bluuebunny/crossref_metadata_2025 huggingface dataset:
Mouse models for BRAF-induced cancers
Authors: Pritchard C. , Carragher L. , Aldridge V. , Giblett S. , Jin H. , Foster C. , Andreadi C. , Kamata T.
Published: November 2007

Oncogenic mutations in the BRAF gene are detected in ∼7% of human cancer samples with a particularly high frequency of mutation in malignant melanomas. Over 40 different missense BRAF mutations have been found, but the vast majority (>90%) represent a single nucleotide change resulting in a valine→glutamate mutation at residue 600 (V600EBRAF). In cells cultured in vitro, V600EBRAF is able to stimulate endogenous MEK [MAPK (mitogen-activated protein kinase)/ERK (extracellular-signal-regulated kinase) kinase] and ERK phosphorylation leading to an increase in cell proliferation, cell survival, transformation, tumorigenicity, invasion and vascular development. Many of these hallmarks of cancer can be reversed by treatment of cells with siRNA (small interfering RNA) to BRAF or by inhibiting MEK, indicating that BRAF and MEK are attractive therapeutic targets in cancer samples with BRAF mutations. In order to fully understand the role of oncogenic BRAF in cancer development in vivo as well as to test the in vivo efficacy of anti-BRAF or anti-MEK therapies, GEMMs (genetically engineered mouse models) have been generated in which expression of oncogenic BRaf is conditionally dependent on the Cre recombinase. The delivery/activation of the Cre recombinase can be regulated in both a temporal and spatial manner and therefore these mouse models can be used to recapitulate the somatic mutation of BRAF that occurs in different tissues in the development of human cancer. The data so far obtained following Cre-mediated activation in haemopoietic tissue and the lung indicate that V600EBRAF mutation can drive tumour initiation and that its primary effect is to induce high levels of cyclin D1-mediated cell proliferation. However, hallmarks of OIS (oncogene-induced senescence) are evident that restrain further development of the tumour.
Conservation of DNA damage tolerance pathways from yeast to humans
Authors: Ulrich H.D.
Published: November 2007

Damage tolerance mechanisms, which allow the bypass of DNA lesions during replication, are controlled in eukaryotic cells by mono- and poly-ubiquitination of the DNA polymerase cofactor PCNA (proliferating-cell nuclear antigen). In the present review, I will summarize our current knowledge of the enzymatic machinery for ubiquitination of PCNA and the way in which the modifications affect PCNA function during replication and lesion bypass in different organisms. Using the budding yeast as a reference model, I will highlight some of the species-specific differences, but also point out the common principles that emerge from the genetic and biochemical studies of damage tolerance in a range of experimental systems.
Role played by BRCA1 in transcriptional regulation in response to therapy
Authors: Murray M.M. , Mullan P.B. , Harkin D.P.
Published: November 2007

BRCA1 (breast-cancer susceptibility gene 1) is a tumour suppressor, implicated in the hereditary predisposition to breast and ovarian cancer. BRCA1 has been implicated in a number of cellular processes including DNA repair and recombination, cell cycle checkpoint control, chromatin remodelling and ubiquitination. In addition, substantial data now exist to suggest a role for BRCA1 in transcriptional regulation; BRCA1 has been shown to interact with the Pol II holoenzyme complex and to interact with multiple transcription factors, such as p53 and c-Myc. We have previously identified a range of BRCA1 transcriptional targets and have linked these to specific cellular pathways, including cell cycle checkpoint activation and apoptosis. Current research is focused on the transcriptional mechanisms that underpin the association of BRCA1 deficiency with increased sensitivity to DNA damage-based chemotherapy and resistance to spindle poisons.
Novel agents for cancer prevention based on nitric oxide
Authors: Rigas B.
Published: November 2007

NO (nitric oxide) biology has provided the impetus for the development of anticancer agents based on their ability to release NO. NO-NSAIDs (NO-donating non-steroidal anti-inflammatory drugs), consisting of a conventional NSAID to which an NO-releasing moiety is covalently attached, are promising chemopreventive agents against cancer. Compared with their parent compounds, NO-NSAIDs are up to several hundred times more potent in inhibiting the growth of cancer cell lines and prevent colon and pancreatic cancer in animal models. Their chemopreventive effect is due to inhibition of proliferation, induction of cell death and inhibition of cell-cycle-phase transitions. NO-ASA (NO-aspirin), the best-studied NO-NSAID, induces oxidative stress in target cells. Major downstream signalling effects involve the Wnt, NOS2 (nitric oxide synthase 2), MAPK (mitogen-activated protein kinase), NF-κB (nuclear factor κB) and Nrf2 (nuclear factor-erythroid 2 p45 subunit-related factor 2) pathways. NO-NSAIDs, particularly NO-ASA, appear to be safe compounds, as suggested by many animal and early human studies. An ongoing clinical trial is designed to determine whether NO-ASA can inhibit early stages of colon carcinogenesis in subjects at risk for colon cancer. It is clinical trials that will ultimately determine the role of NO-NSAIDs in cancer prevention and perhaps treatment.
Inhibitory effect of lycopene on PDGF-BB-induced signalling and migration in human dermal fibroblasts: a possible target for cancer
Authors: Wu W.-B. , Chiang H.-S. , Fang J.-Y. , Hung C.-F.
Published: November 2007

Tumours are complex tissues composed of both matrix proteins and stromal cells such as fibroblasts and inflammatory cells. Tumour progression is often the result of dynamic interactions between the tumour cells and their surroundings. Lycopene, a natural carotenoid that is abundant in tomato, has been shown to inhibit proliferation of several types of cancer cells through arrest of tumour cell-cycle progression, IGF-1 (insulin-like growth factor 1) signalling transduction, induction of apoptosis etc. However, in our recent study, we found that lycopene inhibited PDGF-BB (platelet-derived growth factor-BB)-induced signalling and cell migration in human cultured skin fibroblasts through a novel mechanism of action, i.e. direct binding to PDGF-BB. Trapping of PDGF by lycopene also compromised melanoma-induced fibroblast migration and attenuated signalling transduction in fibroblasts simulated by melanoma-derived conditioned medium, suggesting that lycopene may interfere with tumour–stroma interactions. The trapping activity of lycopene on PDGF suggests that it may act as an inhibitor on stromal cells, tumour cells and their interactions, which may contribute to its anti-tumour activity.
Native and oxidized low-density lipoproteins modulate the vasoactive actions of soluble β-amyloid peptides in rat aorta
Authors: Smith Christopher C. T. , Stanyer Lee , Betteridge D. John , Cooper Michael B.
Published: November 2007

Cerebrovascular accumulation of Aβ (β-amyloid) occurs in aging and AD (Alzheimer's disease). Hypercholesterolaemia, which is associated with raised plasma LDL (low-density lipoprotein), may predispose to AD. Soluble Aβ is found in the circulation and enhances vasoconstriction. Under conditions that may favour the formation of short Aβ oligomers, as opposed to more severe polymerization leading to Aβ fibrillogenesis, we investigated the influence of LDLs on the vasoactive actions of soluble Aβ. Thus the actions of Aβ40 and Aβ42 in combination with native or oxidized LDL on vasoconstriction to NA (noradrenaline) and vasodilatation to ACh (acetylcholine) were examined in rat aortic rings. LDL, particularly when oxidized, potentiated NA-induced constriction when combined with soluble Aβ40 and, especially, Aβ42. Soluble Aβ40 reduced relaxation induced by ACh, but Aβ42 was ineffective. Native and oxidized LDL also attenuated relaxation. Synergism occurred between oxidized LDL and Aβ with respect to ACh-induced relaxation, but not between native LDL and Aβ. We have shown for the first time that, under conditions that may result in Aβ oligomer formation, LDL, particularly when oxidized, modulates the vascular actions of soluble Aβ to extents greater than those reported previously for fibrillar Aβ preparations. Mechanisms whereby a treatable condition, namely hypercholesterolaemia, might contribute to the development of the cerebrovascular component of AD are indicated.
The PCSK9 gene R46L variant is associated with lower plasma lipid levels and cardiovascular risk in healthy U.K. men
Authors: Scartezini Marileia , Hubbart Christina , Whittall Ros A. , Cooper Jackie A. , Neil Andrew H. W. , Humphries Steve E.
Published: November 2007

In the present study, we have determined the relative frequency of the R46L, I474V and E670G variants in the PCSK9 (protein convertase subtilisin/kexin type 9) gene and its association with plasma lipid levels and CHD (coronary heart disease) in healthy U.K. men and patients with clinically defined definite FH (familial hypercholesterolaemia). Genotypes were determined using PCR and restriction enzyme digestion in 2444 healthy middle-aged (50–61 years) men from the prospective NPHSII (Second Northwick Park Heart Study), with 275 CHD events (15 years of follow-up), and in 597 U.K. FH patients from the Simon Broome Register. In the NPHSII healthy men, the R46L genotype distribution was in Hardy–Weinberg equilibrium and the frequency of 46L was 0.010 [95% CI (confidence interval), 0.007–0.013], with one man homozygous for the 46L allele. There was significant association of the 46L allele with lower mean (S.D.) total cholesterol [5.74 (1.01) mmol/l for RR compared with 5.26±1.03 mmol/l for RL; P=0.001], apolipoprotein B [0.87 (0.24) g/l for RR compared with 0.75 (0.26) g/l for RL; P<0.0001] and low-density lipoprotein cholesterol [4.01 (0.95) mmol/l for RR compared with 3.62 (0.97) mmol/l for RL; P=0.02]) levels, after adjustment for age, general medical practice, smoking, body mass index and systolic blood pressure. As expected, 46L carriers had a low risk of definite or possible CHD [hazard ratio, 0.46 (95% CI, 0.11–1.84)], but this was not statistically significant (P=0.27). Two other common PCSK9 variants I474V [V allele frequency, 0.179 (95% CI, 0.17–0.19)] and E670G [G allele frequency, 0.034 (CI, 0.03–0.04)] were not associated with any significant effects on lipid levels or CHD risk. In FH patients, the frequency of 46L was 0.003 (95% CI, 0.00–0.01), which was significantly lower (P=0.037) than the healthy subjects. In the four FH patients carrying 46L, mean untreated total cholesterol levels were not different (P=0.91) in carriers and non-carriers (median, 10.3 mmol/l compared with 10.2 mmol/l respectively, after adjustment for age, gender and mutation type). In conclusion, the PCSK9 46L allele is more frequent in healthy U.K. men than in FH patients and is strongly associated with a protective plasma lipid profile risk for CHD. Its low frequency (approx. 2% carriers) means that it does not make a major contribution to determining population CHD risk in the U.K.
Quasi-Hermitian quantum mechanics in phase space
Authors: Curtright Thomas , Veitia Andrzej
Published: November 2007

We investigate quasi-Hermitian quantum mechanics in phase space using standard deformation quantization methods: Groenewold star products and Wigner transforms. We focus on imaginary Liouville theory as a representative example where exact results are easily obtained. We emphasize spatially periodic solutions, compute various distribution functions and phase-space metrics, and explore the relationships between them.
Low-lying quartet electronic states of nitrogen dioxide
Authors: Bera Partha P. , Yamaguchi Yukio , Schaefer Henry F.
Published: November 2007

The environmentally active molecule nitrogen dioxide (NO2) has been systematically studied using high level theoretical methods. The electronic ground state and the low-lying quartet states of NO2 have been investigated. Single reference restricted open-shell self-consistent field (SCF), complete active space SCF (CASSCF), spin-restricted (R) and spin-unrestricted (U) configuration interaction with single and double excitations (CISD), coupled cluster with single and double excitations (CCSD), CCSD with perturbative triple excitations [CCSD(T)], and internally contracted multireference configuration interaction (ICMRCI) methods along with Dunning’s correlation consistent polarized valence cc-pVXZ and augmented cc-pVXZ (where X=T,Q,5) basis sets were used in this research. At the aug-cc-pV5Z/UCCSD(T) level the classical adiabatic excitation energies (Te values) of the three lowest-lying quartet excited states were predicted to be 83.3kcal∕mol (3.61eV, 29200cm−1) for the ãA24 state, 93.3kcal∕mol (4.05eV, 32600cm−1) for the b̃B24 state, and 100.8kcal∕mol (4.37eV, 35300cm−1) for the c̃A14 state. The quantum mechanical excitation energies (T0 values) were determined to be 81.6kcal∕mol (3.54eV, 28500cm−1) for the ãA24 state and 90.7kcal∕mol (3.93eV, 31700cm−1) for the b̃B24 state. The lowest quartet linear Renner-Teller Π4 state gives rise to the ãA24 state with 112.8° and the b̃B24 state with 124.4° ∠(ONO) bond angles upon bending. The b̃ state shows some peculiar behavior. Although CASSCF, RCISD, UCISD, RCCSD, UCCSD, and RCCSD(T) methods predicted the presence of a Cs equilibrium geometry (a double minimum A′4 state), SCF, UCCSD(T), and ICMRCI wave functions predicted the C2v structure for the b̃B24 state. The importance of both dynamical and nondynamical correlation treatments for the energy difference between C2v and Cs structures of b̃ state is highlighted in this context. The c̃A14 state is predicted to have a very small bond angle of 85.8°. Potential energy diagrams with respect to the bond angles of the ground state and four quartet states are presented.
An improved replica-exchange sampling method: Temperature intervals with global energy reassignment
Authors: Li Xianfeng , O’Brien Christopher P. , Collier Galen , Vellore Nadeem A. , Wang Feng , Latour Robert A. , Bruce David A. , Stuart Steven J.
Published: November 2007

In a molecular dynamics (MD) simulation, representative sampling over the entire phase space is desired to obtain an accurate canonical distribution at a given temperature. For large molecules, such as proteins, this is problematic because systems tend to become trapped in local energy minima. The extensively used replica-exchange molecular dynamics (REMD) simulation technique overcomes this kinetic-trapping problem by allowing Boltzmann-weighted configuration exchange processes to occur between numerous thermally adjacent and compositionally identical simulations that are thermostated at sequentially higher temperatures. While the REMD method provides much better sampling than conventional MD, there are two substantial difficulties that are inherent in its application: (1) the large number of replicas that must be used to span a designated temperature range and (2) the subsequent long time required for configurations sampled at high temperatures to exchange down for potential inclusion within the low-temperature ensemble of interest. In this work, a new method based on temperature intervals with global energy reassignment (TIGER) is presented that overcomes both of these problems. A TIGER simulation is conducted as a series of short heating-sampling-quenching cycles. At the end of each cycle, the potential energies of all replicas are simultaneously compared at the same temperature using a Metropolis sampling method and then globally reassigned to the designated temperature levels. TIGER is compared with regular MD and REMD methods for the alanine dipeptide in water. The results indicate that TIGER increases sampling efficiency while substantially reducing the number of central processing units required for a comparable conventional REMD simulation.
Influence of the native topology on the folding barrier for small proteins
Authors: Prieto Lidia , Rey Antonio
Published: November 2007

The possibility of downhill instead of two-state folding for proteins has been a very controversial topic which arose from recent experimental studies. From the theoretical side, this question has also been accomplished in different ways. Given the experimental observation that a relationship exists between the native structure topology of a protein and the kinetic and thermodynamic properties of its folding process, Gō-type potentials are an appropriate way to approach this problem. In this work, we employ an interaction potential from this family to get a better insight on the topological characteristics of the native state that may somehow determine the presence of a thermodynamic barrier in the folding pathway. The results presented here show that, indeed, the native topology of a small protein has a great influence on its folding behavior, mostly depending on the proportion of local and long range contacts the protein has in its native structure. Furthermore, when all the interactions present contribute in a balanced way, the transition results to be cooperative. Otherwise, the tendency to a downhill folding behavior increases.
Phase diagram for a model of urate oxidase
Authors: Wentzel N. , Pagan D. L. , Gunton J. D.
Published: November 2007

Urate oxidase from Asperigillus flavus has been shown to be a model protein for studying the effects of polyethylene glycol (PEG) on the crystallization of large proteins. Extensive experimental studies based on small angle x-ray scattering [Vivarès and Bonneté, J. Phys. Chem. B 108, 6498 (2004)] have determined the effects of salt, pH, temperature, and most importantly PEG on the crystallization of this protein. Recently, some aspects of the phase diagram have also been determined experimentally. In this paper, we use Monte Carlo techniques to predict the phase diagram for urate oxidase in solution with PEG, including the liquid-liquid and liquid-solid coexistence curves. The model used includes an electrostatic interaction, van der Waals attraction, and a polymer-induced depletion interaction [Vivarès et al., Eur. Phys. J. E 9, 15 (2002)]. Results from the simulation are compared with experimental results.
Single and dual beam optical switching of resonance energy transfer
Authors: Andrews David L. , Crisp Richard G. , Li Shaopeng
Published: November 2007

Through photonic mechanisms based on near-field coupling, laser radiation can engage with resonant energy transfer in a variety of suitably designed materials and molecular structures. Energy that has been acquired, through the initial absorption of resonant laser light, undergoes transfer between chromophores only on the throughput of off-resonant light, the process known as laser-assisted resonance energy transfer. The comprehensive results that are presented here extend and generalize the theory for both single and dual beam configurations, producing results that are applicable to media of various types including doped crystals, heterogeneous multichromophore solids, and solutions. The detailed principles, here explained in terms of both energetics and optical selection rule criteria, are specifically illustrated for a variety of materials. It is shown how general application of the theory can facilitate the elucidation of experiments, by clearly interpreting the effects of laser polarization manipulation. On further analysis of the photophysical mechanisms it is also demonstrated that such effects represent an entirely practicable basis for optical switching and logic gate operation. The additional polarization selectivity afforded by a two-beam setup proves to allow the most complete system control. With such a configuration, there is considerable promise for the realization of new optically driven logic and molecular devices.
Relaxation dynamics in tert-butylpyridine/tristyrene mixture investigated by broadband dielectric spectroscopy
Authors: Kessairi Khadra , Capaccioli Simone , Prevosto Daniele , Lucchesi Mauro , Rolla Pierangelo
Published: November 2007

We investigated, by means of dielectric spectroscopy, the relaxation dynamics of glass forming binary mixtures composed by the quite rigid polar molecules tert-butylpyridine dissolved in the apolar solvent tristyrene. By changing the relative concentration of the components we observed a transition from a relaxation scenario with a structural process and an excess wing to that with a structural process and a well resolved secondary process. Another relaxation process, slower than the latter, was observed, well below Tg. Our detailed analysis evidenced that the secondary relaxation with shorter relaxation time can be identified as the Johari-Goldstein relaxation for all the mixtures, whereas the new relaxation process was attributed to a different type of motion of tert-butylpyridine needing a larger amount of free volume for the molecular rotation.
Reduced magnetohydrodynamic equations with coupled Alfvén and sound wave dynamics
Authors: Denton R. E. , Rogers B. , Lotko W.
Published: November 2007

A set of reduced magnetohydrodynamic equations is described that is appropriate for the simulation of auroral Alfvén waves using curvilinear coordinates. These equations include the parallel electric field, ponderomotive force, diamagnetic drift effects, and gravity and rotation, but do not include the fast mode dynamics. The equations are formulated for multiple species, but quasineutrality is explicitly maintained. The equations have an exact conserved energy.
Hall effects on the steady structure of the rotational layer at the dayside magnetopause
Authors: Westerberg Lars G. , Åkerstedt Hans O.
Published: November 2007

The influence of the Hall term in the generalized Ohm’s law on the large-scale plasma flow during conditions of ongoing magnetic reconnection at the dayside magnetopause (MP) is investigated. Of special interest is the plasma flow behavior during the transition of the MP transition layer as the Hall effect grows in proportion to the viscous-resistive effects. The governing equations are solved approximately by an ordinary perturbation expansion in orders of large Reynolds and Lundqvist numbers. It is shown that the flow pattern is strongly dependent on the magnitude of the Hall parameter; as it approaches zero, the viscous-resistive solution is obtained, while for an ordering of the same magnitude as the resistivity/viscosity, the Hall effect begins to affect the flow structure severely. For an increasing value on the Hall parameter, oscillations are brought into the system, an effect that is enhanced with the magnitude of the Hall parameter. Furthermore, it is shown that as the Hall effect begins to dominate, the transition layer thickens.
Exact-exchange density functional theory for hyperpolarizabilities
Authors: Bokhan Denis , Bartlett Rodney J.
Published: November 2007

Time-dependent density functional theory (TDDFT) employing the exact-exchange functional (TDDFTx) has been formulated using the optimized effective potential method for the β static hyperpolarizabilities, where it reduces to coupled-perturbed Kohn-Sham theory. A diagrammatic technique is used to take the functional derivatives for the derivation of the adiabatic second kernel, which is required for the analytical calculation of the β static hyperpolarizabilities with DFT. The derived formulas have been implemented using Gaussian basis sets. The structure of the adiabatic exact-exchange second kernel is described and numerical examples are presented. It is shown that no current DFT functional satisfies the correct properties of the second kernel. Not surprisingly, TDDFTx, which corrects the self-interaction error in standard DFT methods and has the correct long-range behavior, provides results close to those of time-dependent Hartree-Fock in the static limit.
Interatomic potential-based semiclassical theory for Lennard-Jones fluids
Authors: Raghunathan A. V. , Park J. H. , Aluru N. R.
Published: November 2007

An interatomic potential based semiclassical theory is proposed to predict the concentration and potential profiles of a Lennard-Jones (LJ) fluid confined in a channel. The inputs to the semiclassical formulation are the LJ parameters of the fluid and the wall, the density of channel wall atoms, and the average concentration of the fluid inside the channel. Using the semiclassical formulation, fluid confinement in channel with widths ranging from 2σff to 100σff, where σff is the fluid-fluid LJ distance parameter, is investigated. The concentration and potential predicted by the semiclassical formulation are found to be in good agreement with those from equilibrium molecular dynamics simulations. While atomistic simulations in large channels are computationally expensive, the proposed semiclassical formulation can rapidly and accurately predict the concentration and potential profiles. The proposed semiclassical theory is thus a robust and fast method to predict the interfacial and “bulk” fluid phenomena in channels with widths ranging from the macroscale down to the scale of a few atomic diameters.
Dispersion control in two-dimensional superlattice photonic crystal slab waveguides by atomic layer deposition
Authors: Gaillot D. P. , Graugnard E. , Blair J. , Summers C. J.
Published: November 2007

The frequency and dispersion of photonic bands in two-dimensional triangular-based superlattice photonic crystal Si slab waveguides were manipulated using atomic layer deposition. The samples were conformally coated with increasing thicknesses of TiO2 and characterized by polarized angular-dependent reflectance measurements, which revealed shifts in the photonic band frequencies of 16% as well as continuous changes in band dispersion. The ability to tune toward zero group velocity by tuning band repulsion between same-polarization bands is demonstrated. Finite-difference time-domain calculations, combined with a dielectric weighting model, were used to assess the observed band and dispersion tuning.
Probing elastic modulus and depth of bottom-supported inclusions in model tissues using piezoelectric cantilevers
Authors: Yegingil Hakki , Shih Wan Y. , Shih Wei-Heng
Published: November 2007

We have experimentally investigated the depth sensitivity limit of a piezoelectric cantilever tissue elastic modulus sensor and simultaneously determined the elastic modulus and the depth of a tumor directly. Using model tissues consisting of bottom-supported modeling clay inclusions of various depths in a gelatin matrix, we empirically determined that the depth sensitivity limit of a piezoelectric cantilever sensor was twice the linear dimension of the indentation area (or the cantilever width). Knowing the depth sensitivity limit of the individual cantilever sensor as input and treating a model tissue that has the gelatin matrix on top and the modeling clay inclusion at the bottom as two springs in series, we showed that the elastic moduli and depths of the hard inclusions could be simultaneously determined with the elastic modulus profiles measured by two cantilevers with different widths as input.
Elongational perturbations on nematic liquid crystal polymers under a weak shear
Authors: Zhou Hong , Wang Hongyun
Published: November 2007

The two-dimensional Smoluchowski equation is employed to study the effect of elongational perturbations on nematic liquid crystal polymers under a weak shear. We use the multiscale asymptotic analysis to show that (1) when the elongational perturbation is small relative to the weak shear, the orientational probability density function (pdf) tumbles periodically only in an intermediate range of polymer concentration; outside this intermediate range (i.e., for very small and very large polymer concentration) the orientational pdf converges to a steady state and there is no tumbling. (2) When the elongational perturbation is about 20% of the shear rate or larger, the intermediate range of tumbling disappears and the orientational pdf always converges to a steady state regardless of the polymer concentration. Our theoretical predictions are consistent with various earlier results based on the Leslie–Ericksen theory [C. V. Chaubal and L. G. Leal, J. Non-Newtonian Fluid Mech. 82, 22 (1999)] or analogous 3D numerical simulations [M. G. Forest, R. Zhou, and Q. Wang, Phys. Rev. Lett. 93, 088301 (2004); M. G. Forest, Q. Wang, R. Zhou, and E. Choate, J. Non-Newtonian Fluid Mech. 118, 17 (2004)].
Interaction of CO with Kr: Potential energy surface and bound states
Authors: Feng Eryin , Wang Zhongquan , Gong Mingyan , Cui Zhifeng
Published: November 2007

The first ab initio potential energy surface of the Kr–CO complex is developed using single and double excitation coupled-cluster theory with noniterative treatment of triple excitations. Mixed basis sets, aug-cc-pVQZ for the C and O atoms and aug-cc-pVQZ-PP for the Kr atom, with an additional (3s3p2d2f1g) set of midbond functions are used. The computed interaction energies in 336 configurations are analytically fitted to a two-dimensional potential model by a least squares fit. The potential has a minimum of −119.68cm−1 with Re=7.35a0 at an approximate T-shaped geometry (θe=98.5°). Bound state energies are calculated up to J=12, thus enabling a comprehensive comparison between theory and available experimental data as well as providing detailed guidance for future spectroscopic investigations of higher-lying states. The predicted transition frequencies and spectroscopic constants are in good agreement with the experimental results.
Quantitative investigation of physical properties of mantle plumes in three-dimensional numerical models
Authors: Galsa Attila , Lenkey László
Published: November 2007

Numerical calculations have been carried out to investigate the physical properties of mantle plumes in highly viscous thermal convection depending on the Rayleigh number (Ra). The Boussinesq approximation was applied in a three-dimensional Cartesian domain filled with isoviscous, purely bottom-heated fluid with infinite Prandtl number. In order to monitor the dynamical behavior of plumes an automatic plume detecting routine was developed based on the temperature between the plume and its surroundings. It was established that as the convection becomes more vigorous with increasing Rayleigh number the average cross-sectional area of an individual plume decreases (∼Ra−2∕3), the vertical velocity in plumes increases (∼Ra2∕3), while the average temperature in plumes is independent of Ra. It means that the volume and the heat transport in an individual plume is independent of the Rayleigh number. The number of plumes forming in the box increases (∼Ra1∕3) which is in accordance with the scale analysis using the energy balance and the conservation of momentum. Furthermore, the Rayleigh number influences the temporal behavior of the average surface heat flow [Nusselt number, Nu0(t)] and the heat advected by plumes [Twp(t)]. The characteristic frequencies of Nu0(t) and Twp(t) increase by ∼Ra2∕3 in agreement with the rate of increase of the vertical velocity in plumes. The characteristic frequencies of Nu0(t) and Twp(t) are between the frequency corresponding to the time necessary for a plume to rise from the bottom to the top of the layer and the frequency of a whole convective cycle. The time series of Twp(t) contain larger amplitudes and higher frequencies than Nu0(t). It was assumed that the heat in the top thermal boundary layer (TBL) propagates by conduction and using Twp(t) as an input at the bottom of the top TBL the amplitude and the frequency of the heat flow series on the surface was calculated. It corresponds very well to the amplitude and the frequency of the observed Nu0(t). The correlation analysis between the time series of the surface Nusselt number and the heat advected by hot plumes showed that the time delay between the time series is equal to the time of the heat propagation by conduction through the TBL. The correlation between time series Twp(t) at different depths demonstrated well that the main heat transfer mechanism in plumes is advection.
Random copolymers at a selective interface: Saturation effects
Authors: Kłos J. , Sommer J.-U.
Published: November 2007

Combining scaling arguments and Monte Carlo simulations using the bond fluctuation method we have studied concentration effects for the adsorption of symmetric AB-random copolymers at selective, symmetric interfaces. For the scaling analysis we consider a hierarchy of two length scales given by the excess (adsorption) blobs and by two dimensional thermal blobs in the semidilute surface regime. When both length scales match, a densely packed array of adsorption blobs is formed (saturation). We show that for random copolymer adsorption the interface concentration can be further increased (oversaturation) due to reorganization of excess blobs. Crossing over this threshold results in a qualitative change in the behavior of the adsorption layer which involves a change in the average shape of the adsorbed chains towards a hairpinlike form. We have analyzed the distribution of loops and tails of adsorbed chains in the various concentration regimes as well as the chain order parameter, concentration profiles, and the exchange rate of individual chains. We emphasized the role of saturation scaling which dominates the behavior of static and dynamic quantities at higher surface concentration.
Lifetime, turnover time, and fast magnetic field regeneration in random flows
Authors: Tanner S. E. M.
Published: November 2007

The fast dynamo is thought to be relevant in the regeneration of magnetic fields in astrophysics where the value of the magnetic Reynolds number (Rm) is immense. The fast dynamo picture is one in which chaotic flows provide a mechanism for the stretching of magnetic field lines. Furthermore, a cascade of energy down to small scales results in intermittent regions of a small-scale, intense magnetic field. Given this scenario it is natural to invoke the use of kinematic random flows in order to understand field regeneration mechanisms better. Here a family of random flows is used to study the effects that L, the lifetime of the cell, and τ, the turnover time of the cell, may have on magnetic field regeneration. Defining the parameter Γ=L∕τ, it has been varied according to Γ>1,Γ<1,Γ∼O(1). In the kinematic regime, dynamo growth rates and Lyapunov exponents are examined at varying values of Rm. The possibility of fast dynamo action is considered. In the nonlinear regime, magnetic and kinetic energies are examined. Results indicate that there does appear to be a relationship between Γ and dynamo efficiency. In particular, the most efficient dynamos seem to operate at lower values of Γ.
Comparison of measurements and particle-in-cell simulations of ion energy distribution functions in a capacitively coupled radio-frequency discharge
Authors: O’Connell D. , Zorat R. , Ellingboe A. R. , Turner M. M.
Published: November 2007

The ion dynamics in the high-voltage sheath of a capacitively coupled radio-frequency plasma has been investigated using mass-resolved ion energy analysis in combination with a two-dimensional particle-in-cell (PIC) code. A symmetric confined discharge is designed allowing highly accurate comparisons of measured ion energy distribution functions in high-voltage sheaths with simulation results. Under the conditions investigated, the sheaths are not only collisional, but also chemically complex. This situation is common in applications but rare in laboratory experiments. Excellent agreement has been found for a hydrogen discharge benchmarking the code. Hydrogen is of particular interest since its light mass gives detailed insight into sheath dynamics, and an extensive database of collisional cross sections is available. The H3+ ion was found to be the dominant ion in the sheaths and the plasma bulk under most conditions investigated. H3+ exhibits the typical saddle-shaped ion energy distribution function indicative of ions created in the plasma bulk and traversing the entire sheath potential. H+ and H2+ are predominantly formed through collisions in the high-voltage sheath. H2+ ion energy distribution functions show structures resulting from symmetric charge exchange collisions with the background gas. Minor discrepancies between the experimental results and PIC simulations indicate slightly lower plasma densities in the simulation, resulting in larger sheath width.
A comparison of two methods for selecting vibrational configuration interaction spaces on a heptatomic system: Ethylene oxide
Authors: Bégué Didier , Gohaud Neil , Pouchan Claude , Cassam-Chenaï Patrick , Liévin Jacques
Published: November 2007

Two recently developed methods for solving the molecular vibrational Schrödinger equation, namely, the parallel vibrational multiple window configuration interaction and the vibrational mean field configuration interaction, are presented and compared on the same potential energy surface of ethylene oxide, c-C2H4O. It is demonstrated on this heptatomic system with strong resonances that both approaches converge towards the same fundamental frequencies. This confirms their ability to tackle the vibrational problem of large molecules for which full configuration interaction calculations are not tractable.
Compact terahertz time domain spectroscopy system with diffraction-limited spatial resolution
Authors: Watanabe Shinichi , Shimano Ryo
Published: November 2007

A compact and rigid terahertz time domain spectroscopy system is presented. The size of the device is 20mm diameter times 61mm length with four parabolic-shaped concave mirrors dug in it to effectively focus a terahertz beam on a sample. The device has no chromatic aberration over the whole bandwidth of the beam (0.3–2THz), and an effective numerical aperture of about 0.45 is achieved, which has a capability to image the structure whose size is almost the same as the wavelength. Frequency resolved images clearly show this performance. We also show that quantitative retrieval of the complex refractive index of the structure as small as twice of the wavelength is possible.
Bounds for the adiabatic approximation with applications to quantum computation
Authors: Jansen Sabine , Ruskai Mary-Beth , Seiler Ruedi
Published: November 2007

We present straightforward proofs of estimates used in the adiabatic approximation. The gap dependence is analyzed explicitly. We apply the result to interpolating Hamiltonians of interest in quantum computing.
Examination of near-wall hindered Brownian diffusion of nanoparticles: Experimental comparison to theories by Brenner (1961) and Goldman et al. (1967)
Authors: Choi C. K. , Margraves C. H. , Kihm K. D.
Published: November 2007

Multilayered distributions of hindered mean square displacement (MSD) for nanoparticles are measured in the near-wall region within 500 nm from the solid surface using total internal reflection fluorescence microscopy, an evanescent wave microscopic imaging technique. Examined particles are yellow-green (505/515) polystyrene fluorescent nanospheres of 100, 250, and 500nm radii with a specific gravity of 1.055. To ensure the measurement accuracy, special care is taken to minimize photobleaching of fluorescent particles by adding neutral density filters to optimally reduce the excitation power. The experimental results for parallel MSDs to the solid surface validate the theory of hindered diffusion [A. J. Goldman, R. G. Cox, and H. Brenner, “Slow viscous motion of a sphere parallel to a plane—I: Motion through a quiescent fluid,” Chem. Eng. Sci. 22, 637 (1967)] of spheres based on viscous slow-down in the near-wall region. It is also reported that the effect of adding sodium chloride up to 10mM to the solution has little effect on the parallel diffusive motion of the tested nanoparticles. Experimental evidence shows that normal MSDs, for submicroscopic charged nanoparticles, are substantially different from Einstein’s 2DΔt due to the deterministic motion arising from electrostatic forces.
An atomic jet in a heat pipe for multiphoton spectroscopy
Authors: Philip G.
Published: November 2007

A conventional heat pipe is modified to operate as a novel atomic jet setup with unprecedented advantages for multiphoton spectroscopy of alkaline-earth atoms especially to study the effect of external electric field, controlled excitation of forbidden transitions and for the study of collisional broadening and shift of excited states, and time evolution of Rydberg atoms.
The elastohydrodynamic force on a sphere near a soft wall
Authors: Urzay Javier , Llewellyn Smith Stefan G. , Glover Beverley J.
Published: November 2007

The influence of soft boundaries on the forces experienced by a small sphere undergoing slow translation and rotation near a wall is investigated using asymptotic and numerical methods. The clearance between the sphere and the wall is assumed to be small, so that the lubrication approximation holds in the gap. The forces induced by boundary deformation break the symmetry of the Stokes equations, leading to irreversibility of the motion of the sphere and yielding a nonzero lift force. A general formulation, applicable to any constitutive equation of the wall, is presented, and an asymptotic analysis for slightly soft boundaries is developed and applied to a thin compressible elastic layer coating a rigid surface. Expressions are derived for the elastohydrodynamic lift exerted on a sphere moving parallel to the wall, which include the influence of the sphere rotation in the direction of its motion. The results extend and correct previous work, and are different from those for the elastohydrodynamic motion of a cylinder near a wall, in that the geometry eliminates the occurrence of maximum lift and optimum choice of the material properties of the boundary.
Measurement of thermal diffusivity at high pressure using a transient heating technique
Authors: Beck Pierre , Goncharov Alexander F. , Struzhkin Viktor V. , Militzer Burkhard , Mao Ho-kwang , Hemley Russell J.
Published: November 2007

We describe a flash-heating procedure designed to measure thermal diffusivity of materials at high pressure and temperature in diamond anvil cells. This technique involves time-resolved radiometry combined with a pulsed IR laser source. Results for MgO, NaCl, and KCl are presented (to P=32GPa and T=2600K). These measurements agree with previous studies at low pressure and high temperature and enable to test models for the combined P-T dependence of thermal conductivity. This technique can be extended to a broader range of pressures and can be used to address a variety of problems in geoscience, planetary sciences, and materials science.
A rigorous approach to the Feynman-Vernon influence functional and its applications. I
Authors: Albeverio Sergio , Cattaneo Laura , Mazzucchi Sonia , Di Persio Luca
Published: November 2007

A rigorous representation of the Feynman-Vernon influence functional used to describe open quantum systems is given, based on the theory of infinite dimensional oscillatory integrals. An application to the case of the density matrices describing the Caldeira-Leggett model of two quantum systems with a quadratic interaction is treated.
On the computation of long-range interactions in fluids under confinement: Application to pore systems with various types of spatial periodicity
Authors: Pantatosaki Evangelia , Papadopoulos George K.
Published: November 2007

The problem of computing accurately the long-range Coulomb interactions in physical systems is investigated focusing mainly on the atomistic simulation of fluids sorbed in porous solids. Several articles involving theory and computation of long-range interactions in charged systems are reviewed, in order to explore the possibility of adapting or developing methodology in the field of computer simulation of sorbate molecules inside nanostructures modeled through a three-dimensional (crystal frameworks), two-dimensional (slit-shaped pores), or one-dimensional (cylindrical pores) replication of their unit cell. For this reason we digitally reconstruct selected paradigms of three-dimensional microporous structures which exhibit different spatial periodicities such as the zeolite crystals of MFI and FAU type, graphitic slit-shaped pores, and single-wall carbon nanotubes in order to study the sorption of CO2, N2, and H2 via grand canonical Monte Carlo simulation; the predicted data are compared with experimental measurements found elsewhere. Suitable technical adjustments to the use of conventional Ewald technique, whenever it is possible, prove to be effective in the computation of electrostatic field of all the categories studied in this work.
Observations of image contrast and dimerization of decacyclene by low temperature scanning tunneling microscopy
Authors: Wesoloski Lisa M. , Stieg Adam Z. , Kunitake Masashi , Dultz Shane C. , Gimzewski James K.
Published: November 2007

Low temperature scanning tunneling microscopy studies revealed both monomer and dimer forms of decacyclene (DC) on atomically clean Cu(100) and Cu(111). The observed image contrast in DC is strongly bias dependent and also influenced by tip modifications. Alternatively, dimers appear solely as protrusions and are nearly bias independent. We provide evidence of both dimer formation and dissociation and suggest that two DC molecules stack by aligning their molecular planes in a parallel fashion with respect to the surface. Dimers and their surface-dependent properties demonstrate the interplay between surface-molecule and molecule-molecule interactions.
Optimized effective potentials from electron densities in finite basis sets
Authors: Bulat Felipe A. , Heaton-Burgess Tim , Cohen Aron J. , Yang Weitao
Published: November 2007

The Wu-Yang method for determining the optimized effective potential (OEP) and implicit density functionals from a given electron density is revisited to account for its ill-posed nature, as recently done for the direct minimization method for OEP’s from a given orbital functional [T. Heaton-Burgess, F. A. Bulat, and W. Yang, Phys. Rev. Lett. 98, 256401 (2007)]. To address the issues on the general validity and practical applicability of methods that determine the Kohn-Sham (local) multiplicative potential in a finite basis expansion, a new functional is introduced as a regularized version of the original work of Wu and Yang. It is shown that the unphysical, highly oscillatory potentials that can be obtained when unbalanced basis sets are used are the controllable manifestation of the ill-posed nature of the problem. The new method ensures that well behaved potentials are obtained for arbitrary basis sets.
Near-edge x-ray absorption and natural circular dichroism spectra of L-alanine: A theoretical study based on the complex polarization propagator approach
Authors: Jiemchooroj Auayporn , Ekström Ulf , Norman Patrick
Published: November 2007

The complex polarization propagator method [J. Chem. Phys. 123, 194103 (2005)] has been employed in conjunction with density functional theory and gauge-including atomic orbitals in order to determine the near-edge x-ray absorption and natural circular dichroism spectra of L-alanine in its neutral and zwitterionic forms. Results are presented for the K-edges of carbon, nitrogen, and oxygen. In contrast to traditional methods, the proposed approach enables a direct determination of the spectra at an arbitrary frequency instead of focusing on the rotatory strengths for individual electronic transitions. The propagator includes a complete set of nonredundant electron-transfer operators and allows for full core-hole relaxation. The theoretical spectrum at the nitrogen K-edge of the zwitterion compares well with the experimental spectrum.