bluuebunny/crossref_metadata_2025 huggingface dataset:
Analytical 2D model to invert hydraulic pumping tests in fractured rocks with fractal behavior
Authors: Delay Frederick , Porel Gilles , Bernard Stephane
Published: August 2004

A solution to interference pumping tests in fractal fractured media of Euclidean dimension two has been developed. It is proposed in dimensioned variables with a pre‐conditioning of its most sensitive parameter and a Gauss‐Newton inversion. The method allows for a rapid identification of hydrodynamic parameters by fitting experimental data. The fractal dimension and the scale exponent of the hydraulic diffusion are also determined without any other calculation or reference to a theoretical medium. Thus, the results provide a reliable appraisal of how the hydrodynamic parameters evolve with the size of the system. This feature has important applications in hydrology and petroleum engineering especially when up‐scaling approaches are needed.
Frost flowers on sea ice as a source of sea salt and their influence on tropospheric halogen chemistry
Authors: Kaleschke L. , Richter A. , Burrows J. , Afe O. , Heygster G. , Notholt J. , Rankin A. M. , Roscoe H. K. , Hollwedel J. , Wagner T. , Jacobi H.‐W.
Published: August 2004

Frost flowers grow on newly‐formed sea ice from a saturated water vapour layer. They provide a large effective surface area and a reservoir of sea salt ions in the liquid phase with triple the ion concentration of sea water. Recently, frost flowers have been recognised as the dominant source of sea salt aerosol in the Antarctic, and it has been speculated that they could be involved in processes causing severe tropospheric ozone depletion events during the polar sunrise. These events can be explained by heterogeneous autocatalytic reactions taking place on salt‐laden ice surfaces which exponentially increase the reactive gas phase bromine (“bromine explosion”). We analyzed tropospheric bromine monoxide (BrO) and the sea ice coverage both measured from satellite sensors. Our model based interpretation shows that young ice regions potentially covered with frost flowers seem to be the source of bromine found in bromine explosion events.
Southern Cascadia episodic slow earthquakes
Authors: Szeliga Walter , Melbourne Timothy I. , Miller M. Meghan , Santillan V. Marcelo
Published: August 2004

Continuous GPS and seismic data from northern California show that slow earthquakes periodically rupture the Gorda‐North America plate interface within southern Cascadia. On average, these creep events have occurred every 10.9 ± 1.2 months since at least 1998. Appearing as week‐long GPS extensional transients that reverse secular forearc contraction, the data show a recurrence interval 22% shorter than slow events recognized to the north. Seismic tremor here accompanies the GPS reversals, correlated across as many as 5 northern California seismometers. Tremor occurs sporadically throughout the year, but increases in duration and intensity by a factor of about 10 simultaneous with the GPS reversals. Beneath west‐central Oregon, three reversals are also apparent, but more stations are needed to confirm sporadic slip on the plate interface here. Together, these measurements suggest that slow earthquakes likely occur throughout the Cascadia subduction zone and add further evidence for the role of fault‐fluid migration in controlling transient slow‐slip events here.
Hydrometeor mass, number, and space charge distribution in a “Hector” squall line
Authors: Takahashi Tsutomu , Keenan Thomas D.
Published: August 2004

Videosonde data from an Australian squall line were combined with a radar echo profile to construct a conceptual model of hydrometeor mass, number, and space charge evolution. Two‐step hydrometeor growth modes were suggested: low‐level, warm rain‐frozen drop and high‐level, graupel‐ice crystals. A riming electrification mechanism successfully explained the charge distribution. A warm rain‐frozen drop process was active in the forward area of the convective region, and frozen drop growth was highly active near the 0°C level. Ice crystals, which electrified frozen drops positively, increased in number as they were lifted. Graupel growth was enhanced, and additional charge separation occurred between ice crystals and graupel in the upper level. Large negative graupel fell at the rear of the convective region, while positive ice crystals and small negative graupel were transported into the anvil. The reason for high lightning frequencies in a squall line over a maritime continent is also discussed.
Atmospheric rotational effects on Mars based on the NASA Ames general circulation model: Angular momentum approach
Authors: Sanchez Braulio , Haberle Robert , Schaeffer James
Published: August 2004

The NASA Ames general circulation model has been used to compute time series for atmospheric products of inertia and relative angular momentum terms. Model outputs were used also to compute time series representing the inertia terms due to CO2 condensation and sublimation on the surface of Mars. Some of these terms were used to generate time series representing the forcing functions for the equatorial components of the linearized Liouville equations of rotational motion. These equations were then solved numerically for a period of a Martian year (669 sols) to obtain a time series for the position of the rotation pole on the surface of Mars. The results of the investigation indicate that mass variation in the atmosphere is as important as the formation and sublimation of ice caps on the surface of the planet. Numerical integration of the equations of rotational motion yields pole displacements as large as 30.9 cm (ice caps solution), 39.5 cm (atmospheric effects), or 33 cm (both effects combined). Fourier analysis of the time series corresponding to the equatorial components of pole displacement for the ice caps solution as well as the atmospheric effects solution shows that the (1/3)‐annual harmonic has the largest coefficient in three cases, with magnitudes in the 7–9 cm range. Fourier analysis of the equatorial components of polar motion for the combined solution yields main harmonics of 5.12 cm (x), (1/3)‐annual and 7.50 cm (y), annual.
Managing the externalities of declining dry season river flow: A case study from the Ewaso Ngiro North River Basin, Kenya
Authors: Gichuki Francis N.
Published: August 2004

Upstream‐downstream water conflicts are common phenomenon in most basins. Such conflicts take a different dimension when they occur during dry season with an already low level of river flows. This context aggravates the spatial externalities on downstream communities and water‐dependent ecosystems, causing serious socioeconomic and ecological effects. Utilizing an analytical framework to capture the causes and consequences of the spatial nature of these externalities and relying on both primary and secondary data pertaining to the Upper Ewaso Ngiro North basin in Kenya, this paper (1) shows how these externalities are caused more by upstream land and water use changes than by any climatic and hydrological factors, (2) evaluates the nature and magnitude of their impacts on different downstream community groups, (3) assesses the extent and success of past policy responses and local initiatives, and (4) concludes by indicating the needed approach and interventions for finding a durable solution to the problem of upstream‐downstream water conflicts and externalities.
Short‐term water consumption dynamics in El Paso, Texas
Authors: Fullerton Thomas M. , Elías Arturo
Published: August 2004

Time series analysis of water consumption patterns has been the subject of increasing attention in recent years. For many municipalities such efforts offer a means for developing potentially useful planning tools. Because data requirements are not extensive, model development is feasible for markets where information is limited. The work at hand examines the applicability of such a tool in El Paso, Texas, a growing metropolitan economy located in a semiarid region. Sample data are from January 1994 through December 2002. In addition to estimating a linear transfer function equation of water consumption in this city the model is subjected to a series of simulation benchmark tests.
The relationship between seed size and abundance in plant communities: model predictions and observed patterns
Authors: Leishman Michelle R. , Murray Brad R.
Published: August 2004

Recent studies have suggested that seed size and plant abundance in communities are associated. However, inconsistent patterns have emerged from these studies, with varying mechanisms proposed to explain emergent relationships. We employ a theoretical framework, based on key theory lineages of vegetation dynamics and species coexistence, to examine relationships between species abundance and seed size. From these theory lineages, we identified four models and their predictions: the Seed size/number trade‐off model (SSNTM), the Succession model (SM), the Spatial competition model (SCM), and the Lottery model (LM). We then explored empirical evidence from ten diverse plant communities for seed size and abundance patterns, and related these patterns to model predictions. The SSNTM predicts a negative correlation between seed size and abundance. The SM predicts either a negative, positive or no correlation dependent on time since disturbance, while the SCM and LM make no predictions for a relationship between seed size and abundance. We found no evidence for consistent relationships between seed size and abundance across the ten communities. There were no consistent differences in seed size and abundance relationships between communities dominated by annuals compared to perennials. In three of the ten communities a significant positive seed size and abundance correlation emerged, which falsified the SSNTM as an important determinant of abundance structure in these communities. For sites in coastal woodland, the relationships between seed size and abundance were consistent with the predictions of the SM (although generally not significant), with fire being the disturbance. We suggest that the significant positive seed size and abundance correlations found may be driven by the association between large seeds and large growth forms, as large growth forms tend to be dominant. It seems likely that patterns of seed size and abundance in communities are determined by a complex interaction between environmental factors and correlations of plant attributes that determine a species’ strategy.
Ngongas and ecology: on having a worldview
Authors: Brown Joel S.
Published: August 2004

Ngongas provide a metaphor for some of the opportunities and challenges facing the science of ecology and evolution. Ngongas, the traditional healers of the Shona culture, Zimbabwe, fail in the delivery of quality health by today's standards. Their outdated worldview makes most health related issues seem more complicated and more multi‐factorial than when viewed through the worldviews of modern medicine. With the wrong worldview, one can work very hard, be very bright and dedicated, and still be ineffective. With the right worldview, one can work much less hard and still be extremely effective. As ecologists, we should be opinionated and possess clearly articulated worldviews for filtering and interpreting information. As ecologists we are also a bit like ngongas – we often fail to provide answers for society's ecological questions and problems, and we excuse ourselves with a belief that ecological systems are too complex and have too many factors. Unlike ngongas, this invites us to pay a lot of attention to promoting and assessing competing worldviews. We should be open‐minded to the anomalies in our worldview and the successes of alternative viewpoints. As an admitted ecological ngonga, I discuss the worldview I use in my own research: the Optimization Research Program, a Darwinian research program that uses game theory to conceptualize and understand ecological systems. I use it illustrate how worldviews can synthesize disparate ideas. (I use kin selection and reciprocal altruism as examples.) I use it to show how new ideas and predictions can be generated. (I use root competition in plants and the possibility that increased crop yield may be forthcoming from knowledge of this game.)
From interesting details to dynamical relevance: toward more effective use of empirical insights in theory construction
Authors: Schmitz Oswald J.
Published: August 2004

A perennial challenge in ecology is to develop dynamical systems models that appropriately abstract and characterize the dynamics of natural systems. Deriving an appropriate model of system dynamics can be a long and iterative process whose outcome depends critically on the quality of empirical data describing the long‐term behavior of a natural system. Most ecological time series are insufficient to offer insight into the way organizational hierarchies and spatial scales are causally linked to natural system dynamics. Moreover, the classic tradition of hypothesis testing in ecology is not likely to lead to those key insights. This because empirical research is geared almost exclusively toward testing model predictions based on underlying causal relationships assumed by theorists. So, empirical research relies heavily on theory for guidance on what is or is not dynamically relevant. I argue here that it is entirely possible to reduce much of this guesswork involved with deciding on causal structure by giving empirical research a new role in theory development. In this role, natural history and field observations are used to develop stochastic, individual‐based and spatially explicit computational models or IBMs that can explore the range of contingency and complexity inherent in real‐world systems.  IBMs can be used to run simulations allowing deductions to be made about the causal linkages between organizational hierarchies, spatial scales, and dynamics. These deductions can be tested under field conditions using experiments that manipulate the putative causal structure and evaluate the dynamical consequences. The emerging insights from this stage can then be used to inspire an analytical construct that embodies the dynamically relevant scales and mechanisms. In essence, computational modeling serves as an intermediate step in theory development in that a wide range of possibly important biological details are considered and then reduced to a subset that is dynamically relevant.
Physiologically structured models – from versatile technique to ecological theory
Authors: De Roos André M. , Persson Lennart
Published: August 2004

A ubiquitous feature of natural communities is the variation in size that can be observed between organisms, a variation that to a substantial degree is intraspecific. Size variation within species by necessity implies that ecological interactions vary both in intensity and type over the life cycle of an individual. Physiologically structured population models (PSPMs) constitute a modelling approach especially designed to analyse these size‐dependent interactions as they explicitly link individual level processes such as consumption and growth to population dynamics. We discuss two cases where PSPMs have been used to analyse the dynamics of size‐structured populations. In the first case, a model of a size‐structured consumer population feeding on a non‐structured prey was successful in predicting both qualitative (mechanisms) and quantitative (individual growth, survival, cycle amplitude) aspects of the population dynamics of a planktivorous fish population. We conclude that single generation cycles as a result of intercohort competition is a general outcome of size‐structured consumer–resource interactions. In the second case, involving both cohort competition and cannibalism, we show that PSPMs may predict double asymptotic growth trajectories with individuals ending up as giants. These growth trajectories, which have also been observed in field data, could not be predicted from individual level information, but are emergent properties of the population feedback on individual processes. In contrast to the size‐structured consumer–resource model, the dynamics in this case cannot be reduced to simpler lumped stage‐based models, but can only be analysed within the domain of PSPMs. Parameter values used in PSPMs adhere to the individual level and are derived independently from the system at focus, whereas model predictions involve both population level processes and individual level processes under conditions of population feedback. This leads to an increased ability to test model predictions but also to a larger set of variables that is predicted at both the individual and population level. The results turn out to be relatively robust to specific model assumptions and thus render a higher degree of generality than purely individual‐based models. At the same time, PSPMs offer a much higher degree of realism, precision and testing ability than lumped stage‐based or non‐structured models. The results of our analyses so far suggest that also in more complex species configurations only a limited set of mechanisms determines the dynamics of PSPMs. We therefore conclude that there is a high potential for developing an individual‐based, size‐dependent community theory using PSPMs.
On nonlinear stability of the regular vortex systems on a sphere
Authors: Kurakin L. G.
Published: August 2004

We present the necessary and sufficient conditions for stability and instability of the stationary rotation of a system of n identical point vortices located at the same latitude on a sphere at vertices of a regular n-gon. We also examine stability of the equilibrium configuration of identical point vortices, situated at the vertices of a regular polyhedra. It is proved that vortex tetrahedron, octahedron, and icosahedron are stable, while vortex cube and dodecahedron are unstable.
Adaptation through minimization of the phase lag in coupled nonidentical systems
Authors: Dzakpasu Rhonda , Żochowski Michał
Published: August 2004

We show that the internal control of adaptation can be obtained from the properties of the phase lag that results from phase synchronization of two nonidentical chaotic oscillators. The direction and magnitude of the phase lag depend upon the relative internal properties of the coupled units, and they can be used as indicators during the adjustment of dynamics, i.e., adaptation of the target unit to match that of the control. The properties of the phase lag are obtained using a method based on the estimation of properties of the distributions of relative event times of both (target and control) units. The phase lag dependent mechanism to control the adaptation process was applied to a system of nonidentical Rössler oscillators and a system of nonidentical Lorenz oscillators. We also elucidate its importance as a control mechanism of the changes of neuronal activity showing its application to neural adaptation.
Ab initio calculations of stationary points on the benzene–Ar and p-difluorobenzene–Ar potential energy surfaces: barriers to bound orbiting states
Authors: Moulds Rebecca J. , Buntine Mark A. , Lawrance Warren D.
Published: August 2004

The potential energy surfaces of the van der Waals complexes benzene–Ar and p-difluorobenzene–Ar have been investigated at the second-order Møller–Plesset (MP2) level of theory with the aug-cc-pVDZ basis set. Calculations were performed with unconstrained geometry optimization for all stationary points. This study has been performed to elucidate the nature of a conflict between experimental results from dispersed fluorescence and velocity map imaging (VMI). The inconsistency is that spectra for levels of p-difluorobenzene–Ar and –Kr below the dissociation thresholds determined by VMI show bands where free p-difluorobenzene emits, suggesting that dissociation is occurring. We proposed that the bands observed in the dispersed fluorescence spectra are due to emission from states in which the rare gas atom orbits the aromatic chromophore; these states are populated by intramolecular vibrational redistribution from the initially excited level [S. M. Bellm, R. J. Moulds, and W. D. Lawrance, J. Chem. Phys. 115, 10709 (2001)]. To test this proposition, stationary points have been located on both the benzene–Ar and p-difluorobenzene–Ar potential energy surfaces (PESs) to determine the barriers to this orbiting motion. Comparison with previous single point CCSD(T) calculations of the benzene–Ar PES has been used to determine the amount by which the barriers are overestimated at the MP2 level. As there is little difference in the comparable regions of the benzene–Ar and p-difluorobenzene–Ar PESs, the overestimation is expected to be similar for p-difluorobenzene–Ar. Allowing for this overestimation gives the barrier to movement of the Ar atom around the pDFB ring via the valley between the H atoms as ⩽204 cm−1 in S0 (including zero point energy). From the estimated change upon electronic excitation, the corresponding barrier in S1 is estimated to be ⩽225 cm−1. This barrier is less than the 240 cm−1 energy of 302¯, the vibrational level for which the anomalous “free p-difluorobenzene” bands were observed in dispersed fluorescence from p-difluorobenzene–Ar, supporting our hypothesis for the origin of these bands.
Femtosecond pump-probe spectroscopy of I2 in a dense rare gas environment: A mixed quantum/classical study of vibrational decoherence
Authors: Meier C. , Beswick J. A.
Published: August 2004

The process of decoherence of vibrational states of I2 in a dense helium environment is studied theoretically using the mixed quantum/classical method based on the Bohmian formulation of quantum mechanics [E. Gindensperger, C. Meier, and J. A. Beswick, J. Chem. Phys. 113, 9369 (2000)]. Specifically, the revival of vibrational wave packets is a quantum phenomena which depends sensitively on the coherence between the vibrational states excited by an ultrafast laser pulse. Its detection by a pump-probe setup as a function of rare gas pressure forms a very accurate way of detecting vibrational dephasing. Vibrational revivals of I2 in high pressure rare gas environments have been observed experimentally, and the very good agreement with the simulated spectra confirms that the method can accurately describe decoherence processes of quantum systems in interaction with an environment.
Unbiased expectation values from diffusion quantum Monte Carlo simulations with a fixed number of walkers
Authors: Bosá Ivana , Rothstein Stuart M.
Published: August 2004

We append forward walking to a diffusion Monte Carlo algorithm which maintains a fixed number of walkers. This removes the importance sampling bias of expectation values of operators which do not commute with the Hamiltonian. We demonstrate the effectiveness of this approach by employing three importance sampling functions for the hydrogen atom ground state, two very crude. We estimate moments of the electron-nuclear distance, static polarizabilities, and high-order hyperpolarizabilites up to the fourth power in the electric field, where no use is made of the finite field approximation. The results agree with the analytical values, with a statistical error which increases substantially with decreasing overlap of the guiding function with the exact wave function.
Reconciling semiclassical and Bohmian mechanics. I. Stationary states
Authors: Poirier Bill
Published: August 2004

The semiclassical method is characterized by finite forces and smooth, well-behaved trajectories, but also by multivalued representational functions that are ill behaved at caustics. In contrast, quantum trajectory methods—based on Bohmian mechanics (quantum hydrodynamics)—are characterized by divergent forces and erratic trajectories near nodes, but also well-behaved, single-valued representational functions. In this paper, we unify these two approaches into a single method that captures the best features of both, and in addition, satisfies the correspondence principle. Stationary eigenstates in one degree of freedom are the primary focus, but more general applications are also anticipated.
An approach to chaotic synchronization
Authors: Hramov Alexander E. , Koronovskii Alexey A.
Published: August 2004

This paper deals with the chaotic oscillator synchronization. An approach to the synchronization of chaotic oscillators has been proposed. This approach is based on the analysis of different time scales in the time series generated by the coupled chaotic oscillators. It has been shown that complete synchronization, phase synchronization, lag synchronization, and generalized synchronization are the particular cases of the synchronized behavior called “time-scale synchronization.” The quantitative measure of chaotic oscillator synchronous behavior has been proposed. This approach has been applied for the coupled Rössler systems and two coupled Chua’s circuits.
Continuous polydispersity in a self-consistent field theory for diblock copolymers
Authors: Sides Scott W. , Fredrickson Glenn H.
Published: August 2004

An efficient algorithm is presented for numerically evaluating a self-consistent field theoretic (SCFT) model of an AB diblock copolymer that incorporates continuous polydispersity in one of the blocks. An interesting segregation effect is found in which chains of intermediate molecular weight are concentrated at domain interfaces. This model of continuous polydispersity is also implemented in the random phase approximation (RPA) to study the order-disorder transition and predicts that the stability of the disordered, homogeneous phase decreases as the polydispersity in one of the blocks increases. The RPA predictions are confirmed by SCFT calculations. Our approach and results are particularly relevant to block copolymers prepared by quasiliving synthesis techniques, where the polymerization of one block is much more controlled than the other block.
Analysis of two intramolecular proton transfer processes in terms of the reaction force
Authors: Toro-Labbé Alejandro , Gutiérrez-Oliva Soledad , Concha Monica C. , Murray Jane S. , Politzer Peter
Published: August 2004

The negative derivative of the potential energy along an intrinsic reaction coordinate defines a force that has qualitatively a universal form for any process having an energy barrier: it passes through a negative minimum before the transition state, at which it is zero, followed by a positive maximum. We have analyzed two intramolecular proton transfer reactions in terms of several computed properties: internal charge separation, the electrostatic potentials of the atoms involved, their Fukui functions, and the local ionization energies. The variation of each of these properties along the intrinsic reaction coordinate shows a marked correlation with the characteristic features of the reaction force. We present a description of the proton transfer processes in terms of this force.
Trapping time statistics and efficiency of transport of optical excitations in dendrimers
Authors: Heijs Dirk-Jan , Malyshev Victor A. , Knoester Jasper
Published: August 2004

We theoretically study the trapping time distribution and the efficiency of the excitation energy transport in dendritic systems. Trapping of excitations, created at the periphery of the dendrimer, on a trap located at its core, is used as a probe of the efficiency of the energy transport across the dendrimer. The transport process is treated as incoherent hopping of excitations between nearest-neighbor dendrimer units and is described using a rate equation. We account for radiative and nonradiative decay of the excitations while diffusing across the dendrimer. We derive exact expressions for the Laplace transform of the trapping time distribution and the efficiency of trapping, and analyze those for various realizations of the energy bias, number of dendrimer generations, and relative rates for decay and hopping. We show that the essential parameter that governs the trapping efficiency is the product of the on-site excitation decay rate and the trapping time (mean first passage time) in the absence of decay.
Vibrational dynamics of adsorbed molecules under conditions of photodesorption: Pump-probe SFG spectra of CO/Pt(111)
Authors: Fournier Frédéric , Zheng Wanquan , Carrez Serge , Dubost Henri , Bourguignon Bernard
Published: August 2004

Interaction of CO adsorbed on Pt(111) with electrons and phonons is studied experimentally by means of a pump-probe experiment where CO is probed by IR+visible sum frequency generation under a pump laser intensity that allows photodesorption. Vibrational spectra of CO internal stretch are obtained as a function of pump-probe delay. A two-temperature and anharmonic coupling model is used to extract from the spectra the real time variations of CO peak frequency and dephasing time. The main conclusions are the following: (i) The CO stretch is perturbed by two low-frequency modes, assigned to frustrated rotation and frustrated translation. (ii) The frustrated rotation is directly coupled to electrons photoexcited in Pt(111) by the pump laser. (iii) There is no evidence of Pt-CO stretch excitation in the spectra. The implications for the photodesorption dynamics are discussed.
Simulation of the mechanical unfolding of ubiquitin: Probing different unfolding reaction coordinates by changing the pulling geometry
Authors: Li Pai-Chi , Makarov Dmitrii E.
Published: August 2004

Motivated by the recent experimental atomic force microscopy (AFM) measurements of the mechanical unfolding of proteins pulled in different directions [D. J. Brockwell et al., Nat. Struct. Biol. 10, 731 (2003); M. Carrion-Vazquez et al., ibid 10, 738 (2003)] we have computed the unfolding free energy profiles for the ubiquitin domain when it is stretched between its (A) N and C termini, (B) Lys48 and C terminus, (C) Lys11 and C terminus, and (D) N terminus and Lys63. Our results for cases (A) and (B) are in good agreement with the experimental unfolding forces measured for the N-C and Lys48-C linked polyubiquitin, in particular, indicating a considerably lower unfolding force in the latter case. Mechanical unfolding in case (A) involves longitudinal shearing of the terminal parallel strands while in case (C) the same strands are “unzipped” by the force. The computed unfolding forces in case (C) are found to be very low, less than 50 pN for pulling rates typical of AFM experiments. The unfolding free energy barrier found in case (C) is ∼13 kcal/mol, which corresponds to a zero-force unfolding rate constant that is comparable to the rate of chemical unfolding extrapolated to zero denaturant concentration. The unfolding barrier calculated in case (A) in the limit of zero force is much higher, suggesting that mechanical unfolding in this case follows a pathway that is different from that of thermal/chemical denaturation.
Simulation of the plastic behavior of amorphous glassy bis-phenol-A-polycarbonate
Authors: Fortunelli Alessandro , Geloni Claudio , Lazzeri Andrea
Published: August 2004

A protocol for studying the plastic deformation of amorphous glassy polymers is presented. The protocol is based on a viable computational procedure which combines constant-stress molecular dynamics simulations and fixed-cell energy minimizations, followed by kinetic, configurational, and energy analyses. It is shown that the computational results can be accounted for within a “potential energy landscape” theoretical framework, in which the plastic transition is interpreted as a crossing between and a collapse onto each other of “ideal (thermodynamic) structures.” The procedure is applied to bis-phenol-A-polycarbonate (BPA-PC), but is equally valid for a wide variety of polymeric species. Allowing for the limited size of the simulation cell, the high strain rate, and the fact that the simulation are conducted at low temperature, the values of the density, Young’s modulus, yield strain, yield stress, activation energy, and activation volume are in fair agreement with the experimental data on BPA-PC. The analysis of the results shows that the plastic relaxation for this polymer has both a collective and cooperative character (as in classical percolation theories), involves a significant fraction of the simulation cell, and can be viewed as a “nanoscopic shear band.”
Rate constants from the reaction path Hamiltonian. I. Reactive flux simulations for dynamically correct rates
Authors: Peters Baron , Bell Alexis T. , Chakraborty Arup
Published: August 2004

As ab initio electronic structure calculations become more accurate, inherent sources of error in classical transition state theory such as barrier recrossing and tunneling may become major sources of error in calculating rate constants. This paper introduces a general method for diabatically constructing the transverse eigensystem of a reaction path Hamiltonian in systems with many degenerate transverse frequencies. The diabatically constructed reaction path Hamiltonian yields smoothly varying coupling constants that, in turn, facilitate reactive flux calculations. As an example we compute the dynamically corrected rate constant for the chair to boat interconversion of cyclohexane, a system with 48 degrees of freedom and a number of degenerate frequencies. The transmission coefficients obtained from the reactive flux simulations agree with previous results that have been calculated using an empirical potential. Furthermore, the calculated rate constants agree with experimental values. Comparison to variational transition state theory shows that, despite finding the true bottleneck along the reaction pathway, variational transition state theory only accounts for half of the rate constant reduction due to recrossing trajectories.
Rate constants from the reaction path Hamiltonian. II. Nonseparable semiclassical transition state theory
Authors: Peters Baron , Bell Alexis T. , Chakraborty Arup
Published: August 2004

For proton transfer reactions, the tunneling contributions to the rates are often much larger than thermally activated rates at temperatures of interest. A number of separable tunneling corrections have been proposed that capture the dependence of tunneling rates on barrier height and imaginary frequency size. However, the effects of reaction pathway curvature and barrier anharmonicity are more difficult to quantify. The nonseparable semiclassical transition state theory (TST) of Hernandez and Miller [Chem. Phys. Lett. 214, 129 (1993)] accounts for curvature and barrier anharmonicity, but it requires prohibitively expensive cubic and quartic derivatives of the potential energy surface at the transition state. This paper shows how the reaction path Hamiltonian can be used to approximate the cubic and quartic derivatives used in nonseparable semiclassical transition state theory. This enables tunneling corrections that include curvature and barrier anharmonicity effects with just three frequency calculations as required by a conventional harmonic transition state theory calculation. The tunneling correction developed here is nonseparable, but can be expressed as a thermal average to enable efficient Monte Carlo calculations. For the proton exchange reaction NH2+CH4⇔NH3+CH3, the nonseparable rates are very accurate at temperatures from 300 K up to about 1000 K where the TST rate itself begins to diverge from the experimental results.
Reconstruction of the free energy in the metastable region using the path ensemble
Authors: Bustillos Armando Ticona , Heermann Dieter W. , Cordeiro Claudette E.
Published: August 2004

By quenching into the metastable region of the three-dimensional Ising model, we investigate the paths that the magnetization (energy) takes as a function of time. We accumulate the magnetization (energy) paths into time-dependent distributions from which we reconstruct the free energy as a function of the magnetic field, temperature, and system size. From the reconstructed free energy, we obtain the free-energy barrier that is associated with the transition from a metastable state to the stable equilibrium state. Although mean-field theory predicts a sharp transition between the metastable and the unstable region where the free-energy barrier is zero, the results for the nearest-neighbor Ising model show that the free-energy barrier does not go to zero.
Time resolved infrared absorption studies of geminate recombination and vibrational relaxation in OClO photochemistry
Authors: Bolinger Joshua C. , Hayes Sophia C. , Reid Philip J.
Published: August 2004

Ultrafast time-resolved infrared absorption studies of aqueous chlorine dioxide (OClO) photochemistry are reported. Following photoexcitation at 401 nm, the evolution in optical density at frequencies between 1000 to 1100 cm−1 is monitored to investigate vibrational energy deposition and relaxation along the asymmetric-stretch coordinate following the reformation of ground-state OClO via geminate recombination of the primary photofragments. The measured kinetics are compared to two proposed models for the vibrational-relaxation dynamics along the asymmetric-stretch coordinate. This comparison demonstrates that the perturbation model derived from molecular dynamics studies is capable of qualitatively reproducing the observed kinetics, where the collisional model employed in previous UV-pump, visible probe experiments demonstrates poor agreement with experiment. The ability of the perturbation model to reproduce the optical-density evolution observed in these studies demonstrates that for aqueous OClO, frequency dependence of the solvent–solute coupling is important in defining the level-dependent vibrational relaxation rates along the asymmetric-stretch coordinate. The absence of optical-density evolution corresponding to the population of higher vibrational levels (n>8) along the asymmetric-stretch coordinate suggests that following geminate recombination, energy is initially deposited into a local Cl–O stretch, with the relaxation of vibrational energy from this coordinate providing for delayed vibrational excitation of the asymmetric- and symmetric-stretch coordinates relative to geminate recombination, as previously observed.
Application of time series analysis on molecular dynamics simulations of proteins: A study of different conformational spaces by principal component analysis
Authors: Alakent Burak , Doruker Pemra , Camurdan Mehmet C.
Published: August 2004

Time series analysis is applied on the collective coordinates obtained from principal component analysis of independent molecular dynamics simulations of α-amylase inhibitor tendamistat and immunity protein of colicin E7 based on the Cα coordinates history. Even though the principal component directions obtained for each run are considerably different, the dynamics information obtained from these runs are surprisingly similar in terms of time series models and parameters. There are two main differences in the dynamics of the two proteins: the higher density of low frequencies and the larger step sizes for the interminima motions of colicin E7 than those of α-amylase inhibitor, which may be attributed to the higher number of residues of colicin E7 and/or the structural differences of the two proteins. The cumulative density function of the low frequencies in each run conforms to the expectations from the normal mode analysis. When different runs of α-amylase inhibitor are projected on the same set of eigenvectors, it is found that principal components obtained from a certain conformational region of a protein has a moderate explanation power in other conformational regions and the local minima are similar to a certain extent, while the height of the energy barriers in between the minima significantly change. As a final remark, time series analysis tools are further exploited in this study with the motive of explaining the equilibrium fluctuations of proteins.
X-ray emission spectroscopy of (23×23)R30°CO/Ru(0001): Comparison to c(2×2)CO/Ni(100) and c(2×2)CO/Cu(100)
Authors: Föhlisch A. , Wurth W. , Stichler M. , Keller C. , Nilsson A.
Published: August 2004

The atom specific electronic structure of (2∛×2∛)R30°CO on hcp Ru(0001) has been determined with resonantly excited x-ray emission spectroscopy. We find that the general features of the local adsorbate electronic structure are similar to the situation of CO adsorbed on the fcc metals Ni(100) and Cu(100). The interpretation of the surface chemical bond of (2∛×2∛)R30°CO/Ru(0001) based on the direct application of the local, allylic model from on-top adsorption on the fcc(100) surfaces Ni(100) and Cu(100) explains many aspects of the surface chemical bond. However, also nonlocal contributions like adsorbate-adsorbate interaction and the deviation from upright on-top adsorption on the Ru(0001) surface influence observables like the heat of adsorption and the Me-CO bond strength.
Polarization effects on the hyper-Raman spectra of carbon tetrachloride: A joint experimental-theoretical study
Authors: Quinet Olivier , Champagne Benoı̂t , Rodriguez Vincent
Published: August 2004

Hyper-Raman spectra of pure carbon tetrachloride in the liquid phase are recorded for different combinations of the polarizations of the incident and scattered lights and are compared to ab initio time-dependent Hartree-Fock simulations. Both the calculated intensities of the Raman and hyper-Raman spectra give indeed a quite satisfactory agreement with polarized experimental spectra.
Electronic photodissociation spectroscopy of Aun−⋅Xe (n=7–11) versus time-dependent density functional theory prediction
Authors: Gilb Stefan , Jacobsen Kerstin , Schooss Detlef , Furche Fillip , Ahlrichs Reinhart , Kappes Manfred M.
Published: August 2004

Electronic (one-photon) photodepletion spectra were recorded for gold cluster anions complexed with one xenon atom over the photon energy range 2.1–3.4 eV. Clusters were generated by pulsed laser vaporization and probed under collisionless molecular beam conditions. The spectra obtained are highly structured with the narrowest features—assigned to individual electronic transitions—having bandwidths of less than 40 meV. Time-dependent density functional theory predictions of optically allowed transitions for the most stable—planar—isomers of the corresponding bare metal cluster anions are generally consistent with the experimental observation.
Gaussian-type function set without prolapse H1 through Bi83 for the Dirac-Fock-Roothaan equation
Authors: Tatewaki Hiroshi , Watanabe Yoshihiro
Published: August 2004

We have developed prolapse free Gaussian basis sets which can be used for H1 to Bi83, imposing the condition that the Dirac-Fock-Roothaan (DFR) total energy (TE) decreases monotonically toward the numerical DF (NDF) TE as the expansion term increases. An even-tempered basis set was assumed. The resulting sets gave |TE(DFR)−TE(NDF)|⩽1×10−6 hartree for any atoms less or equal to Bi83; TE(NDF)=−21 565.638 345, and TE(DFR)=−21 565.638 345±0.000 001 hartree for Bi when the expansion terms are in the range (58, 58, 58, 36, 36, 36, and 36) and (72, 72, 72, 36, 36, 36, and 36) for (s+, p−, p+, d−, d+, f−, and f+) symmetries, respectively. A practical set with 44, 44, 44, 36, 36, 32, and 32 for the respective symmetries is also proposed where |TE(DFR)−TE(NDF)|⩽4×10−5.
A discharge investigation of hydrogen and deuterium atom formation, and parahydrogen and orthodeuterium reconversion
Authors: Andrews Lester , Wang Xuefeng
Published: August 2004

Hydrogen is flowed through a mild tesla-coil discharge and trapped at 3.8 K: New infrared absorptions of H2 are induced by interaction with trapped H atoms and H− anions. High purity parahydrogen and orthodeuterium samples are 1%–9% reconverted depending on the discharge pressure and recombination of atoms. Annealing the solid samples to 7 K reveals growth in p-H2 induced by o-H2, which shows that H atom recombination produces thermal nuclear spin populations. Similar results are found in discharge experiments with HD and on annealing solid HD. The observed increase in induced HD absorption by J=1, H2 and D2 molecules formed on recombination gives ≈1% for the H[D] atom concentration in our solid HD samples.
Accurate and highly efficient calculation of the highly excited pure OH stretching resonances of O(1D)HCl, using a combination of methods
Authors: Bian Wensheng , Poirier Bill
Published: August 2004

Accurate calculation of the energies and widths of the resonances of HOCl—an important intermediate in the O(1D)HCl reactive system—poses a challenging benchmark for computational methods. The need for very large direct product basis sets, combined with an extremely high density of states, results in difficult convergence for iterative methods. A recent calculation of the highly excited OH stretch mode resonances using the filter diagonalization method, for example, required 462 000 basis functions, and 180 000 iterations. In contrast, using a combination of new methods, we are able to compute the same resonance states to higher accuracy with a basis less than half the size, using only a few hundred iterations—although the CPU cost per iteration is substantially greater. Similar performance enhancements are observed for calculations of the high-lying bound states, as reported in a previous paper [J. Theo. Comput. Chem. 2, 583 (2003)].
Raman scattering study on structural and dynamical features of noncrystalline selenium
Authors: Yannopoulos S. N. , Andrikopoulos K. S.
Published: August 2004

We report on a detailed, temperature-dependent, off-resonant Raman scattering study of glassy and supercooled selenium. Raman spectra in the frequency regime of the first-order scattering (5–450 cm−1) have been recorded over a wide temperature range, i.e., 143–353 K. To facilitate the analysis, the spectra have intuitively been divided in three spectral regions. The analysis of the high frequency region (bond-stretching vibrational modes) yielded information on the rings-chains equilibrium. In particular, the polymer content was found to amount to more than 85% around the glass transition temperature, exhibiting a weak temperature dependence, which extrapolates nicely to the high-temperature dissolution data. The intermediate frequency range (representative of the medium-range structural order) was treated together with the low frequency regime (where low-energy excitations, i.e., the quasielastic line and the Boson peak are the dominant contributions) owing to their strong overlap. The study of the bond-bending regime revealed information which made it possible to clarify the role of ringlike and chainlike fragments incorporated in polymeric molecules. The temperature evolution of the Boson peak and the frequency dependence of the Raman coupling coefficient C(ω) were also determined. An attempt to decompose the partial contribution of the pure Boson peak to C(ω) revealed valuable information concerning the limiting (ω→0) behavior of the coupling coefficient.
Water network dynamics at the critical moment of a peptide’s β-turn formation: A molecular dynamics study
Authors: Karvounis George , Nerukh Dmitry , Glen Robert C.
Published: August 2004

All-atom molecular dynamics simulations for a single molecule of Leu-Enkephalin in aqueous solution have been used to study the role of the water network during the formation of β-turns. We give a detailed account of the intramolecular hydrogen bonding, the water-peptide hydrogen bonding, and the orientation and residence times of water molecules focusing on the short critical periods of transition to the stable β-turns. These studies suggest that, when intramolecular hydrogen bonding between the first and fourth residue of the β-turn is not present, the disruption of the water network and the establishment of water bridges constitute decisive factors in the formation and stability of the β-turn. Finally, we provide possible explanations and mechanisms for the formations of different kinds of β-turns.