state and subsequent dissociation of vibrationally excited ions, is much faster than triplet–singlet intersystem crossing. We measured lifetimes of 63 μs, 96 μs, and 0.3 ms after 390, 415, and 532 nm excitation, respectively. A fit of a statistical model to the pp− decay results in an Arrhenius activation energy of 0.5±0.2 eV for CO2 loss and a low preexponential factor (106–1010 s−1), indicative of an entropic barrier.
Mass analyzed threshold ionization spectroscopy of 5-methylindole and 3-methylindole cations and the methyl substitution effect
Authors: Lin Jung Lee , Zhang Song , Tzeng Wen Bih
Published: March 2004

The vibrationally resolved mass analyzed threshold ionization spectra of jetcooled 5-methylindole (5MI) and 3-methylindole (3MI) have been recorded by ionizing via various vibronic levels of each species. The adiabatic ionization energies (IEs) of 5MI and 3MI are determined to be 61 696±5 and 60 679±5 cm−1, which are less than that of indole by 895 and 1912 cm−1, respectively. Comparing these data with those of 1-methylindole and indole suggests that the methyl substitution on the pyrrole part leads to a greater redshift in the IE than on the benzene part. These experimental findings are well supported by the theoretical calculations. Analysis on these new data shows that many active vibrations of the 5MI cation are related to the CH3 torsion and in-plane ring bending vibrations. In contrast, the observed vibrational bands of the 3MI cation are very weak due to unfavorable Franck–Condon transition.
A study of the reactions of molecular hydrogen with small gold clusters
Authors: Varganov Sergey A. , Olson Ryan M. , Gordon Mark S. , Mills Greg , Metiu Horia
Published: March 2004

This work presents a study of reactions between neutral and negatively charged Aun clusters (n=2,3) and molecular hydrogen. The binding energies of the first and second hydrogen molecule to the gold clusters were determined using density functional theory (DFT), second order perturbation theory (MP2) and coupled cluster (CCSD(T)) methods. It is found that molecular hydrogen easily binds to neutral Au2 and Au3 clusters with binding energies of 0.55 eV and 0.71 eV, respectively. The barriers to H2 dissociation on these clusters with respect to AunH2 complexes are 1.10 eV and 0.59 eV for n=2 and 3. Although negatively charged Aun− clusters do not bind molecular hydrogen, H2 dissociation can occur with energy barriers of 0.93 eV for Au2− and 1.39 eV for Au3−. The energies of the Au2H2− and Au3H2− complexes with dissociated hydrogen molecules are lower than the energies of Au2−+H2 and Au3−+H2 by 0.49 eV and 0.96 eV, respectively. There is satisfactory agreement between the DFT and CCSD(T) results for binding energies, but the agreement is not as good for barrier heights.
Modeling molecular transport in slit pores
Authors: Jepps Owen G. , Bhatia Suresh K. , Searles Debra J.
Published: March 2004

We examine the transport of methane in microporous carbon by performing equilibrium and nonequilibrium molecular dynamics simulations over a range of pore sizes, densities, and temperatures. We interpret these simulation results using two models of the transport process. At low densities, we consider a molecular flow model, in which intermolecular interactions are neglected, and find excellent agreement between transport diffusion coefficients determined from simulation, and those predicted by the model. Simulation results indicate that the model can be applied up to fluid densities of the order to 0.1–1 nm−3. Above these densities, we consider a slip flow model, combining hydrodynamic theory with a slip condition at the solid–fluid interface. As the diffusion coefficient at low densities can be accurately determined by the molecular flow model, we also consider a model where the slip condition is supplied by the molecular flow model. We find that both density-dependent models provide a useful means of estimating the transport coefficient that compares well with simulation.
Orientational orders of small anisotropic molecules confined in slit pores
Authors: Zhou Xin , Chen Hu , Iwamoto Mitsumasa
Published: March 2004

Based on a constant-pressure Monte Carlo molecular simulation, we have studied orientationally ordered transitions of small anisotropic molecules confined in two parallel hard walls. These molecules are modeled by the hard Gaussian overlap model. The molecular elongations of the chosen molecules are so small that the molecules cannot form stable liquid-crystal (LC) phases in the bulk. But in the slit pores, we found, while the distance between two walls of the pores decreases to the molecular scale, an orientationally ordered phase can form. It shows that even hard confining surfaces favor the alignment of the small anisotropic molecules. Thus we conclude that the required molecular elongation for forming LC phases will decrease in confinement. Our results indicate that some non-LC small molecules may form stable LC phases due to the inducement of confining surfaces.
High-dimensional quantum dynamical study of the dissociation of H2 on Pd(110)
Authors: Dianat Arezoo , Groß Axel
Published: March 2004

We report the first six-dimensional quantum dynamical study of the dissociative adsorption of H2 on a (110) surface. We have performed quantum coupled-channel calculations for the system H2/Pd(110) based on a potential energy surface (PES) that was derived from ab initio electronic structure calculations. In particular, we have focused on the effects of the corrugation and anisotropy of the PES on the H2 dissociation probability. Our results agree well with the available experimental data for the sticking probability as a function of the initial kinetic energy and the angle of incidence. Because of the coupling between the anisotropy and corrugation of the potential energy surface our calculations predict an unusual rotational heating and a rather small rotational alignment in desorption.
Spreading of block copolymer films and domain alignment at moving terrace steps
Authors: Belyi Vladimir A. , Witten Thomas A.
Published: March 2004

We investigate spreading of phase separated copolymer films, where domain walls and thickness steps influence polymer flow. We show that at early stages of spreading its rate is determined by slow activated flow at terrace steps (i.e., thickness steps). At late stages of spreading, on the other hand, the rate is determined by the flow along terraces, with diffusionlike time dependence t−1/2. This dependence is similar to de Gennes and Cazabat’s prediction for generic layered liquids [P. G. de Gennes and A. M. Cazabat, C.R. Acad. Sci. Paris II 310, 1601 (1990)], as opposed to the classical Tanner’s law of drop spreading. We also argue that chain hopping at the spreading terrace steps should lead to the formation of aligned, defect-free domain patterns on the growing terraces.
Structure and dynamics of orientational defects in ice I
Authors: Grishina N. , Buch V.
Published: March 2004

Orientational defects in hexagonal ice were investigated using molecular dynamics simulations. Energy relaxation during L- and D-defect migration was shown to be associated with improved alignment of water molecules along the local electric fields. Two new forms of defects, an “L+D complex,” and a “5+7 defect,” were characterized. These forms appear in ice trajectories close to the melting point, and in the course of L- and D-pair recombination process. Defect pair recombination was shown to be a complex process, involving collective H-bond changes in groups of molecules.