bluuebunny/crossref_metadata_2025 huggingface dataset:
A comparison of latent heat fluxes over global oceans for ERA and NCEP with GSSTF2
Authors: Feng Licheng , Li Jianping
Published: February 2006

The ECMWF Re‐Analysis (ERA) and NCEP reanalysis monthly latent heat flux (LHF) data are compared with those of the Goddard Satellite‐Based Surface Turbulent Fluxes, version2 (GSSTF2), respectively, during the period of 1988–2000, over the global oceans between 60°S and 60°N. Qualitatively, the annual mean LHF fields and monthly variations are similar for GSSTF2, ERA, and NCEP. Quantitatively, however, there are distinct differences among them. The annual mean ERA LHF is closer to GSSTF2 than NCEP in the tropics (5°–25°S and 8°–22°N) and midlatitudes, while the situation is opposite in other zones. The temporal variability of monthly LHF difference (ERA‐GSSTF2) is smaller than that of NCEP‐GSSTF2 in the tropics, yet the former and the latter are similar in other zones. To find causes for the discrepancies of LHF, the differences of both the 10‐m wind speed (U10m) and sea‐air humidity difference (Qs‐a) among these data sets have been studied. The differences of the annual mean fields and the monthly variations of the differences between GSSTF2 and the other two data sets in the tropics may be mainly caused by the discrepancies of both U10m and Qs‐a.
Long dance of the bashful ballerina
Authors: Hiltula T. , Mursula K.
Published: February 2006

In this letter we extend our earlier analysis of the north‐south asymmetry of the heliospheric current sheet (HCS) using a recent data set of heliospheric magnetic field (HMF) sector polarities extracted from ground‐based magnetic observations. We find that the heliospheric current sheet is similarly southward coned or shifted during the late declining to minimum phase of the solar cycle in the early part of the studied data interval (1926–1955), as earlier found for the more recent solar cycles. Accordingly, the HCS has been southward shifted; that is, the solar ballerina has been bashful at least during the last 80 years. We also discuss solar cycle 19 which presents a period of a very curious behaviour for the HCS with an exceptionally large HMF toward sector dominance in 1957, the year of cycle 19 maximum, and an equally strong HMF away sector dominance in 1960, the time of final solar polarity reversal.
Radial anisotropy in seismic reference models of the mantle
Authors: Beghein C. , Trampert J. , van Heijst H. J.
Published: February 2006

Sambridge's Neighborhood Algorithm was applied to normal mode and surface wave phase velocity data to determine the likelihood of radial anisotropy in mantle reference models. This full model space search technique provides probability density functions for each model parameter and therefore reliable estimates of resolution and uncertainty, without having to introduce unnecessary regularization on the model space. Our results for shear wave anisotropy (described by parameter ξ) show a fast decrease with depth with no significant deviation from Preliminary Reference Earth Model (PREM) at any depth. The data do not require strong deviations from PREM for P wave anisotropy either, except between 220 and 400 km depth and in the D″ layer. The intermediate parameter η might depart from PREM between 220 and 670 km depth. This implies a likely deeper P wave anisotropy and η anisotropy than S wave anisotropy. The sign change in the anisotropic parameters across the 670‐km discontinuity found by other authors is not warranted by our data set, which is far more extensive than in previous studies. We found that density needs to be well resolved because we observe a high dependence of the results for P wave‐related parameters on the presence or absence of density in the parameterization. S wave anisotropy and η are less affected by density. A well‐resolved negative density anomaly was found in the uppermost mantle, and a density excess was observed in the transition zone and the lowermost mantle which might be a seismic signature of the recently identified postperovskite phase.
The role of central 5‐hydroxytryptamine (5‐HT, serotonin) receptors in the control of micturition
Authors: Ramage Andrew G.
Published: February 2006

At present the most investigated 5‐HT receptor that has been shown to play a role in the control of micturition is the 5‐HT1Areceptor followed by 5‐HT7, 5‐HT2and 5‐HT3receptors. Most experiments focus on the control these receptors have on the parasympathetic outflow to the bladder and the somatic outflow to the external urethral sphincter (EUS) in the rat. Furthermore, 5‐HT1Aand 5‐HT7receptors have been identified as having an excitatory physiological role in the control of bladder function. 5‐HT1Areceptors act, at least in the rat, at both a spinal (probably a heteroreceptor) and supraspinal (probably an autoreceptor) level, while 5‐HT7receptors only act at a supraspinal level. Additionally, in the rat, 5‐HT administered at a spinal or supraspinal site has an excitatory action, although earlier experiments have shown that activating 5‐HT‐containing brain areas causes inhibition of the bladder. Recent experiments have also indicated that blockade of the 5‐HT1Areceptor pathway shows rapid tolerance. However, no data exist for the development of tolerance for the 5‐HT7receptor pathway. Neither receptor seems to play a role in the control of the urethra. Regarding 5‐HT2receptors, activation of this receptor subtype inhibits micturition, and this inhibitory action may occur at a spinal, supraspinal or both levels. Although no physiological role for 5‐HT2Creceptors can yet be identified, 5‐HT2Creceptors have been implicated in the proposed supraspinal tonically active 5‐HT1Aautoreceptor (negative feedback) pathway. This proposition reconciles the data that central 5‐HT‐containing pathways are inhibitory to micturition, while 5‐HT1Areceptors, although inhibitory to adenylyl cyclase, have an excitatory function. This is because activation of 5‐HT1Aautoreceptors reduces the release of 5‐HT thus reducing the activation of the 5‐HT2Creceptors, which are inhibitory in the control of micturition (disinhibition). Furthermore, 5‐HT2Areceptors in the rat and 5‐HT2Creceptors in the guinea pig cause activation of the EUS. In this respect, 5‐ht5Areceptors have also been identified in Onuf's nucleus, the site of somatic motoneurones controlling this sphincter. In the cat there is very little evidence to indicate that 5‐HT receptors are involved in micturition except under pathological conditions in which activation of 5‐HT1Areceptors causes inhibition of micturition. Interestingly, under such conditions 5‐HT1Areceptors cause excitation of the EUS. Nevertheless, spinal 5HT3receptors have been implicated in the physiological control of micturition in the cat, but not yet in the rat. Overall, the data support the view that 5‐HT receptors are important in the control of micturition. However, many more studies are required to fully understand these roles and why there are such species differences.

British Journal of Pharmacology(2006)147, S120–S131. doi:10.1038/sj.bjp.0706504
In vitromodels: research in physiology and pharmacology of the lower urinary tract
Authors: Moreland Robert B.
Published: February 2006

The physiology and pharmacology of the lower urinary tract has advanced based, in part, due to thein vitroassays that have facilitated this exploration. Such assays have led to the development of novel and selective molecules that have been used to characterize different receptor and enzyme systems in the larger context ofin vivopharmacology. These assays can be classified by sites of action of drugs into the following categories: receptors, effector enzymes and enzymes that terminate the responses. In this review, representative assays are presented based on our experience in male erectile dysfunction.

British Journal of Pharmacology(2006)147, S56–S61. doi:10.1038/sj.bjp.0706505
Muscarinic receptors in the bladder: from basic research to therapeutics
Authors: Hegde Sharath S.
Published: February 2006

Muscarinic receptor antagonists (antimuscarinics) serve as the cornerstone in the pharmacological management of overactive bladder (OAB) by relieving the symptoms of urgency, frequency and incontinence. These drugs operate primarily by antagonizing post‐junctional excitatory muscarinic receptors (M2/M3) in the detrusor. The combination of pharmacological and gene knockout studies has greatly advanced our understanding of the functional role of muscarinic receptors in the bladder. M3receptors produce direct smooth muscle contraction by a mechanism that relies on entry of extracellular calcium through L‐type channels and activation of a rho kinase. M2receptors, which predominate in number, appear to facilitate M3‐mediated contractions. M2receptors can also produce bladder contractions indirectly by reversing cAMP‐dependent β‐adrenoceptor‐mediated relaxation, although the physiological role of β‐adrenoceptors in detrusor relaxation is controversial. Emerging evidence suggests that muscarinic receptors in the urothelium/suburothelium can modulate the release of certain factors, which in turn may affect bladder function at the efferent or afferent axis. Currently, oxybutynin, tolterodine, darifenacin, solifenacin and trospium are the five major antimuscarinics approved for the treatment of OAB. Comparative clinical studies have shown that oxybutynin and solifenacin may be marginally more effective than tolterodine, although the latter seems to be better tolerated. Pharmacokinetic–pharmacodynamic analyses using plasma concentrations of ‘total drug’ indicate that, at therapeutic doses, the clinical efficacy of darifenacin and solifenacin may be driven primarily by selective M3receptor occupation, whereas the pharmacodynamic effects of pan‐selective molecules (such as tolterodine, trospium) may potentially involve multiple receptors, including M2and M3. Furthermore, high M3receptor occupation is the likely explanation for the greater propensity of darifenacin and oxybutynin to cause dry mouth and/or constipation. Although the recently introduced drugs represent a significant improvement over older drugs, especially with respect to the convenience of dosing schedule, their overall efficacy and tolerability profile is still less than optimal and patient persistence with therapy is low. Recent advances in basic research have not yet offered a clear discovery path for improving the therapeutic index of antimuscarinic molecules. There is still an unmet need for an antimuscarinic medicine with superior clinical effectiveness that can translate into better persistence on therapy.

British Journal of Pharmacology(2006)147, S80–S87. doi:10.1038/sj.bjp.0706560
Integrative control of the lower urinary tract: preclinical perspective
Authors: de Groat William C.
Published: February 2006

Storage and periodic expulsion of urine is regulated by a neural control system in the brain and spinal cord that coordinates the reciprocal activity of two functional units in the lower urinary tract (LUT): (a) a reservoir (the urinary bladder) and (b) an outlet (bladder neck, urethra and striated muscles of the urethral sphincter). Control of the bladder and urethral outlet is dependent on three sets of peripheral nerves: parasympathetic, sympathetic and somatic nerves that contain afferent as well as efferent pathways. Afferent neurons innervating the bladder have A‐δ or C‐fibre axons. Urine storage reflexes are organized in the spinal cord, whereas voiding reflexes are mediated by a spinobulbospinal pathway passing through a coordination centre (the pontine micturition centre) located in the brainstem. Storage and voiding reflexes are activated by mechanosensitive A‐δ afferents that respond to bladder distension. Many neurotransmitters including acetylcholine, norepinephrine, dopamine, serotonin, excitatory and inhibitory amino acids, adenosine triphosphate, nitric oxide and neuropeptides are involved in the neural control of the LUT. Injuries or diseases of the nervous system as well as disorders of the peripheral organs can produce LUT dysfunctions including: (1) urinary frequency, urgency and incontinence or (2) inefficient voiding and urinary retention. Neurogenic detrusor overactivity is triggered by C‐fibre bladder afferent axons, many of which terminate in the close proximity to the urothelium. The urothelial cells exhibit ‘neuron‐like’ properties that allow them to respond to mechanical and chemical stimuli and to release transmitters that can modulate the activity of afferent nerves.

British Journal of Pharmacology(2006)147, S25–S40. doi:10.1038/sj.bjp.0706604
Lower urinary tract disease: what are we trying to treat and in whom?
Authors: Heaton Jeremy P W.
Published: February 2006

The diseases of the lower urinary tract are traditionally divided into abnormalities of storage and abnormalities of emptying. The targets for therapy were the organs most responsible for influencing storage and emptying. Modern understanding places the symptomatic status of the patient as the overriding criterion for treatment. It also accommodates a broader understanding of multiple and overlapping systems. Symptoms of voiding dysfunction have been clearly shown to be associated with symptoms of other genitourinary disease, for example, erectile dysfunction (ED). Treatment of voiding dysfunction has also been shown to have effects (adverse or beneficial) in these other domains. Thus, the symptoms of lower urinary tract disease (LUTD) that have to be considered now as targets relevant to these therapies include ED, ejaculatory dysfunction, sexual desire, sexual pain disorders and female sexual dysfunction. The anatomic, neural and endocrine systems that support these symptomatic functions and dysfunctions span the range from the urogenital smooth muscle to the hypothalamus, the bladder sensory output to the micturition centre and growth factors to androgens. Potentially important targets also include vascular and spinal structures, sex hormones and nitric oxide as well as the obvious genes, enzymes and receptors. The epidemiological studies prove the convergence of LUTD when viewed through the lens of the current patient‐related outcomes and problem constructs. This convergence serves as a clear guidance to include wide ranging outcome instruments in all future studies with compounds being investigated for the treatment of LUTD. Out of these will come evidence of expected and unexpected collateral effects. The convergence should open the possibility to a different business model for developing therapeutic concepts. The blockbuster drug for a monolithic indication may be supplemented by agents with single or multiple pathway activity with smaller parallel targets. Using an approach based on patient reported outcomes to therapeutic targets not only widens the range of conditions, but also the patient types who can be considered as having LUTD.

British Journal of Pharmacology (2006) 147, S2–S13. doi:10.1038/sj.bjp.0706620
Integrated control of lower urinary tract – clinical perspective
Authors: Fowler Clare J.
Published: February 2006

The neural mechanisms that determine social bladder control are reviewed, with a particular emphasis on the role played by sensation in the process. Much has been learnt about the neural control of the bladder from studying patients with neurological disease and those disorders that are known to disrupt bladder storage are described. Possible approaches to treatment of the resulting incontinence are reviewed and it is acknowledged that in the future, the optimal treatment for incontinence may be determined by its precise underlying pathophysiology in each instance, for example, suprapontine causes requiring different medication to spinal causes. Although the main emphasis of urological research and development so far has been the treatment of incontinence, effective therapy for other bladder disorders such an impaired emptying or bladder pain could have an important impact on the bladder symptoms of many patients.

British Journal of Pharmacology (2006) 147, S14–S24. doi:10.1038/sj.bjp.0706629
Animal models in urological disease and sexual dysfunction
Authors: McMurray Gordon , Casey James H. , Naylor Alasdair M.
Published: February 2006

There are several conditions associated with dysfunction of the lower urinary tract or which result in a reduction in the ability to engage in satisfactory sexual function and result in significant bother to sufferers, partners and/or carers. This review describes some of the animal models that may be used to discover safe and effective medicines with which to treat them. While alpha adrenoceptor antagonists and 5‐alpha‐reductase inhibitors deliver improvement in symptom relief in benign prostatic hyperplasia sufferers, the availability of efficacious and well‐tolerated medicines to treat incontinence is less well served. Stress urinary incontinence (SUI) has no approved medical therapy in the United States and overactive bladder (OAB) therapy is limited to treatment with muscarinic antagonists (anti‐muscarinics). SUI and OAB are characterised by high prevalence, a growing ageing population and a strong desire from sufferers and physicians for more effective treatment options. High patient numbers with low presentation rates characterizes sexual dysfunction in men and women. The introduction of Viagra™ in 1998 for treating male erectile dysfunction and the success of the phosphodiesterase type 5 inhibitor class (PDE5 inhibitor) have indicated the willingness of sufferers to seek treatment when an effective alternative to injections and devices is available. The main value of preclinical models in discovering new medicines is to predict clinical outcomes. This translation can be established relatively easily in areas of medicine where there are a large number of drugs with different underlying pharmacological mechanisms in clinical usage. However, apart from, for example, the use of PDE5 inhibitors to treat male erectile dysfunction and the use of anti‐muscarinics to treat OAB, this clinical information is limited. Therefore, current confidence in existing preclinical models is based on our understanding of the biochemical, physiological, pathophysiological and psychological mechanisms underlying the conditions in humans and how they are reflected in preclinical models. Confidence in both the models used and the pharmacological data generated is reinforced if different models of related aspects of the same disorder generate confirmatory data. However, these models will only be fully validated in retrospect once the pharmacological agents they have helped identify are tested in humans.

British Journal of Pharmacology(2006)147, S62–S79. doi:10.1038/sj.bjp.0706630
Growth factor signalling in prostatic growth: significance in tumour development and therapeutic targeting
Authors: Reynolds Arich Ryan , Kyprianou Natasha
Published: February 2006

The intricate balance maintained between cell growth and proliferation factors and apoptosis‐inducing factors is fundamental to the regulation of prostate growth. Disruptions in this homeostasis often trigger the loss of apoptosis and the over‐expression of factors promoting cell survival and proliferation, inevitably leading to tumorigenesis and cancer. Deregulation of prostate growth during prostate cancer development and progression is characterized by apoptotic evasion, uncontrolled proliferation, and increased invasive potential. Thus, in advanced stages of disease progression, surviving prostate tumour cells acquire the ability to migrate and invade heterotopic tissues, with the bone and lymph nodes being the most common sites for human prostate cancer metastasis. The challenges in the implementation of effective therapeutic strategies for the treatment of advanced metastatic prostate cancer reflect the multidimensional nature and functional significance of antiapoptotic pathways in the emergence of therapeutic resistance of prostate tumours. In this chapter, we discuss the current understanding of the molecular mechanisms governing growth factor signalling pathways with often overlapping functions that contribute to loss of apoptosis control and activation of cell proliferation towards aggressive prostate tumorigenic growth and metastatic behaviour. While a full understanding of the prosurvival characteristics of these growth factor pathways is still evolving, the impact that growth factors such a epidermal growth factor and transforming growth factor‐β can be recognized by the vigorous attempts at therapeutic targeting of their key signalling steps.

British Journal of Pharmacology (2006) 147, S144–S152. doi:10.1038/sj.bjp.0706635
Late‐stage clinical development in lower urogenital targets: sexual dysfunction
Authors: Azam Usman
Published: February 2006

In recent years, late‐stage clinical drug development that primarily focuses on urogenital targets has centered around four areas of medical need (both unmet need and aiming to improve on existing therapies). These include male sexual dysfunction (MSD), female sexual dysfunction (FSD), prostatic pathology (neoplastic, pre‐neoplasitic, and non‐neoplastic), and improvement in lower urinary tract symptoms. Despite the regulatory approval of compounds to treat erectile dysfunction (ED), benign prostatic hyperplasia, a number of treatments for overactive bladder, and stress urinary incontinence, there remains a deficiency in addressing a number of conditions that arise out of pathophysiological dysfunction resulting in lower urogenital tract sexual conditions. In terms of late‐stage clinical development, significant progress has most recently been made in MSD development, especially in understanding further a common and complex sexual dysfunction – that of premature ejaculation. The search also continues for compounds that improve ED in terms of better efficacy and superior safety profile compared to the currently marketed phosphodiesterase‐5‐inhibitors. Whilst there are no approved medications to treat the subtypes of FSD, there has been significant progress in attempting to better understand how to appropriately assess treatment benefit in clinical trial settings for this difficult to diagnose and treat condition. This review will focus on late‐stage human clinical development pertaining to MSD and FSD.

British Journal of Pharmacology (2006) 147, S153–S159. doi:10.1038/sj.bjp.0706638
Bilirubin Oxidation Products (BOXes) and Their Role in Cerebral Vasospasm after Subarachnoid Hemorrhage
Authors: Clark Joseph F , Sharp Frank R
Published: February 2006

Many factors have been postulated to cause delayed subarachnoid hemorrhage (SAH)-induced vasospasm, including hemoglobin, nitric oxide, endothelin, and free radicals. We propose that free radicals (because of the high levels that are produced in the blood clots surrounding blood vessels after SAH) act on bilirubin, biliverdin, and possibly heme to produce BOXes (Bilirubin OXidized Products). Bilirubin oxidation products act on vascular smooth muscle cells to produce chronic vasoconstriction and vasospasm combined with a vasculopathy because of smooth muscle cell injury. This review summarizes recent evidence that BOXes play a role in SAH-induced vasospasm. The data supporting a role for BOXes includes (1) identification of molecules in cerebrospinal fluid (CSF) of patients with vasospasm after SAH that have structures consistent with BOXes; (2) BOXes are vasoactive in vitro and mimic the biochemical actions of CSF of patients with vasospasm; (3) BOXes are vasoactive in vivo, constricting rat cerebral vessels; and (4) there is a correlation between clinical occurrence of vasospasm and BOXes concentration in our preliminary study of patients with SAH. Since oxidation of bilirubin, biliverdin, and perhaps heme is proposed to produce BOXes that contribute to vasospasm, either blocking bilirubin formation, inactivating bilirubin or BOXes, or removing all of the blood clot before vasospasm are potential treatment targets.
Glucose is Necessary to Maintain Neurotransmitter Homeostasis during Synaptic Activity in Cultured Glutamatergic Neurons
Authors: Bak Lasse K , Schousboe Arne , Sonnewald Ursula , Waagepetersen Helle S
Published: February 2006

Glucose is the primary energy substrate for the adult mammalian brain. However, lactate produced within the brain might be able to serve this purpose in neurons. In the present study, the relative significance of glucose and lactate as substrates to maintain neurotransmitter homeostasis was investigated. Cultured cerebellar (primarily glutamatergic) neurons were superfused in medium containing [U-13C]glucose (2.5 mmol/L) and lactate (1 or 5 mmol/L) or glucose (2.5 mmol/L) and [U-13C]lactate (1 mmol/L), and exposed to pulses of N-methyl-D-aspartate (300 μmol/L), leading to synaptic activity including vesicular release. The incorporation of 13C label into intracellular lactate, alanine, succinate, glutamate, and aspartate was determined by mass spectrometry. The metabolism of [U-13C]lactate under non-depolarizing conditions was high compared with that of [U-13C]glucose; however, it decreased significantly during induced depolarization. In contrast, at both concentrations of extracellular lactate, the metabolism of [U-13C]glucose was increased during neuronal depolarization. The role of glucose and lactate as energy substrates during vesicular release as well as transporter-mediated influx and efflux of glutamate was examined using preloaded D-[3H]aspartate as a glutamate tracer and DL-threo-β-benzyloxyaspartate to inhibit glutamate transporters. The results suggest that glucose is essential to prevent depolarization-induced reversal of the transporter (efflux), whereas vesicular release was unaffected by the choice of substrate. In conclusion, the present study shows that glucose is a necessary substrate to maintain neurotransmitter homeostasis during synaptic activity and that synaptic activity does not induce an upregulation of lactate metabolism in glutamatergic neurons.
The Role of Endothelial Nitric Oxide Synthase (eNOS) Genetic Variants in European Patients with Intracranial Aneurysms
Authors: Krex Dietmar , Fortun Stefanie , Kuhlisch Eberhard , Schackert Hans K , Schackert Gabriele
Published: February 2006

The endothelial nitric oxide synthase (eNOS) gene harbors three well-characterized genetic variants, which have been reported to be associated with various vascular diseases. Recently, conflicting results have been published relating to the role of these genetic variants in the pathogenesis of intracranial aneurysms (IA). Therefore, we analyzed these variants in a large European population of IA patients and controls. In all, 142 patients with IA and 190 controls were enrolled in our study. The −786T > C and 894G > T single-nucleotide polymorphisms (SNPs) were analyzed by direct sequencing of the corresponding sections in the genomic DNA. A variable number tandem repeat (VNTR) located in intron 4 of the gene and consisting of either four or five 27-base pair (bp) repeats was analyzed by polymerase chain reaction amplification and electrophoresis using ALF sequencer™ equipment. Genotype and allele frequencies were determined, and the frequencies in cases and controls were compared. In addition, haplotypes were constructed. There were no deviations from Hardy–Weinberg equilibrium. Genotype and allele frequencies did not differ significantly between cases and controls in any sample group or after stratification for multiple IA or aneurysm size. No single haplotype was significantly associated with the phenotype of an IA. The −786T > C, 894G > T, and 27-bp VNTR genetic variants of the eNOS gene are not associated with IA in the European population.
Analysis of a particle antiparticle description of a soliton cellular automaton
Authors: Takagi Taichiro
Published: February 2006

We present a derivation of a formula that gives dynamics of an integrable cellular automation associated with crystal bases. This automaton is related to type D affine Lie algebra and contains usual box-ball systems as a special case. The dynamics is described by means of such objects as carriers, particles, and antiparticles. We derive it from an analysis of a recently obtained formula of the combinatorial R (an intertwiner between tensor products of crystals) that was found in a study of geometric crystals.
Diffusion-limited deposition with dipolar interactions: Fractal dimension and multifractal structure
Authors: Tasinkevych M. , Tavares J. M. , de los Santos F.
Published: February 2006

Computer simulations are used to generate two-dimensional diffusion-limited deposits of dipoles. The structure of these deposits is analyzed by measuring some global quantities: the density of the deposit and the lateral correlation function at a given height, the mean height of the upper surface for a given number of deposited particles, and the interfacial width at a given height. Evidences are given that the fractal dimension of the deposits remains constant as the deposition proceeds, independently of the dipolar strength. These same deposits are used to obtain the growth probability measure through the Monte Carlo techniques. It is found that the distribution of growth probabilities obeys multifractal scaling, i.e., it can be analyzed in terms of its f(α) multifractal spectrum. For low dipolar strengths, the f(α) spectrum is similar to that of diffusion-limited aggregation. Our results suggest that for increasing the dipolar strength both the minimal local growth exponent αmin and the information dimension D1 decrease, while the fractal dimension remains the same.
Path-integral centroid dynamics for general initial conditions: A nonequilibrium projection operator formulation
Authors: Jang Seogjoo
Published: February 2006

The formulation of path-integral centroid dynamics is extended to the quantum dynamics of density operators evolving from general initial states by means of the nonequilibrium projection operator technique. It is shown that the new formulation provides a basis for applying the method of centroid dynamics to nonequilibrium situations and that it allows the derivation of new formal relations, which can be useful in improving current equilibrium centroid dynamics methods. A simple approximation of uniform relaxation for the unprojected portion of the Liouville space propagator leads to a class of practically solvable equations of motion for the centroid variables, but with an undetermined parameter of relaxation. This new class of equations encompasses the centroid molecular-dynamics (CMD) method as a limiting case, and can be applied to both equilibrium and nonequilibrium situations. Tests for the equilibrium dynamics of one-dimensional model systems demonstrate that the new equations with appropriate choice of the relaxation parameter are comparable to the CMD method.
Highly accurate potential-energy and dipole moment surfaces for vibrational state calculations of methane
Authors: Oyanagi Chikako , Yagi Kiyoshi , Taketsugu Tetsuya , Hirao Kimihiko
Published: February 2006

Full-dimensional ab initio potential-energy surface (PES) and dipole moment surface are constructed for a methane molecule at the CCSD(T)/cc-pVTZ and MP2/cc-pVTZ levels of theory, respectively, by the modified Shepard interpolation method based on the fourth-order Taylor expansion [MSI(4th)]. The reference points for the interpolation have been set in the coupling region of CH symmetric and antisymmetric stretching modes so as to reproduce the vibrational energy levels related to CH stretching vibrations. The vibrational configuration-interaction calculations have been performed to obtain the energy levels and the absorption intensities up to 9000cm−1 with the use of MSI(4th)-PES. The calculated fundamental frequencies and low-lying vibrational energy levels show that MSI(4th) is superior to the widely employed quartic force field, giving a better agreement with the experimental values. The absorption bands of overtones as well as combination bands, which are caused by purely anharmonic effects, have been obtained up to 9000cm−1. Strongly coupled states with visible intensity have been found in the 6500–9000cm−1 region where the experimental data are still lacking.
Atomic force microscopy compatible device for stretching cells and adsorbed proteins
Authors: De Jong K. L. , MacLeod H. C. , Norton P. R. , Petersen N. O. , Jasnin M. F.
Published: February 2006

A device that we term a “microrack” was designed to provide a means to stretch cells and proteins and to permit the measurement of any changes in adhesion forces that might occur as a result of the strain, with an atomic force microscope. The device requires an elastic material that allows adsorption of proteins and attachment of cells. The elastomer polydimethylsiloxane (PDMS) was chosen, and its suitability for short-term cell studies was tested by comparing cell morphology and fiber distribution on PDMS with cells grown on glass, a conventional substrate for cell study. Atomic force microscopy (AFM) images and section analysis of beads and scrape marks on the PDMS surface before and after stretching indicate that the microrack can provide up to 21%–29% deformation of PDMS. AFM images of cells grown on PDMS show that material attached to the surface is also affected by stretching of the microrack. The rupture of the cell after stretching and rippling of the cell under compression can be attributed to the fixation treatment, but indicates that the cell morphology is significantly affected by the movement of the substrate on the microrack.
A second generation mesoscopic lipid bilayer model: Connections to field-theory descriptions of membranes and nonlocal hydrodynamics
Authors: Ayton Gary S. , McWhirter J. Liam , Voth Gregory A.
Published: February 2006

A new mesoscopic membrane model is developed in order to examine long-wavelength structural and dynamical membrane phenomena. Two different explicit mesoscopic solvent models are employed. The first mesoscopic solvent is denoted the big liquid oscillating blob system, which is parametrized to model water at a coarse-grained level and is motivated by a Langevin-like approach; the resulting membrane dynamics predict a solvent viscosity dependence consistent with the known viscosity of water. The second mesoscopic solvent is a Weeks-Chandler-Anderson model. Here, it is found that the correct mesoscopic hydrodynamic scaling of the membrane undulation dynamics is still preserved, although accelerated. When the behavior of the two membranes in close proximity to one another is examined, very little correlated motion is observed. However, the theoretically predicted scaling of the entropic undulation energy is confirmed, demonstrating that the entropic interaction between two membranes becomes increasingly repulsive with decreasing separation.
Thermal contact conductance of ceramic AlN and oxygen-free high-conductivity copper interfaces under low temperature and vacuum for high-temperature superconducting cryocooler cooling
Authors: Wang Jian , Wang Huiling , Zhuang Hanrui
Published: February 2006

In this article, a device for measuring thermal contact conductance under low temperature and vacuum for cryocooler cooling in high-temperature superconducting (HTS) system is presented. Such device may be used to simulate the real running condition of HTS equipments cooled by cryocooler. It is also convenient for temperature controlling. The thermal conductivity of ceramic AlN and the thermal contact conductance (TCC) between AlN and oxygen-free high-conductivity copper for the temperature range of 45–140 K and the vacuum range of 10−3–10−4Pa have been measured using axial steady heat-flow method on the Giffard-McMahon cryocooler with 5 W (20 K) capacity. Investigation shows that the TCC of the AlN∕Cu interface increases as the temperature and the pressure load of contact interface increase, and the conductivity of ceramic AlN increases as temperature rises. An analysis based on micro- and nanocryogenic concepts is made to explain the behaviors of thermal conductivity for AlN and thermal contact conductance for the AlN∕Cu interface.
Covariant equilibrium statistical mechanics
Authors: Lehmann E.
Published: February 2006

A manifest covariant equilibrium statistical mechanics is constructed starting with a 8N dimensional extended phase space which is reduced to the 6N physical degrees of freedom using the Poincaré-invariant constrained Hamiltonian dynamics describing the microdynamics of the system. The reduction of the extended phase space is initiated forcing the particles on energy shell and fixing their individual time coordinates with help of invariant time constraints. The Liouville equation and the equilibrium condition are formulated in respect to the scalar global evolution parameter which is introduced by the time fixation conditions. The applicability of the developed approach is shown for both, the perfect gas as well as the real gas. As a simple application the canonical partition integral of the monatomic perfect gas is calculated and compared with other approaches. Furthermore, thermodynamical quantities are derived. All considerations are shrinked on the classical Boltzmann gas composed of massive particles and hence quantum effects are discarded.
Radiative correction to the helium dimer interaction energy
Authors: Pachucki Krzysztof , Komasa Jacek
Published: February 2006

The leading-order radiative correction to the helium-helium interaction energy at the equilibrium internuclear distance has been calculated for the first time. The result is −1.27(2)mK. The calculations were performed using a new technique of evaluating expectation values of singular operators in connection with the most accurate wave functions of He2 available today—the exponentially correlated Gaussian functions.
Auger decay calculations with core-hole excited-state molecular-dynamics simulations of water
Authors: Takahashi Osamu , Odelius Michael , Nordlund Dennis , Nilsson Anders , Bluhm Hendrik , Pettersson Lars G. M.
Published: February 2006

We report a new theoretical procedure for calculating Auger decay transition rates including effects of core-hole excited-state dynamics. Our procedure was applied to the normal and first resonant Auger processes of gas-phase water and compared to high-resolution experiments. In the normal Auger decay, calculated Auger spectra were found to be insensitive to the dynamics, while the repulsive character of the first resonant core-excited state makes the first resonantly excited Auger decay spectra depend strongly on the dynamics. The ultrafast dissociation of water upon O(1s)→4a1 excitation was analyzed and found to be very sensitive to initial vibrational distortions in the ground state which furthermore affect the excitation energy. Our calculated spectra reproduce the experimental Auger spectra except for the Franck-Condon vibrational structure which is not included in the procedure. We found that the Auger decay of OH and O fragments contributes to the total intensity, and that the contribution from these fragments increases with increasing excitation energy.
Calculating potentials of mean force and diffusion coefficients from nonequilibrium processes without Jarzynski’s equality
Authors: Kosztin Ioan , Barz Bogdan , Janosi Lorant
Published: February 2006

In general, the direct application of the Jarzynski equality (JE) to reconstruct potentials of mean force (PMFs) from a small number of nonequilibrium unidirectional steered molecular-dynamics (SMD) paths is hindered by the lack of sampling of extremely rare paths with negative dissipative work. Such trajectories that transiently violate the second law of thermodynamics are crucial for the validity of JE. As a solution to this daunting problem, we propose a simple and efficient method, referred to as the FR method, for calculating simultaneously both the PMF U(z) and the corresponding diffusion coefficient D(z) along a reaction coordinate z for a classical many-particle system by employing a small number of fast SMD pullings in both forward (F) and time reverse (R) directions, without invoking JE. By employing Crooks [Phys. Rev. E 61, 2361 (2000)] transient fluctuation theorem (that is more general than JE) and the stiff-spring approximation, we show that (i) the mean dissipative work W¯d in the F and R pullings is the same, (ii) both U(z) and W¯d can be expressed in terms of the easily calculable mean work of the F and R processes, and (iii) D(z) can be expressed in terms of the slope of W¯d. To test its viability, the FR method is applied to determine U(z) and D(z) of single-file water molecules in single-walled carbon nanotubes (SWNTs). The obtained U(z) is found to be in very good agreement with the results from other PMF calculation methods, e.g., umbrella sampling. Finally, U(z) and D(z) are used as input in a stochastic model, based on the Fokker-Planck equation, for describing water transport through SWNTs on a mesoscopic time scale that in general is inaccessible to MD simulations.
Freezing line of the Lennard-Jones fluid: A phase switch Monte Carlo study
Authors: McNeil-Watson Graham C. , Wilding Nigel B.
Published: February 2006

We report a phase switch Monte Carlo (PSMC) method study of the freezing line of the Lennard-Jones (LJ) fluid. Our work generalizes to soft potentials the original application of the method to hard-sphere freezing and builds on a previous PSMC study of the LJ system by Errington [J. Chem. Phys. 120, 3130 (2004)]. The latter work is extended by tracing a large section of the Lennard-Jones freezing curve, the results of which we compare with a previous Gibbs-Duhem integration study. Additionally, we provide new background material regarding the statistical-mechanical basis of the PSMC method and extensive implementation details.
On the calculation of absolute free energies from molecular-dynamics or Monte Carlo data
Authors: Huang Lei , Makarov Dmitrii E.
Published: February 2006

We propose a method for calculating absolute free energies from Monte Carlo or molecular-dynamics data. The method is based on the identity that expresses the partition function Q as a Boltzmann average: 1∕Q=⟨w(p,x)exp[βH(p,x)]⟩, where w(p,x) is an arbitrary weight function such that its integral over the phase space is equal to 1. In practice, to minimize statistical errors the weight function is chosen such that the regions of the phase space where sampling statistics are poor are excluded from the average. The “ideal” weight function would be the equilibrium phase-space density exp[−βH(p,x)]∕Q itself. We consider two methods for constructing the weight function based on different estimates of the equilibrium phase-space density from simulation data. In the first method, it is chosen to be a Gaussian function, whose parameters are obtained from the covariance matrix of the atomic coordinates. In the second, a clustering algorithm is used to attempt partitioning the data into clusters corresponding to different basins of attraction visited by the system. The weight function is then constructed as a superposition of Gaussians calculated for each cluster separately. We show that these strategies can be used to improve upon previous methods of estimating absolute entropies from covariance matrices.
A new atomic force microscope probe with force sensing integrated readout and active tip
Authors: Onaran A. G. , Balantekin M. , Lee W. , Hughes W. L. , Buchine B. A. , Guldiken R. O. , Parlak Z. , Quate C. F. , Degertekin F. L.
Published: February 2006

We introduce a novel probe structure for the atomic force microscope. The probe has a sharp tip placed on a micromachined membrane with an integrated displacement sensor, a diffraction-based optical interferometer. We use this probe in a microscope to directly measure the transient interaction forces between the probe tip and the sample when operating in a dynamic mode. We form images related to viscoelasticity and adhesion of the samples by recording salient features of individual tap signals. We also produce tapping mode images of sample topography an order of magnitude faster than current probe microscopes using an integrated electrostatic actuator to move the probe tip. We envision a broad range of applications for this device that range from life sciences to microelectronics.
Design of a high-efficiency grazing incidence monochromator with multilayer-coated laminar gratings for the 1–6 keV region
Authors: Koike Masato , Ishino Masahiko , Sasai Hiroyuki
Published: February 2006

A grazing incidence objective monochromator consisting of a spherical mirror, a varied-line-spacing plane grating with multilayered coating, a movable plane multilayered mirror, and a fixed exit slit for the 1–6 keV region has been designed. The included angle at the grating was chosen to satisfy the grating equation and extended Bragg condition simultaneously. The aberration was corrected by means of a hybrid design method. A spectral resolving power of ∼600–∼6000 and a throughput of ∼2%–∼40% is expected for the monochromator when used in an undulator beamline.
Infrared vibrational spectroscopy of cis-dichloroethene in Rydberg states
Authors: Wang P. , Woo H. K. , Lau K.-C. , Xing X. , Ng C. Y. , Zyubin A. S. , Mebel A. M.
Published: February 2006

We have measured the infrared (IR) vibrational spectrum for cis-dichloroethene (cis-ClCHCHCl) in excited Rydberg states with the effective principal quantum numbers n*=9, 13, 17, 21, 28, and 55 using the vacuum ultraviolet-IR-photoinduced Rydberg ionization (VUV-IR-PIRI) scheme. Although the IR frequencies observed for the vibrational bands ν11* (asymmetric C–H stretch) and ν12* (symmetric C–H stretch) are essentially unchanged for different n* states, suggesting that the IR absorption predominantly involves the ion core and that the Rydberg electron behaves as a spectator; the intensity ratio for the ν11* and ν12* bands [R(ν11*∕ν12*)] is found to decrease smoothly as n* is increased. This trend is consistent with the results of a model ab initio quantum calculation of R(ν11*∕ν12*) for excited cis-ClCHCHCl in n*=3–18 states and the MP2∕6-311++G(2df,p) calculations of R(ν11∕ν12) and R(ν11+∕ν12+), where R(ν11∕ν12)[R(ν11+∕ν12+)] represents the intensity ratio of the ν11(ν11+) asymmetric C–H stretching to the ν12(ν12+) symmetric C–H stretching vibrational bands for cis-ClCHCHCl (cis-ClCHCHCl+). We have also measured the IR-VUV-photoion (IR-VUV-PI) and IR-VUV-pulsed field ionization-photoelectron depletion (IR-VUV-PFI-PED) spectra for cis-ClCHCHCl. These spectra are consistent with ab initio calculations, indicating that the IR absorption cross section for the ν12 band is negligibly small compared to that for the ν11 band. While the VUV-IR-PIRI measurements have allowed the determination of ν11+=3067±2cm−1, ν12+=3090±2cm−1, and R(ν11+∕ν12+)≈1.3 for cis-ClCHCHCl+, the IR-VUV-PI and IR-VUV-PFI-PED measurements have provided the value ν11=3088.5±0.2cm−1 for cis-ClCHCHCl.
Thermodynamically self-consistent liquid state theories for systems with bounded potentials
Authors: Mladek Bianca M. , Kahl Gerhard , Neumann Martin
Published: February 2006

The mean spherical approximation (MSA) can be solved semianalytically for the Gaussian core model (GCM) and yields exactly the same expressions for the energy and the virial equations. Taking advantage of this semianalytical framework, we apply the concept of the self-consistent Ornstein-Zernike approximation (SCOZA) to the GCM: a state-dependent function K is introduced in the MSA closure relation which is determined to enforce thermodynamic consistency between the compressibility route and either the energy or virial route. Utilizing standard thermodynamic relations this leads to two differential equations for the function K that have to be solved numerically. Generalizing our concept we propose an integrodifferential-equation-based formulation of the SCOZA which, although requiring a fully numerical solution, has the advantage that it is no longer restricted to the availability of an analytic solution for a particular system. Rather it can be used for an arbitrary potential and even in combination with other closure relations, such as a modification of the hypernetted chain approximation.