Larger Root Mean Square Research Articles

The influence of geometrical and rheological non-linearity on the calculation of rubber friction

We discuss the influence of geometrical and rheological non-linearities on the prediction of rubber friction and true contact area for rough sliding interactions. In particular, we compare the results of a linearly-viscoelastic linear-contact model, formulated in the Fourier space, with those obtained from non-linear finite element calculations. A sinusoidal rigid profile indenting a rubber block is here considered for simplicity, whereas the effects of non-linearity are evaluated by varying the aspect ratio, loading conditions and sliding speed of the contact interface. It is found that accurate friction predictions can be obtained through the linear viscoelastic model, provided that the roughness under investigation features moderate values of root mean square slopes, whereas non-linear finite element computations should be adopted for large root mean square slopes.

Impacts of AMSU-A, MHS and IASI data assimilation on temperature and humidity forecasts with GSI–WRF over the western United States

Abstract. Using NOAA's Gridpoint Statistical Interpolation (GSI) data assimilation system and NCAR's Advanced Research WRF (Weather Research and Forecasting) (ARW-WRF) regional model, six experiments are designed by (1) a control experiment (CTRL) and five data assimilation (DA) experiments with different data sets, including (2) conventional data only (CON); (3) microwave data (AMSU-A + MHS) only (MW); (4) infrared data (IASI) only (IR); (5) a combination of microwave and infrared data (MWIR); and (6) a combination of conventional, microwave and infrared observation data (ALL). One-month experiments in July 2012 and the impacts of the DA on temperature and moisture forecasts at the surface and four vertical layers over the western United States have been investigated. The four layers include lower troposphere (LT) from 800 to 1000 hPa, middle troposphere (MT) from 400 to 800 hPa, upper troposphere (UT) from 200 to 400 hPa, and lower stratosphere (LS) from 50 to 200 hPa. The results show that the regional GSI–WRF system is underestimating the observed temperature in the LT and overestimating in the UT and LS. The MW DA reduced the forecast bias from the MT to the LS within 30 h forecasts, and the CON DA kept a smaller forecast bias in the LT for 2-day forecasts. The largest root mean square error (RMSE) is observed in the LT and at the surface (SFC). Compared to the CTRL, the MW DA produced the most positive contribution in the UT and LS, and the CON DA mainly improved the temperature forecasts at the SFC. However, the IR DA gave a negative contribution in the LT. Most of the observed humidity in the different vertical layers is overestimated in the humidity forecasts except in the UT. The smallest bias in the humidity forecast occurred at the SFC and in the UT. The DA experiments apparently reduced the bias from the LT to UT, especially for the IR DA experiment, but the RMSEs are not reduced in the humidity forecasts. Compared to the CTRL, the IR DA experiment has a larger RMSE in the moisture forecast, although the smallest bias is found in the LT and MT.

Hoyle band andαcondensation inC12

The excited states in ${^{12}{\rm C}}$ are investigated by using an extended version of the so-called Tohsaki-Horiuchi- Schuck-R\"opke (THSR) wave function, where both the $3\alpha$ condensate and ${^{8}{\rm Be}} + \alpha$ cluster asymptotic configurations are included. A new method is also used to resolve spurious continuum coupling with physical states. We focus on the structures of the "Hoyle band" states, $2_2^+$, and $4_2^+$ states, which are recently observed above the Hoyle state and of the $0_3^+$ and $0_4^+$ states, which are also quite recently identified in experiment. Their resonance parameters and decay properties are reasonably reproduced. All these states have gaslike configurations of the $3\alpha$ clusters with larger root mean square radii than that of the Hoyle state. The Hoyle band is not simply considered to be the ${^{8}{\rm Be}}(0^+) +\alpha$ rotation as suggested by previous cluster model calculations, nor to be a rotation of a rigid-body triangle-shaped object composed of the $3\alpha$ particles. This is mainly due to the specificity of the Hoyle state, which has the $3\alpha$ condensate structure and gives a rise to the $0_3^+$ state with a prominent ${^{8}{\rm Be}}(0^+)+\alpha$ structure as a result of very strong monopole excitation from the Hoyle state.

Calculations of electron inelastic mean free paths. X. Data for 41 elemental solids over the 50 eV to 200 keV range with the relativistic full Penn algorithm

We have calculated inelastic mean free paths (IMFPs) for 41 elemental solids (Li, Be, graphite, diamond, glassy C, Na, Mg, Al, Si, K, Sc, Ti, V, Cr, Fe, Co, Ni, Cu, Ge, Y, Nb, Mo, Ru, Rh, Pd, Ag, In, Sn, Cs, Gd, Tb, Dy, Hf, Ta, W, Re, Os, Ir, Pt, Au, and Bi) for electron energies from 50 eV to 200 keV. The IMFPs were calculated from measured energy loss functions for each solid with a relativistic version of the full Penn algorithm. The calculated IMFPs could be fitted to a modified form of the relativistic Bethe equation for inelastic scattering of electrons in matter for energies from 50 eV to 200 keV. The average root‐mean‐square (RMS) deviation in these fits was 0.68%. The IMFPs were also compared with IMFPs from a relativistic version of our predictive Tanuma, and Powell and Penn (TPP‐2M) equation that was developed from a modified form of the relativistic Bethe equation. In these comparisons, the average RMS deviation was 11.9% for energies between 50 eV and 200 keV. This RMS deviation is almost the same as that found previously in a similar comparison for the 50 eV to 30 keV range (12.3%). Relatively large RMS deviations were found for diamond, graphite, and cesium as in our previous comparisons. If these three elements were excluded in the comparisons, the average RMS deviation was 8.9% between 50 eV and 200 keV. The relativistic TPP‐2M equation can thus be used to estimate IMFPs in solid materials for energies between 50 eV and 200 keV. We found satisfactory agreement between our calculated IMFPs and those from recent calculations and from measurements at energies of 100 and 200 keV. Copyright © 2015 John Wiley & Sons, Ltd.

English

Crop models known to be based on the theory of crop physiology for describing the dynamic process of crop growth are recently explored for their uncertainties in model application under resource limited conditions. The aim of this study was to test Environmental Policy Integrated Climate (EPIC), on upland land rice production by taking into account seasonal variability in Guinean and Guinean-Sudanian zones in Benin and Nigeria (West Africa). A range of data available under farmer or experimental conditions in rainfed agriculture were measured or used from literature. The results show the accuracy of the model to simulate LAI, total above ground biomass and grain yield of upland rice for 2 NERICA rice cultivars. After calibration, the model showed average mean relative error between 0.06 and 0.15 with the model efficiency up to 0.98% in the case of LAI. The assessment of the model performances about sensitivity to N or P fertilizer application is also discussed under Ultisols. Large root mean square (RMSE) in calibration and the validation (>100) process suggested that robustness of the model became restrictive under severe environmental conditions such as in drought or flooding condition. Performance of the model at large scale should be executed of with land marginality classification. Key words: Environmental Policy Integrated Climate (EPIC), modeling, upland rice, West Africa.

Predicting the EQ-5D-3L Preference Index from the SF-12 Health Survey in a National US Sample: A Finite Mixture Approach.

Background. When data on preferences are not available, analysts rely on condition-specific or generic measures of health status like the SF-12 for predicting or mapping preferences. Such prediction is challenging because of the characteristics of preference data, which are bounded, have multiple modes, and have a large proportion of observations clustered at values of 1. Methods. We developed a finite mixture model for cross-sectional data that maps the SF-12 to the EQ-5D-3L preference index. Our model characterizes the observed EQ-5D-3L index as a mixture of 3 distributions: a degenerate distribution with mass at values indicating perfect health and 2 censored (Tobit) normal distributions. Using estimation and validation samples derived from the Medical Expenditure Panel Survey 2000 dataset, we compared the prediction performance of these mixture models to that of 2 previously proposed methods: ordinary least squares regression (OLS) and two-part models. Results. Finite mixture models in which predictions are based on classification outperform two-part models and OLS regression based on mean absolute error, with substantial improvement for samples with fewer respondents in good health. The potential for misclassification is reflected on larger root mean square errors. Moreover, mixture models underperform around the center of the observed distribution. Conclusions. Finite mixtures offer a flexible modeling approach that can take into account idiosyncratic characteristics of the distribution of preferences. The use of mixture models allows researchers to obtain estimates of health utilities when only summary scores from the SF-12 and a limited number of demographic characteristics are available. Mixture models are particularly useful when the target sample does not have a large proportion of individuals in good health.

Forecasting of ionospheric vertical TEC 1-h ahead using a genetic algorithm and neural network

A hybrid back propagation artificial neural network (ANN) with a genetic algorithm (GA) is built to predict 1-h ahead vertical total electron content (TEC) of single station in China. An ionospheric TEC forecast model was developed based on TEC data from four dual-frequency GPS stations of BJFS (39.61°N, 115.89°E), XIAN (34.18°N, 108.99°E), WUHN (30.53°N, 114.36°E), and KUNM (25.03°N, 102.80°E) in both 2007 and 2011. The results show the mean relative errors of the model are smaller than 10% and the root mean square (RMS) error is less than 1 TECU at mid-high-latitudes during the period of low solar activity in 2007. Some large RMS errors with more than 5 TECU can be observed at low latitude during the medium solar activity period of 2011. Compared to the traditional BP algorithm, the new algorithm is a promising and reliable alternative forecast technology for ionospheric TEC.

Estimating global solar radiation using a hybrid parametric model from MODIS data over the Tibetan Plateau

The Tibetan Plateau plays an important role in global atmospheric circulation with its complex terrain. The downward surface shortwave radiation (DSSR) can be obtained from remote sensing data because of its sparse observations and rugged surface. In this paper, a satellite-based scheme is presented to retrieve all-sky downward surface shortwave radiation, which links a look-up table algorithm and satellite images. The look-up table for clear sky and cloudy sky was created separately using a comprehensive 1D physically based radiative transfer model SBDART to achieve a higher computational accuracy and efficiency compared to the comprehensive radiative transfer model. The estimated DSSR was validated using one year pyranometer measurements from 8 stations in the Tibetan Plateau and compared with GEWEX–SRB data with 1° spatial resolution. The result shows that the largest root mean square error was 60W/m2 (32%) at Guoluo station, and the least root mean square error was 13W/m2 (13%) at Golmud station. The bias was larger in summer and smaller in winter, which may be caused by uncertainties in the assumption from the 1D radiative transfer model and MODIS cloud properties product for broken and inhomogeneous clouds. The algorithm we proposed can be applied globally without local calibration because it is independent of climate and the surface elevation.

Rapid Analysis of Deoxynivalenol in Durum Wheat by FT-NIR Spectroscopy

Fourier-transform-near infrared (FT-NIR) spectroscopy has been used to develop quantitative and classification models for the prediction of deoxynivalenol (DON) levels in durum wheat samples. Partial least-squares (PLS) regression analysis was used to determine DON in wheat samples in the range of <50–16,000 µg/kg DON. The model displayed a large root mean square error of prediction value (1,977 µg/kg) as compared to the EU maximum limit for DON in unprocessed durum wheat (i.e., 1,750 µg/kg), thus making the PLS approach unsuitable for quantitative prediction of DON in durum wheat. Linear discriminant analysis (LDA) was successfully used to differentiate wheat samples based on their DON content. A first approach used LDA to group wheat samples into three classes: A (DON ≤ 1,000 µg/kg), B (1,000 < DON ≤ 2,500 µg/kg), and C (DON > 2,500 µg/kg) (LDA I). A second approach was used to discriminate highly contaminated wheat samples based on three different cut-off limits, namely 1,000 (LDA II), 1,200 (LDA III) and 1,400 µg/kg DON (LDA IV). The overall classification and false compliant rates for the three models were 75%–90% and 3%–7%, respectively, with model LDA IV using a cut-off of 1,400 µg/kg fulfilling the requirement of the European official guidelines for screening methods. These findings confirmed the suitability of FT-NIR to screen a large number of wheat samples for DON contamination and to verify the compliance with EU regulation.

The effect of Fermi momentum cutoff on the binding energy of closed shell nuclei in the LOCV framework

The ground state binding energies of the light symmetric closed-shell nuclei, i.e., 4He, 12C, 16O and 40Ca and the heavy asymmetric ones, i.e., 48Ca, 90Zr and 120Sn are calculated in the harmonic oscillator (HOS) basis, by imposing the relative Fermi momentum cutoff of two point-like interacting nucleons on the density dependent average effective interactions (DDAEI). The DDAEI are generated through the lowest order constrained variational (LOCV) method calculations for the asymmetric nuclear matter with the operator and the channel dependent type bare nucleon-nucleon potentials, such as the Argonne \(Av_{18}^{j_{\max } = 2}\) and the Reid soft core, Reid68, interactions. In the framework of harmonic oscillator shell model, the cutoff is imposed by defining the maximum value of the relative quantum numbers (RQNmax) in two ways: (1) The RQNmax of the last shell and (2) the RQNmax of each shell, in the ground state of the nucleus. It is shown that present results on the binding energies and the root means square radius are closer to the corresponding experimental data than, our previous works with the same DDAEI potentials, but without the cutoff constraint. However, for the light symmetric nuclei, the second scheme gives less binding energy and larger root mean square radius compare to the first one. While the situation is reversed for the heavier nuclei.

Performance assessment of the successive Version 6 and Version 7 TMPA products over the climate-transitional zone in the southern Great Plains, USA

Summary This study assesses the latest version, Version 7 (V7) Tropical Rainfall Measuring Mission (TRMM) Multi-satellite Precipitation Analysis (TMPA) rainfall estimates by comparison with the previous version, Version 6 (V6), for both near-real-time product (3B42RT) and post-real-time research products (3B42) over the climate-transitional zone in the southern Great Plains, USA. Two basins, the Verdigris River Basin (VRB) in the east and the Upper Washita Basin (UWB) in the west, with distinctive precipitation but similar vegetation and elevation, were selected to evaluate the TMPA products using rain gauge-blended products with WSR-88D NEXRAD Stage IV. This study sheds important insights into the detailed spatiotemporal precipitation errors, and also reveals algorithm performance during extreme events over the two low-relief basins within a high precipitation gradient zone. Based on nine years of measurements (2002–2010), this study shows that: (1) 3B42V7 corrects the widespread rainfall underestimation from research product 3B42V6, especially for the drier UWB with relative bias (RB) improvement from −23.24% to 2.24%. (2) 3B42RTV7 reduces the widespread, notable overestimation from the real-time product 3B42RTV6, with minor overestimation in the wet VRB and underestimation in the dry UWB. (3) For both versions of TMPA products, larger root mean square error (RMSE) but higher correlation coefficients (CCs) tend to appear for the wet VRB, while lower RMSE and CC mostly occur in the dry UWB. 3B42RTV7 shows a drawback that the CC declines significantly, especially in the dry region where it drops below 0.5. (4) Seasonally, autumn rainfall estimations in both versions and basins have the least bias. The 3B42RTV6 overestimation and 3B42V6 underestimation of spring and summer rainfall, which dominate the annual total bias, are significantly reduced for both basins in the V7 products. Winter precipitation estimation improvement is also noticeable with significant RB and RMSE reductions. However, considerable overestimation in summer rainfall still exists for the wet basin. (5) Although V7 has the overall best performance, it still shows deficiency in detecting extreme rainfall events in low-relief regions, tending to underestimate peak rainfall intensity and to misrepresent timing and locations. Results from this study can be used for reference in the algorithm development of the next generation of Integrated Multi-Satellite Retrievals for Global Precipitation Measurement (GPM) scheduled to launch in 2014.

An investigation of p+8He elastic scattering

The vector analyzing power and differential cross-section for the elastic scattering of 8 He nucleus from polarized protons at 71 MeV/nucleon have been analyzed in the framework of the optical model potentials. Microscopic single folding (SF) optical potentials (OP) have been constructed based upon two different effective nucleon–nucleon (NN) interactions, namely Jeukenne–Lejeune–Mahaux (JLM) and BDM3Y1 effective interactions. The effect of 8 He nuclear structure has been tested through two different choices of the nuclear density distribution. It is concluded that the nucleus 8 He may be considered as a thick skin exotic nucleus. In order to investigate the vector analyzing power data, besides the Thomas phenomenological representation, three different forms of the spin–orbit (SO) part of the OP have been considered. These forms are based directly or indirectly upon the density distribution of 8 He nucleus. It is found that SO potentials of larger root mean square radii are able to successfully describe the vector analyzing power data more than those of shorter radii.

Roughness and Lubricant Effect on 3D Atomic Asperity Contact

Large-scale molecular dynamics simulations were performed to study the sliding process of rough surfaces with and without lubricant. In the dry contact, a linear relationship has been observed between the load and the contact area for surfaces with large root mean square (RMS) roughness. However, it becomes nonlinear when the RMS is small. In the presence of adhesion, small roughness results in a large friction force when the surfaces are flattened and the contact area reaches 60 %. In order to confirm this observation, nonadhesive models have been established with an observation that under the combined influence from roughness and adhesion, the contact area plays a crucial role to determine whether the dry sliding is under the domination of roughness or adhesion. In the lubricated sliding, an increase in friction force has been found for the partially lubricated condition because the asperity contact still accounts for a great deal of resisting force. Besides, the lubricant exerts a comparable resisting force to the sliding.

Improving estimates of critical lower percentiles by induced censoring

In this article, we present an approach based on induced censoring for improving the estimation of critical lower percentiles. We validate this technique via simulation results and practical industrial insights. Data from product components that have at least two aging periods (e.g., bathtub failure rate) is investigated. When such data are improperly fit by certain reliability distributions, estimates of lower percentiles are impacted by longer-lasting failures, resulting in larger root mean square errors (RMSE) and bias. In lieu of utilizing a more complex bathtub model, we propose induced right censoring of data at various points to substantially reduce RMSE and bias of lower percentile estimates. A technique for finding optimal or near optimal censoring points is discussed and two real world examples illustrate how this works in practice.

Impact of derived global weather data on simulated crop yields

Crop simulation models can be used to estimate impact of current and future climates on crop yields and food security, but require long-term historical daily weather data to obtain robust simulations. In many regions where crops are grown, daily weather data are not available. Alternatively, gridded weather databases (GWD) with complete terrestrial coverage are available, typically derived from: (i) global circulation computer models; (ii) interpolated weather station data; or (iii) remotely sensed surface data from satellites. The present study's objective is to evaluate capacity of GWDs to simulate crop yield potential (Yp) or water-limited yield potential (Yw), which can serve as benchmarks to assess impact of climate change scenarios on crop productivity and land use change. Three GWDs (CRU, NCEP/DOE, and NASA POWER data) were evaluated for their ability to simulate Yp and Yw of rice in China, USA maize, and wheat in Germany. Simulations of Yp and Yw based on recorded daily data from well-maintained weather stations were taken as the control weather data (CWD). Agreement between simulations of Yp or Yw based on CWD and those based on GWD was poor with the latter having strong bias and large root mean square errors (RMSEs) that were 26–72% of absolute mean yield across locations and years. In contrast, simulated Yp or Yw using observed daily weather data from stations in the NOAA database combined with solar radiation from the NASA-POWER database were in much better agreement with Yp and Yw simulated with CWD (i.e. little bias and an RMSE of 12–19% of the absolute mean). We conclude that results from studies that rely on GWD to simulate agricultural productivity in current and future climates are highly uncertain. An alternative approach would impose a climate scenario on location-specific observed daily weather databases combined with an appropriate upscaling method.

Direct numerical simulation of ellipsoidal particles in turbulent channel flow

This paper investigates the behaviour of elongated, axi-symmetric ellipsoidal particles, their interaction with turbulence, and the effects of the ellipsoids on turbulence in a turbulent channel flow with Reτ = 150. The simulations are carried out with full four-way coupling using the point-source approach: the particles are affected by the fluid, the particles affect the fluid, and the particles can collide with each other or the wall using a realistic collision algorithm. The trajectories of the ellipsoids are tracked by solving the translational and rotational equations of motion in a Quaternion framework and are closed with hydrodynamic drag and torque laws. To specifically identify the effect of particle shape, simulations of single phase channel flow are compared to simulations with spherical particles and to simulations with ellipsoids. In all cases, the driving pressure drop, to establish a flow with Reτ = 150, is kept constant. Both the spherical particles and the ellipsoidal particles have a Stokes number of 5. Although the volume fraction is very low, 0.00725 and 0.0219 % for the spheres and ellipsoids, respectively, there is some effect of the particles and the ellipsoids on the turbulence. Although the transport terms in the turbulent kinetic energy equation of the fluid are hardly affected, the turbulence kinetic energy itself decreases by 6.0 % for the flow laden with spherical particles and 4.8 % for the ellipsoidal particles. The homogeneous dissipation of turbulence kinetic energy by the fluid decreases due to the addition of particles, and the production also decreases. The particles dissipate turbulence kinetic energy of the fluid phase, predominantly in the near-wall region. Because there is a high average slip velocity in the stream-wise direction between the particles and the fluid in the near-wall region, the root mean square of the particle velocity is higher than that of the fluid velocity in this direction. In the other directions, the root mean square velocities of the particles are significantly lower than of the fluid. There is, however, a positive slip velocity between the particles and the fluid in the wall-normal direction, indicating that the particles move towards the wall with a higher momentum than that they return to the centre of the channel with. As a result, there is a 4–5 times higher concentration of particles near the wall than in the centre of the channel. As both the spherical and the ellipsoidal particles are very small, there is no major difference in their overall behaviour. However, in the near-wall region, there are some profound differences. The collision mechanism of ellipsoids with the walls is significantly different compared to spheres, the former predominantly inducing rotation resulting from a collision and the latter predominantly moving away from the wall after colliding. This is confirmed by the strong rotation as well as large root mean square of rotation of the ellipsoidal particles in the near-wall region. This results in a slight inward shift of the peak of the root mean square velocities of the fluid and the ellipsoidal particles as well as the peak in slip velocity, driving the momentum transfer, compared to the simulations with the spheres. Finally, the statistics of the orientation show that the ellipsoids align in the stream-wise direction in the near-wall region, because of the fluid boundary layer as well as the particle–wall collisions, but that there is no significant orientation of the ellipsoids outside of the near-wall region.

Structural investigation of deleterious non-synonymous SNPs of EGFR gene

Epidermal Growth Factor Receptor (EGFR), a member of the receptor tyrosine kinase family has shown to be implicated in the development and progression of various cancers due to mutations in the tyrosine kinase domain (TKD). It is important to understand the functional significance of amino acid variation occurring within TKD due to non-synonymous Single Nucleotide Polymorphism (nsSNPs). Therefore, we have evaluated the influence of nsSNPs on the structure of EGFR-TKD using computational methods. Out of 2,493 SNPs in the EGFR gene, only 41 were found to be non-synonymous. In silico evaluation of these nsSNPs using a sequence based SIFT tool and structure based PolyPhen algorithm revealed that 13 nsSNPs disrupted the conformation of EGFR-TKD. Protein stability analysis using CUPSAT, I-mutant2.0 and iPTree-STAB identified 6 mutants that are less stable than the wild structure. Thereafter, to evaluate the structural impact of 5 mutants (G719A, P733L, V742A, S768I and H773R) the molecular dynamics (MD) simulation for 2 ns was performed. The MD trajectories showed that the native EGFR was stabilized after 0.9 ns while the stability of mutants was achieved after longer simulation. The RMSF profile of P-loop and A-loop shows an increased flexibility for all the mutants. We also observed that the 3 mutants (V742A, P733L and H773R) showed large root mean square deviation (2.075, 2.59 and 2.752 Å respectively) compared to the native EGFR. Further docking studies indicate that gefitinib can be administered for combating cancer occurring due to presence of these mutations.

Lattice summations for spread out particles: Applications to neutral and charged systems

This work is concerned with the lattice energy of periodic assemblies of mass and charge distributions of the form, exp (-αp(2)), where α is an adjustable positive variable and p(̱) is the vector from the lattice site or average position. The energy of interaction between two distributions is the density-weighted integral of the interactions between the volume elements of each distribution. Reciprocal space lattice summation formulas derived for particles represented by gaussian smeared-out density distributions are applied to the gaussian potential and a bounded version of the soft-sphere potential for a range of exponents. Two types of spatial broadening are considered, continuous or physical broadening (PB) and broadening resulting from the time average of point particle positions, so-called "time" broadening (TB). For neutral mass distributions a reciprocal space lattice summation formula is derived which is applied to the bounded soft-sphere potential. For the charged systems, the methodology described in Heyes [J. Chem. Phys. 74, 1924 (1981)] is used, which for the PB case gives the Ewald-like formulas derived by Gingrich and Wilson [Chem. Phys. Lett. 500, 178 (2010)] using a different method. Another expression for the lattice energy of the spread out charge distributions is derived which is cast entirely in terms of a summation over the reciprocal lattice vectors, without the arbitrary charge spreading function used in the Ewald method. The effects of charge spreading on a generalized definition of the Madelung constant (M) for a selection of crystal lattices are shown to be insignificant for route mean square displacements up to values typical of melting of an ionic crystal. When the length scale of the charge distribution becomes comparable to or greater than the mean inter particle spacing, however, the effects of charge broadening on the lattice energy are shown to be significant. In the PB case, M → 0 for the uniform charge density or α → 0 limit, and M ultimately becomes negative in the TB case for a large enough root mean square displacement (or small enough α).

Evaluation of multiple protein docking structures using correctly predicted pairwise subunits

BackgroundMany functionally important proteins in a cell form complexes with multiple chains. Therefore, computational prediction of multiple protein complexes is an important task in bioinformatics. In the development of multiple protein docking methods, it is important to establish a metric for evaluating prediction results in a reasonable and practical fashion. However, since there are only few works done in developing methods for multiple protein docking, there is no study that investigates how accurate structural models of multiple protein complexes should be to allow scientists to gain biological insights.MethodsWe generated a series of predicted models (decoys) of various accuracies by our multiple protein docking pipeline, Multi-LZerD, for three multi-chain complexes with 3, 4, and 6 chains. We analyzed the decoys in terms of the number of correctly predicted pair conformations in the decoys.Results and conclusionWe found that pairs of chains with the correct mutual orientation exist even in the decoys with a large overall root mean square deviation (RMSD) to the native. Therefore, in addition to a global structure similarity measure, such as the global RMSD, the quality of models for multiple chain complexes can be better evaluated by using the local measurement, the number of chain pairs with correct mutual orientation. We termed the fraction of correctly predicted pairs (RMSD at the interface of less than 4.0Å) as fpair and propose to use it for evaluation of the accuracy of multiple protein docking.

Possible deuteronlike molecular states composed of heavy baryons

We perform a systematic study of the possible loosely bound states composed of two charmed baryons or a charmed baryon and an anti-charmed baryon within the framework of the one boson exchange (OBE) model. We consider not only the $\pi$ exchange but also the $\eta$, $\rho$, $\omega$, $\phi$ and $\sigma$ exchanges. The $S-D$ mixing effects for the spin-triplets are also taken into account. With the derived effective potentials, we calculate the binding energies and root-mean-square (RMS) radii for the systems $\Lambda_c\Lambda_c(\bar{\Lambda}_c)$, $\Xi_c\Xi_c(\bar{\Xi}_c)$, $\Sigma_c\Sigma_c(\bar{\Sigma}_c)$, $\Xi_c^\prime\Xi_c^\prime(\bar{\Xi}_c^\prime)$ and $\Omega_c\Omega_c(\bar{\Omega}_c)$. Our numerical results indicate that: (1) the H-dibaryon-like state $\Lambda_c\Lambda_c$ does not exist; (2) there may exist four loosely bound deuteron-like states $\Xi_c\Xi_c$ and $\Xi_c^\prime\Xi_c^\prime$ with small binding energies and large RMS radii.