bluuebunny/crossref_metadata_2025 huggingface dataset:
Trends in performance of Turkish durum wheats derived from the International Maize and Wheat Improvement Center in an irrigated West Asian and North African environment
Authors: BARUTÇULAR C. , KOÇ M. , TIRYAKIOĞLU M. , YAZAR A.
Published: July 2006

Turkey is one of the most important durum wheat (T. turgidum L. var. durum Desf.) producers in West Asia and North Africa (WANA). There appears to have been a lack of progress in wheat yields in WANA over recent decades. Most of the modern cultivars grown in WANA are related to crosses produced by the International Maize and Wheat Improvement Center (CIMMYT). During 1999 and 2000, a chronological set of 11 cultivars related to CIMMYT crosses was evaluated using two irrigation regimes near Şanlıurfa, Turkey.

Average yields ranged from 386 g/m2 (local cultivar, Karakılçık-33) to 614 g/m2 (Ege-88). When wheat cultivars were grown with irrigation until physiological maturity, cessation of irrigation near anthesis reduced average grain yields of all cultivars by 6·2–25·7%. Since the introduction of the first generation of CIMMYT cultivars in 1975, CIMMYT grain yields have increased by about 0·60% per year compared with that of Karakılçık-33. This rate increased up to 1·08% per year until 1988. No further progress in yield was measured for varieties released in the 1990s. The average rate was 0·76% per year. After the introduction of the CIMMYT cultivars, yield changes fitted better in a quadratic function. Compared with Karakılçık-33, the yield increases of CIMMYT cultivars have resulted from an increase in harvest index associated with reduced height and the development of more and heavier grains. Grain quality traits decreased with the introduction of the first CIMMYT cultivar but recovered slightly thereafter with no clear trend. The results are discussed with consideration of breeding priorities and specific WANA conditions.
Effects of dietary conjugated linoleic acid on production and metabolic parameters in transition dairy cows grazing fresh pasture
Authors: Kay Jane K , Roche John R , Moore Chel E , Baumgard Lance H
Published: July 2006

Supplementation with a high dose (600 g/d) of rumen inert conjugated linoleic acids (RI-CLA) inhibits milk fat synthesis in total mixed ration (TMR)-fed dairy cows immediately post partum. However, effects of RI-CLA on milk fat and bioenergetic parameters during the transition period in grazing cows have not been investigated. Multiparous Holstein cows (n=39) grazing pasture were randomly assigned to one of three treatments: (1) pasture (PAS), (2) PAS+540 g/d Hyprofat (palm oil; HYPRO) and (3) PAS+600 g/d RI-CLA. HYPRO and RI-CLA supplements were isoenergetic, fed twice daily at 7.00 and 16.00 and provided 0 and 125 g CLA/d, respectively. Treatments began 27±10 d prepartum and continued until 36±1 days in milk (DIM). There was little or no overall effect of RI-CLA on content or yield of milk protein and lactose. RI-CLA supplementation decreased overall milk fat content and yield with RI-CLA-induced milk fat depression (MFD) becoming significant by day 3 when compared with PAS and by day 6 when compared with HYPRO. MFD continued to increase in severity during the first 24 d post partum after which MFD reached a plateau (~40%; RI-CLA v. HYPRO). Pasture-fed cows produced less milk (19·4 kg/d) than the lipid-supplemented groups and although there were no overall differences in milk yield between RI-CLA and HYPRO (22·3 kg/d) a curvilinear relationship (R2=0·57) existed between the RI-CLA-induced milk yield response and extent of MFD. RI-CLA tended to increase milk yield (1·8 kg/d) compared with HYPRO until MFD exceeded 35% (~day 21), after which point the positive milk yield response was eliminated. Milk fat trans-10, cis-12 CLA content averaged 0·25 g/100 g in the RI-CLA treatment, was temporally independent, and was undetectable in PAS and HYPRO treatments. Based on the milk fat 14[ratio ]1/14[ratio ]0 ratio, RI-CLA decreased the overall Δ9-desaturase system compared with PAS and HYPRO. Compared with HYPRO, RI-CLA had no effect on plasma glucose, insulin, leptin, or NEFA concentrations. Results indicate that a high RI-CLA dose decreases milk fat synthesis and tends to increase milk yield immediately post partum in pasture-fed cows; however, excessive MFD (>35%) appears to be associated with a diminished milk yield response.
Importance of the host specificity in the selection of probiotic bacteria
Authors: Dogi Cecilia A , Perdigón Gabriela
Published: July 2006

The gastrointestinal tract is a complex and dynamic ecosystem. Commensal microorganisms (C), which proliferate in the intestine from birth, are crucial for gut homeostasis while non commensal (NC) microorganisms are transient and enter the organism from the environment and foods. We studied comparatively the influence of oral administration of C and NC Lactobacillus fermentum and Lactobacilus acidophilus on the gut-associated lymphoid tissue (GALT) of conventional mice. To determine the importance of the selection of probiotic host-specificity bacteria with immunomodulating capacity, we examined the interaction with the gut by transmission electron microscopy and FITC-labelled bacteria. We compared the immunomodulation capacities of C and NC strains by studying the number of IgA secreting cells and cytokine profile. No differences were found in the number of IgA+ cells; however, the pattern of cytokine response to C and NC bacteria was different. With regard to proinflammatory cytokine (IFNγ and TNFα), we found that TNFα was mainly produced by NC bacteria, while C bacteria were able to elicit mainly IFNγ. The regulatory cytokines (IL-10 and IL-4) were induced with different patterns for both C and NC strains. No differences in the pathway of internalization to the gut between C and NC were found. In summary, we determined that C and NC bacteria interact with the intestine in the same way; both C and NC bacteria were able to reinforce the surveillance of the gut mucosal immune system. The cytokine profile showed that C bacteria would be involved in the regulation of intestinal homeostasis rather than in the immune activation as the NC bacteria.
Performance and behaviour of calves reared in groups or individually following an enhanced-growth feeding programme
Authors: Terré Marta , Bach Alex , Devant Maria
Published: July 2006

Nineteen calves were reared in individual pens (IP), and twenty calves were grouped in four pens of five calves each (GP) to study the effects of grouping on behaviour and performance. All calves were on an enhanced-growth feeding programme and had unlimited access to starter. Total dry matter intake (DMI) body weight (BW), serum urea, non-esterified fatty acid (NEFA), cortisol, insulin, and glucose concentrations, and immune response to vaccination were measured. Behaviour patterns categorized as: non-nutritive oral behaviour, cross-sucking, inter-sucking, and self-grooming, were monitored 20 min following the morning and afternoon milk replacer consumption, and at the same times after weaning. There were no differences in final BW and starter DMI between treatments. The decrease of average daily gain (ADG) during the week following weaning was more pronounced in GP than in IP calves. Serum NEFA concentration increased at the beginning of the study in IP calves but serum urea concentrations were greater in GP than in IP calves the week after weaning. Self-grooming increased in both treatments throughout the study but GP calves increased non-nutritive oral behaviour and decreased cross-sucking and inter-sucking behaviours throughout the study. Rearing calves in groups following an enhanced-growth feeding programme did not increase starter intake. Furthermore, cross-sucking and inter-sucking behaviours in calves reared in groups did not seem to cause increased metabolic or immunological distress.
The End of the Road for the Prince? Sixty Years after the Czechoslovak Confiscation of Liechtenstein Property
Authors: DELMARTINO BART
Published: July 2006

In 1945 Czechoslovakia confiscated Liechtenstein property as reparation for the damage done by Nazi Germany. Private claims failed before the courts of Czechoslovakia, and international law did not provide Liechtenstein with a means of action against Czechoslovakia. When the property was on loan in Germany, a private case for recovery was declared inadmissible by the German courts, in line with Germany's international obligations. The European Court of Human Rights accepted these decisions. Liechtenstein, on the other hand, considered them to violate its sovereignty. In 2005, the International Court of Justice decided that it lacked temporal jurisdiction to rule on the issue.
The First Trial of Former Members of the Kosovo Liberation Army: Prosecutor v. Fatmir Limaj, Haradin Bala, and Isak Musliu
Authors: CHIFFLET PASCALE
Published: July 2006

In its Judgement issued on 30 November 2005 in Prosecutor v. Limaj et al., Trial Chamber II of the ICTY found that an armed conflict existed in Kosovo between the Kosovo Liberation Army and the Serbian forces as of the end of May 1998. It held, however, that the evidence did not establish that there was a widespread or systematic attack by the KLA directed against a civilian population at the relevant time. The first trial of former members of the Kosovo Liberation Army also gave rise to a number of significant developments in the ICTY's jurisprudence relating to issues of international criminal law and procedure, such as the treatment of hostile witnesses and of eyewitness identification evidence, as well as the proof of the existence of a joint criminal enterprise.
The Judgment of the International Criminal Tribunal for the Former Yugoslavia in Prosecutor v. Pavle Strugar
Authors: HINEK SILVA
Published: July 2006

This case note focuses on two aspects of the January 2005 Strugar Judgment of the ICTY. The first is the trial chamber's finding that the accused was not aiding and abetting his subordinates in the commission of the crimes charged through his failure to discharge his duty to prevent the crimes and/or punish the perpetrators. The second is the trial chamber's definition of one of the alternative mental states a superior must possess before a conviction can be entered against him on the basis of Article 7(3).
Testing Compliance Theories: Towards US Obedience of International Law in the Avena Case
Authors: PULKOWSKI DIRK
Published: July 2006

Eyal Benvenisti and Moshe Hirsch (eds.), The Impact of International Law on International Cooperation: Theoretical Perspectives, Cambridge, Cambridge University Press, 2004, ISBN 0521835542, 330 pp., £55.00 (hb).

Markus Burgstaller, Theories of Compliance with International Law, Leiden, Martinus Nijhoff, 2005, ISBN 9004141936, 244 pp., €98.00 (hb).

Constanze Schulte, Compliance with Decisions of the International Court of Justice, Oxford, Oxford University Press, 2004, ISBN 0199276722, 500 pp., £75.00 (hb).

Science is organized common sense where many a beautiful theory was killed by an ugly fact.

Thomas H. Huxley
New Approaches to the History of International Law
Authors: BAXI UPENDRA
Published: July 2006

Anthony Anghie, Imperialism, Sovereignty, and the Making of International Law, Cambridge, Cambridge University Press, 2005, ISBN 0521828929, 356 pp., £60.00 (hb).

Gerry Simpson, Great Powers and Outlaw States: Unequal Sovereigns in the International Legal Order, Cambridge, Cambridge University Press, 2004, ISBN 0521827612, 414 pp., £65.00 (hb).
Sentinel laboratory surveillance of hepatitis C antibody testing in England: understanding the epidemiology of HCV infection
Authors: BRANT L. J. , HURRELLE M. , BALOGUN M. A. , KLAPPER P. , AHMAD F. , BOXALL E. , HALE A. , HOLLYOAK V. , IBRAHIM I. B. , IRVING W. , MEIGH R. , MUTTON K. J. , PATEL B. C. , PAVER W. K. , PUGH S. , TAYLOR C. , TURNER A. J. , RAMSAY M. E.
Published: July 2006

This paper describes sentinel laboratory surveillance of hepatitis C antibody testing in England. Demographic and test result data were supplemented by follow-up questionnaires sent to the requesting clinician. Between October 2002 and September 2003 almost 75000 anti-HCV tests were performed in eight sentinel centres. More males were tested than females and over half of those tested were aged 25–44 years. Overall 5·7% (3333/58144, range 2·8–7·7%) individuals tested positive. Follow-up questionnaire data showed that 82% (1043/1277) of the positives had injecting drug use reported as the main risk exposure. The majority of negative individuals were undergoing routine screening as recommended for specific patient groups. Most individuals were asymptomatic. Antibody prevalence was estimated to be 34% in current injecting drug users and 42% in former injectors. Comparing positives to routine national surveillance suggests that only 53% (1782/3333) of diagnosed cases were reported. Sentinel laboratory data can provide valuable supplementary data to national surveillance.
Screening strategies in surveillance and control of methicillin-resistant Staphylococcus aureus (MRSA)
Authors: ROBOTHAM J. V. , JENKINS D. R. , MEDLEY G. F.
Published: July 2006

With reports of hospital-acquired methicillin-resistant Staphylococcus aureus (MRSA) continuing to increase and therapeutic options decrease, infection control methods are of increasing importance. Here we investigate the relationship between surveillance and infection control. Surveillance plays two roles with respect to control: it allows detection of infected/colonized individuals necessary for their removal from the general population, and it allows quantification of control success. We develop a stochastic model of MRSA transmission dynamics exploring the effects of two screening strategies in an epidemic setting: random and on admission. We consider both hospital and community populations and include control and surveillance in a single framework. Random screening was more efficient at hospital surveillance and allowed nosocomial control, which also prevented epidemic behaviour in the community. Therefore, random screening was the more effective control strategy for both the hospital and community populations in this setting. Surveillance strategies have significant impact on both ascertainment of infection prevalence and its control.
Resilience and sustainable development
Authors: PERRINGS CHARLES
Published: July 2006

This special issue results from a call for papers to address the connection between resilience and sustainability, and stems from the fact that the ecological concept of resilience has been exercising an increasing influence on the economics of development. Resilience is interpreted in two different ways by ecologists: one capturing the speed of return to equilibrium following perturbation (Pimm, 1984), the other capturing the size of a disturbance needed to dislodge a system from its stability domain (Holling, 1973). The latter may be interpreted as the conditional probability that a system in one stability domain will flip into another stability domain given its current state and the disturbance regime (Perrings, 1998). The relevance of this concept for the problem of sustainable economic development has been recognized for at least fifteen years (Common and Perrings, 1992). Indeed, Levin et al. (1998) claimed that resilience is the preferred way to think about sustainability in social as well as natural systems, and a research network – the Resilience Alliance – has subsequently developed around the idea.
Pollution thresholds under uncertainty
Authors: WIRL FRANZ
Published: July 2006

This study investigates the optimal use of ‘dirty’ technologies for economic development and when to stop polluting (either temporarily or forever). This question is addressed within a real option framework where three different kinds of options arise: for stopping pollution temporarily or forever and for re-starting. The possibility to shelve a polluting technology temporarily allows for a more conservationist policy. Costs associated with the option of a re-start lead to hystereses effects that complicate empirical cross-country comparisons of environmental policies.
Firm size diversity, functional richness, and resilience
Authors: GARMESTANI AHJOND S. , ALLEN CRAIG R. , MITTELSTAEDT JOHN D. , STOW CRAIG A. , WARD WILLIAM A.
Published: July 2006

This paper applies recent advances in ecology to our understanding of firm development, sustainability, and economic development. The ecological literature indicates that the greater the functional richness of species in a system, the greater its resilience – that is, its ability to persist in the face of substantial changes in the environment. This paper focuses on the effects of functional richness across firm size on the ability of industries to survive in the face of economic change. Our results indicate that industries with a richness of industrial functions are more resilient to employment volatility.
Growth factor pathway switching: implications for the use of gefitinib and trastuzumab
Authors: Jones H. E. , Gee J. M. W. , Hutcheson I. R. , Nicholson R. I.
Published: July 2006

Over-expression or aberrant signalling of the erbB family members epidermal growth factor receptor (EGFR) and HER2 (erbB2/neu) have been associated with the pathogenesis of the malignant phenotype. In addition, high levels of EGFR and HER2 expression have been shown to correlate with poor prognosis and also implicated in disease progression. Signal transduction inhibitors (STIs) have been developed with specifically target these receptors and include the small molecule tyrosine kinase inhibitor gefitinib (IressaTM) which targets the EGFR and the humanised monoclonal antibody trastuzumab (HerceptinTM), which has anti-tumour activity against HER2. Studies however, have indicated that de novo or acquired resistance to these agents is a major clinical problem. Cancer cells are highly adaptive and can readily switch from one receptor signalling pathway to another in order to maintain growth or cell survival, a process paradoxically, that in many instances is induced by the anti-tumour agents themselves, ultimately limiting their activity and promoting resistance. Evidence is accumulating which demonstrates that signalling interplay occurs between the EGFR/HER2 and the insulin-like growth factor -1 receptor (IGF-1R) and the article will focus on the growth factor pathway switching that occurs between these receptors which can influence the effectiveness gefitinib and trastuzumab.
Evaluation of the simulation of the annual cycle of Arctic and Antarctic sea ice coverages by 11 major global climate models
Authors: Parkinson Claire L. , Vinnikov Konstantin Y. , Cavalieri Donald J.
Published: July 2006

Comparison of polar sea ice results from 11 major global climate models (GCMs) and satellite‐derived observations for 1979–2004 reveals that each of the models is simulating annual cycles that are phased at least approximately correctly in both hemispheres. Each is also simulating various key aspects of the observed ice cover distributions, such as winter ice not only throughout the central Arctic basin but also throughout Hudson Bay, despite its relatively low latitudes. However, some of the models simulate too much ice, others simulate too little ice (in some cases depending on hemisphere and/or season), and some match the observations better in one season versus another. Several models do noticeably better in the Northern Hemisphere than in the Southern Hemisphere, and one does noticeably better in the Southern Hemisphere. In the Northern Hemisphere all simulate monthly average ice extents to within ±5.1 × 106 km2 of the observed ice extent throughout the year; in the Southern Hemisphere all except one simulate the monthly averages to within ±6.3 × 106 km2 of the observed values. All the models properly simulate a lack of winter ice to the west of Norway; however, most obtain more ice immediately north of Norway than the observations show, suggesting an under simulation of the North Atlantic Current. The spread in monthly averaged ice extents among the 11 model simulations is greater in the Southern Hemisphere than in the Northern Hemisphere and greatest in the Southern Hemisphere winter and spring.
A remote sensing observatory for hydrologic sciences: A genesis for scaling to continental hydrology
Authors: Krajewski Witold F. , Anderson Martha C. , Eichinger William E. , Entekhabi Dara , Hornbuckle Brian K. , Houser Paul R. , Katul Gabriel G. , Kustas William P. , Norman John M. , Peters‐Lidard Christa , Wood Eric F.
Published: July 2006

Uncertainties in assessing the effects of global‐scale perturbations on the climate system arise primarily from an inadequate understanding of the hydrological cycle: on land, in oceans, and in the atmosphere and biosphere. Because of this uncertainty, almost all science‐based initiatives have expressed the need for continued advances in global observations and modeling of the Earth system. It is in this spirit that we advocate establishing a hydrologic remote sensing observatory (RSO) to advance sensing technologies and their use in scientific inquiry into hydrologic processes. There are two fundamental reasons why establishing such a RSO is timely. The first is operational: Developing assimilation techniques to estimate unobserved fluxes and uncertainties in hydrologic forecasts has sufficiently matured to take advantage of computing facilities and detailed hydrologic observations shaped by the RSO. The second is scientific: This RSO will permit us to refine knowledge from physical and hydrologic models that can then be converted to local and global strategies for water resources management and ecosystem health evaluation. The authors outline the conceptual design, scope, and functionality of a RSO and present four examples to illustrate how the hydrologic community can take advantage of such facility.
Quantitative network model predictions of saturation behind infiltration fronts and comparison with experiments
Authors: DiCarlo David A.
Published: July 2006

Infiltrations with certain boundary and initial conditions show an anomalous behavior where the water saturation and pressure profile are inverted in the vertical direction. This occurs when the water at the infiltration front oversaturates the porous medium, causing drainage behind the front, and is most likely due to the front being sharp at the pore scale. Here we attempt to quantitatively model water flow at infiltration fronts by using a physically based network model that includes viscous effects. The network model includes pore and throat elements of different shapes and sizes, and a connection topology based on geologic media. Viscous effects are added quasi‐statically through calculating the water pressure in each element for a particular applied flux. For media with a small initial saturation, the infiltration flux range for which saturation overshoot occurs is predicted by the network model. For initially dry media, the model predictions scale correctly with media size but require an independent parameter to predict the absolute transition flux. The predicted magnitude of the overshoot does not match particularly well with the measured magnitude for coarse media, although this may be the result of certain simplified assumptions in the model. The results suggest that pore‐scale modeling can make certain quantitative predictions of saturation overshoot.
Three‐dimensional investigation of volcanic textures by X‐ray microtomography and implications for conduit processes
Authors: Polacci Margherita , Baker Don R. , Mancini Lucia , Tromba Giuliana , Zanini Franco
Published: July 2006

Synchrotron X‐ray computed microtomography (μCT) was applied for the first time to clasts of pumice and scoria generated by active, explosive volcanoes characterized by a range of eruptive styles (mild Strombolian to Plinian) and magmatic composition (basaltic to trachytic). The obtained two‐dimensional (2D) tomographic images, corresponding to sample views at different rotation angles, were processed to reconstruct three‐dimensional (3D) volumes and then used to make 3D measurements of vesicularity, vesicle number density, volume and connectivity for quantitative characterization of the investigated tephras. The results indicate a positive correlation between vesicle number density and eruption intensity that is used to investigate modes of magma degassing in explosive eruptions. In addition, the vesicle geometry affecting the connected gas flow pathways in pyroclasts from Strombolian eruptions is determined and related to the known permeabilities. Implications on the dynamics of explosive eruptions is discussed and, ultimately, used to quantitatively discriminate between different eruptive styles.
Effects of continental insulation and the partitioning of heat producing elements on the Earth's heat loss
Authors: Cooper C. M. , Lenardic A. , Moresi L.
Published: July 2006

Continental lithosphere influences heat loss by acting as a local insulator to the convecting mantle and by sequestering heat‐producing radioactive elements from the mantle. Continental heat production can have a two‐part effect since it decreases the amount of internal heat driving convection, which lowers mantle temperature, while also increasing the local insulating effect of continental lithosphere, which raises mantle temperature. We explored these competing effects using simulations that incorporated enriched continents within a mixed internal‐ and bottom‐heated convecting mantle. Increasing continental surface area was found to enhance global heat loss for a range of heat production distributions and Rayleigh numbers. The effect of enriched continents was evident as a double peak in the continental surface area values that maximize global heat loss. That the presence of continental lithosphere could increase average mantle temperature despite the mantle being depleted suggests that continents can significantly influence mantle potential temperature.
The Concept Plot: A Concept Mapping Visualization Tool for Asynchronous Web-Based Brainstorming Sessions
Authors: Ivanov Alex , Cyr Dianne
Published: July 2006

Electronic brainstorming systems have been shown to lead to more ideas, yet unsupported face-to-face brainstorming is still widely preferred. This paper proposes a graphical user interface for a web-based system for design problem-solving or other intellective tasks involving convergent and divergent thinking. Referring to the literature on group support systems and information and knowledge visualization, the study extends features of concept mapping and synthesizes these into a prototype called the Concept Plot (CP). Based on an advertising design task, the paper shows how the CP can be collaboratively constructed in two directions, as text and pictures are uploaded onto nodes, and these nodes scaled up or down as users click to evaluate ideas. The expectation is that this integrated visualization would diminish information overload, while enhancing the social dynamics of the process. Also presented is the pilot deployment of a Flash prototype. The results were inconclusive, yet promising that a study with more participants might demonstrate the functional and affective benefits of the CP.
A second-quantization framework for the unified treatment of relativistic and nonrelativistic molecular perturbations by response theory
Authors: Helgaker Trygve , Hennum Alf Christian , Klopper Wim
Published: July 2006

A formalism is presented for the calculation of relativistic corrections to molecular electronic energies and properties. After a discussion of the Dirac and Breit equations and their first-order Foldy-Wouthuysen [Phys. Rev. 78, 29 (1950)] transformation, we construct a second-quantization electronic Hamiltonian, valid for all values of the fine-structure constant α. The resulting α-dependent Hamiltonian is then used to set up a perturbation theory in orders of α2, using the general framework of time-independent response theory, in the same manner as for geometrical and magnetic perturbations. Explicit expressions are given to second order in α2 for the Hartree-Fock model. However, since all relativistic considerations are contained in the α-dependent Hamiltonian operator rather than in the wave function, the same approach may be used for other wave-function models, following the general procedure of response theory. In particular, by constructing a variational Lagrangian using the α-dependent electronic Hamiltonian, relativistic corrections can be calculated for nonvariational methods as well.
Singly and doubly excited states of butadiene, acrolein, and glyoxal: Geometries and electronic spectra
Authors: Saha Biswajit , Ehara Masahiro , Nakatsuji Hiroshi
Published: July 2006

Excited-state geometries and electronic spectra of butadiene, acrolein, and glyoxal have been investigated by the symmetry adapted cluster configuration interaction (SAC-CI) method in their s-trans conformation. Valence and Rydberg states below the ionization threshold have been precisely calculated with sufficiently flexible basis sets. Vertical and adiabatic excitation energies were well reproduced and the detailed assignments were given taking account of the second moments. The deviations of the vertical excitation energies from the experiment were less than 0.3eV for all cases. The SAC-CI geometry optimization has been applied to some valence and Rydberg excited states of these molecules in the planar structure. The optimized ground- and excited-state geometries agree well with the available experimental values; deviations lie within 0.03Å and 0.7° for the bond lengths and angles, respectively. The force acting on the nuclei caused by the excitations has been discussed in detail by calculating the SAC-CI electron density difference between the ground and excited states; the geometry relaxation was well interpreted with the electrostatic force theory. In Rydberg excitations, geometry changes were also noticed. Doubly excited states (so-called 2Ag1 states) were investigated by the SAC-CI general-R method considering up to quadruple excitations. The characteristic geometrical changes and large energetic relaxations were predicted for these states.
Post-transition state dynamics for propene ozonolysis: Intramolecular and unimolecular dynamics of molozonide
Authors: Vayner Grigoriy , Addepalli Srirangam V. , Song Kihyung , Hase William L.
Published: July 2006

A direct chemical dynamics simulation, at the B3LYP∕6-31G(d) level of theory, was used to study the post-transition state intramolecular and unimolecular dynamics for the O3+propene reaction. Comparisons of B3LYP∕6-31G(d) with CCSD(T)/cc-pVTZ and other levels of theory show that the former gives accurate structures and energies for the reaction’s stationary points. The direct dynamics simulations are initiated at the anti and syn O3+propene transition states (TSs) and the TS symmetries are preserved in forming the molozonide intermediates. Anti↔syn molozonide isomerization has a very low barrier of 2–3kcal∕mol and its Rice-Ramsperger-Kassel-Marcus (RRKM) lifetime is 0.3ps. However, the trajectory isomerization is slower and it is unclear whether this anti↔syn equilibration is complete when the trajectories are terminated at 1.6ps. The syn (anti) molozonides dissociate to CH3CHO+H2COO and H2CO+syn (anti) CH3CHOO. The kinetics for the latter reactions are in overall good agreement with RRKM theory, but there is a symmetry preserving non-RRKM dynamical constraint for the former. Dissociation of anti molozonide to CH3CHO+H2COO is enhanced and suppressed, respectively, for the trajectory ensembles initiated at the anti and syn O3+propene TSs. The dissociation of syn molozonide to CH3CHO+H2COO may also be enhanced for trajectories initiated at the syn O3+propene TS. At the time the trajectories are terminated at 1.6ps, the ratio of the trajectory and RRKM values of the CH3CHO+H2COO product yield is 1.6 if the symmetries of the initiation and dissociation TSs are the same and 0.6 if their symmetries are different. There are coherences in the intramolecular energy flow, which depend on molozonide’s symmetry (i.e., anti or syn). This symmetry related dynamics is not completely understood, but it is clearly related to the non-RRKM dynamics for anti↔syn isomerization and anti molozonide dissociation to CH3CHO+H2COO. Correlations are found between the stretching motions of molozonide, indicative of nonchaotic and non-RRKM dynamics. The non-RRKM dynamics of molozonide dissociation partitions vibration energy to H2COO that is larger than statistical partitioning. Though the direct dynamics simulations are classical, better agreement is obtained using quantum instead of classical harmonic RRKM theory. This may result from the neglect of anharmonicity in the RRKM calculations, the non-RRKM dynamics of the classical trajectories, or a combination of these two effects. The trajectories suggest that the equilibrium syn/anti molozonide ratio is approximately 1.1–1.2 times larger than that predicted by the harmonic densities of state, indicating an anharmonic correction.
Seven-dimensional microcanonical treatment of hydrogen dissociation dynamics on Cu(111): Clarifying the essential role of surface phonons
Authors: Abbott H. L. , Harrison I.
Published: July 2006

A simple picture of the hydrogen dissociation/associative desorption dynamics on Cu(111) emerges from a two-parameter, full dimensionality microcanonical unimolecular rate theory (MURT) model of the gas-surface reactivity. Vibrational frequencies for the reactive transition state were taken from density functional theory calculations of a six-dimensional potential energy surface [Hammer et al., Phys. Rev. Lett. 73, 1400 (1994)]. The two remaining parameters required by the MURT were fixed by simulation of experiments. These parameters are the dissociation threshold energy, E0=79kJ∕mol, and the number of surface oscillators involved in the localized H2∕Cu(111) collision complex, s=1. The two-parameter MURT quantitatively predicts much of the varied behavior observed for the H2 and D2∕Cu(111) reactive systems, including the temperature-dependent associative desorption angular distributions, mean translational energies of the associatively desorbing hydrogen as a function of rovibrational eigenstate, etc. The divergence of the statistical theory’s predictions from experimental results at low rotational quantum numbers, J≲5, suggests that either (i) rotational steering is important to the dissociation dynamics at low J, an effect that washes out at high J, or (ii) molecular rotation is approximately a spectator degree of freedom to the dissociation dynamics for these low J states, the states that dominate the thermal reactivity. Surface vibrations are predicted to provide ∼30% of the energy required to surmount the activation barrier to H2 dissociation under thermal equilibrium conditions. The MURT with s=1 is used to analytically confirm the experimental finding that ∂“Ea(Ts)”∕∂Et=−1 for eigenstate-resolved dissociative sticking at translational energies Et<E0−Ev−Er. Explicit treatment of the surface motion (i.e., surface not frozen at Ts=0K) is a relatively novel aspect of the MURT theoretical approach.
Stability of discrete memory states to stochastic fluctuations in neuronal systems
Authors: Miller Paul , Wang Xiao-Jing
Published: July 2006

Noise can degrade memories by causing transitions from one memory state to another. For any biological memory system to be useful, the time scale of such noise-induced transitions must be much longer than the required duration for memory retention. Using biophysically-realistic modeling, we consider two types of memory in the brain: short-term memories maintained by reverberating neuronal activity for a few seconds, and long-term memories maintained by a molecular switch for years. Both systems require persistence of (neuronal or molecular) activity self-sustained by an autocatalytic process and, we argue, that both have limited memory lifetimes because of significant fluctuations. We will first discuss a strongly recurrent cortical network model endowed with feedback loops, for short-term memory. Fluctuations are due to highly irregular spike firing, a salient characteristic of cortical neurons. Then, we will analyze a model for long-term memory, based on an autophosphorylation mechanism of calcium/calmodulin-dependent protein kinase II (CaMKII) molecules. There, fluctuations arise from the fact that there are only a small number of CaMKII molecules at each postsynaptic density (putative synaptic memory unit). Our results are twofold. First, we demonstrate analytically and computationally the exponential dependence of stability on the number of neurons in a self-excitatory network, and on the number of CaMKII proteins in a molecular switch. Second, for each of the two systems, we implement graded memory consisting of a group of bistable switches. For the neuronal network we report interesting ramping temporal dynamics as a result of sequentially switching an increasing number of discrete, bistable, units. The general observation of an exponential increase in memory stability with the system size leads to a trade-off between the robustness of memories (which increases with the size of each bistable unit) and the total amount of information storage (which decreases with increasing unit size), which may be optimized in the brain through biological evolution.
The effect of negative feedback on noise propagation in transcriptional gene networks
Authors: Hooshangi Sara , Weiss Ron
Published: July 2006

This paper analyzes how the delay and repression strength of negative feedback in single-gene and multigene transcriptional networks influences intrinsic noise propagation and oscillatory behavior. We simulate a variety of transcriptional networks using a stochastic model and report two main findings. First, intrinsic noise is not attenuated by the addition of negative or positive feedback to transcriptional cascades. Second, for multigene negative feedback networks, synchrony in oscillations among a cell population can be improved by increasing network depth and tightening the regulation at one of the repression stages. Our long term goal is to understand how the noise characteristics of complex networks can be derived from the properties of modules that are used to compose these networks.
Chemical oscillations and Turing patterns in a generalized two-variable model of chemical self-replication
Authors: Beutel Kathleen M. , Peacock-López Enrique
Published: July 2006

Chemical self-replication of oligonucleotides and helical peptides show the so-called square root rate law. Based on this rate we extend our previous work on ideal replicators to include the square root rate and other possible nonlinearities, which we couple with an enzimatic sink. Although the nonlinearity is necessary for complex dynamics, the nature of the sink is the essential feature in the mechanism that allows temporal and spatial patterns. We obtain exact general relations for the Poincare-Adronov-Hopf and Turing bifurcations, and our generalized results include the Higgins, autocatalator, and templator models as specific cases.
Synaptic input statistics tune the variability and reproducibility of neuronal responses
Authors: Dorval Alan D. , White John A.
Published: July 2006

Synaptic waveforms, constructed from excitatory and inhibitory presynaptic Poisson trains, are presented to living and computational neurons. We review how the average output of a neuron (e.g., the firing rate) is set by the difference between excitatory and inhibitory event rates while neuronal variability is set by their sum. We distinguish neuronal variability from reproducibility. Variability quantifies how much an output measure is expected to vary; for example, the interspike interval coefficient of variation quantifies the typical range of interspike intervals. Reproducibility quantifies the similarity of neuronal outputs in response to repeated presentations of identical stimuli. Although variability and reproducibility are conceptually distinct, we show that, for ideal current source synapses, reproducibility is defined entirely by variability. For physiologically realistic conductance-based synapses, however, reproducibility is distinct from variability and average output, set by the Poisson rate and the degree of synchrony within the synaptic waveform.
Stochastically driven genetic circuits
Authors: Tsimring L. S. , Volfson D. , Hasty J.
Published: July 2006

Transcriptional regulation in small genetic circuits exhibits large stochastic fluctuations. Recent experiments have shown that a significant fraction of these fluctuations is caused by extrinsic factors. In this paper we review several theoretical and computational approaches to modeling of small genetic circuits driven by extrinsic stochastic processes. We propose a simplified approach to this problem, which can be used in the case when extrinsic fluctuations dominate the stochastic dynamics of the circuit (as appears to be the case in eukaryots). This approach is applied to a model of a single nonregulated gene that is driven by a certain gating process that affects the rate of transcription, and to a simplified version of the galactose utilization circuit in yeast.
Franck-Condon factors based on anharmonic vibrational wave functions of polyatomic molecules
Authors: Rodriguez-Garcia Valerie , Yagi Kiyoshi , Hirao Kimihiko , Iwata Suehiro , Hirata So
Published: July 2006

Franck-Condon (FC) integrals of polyatomic molecules are computed on the basis of vibrational self-consistent-field (VSCF) or configuration-interaction (VCI) calculations capable of including vibrational anharmonicity to any desired extent (within certain molecular size limits). The anharmonic vibrational wave functions of the initial and final states are expanded unambiguously by harmonic oscillator basis functions of normal coordinates of the respective electronic states. The anharmonic FC integrals are then obtained as linear combinations of harmonic counterparts, which can, in turn, be evaluated by established techniques taking account of the Duschinsky rotations, geometry displacements, and frequency changes. Alternatively, anharmonic wave functions of both states are expanded by basis functions of just one electronic state, permitting the FC integral to be evaluated directly by the Gauss-Hermite quadrature used in the VSCF and VCI steps [Bowman et al., Mol. Phys. 104, 33 (2006)]. These methods in conjunction with the VCI and coupled-cluster with singles, doubles, and perturbative triples [CCSD(T)] method have predicted the peak positions and intensities of the vibrational manifold in the X̃B12 photoelectron band of H2O with quantitative accuracy. It has revealed that two weakly visible peaks are the result of intensity borrowing from nearby states through anharmonic couplings, an effect explained qualitatively by VSCF and quantitatively by VCI, but not by the harmonic approximation. The X̃B22 photoelectron band of H2CO is less accurately reproduced by this method, likely because of the inability of CCSD(T)/cc-pVTZ to describe the potential energy surface of open-shell H2CO+ with the same high accuracy as in H2O+.
Symmetrized correlation function for liquidpara-hydrogen using complex-time pair-product propagators
Authors: Nakayama Akira , Makri Nancy
Published: July 2006

We present a simple and efficient method for calculating symmetrized time correlation functions of neat quantum fluids. Using the pair-product approximation to each complex-time quantum mechanical propagator, symmetrized correlation functions are written in terms of a double integral for each degree of freedom with a purely positive integrand. At moderate temperatures and densities, where the pair-product approximation to the Boltzmann operator is sufficiently accurate, the method leads to quantitative results for the early time part of the correlation function. The method is tested extensively on liquid para-hydrogen at 25K and used to obtain accurate quantum mechanical results for the initial 0.2ps segment of the symmetrized velocity autocorrelation function of this system, as well as the incoherent dynamic structure factor at certain momentum transfer values.
The dynamics of small excitable ion channel clusters
Authors: Shuai J.W. , Jung P.
Published: July 2006

Through computational modeling we predict that small sodium ion channel clusters on small patches of membrane can encode electric signals most efficiently at certain magic cluster sizes. We show that this effect can be traced back to algebraic features of small integers and are universal for channels with a simple gating dynamics. We further explore physiologic conditions under which such effects can occur.
Effects of the radial electric field on the confinement of trapped fast ions in the Wendelstein 7-X and Helias reactor
Authors: Kolesnichenko Ya. I. , Lutsenko V. V. , Tykhyy A. V. , Weller A. , Werner A. , Wobig H. , Geiger J.
Published: July 2006

Confinement of trapped fast ions in the Wendelstein-line stellarators in the presence of the radial electric field, Er, is studied. It is shown that negative electric field improves the confinement; in particular, a radially localized field can play the role of a transport barrier for the ions escaping from the plasma when Er=0. In contrast to this, the positive electric field tends to deteriorate the ion confinement, unless its magnitude is very large. Such a field accompanied by the plasma rotation with the frequency around a certain magnitude, which we refer to as the resonance rotation frequency, leads to a quick particle loss. A possibility of using the plasma rotation with the resonance frequency for the ash removal in a Helias reactor is considered. The mentioned results are obtained analytically and numerically. The analytical consideration was done on the basis of the derived bounce-averaged equations of the particle motion. The numerical calculations were carried out for Wendelstein 7-X [G. Grieger et al., J. Plasma Fusion Res. Series 1, 53 (1998)] and a Helias reactor [J. Kisslinger et al., Proceedings of the 17th International Conference, Yokohama, 1998 (1999), Vol. 4, p. 1239] by the guiding center code ORBIS (ORBits In Stellarators) developed in this work.
Circadian rhythms and molecular noise
Authors: Gonze Didier , Goldbeter Albert
Published: July 2006

Circadian rhythms, characterized by a period of about 24h, are the most widespread biological rhythms generated autonomously at the molecular level. The core molecular mechanism responsible for circadian oscillations relies on the negative regulation exerted by a protein on the expression of its own gene. Deterministic models account for the occurrence of autonomous circadian oscillations, for their entrainment by light-dark cycles, and for their phase shifting by light pulses. Stochastic versions of these models take into consideration the molecular fluctuations that arise when the number of molecules involved in the regulatory mechanism is low. Numerical simulations of the stochastic models show that robust circadian oscillations can already occur with a limited number of mRNA and protein molecules, in the range of a few tens and hundreds, respectively. Various factors affect the robustness of circadian oscillations with respect to molecular noise. Besides an increase in the number of molecules, entrainment by light-dark cycles, and cooperativity in repression enhance robustness, whereas the proximity of a bifurcation point leads to less robust oscillations. Another parameter that appears to be crucial for the coherence of circadian rhythms is the binding/unbinding rate of the inhibitory protein to the promoter of the clock gene. Intercellular coupling further increases the robustness of circadian oscillations.
Dust clusters with non-Hamiltonian particle dynamics
Authors: Kompaneets R. , Vladimirov S. V. , Ivlev A. V. , Tsytovich V. , Morfill G.
Published: July 2006

The modes of clusters formed by two or three charged dust particles in a plasma are analyzed. The non-Hamiltonian dynamics of the particles is taken into account, which includes (i) nonreciprocal interaction forces due to wake effects and (ii) spatial variations of the particle charge and shielding parameters. It is shown that these effects can trigger an oscillatory instability under realistic experimental conditions. An experiment is suggested to observe this instability.