Use Of Model Potentials Research Articles

Modelling CO2 and CH4 emissions from drained peatlands with grass cultivation by the BASGRA-BGC model

Cultivated peatlands under drainage practices contribute significant carbon losses from agricultural sector in the Nordic countries. In this research, we developed the BASGRA-BGC model coupled with hydrological, soil carbon decomposition and methane modules to simulate the dynamic of water table level (WTL), carbon dioxide (CO2) and methane (CH4) emissions for cultivated peatlands. The field measurements from four experimental sites in Finland, Denmark and Norway were used to validate the predictive skills of this novel model under different WTL management practices, climatic conditions and soil properties. Compared with daily observations, the model performed well in terms of RMSE (Root Mean Square Error; 0.06–0.11 m, 1.22–2.43 gC/m2/day, and 0.002–0.330 kgC/ha/day for WTL, CO2 and CH4, respectively), NRMSE (Normalized Root Mean Square Error; 10.3–18.3%, 13.0–18.6%, 15.3–21.9%) and Pearson's r (Pearson correlation coefficient; 0.60–0.91, 0.76–0.88, 0.33–0.80). The daily/seasonal variabilities were therefore captured and the aggregated results corresponded well with annual estimations. We further provided an example on the model's potential use in improving the WTL management to mitigate CO2 and CH4 emissions while maintaining grass production. At all study sites, the simulated WTLs and carbon decomposition rates showed a significant negative correlation. Therefore, controlling WTL could effectively reduce carbon losses. However, given the highly diverse carbon decomposition rates within individual WTLs, adding indicators (e.g. soil moisture and peat quality) would improve our capacity to assess the effectiveness of specific mitigation practices such as WTL control and rewetting.

Clusters of lysozyme in aqueous solutions

Equilibrium clusters of protein lysozyme are at the center of an ongoing scientific debate. Previous attempts to provide a microscopic description of the clusters that is consistent with all experimental evidence have not been fully successful. The primary reason is the use of model potentials that have a predefined shape. In this paper we derive a model-free interprotein potential directly from experimental structure factor. The derived potential is globally repulsive but has a local minimum at short distances. The minimum is essential for the correct behavior of the structure factor with protein concentration, in particular the shifting pattern of the signature maximum at short wave vectors. Equilibrium clusters are observed throughout the entire range of concentrations, but their nature differs in the low and high concentration limits. At low concentrations, the clusters are extended in shape. As the concentration is increased, small clusters collapse while large clusters are assembled from the small ones. Hydrodynamic interactions drive a kinetic slowdown at high concentrations, where a transition into a fluid of permanent clusters of specific size is observed. In good agreement with the available experimental data, our simulations shed light on the microscopic nature of protein clusters.

Natural extension of fast-slow decomposition for dynamical systems.

Modeling and parameter estimation to capture the dynamics of physical systems are often challenging because many parameters can range over orders of magnitude and are difficult to measure experimentally. Moreover, selecting a suitable model complexity requires a sufficient understanding of the model's potential use, such as highlighting essential mechanisms underlying qualitative behavior or precisely quantifying realistic dynamics. We present an approach that can guide model development and tuning to achieve desired qualitative and quantitative solution properties. It relies on the presence of disparate time scales and employs techniques of separating the dynamics of fast and slow variables, which are well known in the analysis of qualitative solution features. We build on these methods to show how it is also possible to obtain quantitative solution features by imposing designed dynamics for the slow variables in the form of specified two-dimensional paths in a bifurcation-parameter landscape.

A Survey-Based Method to Evaluate Optimal Treatment Selection for Escape-Maintained Problem Behavior.

Geiger, Carr, and LeBlanc (2010) developed a decision-making model for escape-maintained problem behavior that could be used to guide the course of treatment selection. We used a digital survey to evaluate the model's potential usefulness. We presented novice and expert practitioners' written hypothetical scenarios and asked them to determine the optimal treatment in a given situation. Some participants were given the model, whereas others were instructed to use their best clinical judgment. Using logistic regression analyses, the general findings for our scenarios were the following: (a) experts without the aid of a decision model had better odds of selecting the optimal treatment than novices without the decision model, (b) experts with the decision model did not have greater odds of selecting optimal treatment than experts without the model, and

Observing live actin in the human trabecular meshwork

The actomyosin network of trabecular meshwork (TM) cells influences intraocular pressure (IOP) and aqueous humor drainage resistance1 and represents an important therapeutic target for glaucoma. The biology of actin in the TM and effect of agents that alter actin have been studied primarily in cultured TM cells. We are developing a tissue-based model of the human TM in which live cells and cellular interactions can be directly observed in situ.2,3 Here we report our initial novel observations of actin in live cells within the human TM following in situ baculovirus transduction with actin-RFP. Human donor corneoscleral tissue was received in Optisol GS (Bausch & Lomb, Rochester, NY). For institutional reasons, age, death and other patient information were not available to us. Typical age at death ranged from 40-70 years and typical post-mortem age was 7-days (oral communication, Dr. Martin Heur), with experiments begun within a day of receipt.2-5 TM was cut into segments (Fig. 1) and representative segments were randomly selected for viability analysis, as previously described,2 prior to incubations for F-actin labeling. Briefly, tissue was co-incubated with Calcein AM and propidium iodide at 37°C and 8% CO2 prior to live cell imaging. Tissues with at least 50% Calcein-positive cells were considered viable.2 Viable tissue was incubated with Cellular Lights™ Actin-RFP (Life Technologies; n=5) following manufacturer's instructions. Cellular Lights uses a baculovirus delivery vector (BacMam technology) that transduces mammalian cells and directs fluorescence expression by TagRFP fusion to the N-terminus of beta-actin. Some specimens were co-incubated with Hoechst 33342 to label cell nuclei. For comparison, different tissue segments were fixed (4% parformaldehyde), permeabilized in 5% Triton X-100 (2h, 4°C), and incubated with Alexa Fluor 568®-conjugated phalloidin (n=40).4 Figure 1 A: Location of trabecular meshwork (TM) in human corneoscleral tissue. Bar=1mm. B: Examples of wedges cut from corneoscleral donor tissue. Hashed lines indicate the anterior and posterior borders of the TM. Blood is present in Schlemm's canal, immediately ... The tissue was imaged on a PerkinElmer™ Ultraviewer spinning disk confocal microscopy system with 63× water immersion objective. Excitation/emission: 488/525nm (autofluorescence); 555/584nm (Actin-RFP; phalloidin) and 350/460nm (Hoechst) Following baculovirus transduction, cell clusters expressing actin-RFP (red fluorescence) were seen associated with autofluorescent TM uveal beams (Fig. 2A), corneoscleral pores (Fig. 2B,C) and juxtacanalicular fibers (Fig. 2D). Actin-RFP had a primarily cortical distribution and outlined cell borders, comparable with phalloidin labeling (compare figs. 2E-H). Actin distribution in the cytosol was perinuclear (Figs. 2D, 2H; closed arrowheads), punctate (Figs. 2A, 2C, 2D-H; open arrowheads) and filamentous (Figs. 2B-D; open arrows). In some sections, actin filaments were aligned along uveal beams (Figs. 2A, 2E) and corneoscleral pores (Figs. 2B, 2F). Some cell borders had an appearance resembling membrane ruffles typically seen in cultured cells (Fig. 2B, 2C; closed arrows). These ruffle-like structures were not observed in phalloidin-labeled cells. Nuclei were closely associated with fluorescence-labeled actin (Figs. 2A, 2D-H; asterisks). No nuclear fragmentation was seen. Figure 2 Clusters of live TM cells expressing Actin-RPF (red; A-D) or fixed, phalloidin-labeled (red) TM cells in the uveal (A, E), corneoscleral (B, C, F, G) and juxtacanalicular (D, H) regions. Membrane ruffle-like structures (closed arrows) were apparent in ... We have observed the actin cytoskeleton of live cells in the human TM following baculovirus transduction with actin-RFP. Optical sections captured various aspects of the actin cytoskeleton at different TM depths. Actin distribution was perinuclear, punctate, filamentous, and prominent in cell cortices and borders. Notably, prominent stress fibers were not seen. This may be due to the tissue micro-environment that differs from that of rigid-surfaced 2D culture; lack of serum or endogenous factors that enhance actin polymerization; or optical sectioning of cells in 3D tissue that masks stress fibers. Alternatively, the lack of uveal and posterior tissue attachments in donor tissue rims could result in decreased tensions across the TM, and explain the lack of stress fibers. Actin-RFP labeling showed similarities with phalloidin-labeled actin with one caveat. Actin-RFP revealed the presence of membrane protrusions reminiscent of ruffles that were not evident in fixed and permeabilized phalloidin-labeled cells. It could be that Actin-RFP (or GFP) labeling has particular benefits for visualizing less stable actin structures (lamellipodia, filopodia) in live cells, a possibility we plan to explore in future studies using 2-photon microscopy. We used spinning disk laser confocal microscopy that limits phototoxicity during live cell imaging. We are now optimizing our transduction protocols and using 2-photon microscopy that is less phototoxic and penetrates deeper than 1-photon microscopy. We have reported the utility of our human TM tissue-based system for live cell analysis and analysis of protein induction and expression, extracellular matrix and glaucoma markers.2-6 Our present report expands the findings of our prior studies with evidence for the model's potential use in tissue-based real-time studies of actin dynamics and testing of actin-targeting glaucoma therapies.

A Client-centered Nutrition Education Model: Lessons Learned from Texas WIC

To examine the implementation of client-centered nutrition education in Texas Special Supplemental Program for Women, Infants, and Children as it relates to the Participant-Centered Education (PCE) model and identify additional components relevant to practical application. Implementation evaluation at Texas Special Supplemental Program for Women, Infants, and Children state and local agencies, including online surveys, telephone interviews, field observations/interviews, and meeting notes collected from 2009 to 2011. Data analyzed using deductive and inductive coding to investigate research questions. The data aligned with the PCE model domains and suggested elements for practical application. Communication, training, evaluation, and client participation emerged as additional components to support client-centered nutrition education. The new model captures the way the domains influence each other and the importance of 2-way interactions between the client and the other domains. The findings document the model's potential usefulness for programs with similar audiences and goals. This research highlights an expanded PCE model to assist practitioners in implementation of similar client centered programs.

A physiologically based pharmacokinetic model for atrazine and its main metabolites in the adult male C57BL/6 mouse

Atrazine (ATR) is a chlorotriazine herbicide that is widely used and relatively persistent in the environment. In laboratory rodents, excessive exposure to ATR is detrimental to the reproductive, immune, and nervous systems. To better understand the toxicokinetics of ATR and to fill the need for a mouse model, a physiologically based pharmacokinetic (PBPK) model for ATR and its main chlorotriazine metabolites (Cl-TRIs) desethyl atrazine (DE), desisopropyl atrazine (DIP), and didealkyl atrazine (DACT) was developed for the adult male C57BL/6 mouse. Taking advantage of all relevant and recently made available mouse-specific data, a flow-limited PBPK model was constructed. The ATR and DACT sub-models included blood, brain, liver, kidney, richly and slowly perfused tissue compartments, as well as plasma protein binding and red blood cell binding, whereas the DE and DIP sub-models were constructed as simple five-compartment models. The model adequately simulated plasma levels of ATR and Cl-TRIs and urinary dosimetry of Cl-TRIs at four single oral dose levels (250, 125, 25, and 5 mg/kg). Additionally, the model adequately described the dose dependency of brain and liver ATR and DACT concentrations. Cumulative urinary DACT amounts were accurately predicted across a wide dose range, suggesting the model's potential use for extrapolation to human exposures by performing reverse dosimetry. The model was validated using previously reported data for plasma ATR and DACT in mice and rats. Overall, besides being the first mouse PBPK model for ATR and its Cl-TRIs, this model, by analogy, provides insights into tissue dosimetry for rats. The model could be used in tissue dosimetry prediction and as an aid in the exposure assessment to this widely used herbicide.

MOLE: A system for quantum chemistry. II. recent developments

The concept of a quantum chemical system (QCS) as a viable and useful tool in quantum chemical calculations requires that the system be continuously modified and expanded to handle new developments. The MOLE QCS, as originally conceived, was designed to handle the study of molecular electronic structure by means of the following types of calculations: (1) semiempirical (CNDO/2, Hueckel, extended Hueckel); (2) ab initio SCF; (3) configuration interaction (CI); (4) natural orbital analysis; and (5) expectation values (electronic moments and point properties). Since 1968, MOLE has been continuously modified to improve the efficiency of the algorithms which accomplish the above. Recently major additions have altered MOLE sufficiently to justify reporting its new capabilities. The additions are as follows: (1) extended CI capability; (2) perturbation theory CI for the choosing of optimal configurations; (3) configuration generation capability; (4) improved SCF proficiency; and (5) valence-only electronic structure capability based on the use of model potentials for core electrons. The present paper describes the current status of the MOLE system.

Restructuring the On‐Campus Counselor Education Laboratory: Contemporary Professional Issues

An accountability model for addressing contemporary issues in the development and operation of on‐campus practicum laboratories is presented. A case illustration provides an example of the model's potential use. Implications for counselor education programs are discussed.

Models and Algorithms for Transient Queueing Congestion at Airports

We develop a new model for studying the phenomenon of congestion in a transient environment, focusing on the problem of aircraft landings at a busy “hub” airport. Our model is based on a Markov/semi-Markov treatment of changes in the weather, the principal source of uncertainty governing service times, together with a treatment of the arrival stream as time-varying but deterministic. The model is employed to compute moments of queue length and waiting time via a recursive algorithm. To test the model, we conduct a case study using traffic and capacity data for Dallas-Fort Worth International Airport. Our results show that the model's estimates are reasonable, though substantial data difficulties make validation difficult. We explore, as examples of the model's potential usefulness, two policy questions: schedule interference between the two principal carriers, and the likely effects of demand smoothing policies on queueing delays.

The 4s2 1S0 -4s4p 3P1o intercombination line in the zinc-like ions: Ga II, Kr VII, Sr IX, Nb XII, Mo XIII, Rh XVI and Ag XVIII

Transition probabilities are calculated for the 4s2 1S0 -4s4p 3P1o intercombination line in the zinc-like ions Ga II, Kr VII, Sr IX, Nb XII, Mo XIII, Rh XVI and Ag XVIII using the configuration interaction (CI) code CIV3. The calculation involves valence shell correlation, use of model potentials to account for core polarization and the inclusion of relativistic effects. Adjustments are made to the diagonal elements of the Hamiltonian matrix so that eigenvalue differences agree with experimental energy differences, so effectively experimental energies are used for transition energies and to refine the CI mixing coefficients of the wave functions. Both the A-values and the lifetimes of the transition for the various ions are compared with recent experimental and other theoretical results. The present results are sufficiently accurate to provide a benchmark for the analysis of the experimental data.

The 1909 Å intercombination line in C III

The configuration interaction code CIV3 is used to calculate the A-value for the 1909 Å 2s2 1S0-2s2p 3Po1 intercombination line in C III. An extensive calculation of valence shell correlation is augmented by the inclusion of core polarization effects both explicitly through further configurations with one or both 1s orbitals replaced by correlation orbitals, and also by the use of model potentials. Our recommended value of 104 ± 4s−1 for the A-value lies somewhat lower than the experimentally determined value of 121 ± 7s−1. We have estimated the expected error in our work by considering the extent of the convergence of our calculation. We also calculated the resonance transition and obtain an oscillator strength in excellent agreement with experiment.

Core polarization effects on oscillator strengths in neutral zinc

The effect of core polarization on the oscillator strength for the resonance transition in neutral zinc is investigated using the multiconfiguration Hartree Fock approach. The use of model potentials and corrections to the dipole operator is compared to a method, where the core polarization is represented by including configuration state functions, with one hole in the 3d core subshell in the CI-expansion. The latter, which is labeled explicit CI, gives results in good agreement with experiment. The reason for deviations in earlier calculations is discussed, together with the validity of the comparison of length and velocity forms of oscillator strengths, as a test of accuracy. The dependence of the model potential results on the choice of cut-off radius is investigated.

A dynamic almost ideal demand system incorporating consumer expectations

AbstractIn this paper a theoretical framework is presented for the analysis of the effects of psychological, perceptual or expectational factors on household expenditure within a complete demand system. The model was estimated using the Consumer Sentiment Index, which represents an index of consumer perceptions of economic conditions. Evidence was found for significant expectational effects on five of nine expenditure categories—food at home, alcohol, housing, durables and other services. The direct expectation effects were found to be small in size. The results demonstrate the model's potential usefulness as a framework for modelling consumer behavioral responses to expectations and for evaluating the welfare implications of policy‐induced changes in expectations.

An analysis of consumer expectation effects on demand in a dynamic almost ideal demand system

A theoretical framework is presented for analyzing psychological, perceptual, or expectational effects on household expenditure within a complete demand system that is also consistent with household utility-maximizing behavior. The model was estimated with the Consumer Sentiment Index (CSI), which represents an index of consumer perceptions of future economic conditions, and was re-estimated for several CSI components separately. From the CSI, evidence was found for significant expectational effects for 4 of the 11 expenditure categories: alcohol, housing services, durable goods, and other services. The results demonstrate the model's potential usefulness for both demand forecasting and policy analysis.

Effects of a quantum-mechanical lattice on the electronic structure and d–d spectrum of the (MnF6)4− cluster in Mn2+ :KZnF3

The electronic structure of the Mn2+ :KZnF3 impurity system has been computed by means of a Hartree–Fock–Roothaan cluster model. First, the Mn2+ center has been simulated by the (MnF6 )4− unit in vacuo. Then, the effects of the KZnF3 lattice have been included in the cluster calculation using three different lattice models. The well-known point–charge approximation has been compared with two rigorous quantum–lattice models derived from the ideas of the theory of electronic separability. In these two models the lattice ions are represented by an effective lattice potential and a lattice projection operator that enforces the cluster–lattice orthogonality. In the Coulomb or Hartree model the cluster–lattice exchange interactions are neglected. The ab initio model potential (MP) lattice model makes use of model potentials for representing the lattice ions and includes an accurate nonlocal exchange operator. According to the present results, the point–charge lattice model destroys the acceptable picture of the electronic ground state of the (MnF6 )4− unit obtained at the cluster-in vacuo stage, giving a continuously repulsive nuclear potential. The quantum–lattice models restore the bound ground state and give an equilibrium geometry qualitatively correct and quantitatively reasonable. The seven d–d electronic transitions observed in this system are computed within a quarter of eV after correcting the Hartree–Fock description with a configuration interaction limited to the octahedral configurations of the d5 problem and a semiempirical correlation-energy correction. Lattice effects on vertical transition energies turn out to be small. However, important indirect lattice effects are encountered in the theoretical spectrum as a consequence of the lattice-induced modification of the equilibrium geometry of the ground state.

The use of model potentials in oscillator strength calculations

We review recent calculations of oscillator strengths for medium to heavy ions in which the influence of the core on the valence electrons has been treated by the use of model potentials. In particular, we consider core polarisation both with model potentials and with explicit configuration interaction, so that valence-shell correlation is incorporated in the same way in both approaches. These two approaches yield very similar results. This allows the confident use of model potentials for heavy ions and atoms, thus saving considerable computer time when compared with all-electron calculations.

A STOCHASTIC ADAPTATION OF THE VOLLENWEIDER PHOSPHORUS MODEL

ABSTRACT A stochastic modification of the basic Vollenweider model was used to represent variability in daily phosphorus concentrations in a small southern hypereutrophic lake. Uncertainty measurements, arising from defining initial conditions such as loading estimates, and a lumped white-noise parameter were used to project probability distributions of mean daily in-lake phosphorus concentrations. Additional consideration of spatial variability permitted comparison of model projections with monitoring data. Model calibration was performed with over 500 temporally and spatially distributed total phosphorus observations, ranging from 0.171 to 1.575 mg/L, taken from a 70-day intensive monitoring program in 1983. Results indicate the model's potential usefulness, particularly in unstable systems, although short-term oxygen depression, stratification, and catastrophic events, such as a 12.7 cm rainstorm, limited its predictive capabilities.

Comparative study of low-energyΣg+2andΠg2scattering in molecular nitrogen

The linear-algebraic---optical-potential method is applied to low-energy $^{2}\ensuremath{\Sigma}_{g}^{+}$ and $^{2}\ensuremath{\Pi}_{g}e+{\mathrm{N}}_{2}$ scattering in order to understand the nature of the correlation effects in these two symmetries. The calculations clearly show that the two symmetries are dominated by quite different physical effects. The $^{2}\ensuremath{\Sigma}_{g}^{+}$ scattering is sensitive to long-range dipole distortions of the ${\mathrm{N}}_{2}$ core, while $^{2}\ensuremath{\Pi}_{g}$ symmetry is critically dependent on short-range correlations which conserve the ${\ensuremath{\Sigma}}_{g}^{+}$ symmetry of the ${\mathrm{N}}_{2}$ core electrons. Quantitative results which support these conclusions are presented and implications of the calculations on the construction and use of model potentials and polarized orbitals are briefly discussed.

A systems model of rural development

This paper presents a systems model that views rural development as the outcome of interactions between various rural system components - pattern of asset distribution, organizations and institutions and incentive structure in the region and the external relations to the outside world. It uses the model to interpret the rural development experience in Bangladesh, Brazil, China, Indonesia and Nigeria, identifying the links between the asset-organizational-incentive-relational mix in these countries and their respective developmental styles and achievements. Finally, the model's potential use for generation of coherent developmental interventions consistent with and supportive of desired developmental objective is illustrated.