bluuebunny/crossref_metadata_2025 huggingface dataset:
Fundamental Issues of Nanofluid Behavior
Authors: Williams Wesley C.
Published: September 2008

This paper will elucidate some of the behaviors of nanofluids other than the abnormal conductivity enhancement, which are of importance to the experimental and engineering use of nanofluids. Nanofluid is the common name of any sol colloid involving nanoscale (less than 100nm) sized particles dispersed within a base fluid. It has been shown previously that the dispersion of nano-particulate metallic oxides into water can increase thermal conductivity up to 30–40% over that of the base fluid and anomalously more than the mere weighed average of the colloid. There is a great potential for the use of nanofluids as a way to enhance fluid/thermal energy transfer systems. Due to the recentness of nanofluid science, there are still many issues which have not been fully investigated. This paper should act as a primer for the basic understanding of nanofluid behavior. Particle size and colloid stability are of key importance to the functionality of nanofluids. The pH and concentration/loading of nanofluids can alter the size of the nanoparticles and also the stability of the fluids. It will be shown through experiment and colloid theory the importance of these parameters. Furthermore, most of the existing literature uses volume percentage as the measure of particle loading, which can often be misleading. There will be discussion of this and other misleading ideas in nanofluid science.
Formulation Study on Immobilization of Spent Ion Exchange Resins in Polymer Cements
Authors: Xia Lili , Lin Meiqiong , Liangjin Bao
Published: September 2008

Applying normal design and correlative computer software, a new matrix material and an excellent waste formulation were developed. Based on the theory calculations and normal design in this paper, using polymer complex cement as immobilization matrix that mixed with simulating spent ion exchange resin a new waste formulation was carried out. The characterization of solidified waste had been done after 28 days curing. The results conformed to the treatment of the waste about the requests of the national standard [GB14569-93-1]. Leach index of the solidified waste was excellent. An optimized formulation was recommended.
Evaluation and Numerical Simulation of Tsunami for Coastal Nuclear Power Plants of India
Authors: Sharma Pavan K. , Ghosh B. , Singh R. K. , Ghosh A. K. , Kushwaha H. S.
Published: September 2008

Recent tsunami generated on December 26, 2004 due to Sumatra earthquake of magnitude 9.3 resulted in inundation at the various coastal sites of India. The site selection and design of Indian nuclear power plants demand the evaluation of run up and the structural barriers for the coastal plants: Besides it is also desirable to evaluate the early warning system for tsunamigenic earthquakes. The tsunamis originate from submarine faults, underwater volcanic activities, sub-aerial landslides impinging on the sea and submarine landslides. In case of a submarine earthquake-induced tsunami the wave is generated in the fluid domain due to displacement of the seabed. There are three phases of tsunami: generation, propagation, and run-up. Reactor Safety Division (RSD) of Bhabha Atomic Research Centre (BARC), Trombay has initiated computational simulation for all the three phases of tsunami source generation, its propagation and finally run up evaluation for the protection of public life, property and various industrial infrastructures located on the coastal regions of India. These studies could be effectively utilized for design and implementation of early warning system for coastal region of the country apart from catering to the needs of Indian nuclear installations. This paper presents some results of tsunami waves based on different analytical/numerical approaches with shallow water wave theory.
Study on Off-Design Steady State Performances of Helium Gas Turbocompressor for HTGR-GT
Authors: Ren Qisen , Yang Xiaoyong , Huang Zhiyong , Wang Jie
Published: September 2008

The high temperature gas-cooled reactor (HTGR) coupled with direct gas turbine cycle is a promising concept in the future of nuclear power development. Both helium gas turbine and compressor are key components in the cycle. Under normal conditions, the mode of power adjustment is to control total helium mass in the primary loop using gas storage vessels. Meanwhile, thermal power of reactor core is regulated. This article analyzes off-design performances of helium gas turbine and compressors for high temperature gas-cooled reactor with gas turbine cycle (HTGR-GT) at steady state level of electric power adjustment. Moreover, performances of the cycle were simply discussed. Results show that the expansion ratio of turbine decreases as electric power reduces but the compression ratios of compressors increase, efficiencies of both turbine and compressors decrease to some extent. Thermal power does not vary consistently with electric power, the difference between these two powers increases as electric power reduces. As a result of much thermal energy dissipated in the temperature modulator set at core inlet, thermal efficiency of the cycle has a widely reduction under partial load conditions.
Spent Nuclear Fuel Transportation Risk Assessment Methodology for Homeland Security
Authors: Teagarden Grant A. , Canavan Kenneth T. , Nickell Robert E.
Published: September 2008

In response to increased interest in risk-informed decision making regarding terrorism, EPRI was selected by U.S. DHS and ASME to develop and demonstrate a nuclear sector specific methodology for owner / operators to utilize in performing a Risk Analysis and Management for Critical Asset Protection (RAMCAP) assessment for the transportation of spent nuclear fuel (SNF). The objective is to characterize SNF transportation risk for risk management opportunities and to provide consistent information for DHS decision making. The method uses a characterization of risk as a function of Consequence, Vulnerability, and Threat. Worst reasonable case scenarios characterize risk for a benchmark set of threats and consequence types. A trial application was successfully performed and implementation is underway by one utility.
Room at the Mountain: Estimated Maximum Amounts of Commerical Spent Nuclear Fuel Capable of Disposal in a Yucca Mountain Repository
Authors: Kessler John H. , Apted Michael J. , Zhou Wei , Kemeny John , King Fraser , Ross Alan M. , Ross Benjamen , Schwartz Franklin W.
Published: September 2008

The purpose of this paper is to present an initial analysis of the maximum amount of commercial spent nuclear fuel (CSNF) that could be emplaced into a geological repository at Yucca Mountain. This analysis identifies and uses programmatic, material, and geological constraints and factors that affect this estimation of maximum amount of CSNF for disposal. The conclusion of this initial analysis is that the current legislative limit on Yucca Mountain disposal capacity, 63,000 MTHM of CSNF, is a small fraction of the available physical capacity of the Yucca Mountain system assuming the current high-temperature operating mode (HTOM) design. EPRI is confident that at least four times the legislative limit for CSNF (∼260,000 MTHM) can be emplaced in the Yucca Mountain system. It is possible that with additional site characterization, upwards of nine times the legislative limit (∼570,000 MTHM) could be emplaced.
Development, Application, and Implementation of RAMCAP to Characterize Nuclear Power Plant Risk From Terrorism
Authors: Gaertner John P. , Teagarden Grant A.
Published: September 2008

In response to increased interest in risk-informed decision making regarding terrorism, EPRI and ERIN Engineering were selected by U.S. DHS and ASME to develop and demonstrate the RAMCAP method for nuclear power plant (NPP) risk assessment. The objective is to characterize plant-specific NPP risk for risk management opportunities and to provide consistent information for DHS decision making. This paper is an update of this project presented at the American Nuclear Society (ANS) International Topical Meeting on Probabilistic Safety Analysis (PSA05) in September, 2005. The method uses a characterization of risk as a function of Consequence, Vulnerability, and Threat. For each site, worst case scenarios are developed for each of sixteen benchmark threats. Nuclear RAMCAP hypothesizes that the intent of the perpetrator is to cause offsite radiological consequences. Specific targets are the reactor core, the spent fuel pool, and nuclear spent fuel in a dry storage facility (ISFSI). Results for each scenario are presented as conditional risk for financial loss, early fatalities and early injuries. Expected consequences for each scenario are quantified, while vulnerability is estimated on a relative likelihood scale. Insights for other societal risks are provided. Although threat frequencies are not provided, target attractiveness and threat deterrence are estimated. To assure efficiency, completeness, and consistency; results are documented using standard RAMCAP Evaluator software. Trial applications were successfully performed at four plant sites. Implementation at all other U.S. commercial sites is underway, supported by the Nuclear Sector Coordinating Council (NSCC). Insights from RAMCAP results at 23 U.S. plants completed to date have been compiled and presented to the NSCC. Results are site-specific. Physical security barriers, an armed security force, preparedness for design-basis threats, rugged design against natural hazards, multiple barriers between fuel and environment, accident mitigation capability, severe accident management procedures, and offsite emergency plans are risk-beneficial against all threat types.
A Review of Some Degradation Mechanisms in CANDU Steam Generator Tubing
Authors: Ogundele G. , Clark M. , Goszczynski G. , Lloyd A. , Pagan S. , Sedman K. , King P.
Published: September 2008

The first CANDU (CANadian Deuterium Uranium) pressurized heavy water reactor (PHWR) went into operation in July 1971. Today, there are several units in operation at the Pickering, Bruce, and Darlington sites in Ontario, Canada. The steam generator tubing materials were manufactured from Monel 400, Inconel 600, and Incoloy 800 for the Pickering, Bruce, and Darlington respectively and are subjected to different operating conditions. This paper presents a review of some of the various types of degradation mechanisms that have been observed on these tubing materials over the operating period of the respective plants. The results presented are based on the metallurgical examination of removed tubes. The mechanisms that have been observed include pitting, stress corrosion cracking, intergranular attack, fretting, and erosion corrosion. The nature of the flaws and causative factors (if known) are discussed.
Large Break LOCA Accident Management Strategies for Accidents With Large Containment Leaks
Authors: Sdouz Gert
Published: September 2008

The goal of this work is the investigation of the influence of different accident management strategies on the thermal-hydraulics in the containment during a Large Break Loss of Coolant Accident with a large containment leak from the beginning of the accident. The increasing relevance of terrorism suggests a closer look at this kind of severe accidents. Normally the course of severe accidents and their associated phenomena are investigated with the assumption of an intact containment from the beginning of the accident. This intact containment has the ability to retain a large part of the radioactive inventory. In these cases there is only a release via a very small leakage due to the untightness of the containment up to cavity bottom melt through. This paper represents the last part of a comprehensive study on the influence of accident management strategies on the source term of VVER-1000 reactors. Basically two different accident sequences were investigated: the “Station Blackout”-sequence and the “Large Break LOCA”. In a first step the source term calculations were performed assuming an intact containment from the beginning of the accident and no accident management action. In a further step the influence of different accident management strategies was studied. The last part of the project was a repetition of the calculations with the assumption of a damaged containment from the beginning of the accident. This paper concentrates on the last step in the case of a Large Break LOCA. To be able to compare the results with calculations performed years ago the calculations were performed using the Source Term Code Package (STCP), hydrogen explosions are not considered. In this study four different scenarios have been investigated. The main parameter was the switch on time of the spray systems. One of the results is the influence of different accident management strategies on the source term. In the comparison with the sequence with intact containment it was demonstrated that the accident management measures have quite lower consequences. In addition it was shown that in the case of a “Large Break LOCA”-sequence the intact containment retains the nuclides up to a factor of 20 000. This is much more than in the case of a “Station Blackout”-sequence. Within the frame of the study 17 source terms have been generated to evaluate in detail accident management strategies for VVER-1000 reactors.
Dimensionless Parameters in Stability Analysis of Heated Channels With Fluids at Supercritical Pressures
Authors: Ambrosini Walter , Sharabi Medhat
Published: September 2008

The paper proposes dimensionless parameters for the analysis of stability in heated channels with supercritical fluids. The parameters are devised basing on the classical phase change and subcooling numbers adopted in the case of boiling channels, proposing a novel formulation making use of fluid properties at the pseudo-critical temperature as a function of pressure. The adopted formulation for dimensionless density of a given fluid provides a unique dependence with respect to dimensionless enthalpy, in a reasonably wide range of system pressures, thus giving generality to the predictions of unstable conditions obtained as a function of dimensionless parameters. It is shown that these parameters allow setting up quantitative stability maps for a single heated channel with imposed overall pressure drop, in analogy with the ones proposed in previous work concerning boiling channels. Similarities with the boiling channel stability phenomena are pointed out, also supporting the conclusions with system code predictions.
Analysis of Basic Phenomena in Boiling Channel Instabilities With Different Flow Models and Numerical Schemes
Authors: Ambrosini Walter , Ferreri Juan Carlos
Published: September 2008

The results of a computational study on boiling channel stability are here discussed. The study compares the information obtained by two programs, developed in previous work for the linear and the nonlinear stability analysis of boiling channels basing on a simplified flow model, with the predictions of a well known system code. The phenomena highlighted by the results of the system code, adopted with different flow models and numerical methods, are discussed in a systematic way with the aid of the description obtained by the simplified model, in order to obtain a clearer picture than could be achieved by the mere application of the system code to conditions of interest for boiling water reactor stability. The effects on the obtained results of non-equilibrium, numerical discretization and number of nodes are considered, evaluating their influence on the predicted stability boundaries. Some physical aspects of the density-wave mode of instability are finally discussed basing on the predictions obtained by the different models.
IAEA INPRO Project: A Vision of How to Meet the Opportunities and Challenges of Large-Scale Nuclear Energy Development
Authors: Khoroshev M. , Depisch F. , Subbotin S.
Published: September 2008

The IAEA International Project on Innovative Nuclear Reactors and Fuel Cycles (INPRO) can be considered as the IAEA’s response to the challenges of growing energy demand. INPRO’s activities are intended to help to achieve one of the main objectives of the IAEA — to promote the development and peaceful use of nuclear energy. INPRO applies a carefully developed Methodology to assess Innovative Nuclear Energy Systems (INS) and to define R&D needs and deployment strategies for the development of large-scale regional and global INS. The purpose is to match the opportunities and challenges of sustainable energy supply provided by nuclear energy (NE) to the global balance of demands and resources.
Design Configurations for Very High Temperature Gas-Cooled Reactor Designed to Generate Electricity and Hydrogen
Authors: Oh Chang H. , Davis Cliff , Barner Robert , Sherman Steven
Published: September 2008

The High Temperature Gas-Cooled Reactor is being envisioned that will generate not just electricity, but also hydrogen to charge up fuel cells for cars, trucks and other mobile energy uses. INL engineers studied various heat-transfer working fluids—including helium and liquid salts—in seven different configurations. In computer simulations, serial configurations diverted some energy from the heated fluid flowing to the electric plant and hydrogen production plant. In anticipation of the design, development and procurement of an advanced power conversion system for HTGR, this study was initiated to identify the major design and technology options and their tradeoffs in the evaluation of power conversion system (PCS) coupled to hydrogen plant. In this study, we investigated a number of design configurations and performed thermal hydraulic analyses using various working fluids and various conditions (Oh, 2005). This paper includes a portion of thermal hydraulic results based on a direct cycle and a parallel intermediate heat exchanger (IHX) configuration option.
Multidimensional Model of Fluid Flow and Heat Transfer in Generation-IV Supercritical Water Reactors
Authors: Gallaway Tara , Antal Steven P. , Podowski Michael Z.
Published: September 2008

This paper is concerned with the mechanistic modeling and theoretical/computational analysis of flow and heat transfer in future Generation-IV Supercritical Water Cooled Reactors (SCWR). The issues discussed in the paper include: the development of analytical models of the properties of supercritical water, and the application of full three-dimensional computational modeling framework to simulate fluid flow and heat transfer in SCWRs. Several results of calculations are shown, including the evaluation of water properties (density, specific heat, thermal conductivity, viscosity, and Prandtl number) near the pseudo-critical temperature for various supercritical pressures, and the CFD predictions using the NPHASE computer code. It is demonstrated that the proposed approach is very promising for future mechanistic analyses of SCWR thermal-hydraulics and safety.
International Training Program in Support of Safety Analysis: 3D S.UN.COP—Scaling, Uncertainty and 3D Thermal-Hydraulics/Neutron-Kinetics Coupled Codes Seminars
Authors: Petruzzi Alessandro , D’Auria Francesco , Bajs Tomislav , Reventos Francesc
Published: September 2008

Thermal-hydraulic system computer codes are extensively used worldwide for analysis of nuclear facilities by utilities, regulatory bodies, nuclear power plant designers and vendors, nuclear fuel companies, research organizations, consulting companies, and technical support organizations. The computer code user represents a source of uncertainty that can influence the results of system code calculations. This influence is commonly known as the ‘user effect’ and stems from the limitations embedded in the codes as well as from the limited capability of the analysts to use the codes. Code user training and qualification is an effective means for reducing the variation of results caused by the application of the codes by different users. This paper describes a systematic approach to training code users who, upon completion of the training, should be able to perform calculations making the best possible use of the capabilities of best estimate codes. In other words, the program aims at contributing towards solving the problem of user effect. The 3D S.UN.COP (Scaling, Uncertainty and 3D COuPled code calculations) seminars have been organized as follow-up of the proposal to IAEA for the Permanent Training Course for System Code Users [1]. Five seminars have been held at University of Pisa (2003, 2004), at The Pennsylvania State University (2004), at University of Zagreb (2005) and at the School of Industrial Engineering of Barcelona (2006). It was recognized that such courses represented both a source of continuing education for current code users and a mean for current code users to enter the formal training structure of a proposed ‘permanent’ stepwise approach to user training. The 3D S.UN.COP 2006 was successfully held with the attendance of 33 participants coming from 18 countries and 28 different institutions (universities, vendors, national laboratories and regulatory bodies). More than 30 scientists (coming from 13 countries and 23 different institutions) were involved in the organization of the seminar, presenting theoretical aspects of the proposed methodologies and holding the training and the final examination. A certificate (LA Code User grade) was released to participants that successfully solved the assigned problems. A sixth seminar will be organized in 2007 at the Texas A&M University involving more than 30 scientists between lecturers and code developers. (http://dimnp.ing.unipi.it/3dsuncop/2007)
Quad Cities Unit 2 Main Steam Line Acoustic Source Identification and Load Reduction
Authors: DeBoo Guy , Ramsden Kevin , Gesior Roman
Published: September 2008

The Quad Cities Units 1 and 2 have a history of steam line vibration issues. The implementation of an Extended Power Uprate resulted in significant increases in steam line vibration as well as acoustic loading of the steam dryers, which led to equipment failures and fatigue cracking of the dryers. This paper discusses the results of extensive data collection on the Quad Cities Unit 2 replacement dryer and the Main Steam Lines. This data was taken with the intent of identifying acoustic sources in the steam system. Review of the data confirmed that vortex shedding coupled column resonance in the relief and safety valve stub pipes were the principal sources of large magnitude acoustic loads in the main steam system. Modifications were developed in subscale testing to alter the acoustic properties of the valve standpipes and add acoustic damping to the system. The modifications developed and installed consisted of acoustic side branches that were attached to the Electromatic Relief Valve (ERV) and Main Steam Safety Valve (MSSV) attachment pipes. Subsequent post-modification testing was performed in plant to confirm the effectiveness of the modifications. The modifications have been demonstrated to reduce vibration loads at full Extended Power Uprate (EPU) conditions to levels below those at Original Licensed Thermal Power (OLTP).
On the C-C Coupling of the Naphthylium Ion with Methane
Authors: Roithová Jana , Ricketts Claire L. , Schröder Detlef
Published: September 2008

Unlike other medium-sized hydrocarbon cations CmHn+ (m = 7-11, n = 6-12), the naphthylium ion C10H7+ undergoes a thermal reaction with methane to form the C-C coupled product C11H9+ concomitant with dehydrogenation. This reaction, which might be of relevance in the context of the growth of hydrocarbon species under extreme conditions, is suggested to lead to a benzylium-type cation in analogy to the C-C coupling of phenyl cations with methane.
The Position-Dependent Reaction Force Constant in Bond Dissociation/Formation
Authors: Politzer Peter , Murray Jane S.
Published: September 2008

The concept of a position-dependent reaction force constant κ(R) can be used to distinguish the two phases of bond dissociation or formation: stretched bond, κ(R) > 0, and interacting but separate fragments, κ(R) < 0. The transition between these phases is at κ(R) = 0, which coincides with the minimum (for dissociation) or maximum (for formation) of the reaction force. As was shown earlier, all of these occur (for diatomic molecules) at the separation R at which the system's energy relative to equilibrium is about 27% of its dissociation energy.
Absence of Conjugation in Vibrational Spectra and Assignments of Dichloro(vinyl)phosphine and Dichloro(phenyl)phosphine Oxides and Sulfides
Authors: Förner Wolfgang , Badawi Hassan M.
Published: September 2008

The structure and conformational stability of dichloro(vinyl)phosphine and dichloro(phenyl)- phosphine oxides and sulfides were investigated using calculations at the DFT/6-311G** and ab initio ones at the MP2/6-311G** level. We know from our previous results that the addition of diffuse functions to a valence triple zeta basis with polarization functions might lead to an unbalanced basis, which performs even worse than the smaller basis without diffuse functions, as it is the case for the 6-311++G** basis set in the Gaussian program. For large energy differences between conformers, DFT works very well, in some cases even better than MP3 or MP4. The vinyl derivatives were predicted to exist in a cis/gauche conformational equilibrium with cis (the PX bond, X being oxygen or sulfur eclipses the vinyl groups) being the predominant conformer at ambient temperature. In the phenyl case case the two planar forms are equivalent minima. The asymmetric potential function for the internal rotation was determined for each of the molecules. The vibrational frequencies were computed and the spectra, where possible, were compared with the experimental ones. Normal coordinate calculations were carried out and potential energy distributions were calculated for the molecules in the cis and gauche conformations (in the vinyl case, planar one for phenyl), providing a complete assignment of the vibrational lines to symmetry coordinates in the molecules. From our results and their analysis we conclude, in agreement with literature results based on localized orbitals, that conjugation effects are absent - or at least negligible - as compared with electrostatic ones in determining the structures of the stable conformers in both the vinyl and the phenyl derivatives. The P-O bond should be a highly polarized triple bond, as confirmed by analysis of Mulliken populations. The polarization turned out to be much less in the sufides due to the much smaller electronegativity of sulfur as compared with oxygen.
Application of Berlin's Theorem to Bond-Length Changes in Isolated Molecules and Red- and Blue-Shifting H-Bonded Clusters
Authors: Wang Weizhou , Hobza Pavel
Published: September 2008

The origin of the bond-length change in molecule or molecular cluster has been investigated at the MP2/aug-cc-pVDZ level of theory using the electrostatic potential or the electron density difference analysis method. Our results have clearly shown that the bond-length change of a chemical bond is determined mainly by the balance of the electrostatic forces exerted by electrons on the two nuclei. The factors that affect the balance of the electrostatic forces include four parts: (i) The abstraction of the electron density from Berlin's binding region between the two nuclei. (ii) The accumulation of the electron density in Berlin's antibinding regions. (iii) The accumulation of the electron density in Berlin's binding region between the two nuclei. (iv) The abstraction of the electron density from Berlin's antibinding regions. Using the change of the electron density around the two nuclei of a chemical bond, we have succeeded in explaining two important chemical phenomena: (i) breakdown of bond length-bond strength correlation; (ii) the bond-length change in the hydrogen bond.
Energies and Electric Dipole Moments of the Bound Vibrational States of HN2+ and DN2+
Authors: Špirko Vladimír , Bludský Ota , Kraemer Wolfgang P.
Published: September 2008

The adiabatic three-dimensional potential energy surface and the corresponding dipole moment surface describing the ground electronic state of HN2+ (Χ1Σ+) are calculated at different levels of ab initio theory. The calculations cover the entire bound part of the potential up to its lowest dissociation channel including the isomerization barrier. Energies of all bound vibrational and low-lying ro-vibrational levels are determined in a fully variational procedure using the Suttcliffe-Tennyson Hamiltonian for triatomic molecules. They are in close agreement with the available experimental numbers. From the dipole moment function effective dipoles and transition moments are obtained for all the calculated vibrational and ro-vibrational states. Statistical tools such as the density of states or the nearest-neighbor level spacing distribution (NNSD) are applied to describe and analyse general patterns and characteristics of the energy and dipole results calculated for the massively large number of states of the strongly bound HN2+ ion and its deuterated isotopomer.
Assessment of the Accuracy of TD-DFT Absorption Spectra: Substituted Benzenes
Authors: André Jean-Marie , Jacquemin Denis , Perpete Eric A. , Vercauteren Daniel P. , Wathelet Valérie
Published: September 2008

Using the parameter-free PBE0 hybrid functional in conjunction with the conducting PCM model, we compute the UV/VIS spectra of a series of solvated phenol and nitrobenzene chromogens. For the first series, the average deviation with respect to experiment is large (about 0.5 eV) but the auxochromic shifts are very accurately and consistently predicted. Therefore, after a statistical treatment, the TD-DFT values are within 0.02 eV of the experimental data. For nitrobenzenes, the average discrepancy is smaller than for phenols, though the impact of individual substitution is much less consistent with experimental trends. We also confirm that push-pull compounds with donor and acceptor groups in meta positions are especially problematic for TD-DFT calculations relying on conventional hybrids, and we unravel the origin of this specific difficulty.
The Stabilization Energy of the GLU-LYS Salt Bridge in the Protein/Water Environment: Correlated Quantum Chemical ab initio, DFT and Empirical Potential Studies
Authors: Řezáč Jan , Berka Karel , Horinek Dominik , Hobza Pavel , Vondrášek Jiří
Published: September 2008

The stabilization energies of Glu-Lys salt bridges are calculated at the CCSD(T) complete basis set limit to provide a reasonable description of the strength of the ion-pair bond in the gas phase. The effect of the environment (protein with ε = 4 and water with ε = 80) on the stabilization energy was introduced via a modification of the quantum chemical DFT energy, for which the COSMO methodology was adopted. The other (standard) approach was based on incorporating a dielectric constant into the Coulomb electrostatic term of the Amber empirical potential function and utilizing the generalized Born model implemented in the Amber program. The environment affects the stabilization energy of the salt bridge dramatically: The protein reduces the energy to less than one half of the original value, whereas water sometimes changes stabilization to destabilization. Both theoretical procedures, based on completely different theoretical backgrounds, yield very similar results, which strongly support their validity. An ion pair is converted to an ion-neutral pair when its pH is changed. This transformation is connected with a strong reduction of the stabilization energy regardless of the environment. The substantial differences in the stabilization energies of ion pairs and ion-neutral pairs contradict the negligible changes of free energy detected experimentally. Evidently, the contribution of formation and hydration entropy is significant and compensates for the large stabilization energies.
A Note on the Symmetry Properties of Löwdin's Orthogonalization Schemes
Authors: Rokob András T. , Szabados Ágnes , Surján Peter R.
Published: September 2008

We point out that the well-known symmetry properties of the symmetrically and canonically orthogonalized vectors hold only under certain conditions on the overlapping vectors. In particular, the matrix of the transformation induced by the symmetry operator must be unitary. This requirement is not fulfilled if Cartesian d or f functions are used in the basis set. If such functions are present, canonically orthogonalized orbitals do not transform according to representations of the molecular point group; nor do Löwdin orthogonalized vectors preserve symmetry relation of the original vectors.
The origins ofErigeron trifidus(Asteraceae), an agamospermous rare species in AlbertaThis paper is one of a selection of papers published in the Special Issue on Systematics Research.
Authors: Burke J. L. , Bain J. F.
Published: September 2008

Erigeron trifidus Hook. (Asteraceae) is a rare species in Alberta thought to have originated via hybridization between Erigeron compositus Pursh and Erigeron lanatus Hook., and is disjunct in three alpine regions of Alberta. An analysis of uni- and bi-parentally inherited molecular markers from E. trifidus and its putative parents yielded data that support the hybridization hypothesis for some of the populations. In most cases, cpDNA haplotypes in E. trifidus were the same as in E. lanatus, suggesting that E. lanatus is the maternal parent. Sequencing and cloning the nuclear ETS region revealed multiple repeat types in most individuals. Erigeron trifidus contained only the repeat types also present in the putative parents. In addition, E. trifidus displayed the highest percentage of intra-individual repeat type polymorphism, consistent with a hybrid origin. All northern populations of E. trifidus exhibited a particular pattern of repeat type variation that was absent in central and southern populations. Since E. lanatus is absent from Ram Mountain (in central Alberta), it is likely that populations from this locality, previously identified as E. trifidus, are instead a different agamospermous variant of E. compositus. In southern Alberta (Waterton Lakes), populations of E. trifidus are thought to be the product of local hybridization, and are therefore of different origin from the northern populations. The identity of the putative parents in the southern region remains uncertain.
Evaluating species limits and hybridization in theCarex complanatacomplex using morphology, amplified fragment length polymorphisms, and restriction fragment analysisThis paper is one of a selection of papers published in the Special Issue on Systematics Research.
Authors: Smith Tyler W. , Waterway Marcia J.
Published: September 2008

We used a combination of morphology, amplified fragment length polymorphisms (AFLP), and restriction-site data from 252 individuals from 51 populations to investigate species limits and hybridization in the Carex complanata complex. Principal coordinate analysis of the morphological data shows clear separation of entities corresponding to Carex bushii Mackenzie and Carex caroliniana Schwein. However, only leaf indumentum reliably distinguished between Carex hirsutella Mackenzie and Carex complanata Torr. & Hook. Despite this very subtle difference, AFLP data reveal very clear genetic separation of these two taxa. Contrary to the assertions of previous authors, we found no evidence of introgression among C. complanata, C. caroliniana, and C. bushii. Relatively high genetic variation within C. hirsutella may be an indication of gene-flow between this species and one or more other species, but further work is necessary to clarify this issue. We document six previously undescribed sterile or nearly sterile hybrids involving the species in this complex.
Reticulate evolution in the parasitic genusCuscuta(Convolvulaceae): over and over againThis paper is one of a selection of papers published in the Special Issue on Systematics Research.
Authors: Stefanović Saša , Costea Mihai
Published: September 2008

The frequency and relative importance of hybridization in plants has been an area of intense debate. Although this evolutionary phenomenon has received considerable attention from plant biologists, there are no well-supported cases of reticulate evolution involving parasitic plants, to date. Recent molecular phylogenetic analyses revealed that the subgenus Grammica , the largest and most diverse group of the stem-parasitic genus Cuscuta (dodder), consists of 15 major clades. We describe here five cases of strongly supported discordance between phylogenies derived from plastid and nuclear data, and interpret them as results of five independent hybridization events. Three of these cases could represent relatively recent reticulations, as each of them involves more closely related species, always confined within the same major clade as their putative parental species, and are currently sympatric or parapatric with them. The two remaining cases involve species whose potential progenitors are derived from different major groups of Grammica, and which are allopatric in their present distribution. A series of statistical tests was conducted to assess and further explore the significance of this phylogenetic incongruence. Alternative explanations for discordant gene topologies are explored. Cuscuta liliputana sp. nov., a new Mexican species of hybrid origin is described.
Insights into the evolution of duplicate gene expression in polyploids fromGossypiumThis paper is one of a selection of papers published in the Special Issue on Systematics Research.
Authors: Adams Keith L.
Published: September 2008

Polyploidy is a prominent mechanism of speciation in plants that can lead to novel phenotypes. Polyploidy is characterized by novel genetic and genomic consequences that provide raw material for morphological evolution. Polyploids often exhibit changes in genome organization and gene expression compared with their diploid progenitors. The five allopolyploid cotton (Gossypium) species and newly created cotton neopolyploids have been developed as a useful group for studies of duplicated gene expression in polyploids. Here I review recent studies on the evolution of duplicate gene expression in polyploid cotton. In addition I present new expression data from cotton neopolyploids that address the effects on expression of adding a third genome in an allohexaploid, and that provide insights into fine scale organ-specific silencing. Substantial changes in gene expression have occurred in homoeologous genes (gene pairs duplicated by polyploidy), including organ-specific gene silencing and subfunctionalization. Many of the changes in gene expression have occurred on an evolutionary timescale, whereas others occur immediately after genome merger and within a few generations. Abiotic stress can affect the expression of homoeologous gene expression, causing expression partitioning between homoeologs. To examine the effects of interspecific hybridization, without chromosome doubling, on gene expression, interspecific hybrids have been studied. Extensive variation in allelic expression was observed upon hybridization that varied by gene, organ, and genotype. Several hypotheses have been proposed for why gene expression is altered in allopolyploids and interspecific hybrids.
The origins of polyploids in western North American fawn-lilies (Erythronium)This paper is one of a selection of papers published in the Special Issue on Systematics Research.
Authors: Allen Geraldine A.
Published: September 2008

Two rare tetraploid fawn-lilies, Erythronium elegans P.C. Hammond & K.L. Chambers in western Oregon and Erythronium quinaultense G.A. Allen in northwestern Washington, are hypothesized to be of hybrid origin, on the basis of morphological evidence. I tested these hypotheses using DNA sequences of the nuclear ribosomal ITS region and of two plastid intergenic spacer regions (trnH-psbA and trnS-trnG) from the two tetraploids and the five relevant diploid taxa. ITS sequences indicated that the low-elevation diploid species Erythronium revolutum Sm. and Erythronium oregonum Applegate are recently diverged, and gave rise (at least in part) to the two tetraploids. Both E. elegans and E. quinaultense yielded multiple chloroplast DNA haplotypes that were of two distinct types. One plastid haplotype found in both E. elegans (four populations) and E. quinaultense (one population) exactly matched the most common haplotype of E. revolutum; other haplotypes of E. elegans (four populations) and E. quinaultense (two populations) were similar to those of E. oregonum. These results are consistent with derivation of the plastid genomes of different polyploid populations from either E. revolutum or E. oregonum (or their respective recent ancestors), and suggest recurrent formation of each tetraploid species. The two tetraploids are examples of allopolyploid species in which morphological and molecular evidence of their origins are in striking contrast, reflecting very different aspects of their genomes.
Cytotaxonomy and cytogeography of the goldenaster genus Heterotheca (Asteraceae: Astereae)This paper is one of a selection of papers published in the Special Issue on Systematics Research.
Authors: Semple John C.
Published: September 2008

Between 1948 and 2008, 668 chromosome number determinations have been reported for individuals of the goldenaster genus Heterotheca Cass. (Asteraceae: Astereae) from Canada, Mexico, and the United States, including 285 newly reported here. This common group of mostly western North American herbaceous annuals and perennials is subdivided into three sections, the most complex of which is section Phyllotheca . Differences of opinion about the taxonomy of the goldenasters, numerous synonyms, and the lack of a comprehensive treatment of the polymorphic villosa complex and other species complexes in section Phyllotheca made it difficult to organize the data into a meaningful discussion of the cytotaxonomy and cytogeography of this genus. Here I present the geographic distribution of all published counts and cytogeography maps of all species of Heterotheca, assigning taxa following recent taxonomic revisions. The sample sizes for species sampled ranged from 1 to 228 reports. All species have a base number of x = 9. Only diploids (2n = 9II or 2n = 18) were found in Heterotheca oregona (Nutt.) Shinners (the single species of sect. Ammodia ) and in the three species of section Heterotheca. Both diploids and (or) tetraploids were found across 18 sampled species of section Phyllotheca, with the frequency varying among them; nine species are known only at one ploidy level (either diploid or tetraploid; three species each). Only four triploids (2n = 9III or 2n = 27) were encountered in section Phyllotheca; two were putative interspecific hybrids. One new nomenclatural combination is proposed: Heterotheca inuloides var. leptoglossa .
Molecular and morphological evidence for and against gene flow in sympatric apomicts of the North American Crepis agamic complex (Asteraceae)This paper is one of a selection of papers published in the Special Issue on Systematics Research.
Authors: Whitton Jeannette , Dlugosch Katrina M. , Sears Christopher J.
Published: September 2008

The study of sympatric populations of closely related plant species often reveals evidence of hybridization. Mechanisms that reduce outcrossing (e.g., selfing, apomixis) may allow co-occurrence without gene flow. In this study, we describe patterns of genetic variation in two contact zones, each comprising three closely related morphological types, that key to three distinct species in the North American Crepis agamic (apomictic) complex. We used RAPD markers to characterize individuals from two sites: one in northern California (Sardine Lookout) and another in northwestern Oregon (Summit Road). At Sardine Lookout, we discerned a total of four multilocus genotypes, two in one species, and one each in the other two species. Our findings suggest that distinct morphological types are maintained by absolute barriers to gene flow at this site. At Summit Road, we found greater genotypic diversity, with a total of 24 genotypes across 30 individuals. One of the morphological types was clearly genetically differentiated from the other two, with no variable markers shared with other species at this site. The two remaining species showed evidence of gene flow, with no unique markers discerning them. Morphological data tend to support this conclusion, with univariate and multivariate analyses indicating a pattern of variation spanning the two species. Taken together, these patterns suggest that contact zones need not represent hybrid zones, and that apomixis can serve as an effective barrier to gene flow that may allow for stable coexistence of close relatives.
The effect of pH and ABA on the hydraulic conductivity of Nitella membranes
Authors: Ord G. N. St.G. , Cameron I. F. , Fensom D. S.
Published: September 2008

The method of transcellular osmosis was used to compare the hydraulic permeability (LP) of Nitella membranes at different pH's. LP did not change when the pH ranged from 5.0 to 7.0 but dropped slightly when the pH was 4.4 or below. Tris(hydroxymethyl)aminomethane buffer and abscissic acid (ABA) both increased LP significantly.
Ultrastructure of the appressorium of Spilocaea pomi
Authors: Corlett Michael , Chong James
Published: September 2008

The appressorium, seen after penetration of the apple leaf cuticle, has a two-layered wall, an electron-dense outer layer, and an electron-transparent inner layer. The pore of the appressoriumis bordered by the electron-dense outer layer, which tapers at the margin of the pore. The penetration hypha is derived from the infection sac, a structure or organelle within the appressorium.
Fusarium in barley and corn roots
Authors: McKeen W. E.
Published: September 2008

In the root cortex, Fusarium usually grows in the walls and intercellular spaces, but in the stele it grows within the cells. It does not appear in the large central tracheal tubes. Hyphal strands have a tendency to grow longitudinally in and on the root. Mechanical force is involved in splitting the walls as the fungus grows within the walls. Chemical action is involved in wall penetration. Papillae form opposite penetrating pegs but disappear soon after the Fusarium hyphae have penetrated the wall or passed through the papillae.
Lack of relationship between ability to kill plants and ability to inhibit plant growth among Phytophthora species
Authors: Kanlong Somchai , Hendrix James W.
Published: September 2008

Nineteen isolates of Phytophthora species and two isolates of Pythium species, most of them selected because they were originally isolated from the host families Solanaceae. Malvaceae, and Leguminosae, were evaluated for their ability to cause disease when inoculated into stems of plants of these families or when incorporated into soil into which plants were transplanted. When inoculated into stems, some isolates were extremely host-specific, parasitizing and killing only one plant species, while other isolates were parasitic to several. The isolates parasitic to three hosts all attacked the same hosts: snap bean, okra, and tomato. Plant species also varied insusceptibility to parasitism. Tomato, okra, and snap bean were attacked by a number of isolates, while tobacco, pepper, cotton, soybean, and lima bean were attacked by one isolate or none. In nearly every case, stem inoculation with an isolate produced a brown, necrotic reaction readily distinguishable from the reaction of control plants, which were wounded but not inoculated. Growth of plants transplanted into infested soil was often inhibited by isolates which were unable to parasitize the plants when inoculated by either stem inoculation or soil infestation. Ability to parasitize plants, ability to produce a necrotic reaction in stems without killing plants, and ability to stunt growth of plants transplanted into infested soil were not related. The Pythiaceae apparently possess mechanisms of pathogenesis not dependent on parasitism.