Unifying temperature definition in atomistic and field representations of conservation laws

This work presents a formalism to derive field quantities and conservation laws from the atomistic using the theory of distributions as the mathematical tool. By defining temperature as a derived quantity, as that in molecular kinetic theory and atomistic simulations, a field representation of the conservation law of linear momentum is precisely derived and expressed in terms of temperature field, leading to a unified atomistic and continuum description of temperature and a new conservation equation of linear momentum that, supplemented by an interatomic potential, completely governs thermal and mechanical processes across multiple scales from the atomic to the continuum and can solve for atomistic trajectories for systems at finite temperatures, as well as the evolution of local field quantities in space and time with atomic or multiscale resolution. Four sets of numerical examples are presented to demonstrate the efficacy of the formulation in capturing the effect of temperature or thermal fluctuations, including phonon density of states, thermally activated dislocation motion, dislocation formation during heteroepitaxy, and attenuation of longitudinal acoustic waves as a result of their interaction with thermal phonons

Nucleosome Structure Incorporated Histone Acetylation Site Prediction in \u3ci\u3eArabidopsis thaliana\u3c/i\u3e

BackgroundAcetylation is a crucial post-translational modification for histones, and plays a key role in gene expression regulation. Due to limited data and lack of a clear acetylation consensus sequence, a few researches have focused on prediction of lysine acetylation sites. Several systematic prediction studies have been conducted for human and yeast, but less for Arabidopsis thaliana. ResultsConcerning the insufficient observation on acetylation site, we analyzed contributions of the peptide-alignment-based distance definition and 3D structure factors in acetylation prediction. We found that traditional structure contributes little to acetylation site prediction. Identified acetylation sites of histones in Arabidopsis thaliana are conserved and cross predictable with that of human by peptide based methods. However, the predicted specificity is overestimated, because of the existence of non-observed acetylable site. Here, by performing a complete exploration on the factors that affect the acetylability of lysines in histones, we focused on the relative position of lysine at nucleosome level, and defined a new structure feature to promote the performance in predicting the acetylability of all the histone lysines in A. thaliana. ConclusionWe found a new spacial correlated acetylation factor, and defined a ε-N spacial location based feature, which contains five core spacial ellipsoid wired areas. By incorporating the new feature, the performance of predicting the acetylability of all the histone lysines in A. Thaliana was promoted, in which the previous mispredicted acetylable lysines were corrected by comparing to the peptide-based prediction

Comparing the Salt Tolerance of Three Landscape Plants Using a Near-Continuous Gradient Dosing System

Screening salinity-tolerant plants is usually time intensive and only applicable to a limited number of salinity levels. A near-continuous gradient dosing (NCGD) system allows researchers to evaluate a large number of plants for salinity tolerance with multiple treatments, more flexibility, and reduced efforts of irrigation. Rose of sharon (Hibiscus syriacus), ninebark (Physocarpus opulifolius), and japanese spirea (Spiraea japonica) were irrigated using an NCGD system with eight electrical conductivity (EC) levels ranging from 0.9 to 6.5 dS·m–1. At 11 weeks after irrigation was initiated, there were no significant differences among EC levels in terms of visual score, growth index [(Height + Width 1 + Width 2)/3], stem diameter, number of inflorescences, and shoot dry weight (DW) of rose of sharon. However, the root DW, relative chlorophyll content (SPAD), and net photosynthesis rate (Pn) of rose of sharon decreased linearly as EC levels increased. Ninebark and japanese spirea had increased foliar salt damage with increasing EC levels. The growth index, stem diameter, number of inflorescences, shoot and root DW, SPAD, and Pn of ninebark decreased linearly as EC levels increased. The growth index and SPAD of japanese spirea decreased quadratically with increasing EC levels, but its stem diameter, number of inflorescences, shoot and root DW, and Pn decreased linearly with increasing EC levels. The salinity threshold (50% loss of shoot DW) was 5.4 and 4.6 dS·m–1, respectively, for ninebark and japanese spirea. We were not able to define the salinity threshold for rose of sharon in this study. However, rose of sharon was the most salinity-tolerant species among the three landscape plants

Passing Waves from Atomistic to Continuum

Progress in the development of coupled atomistic-continuum methods for simulations of critical dynamic material behavior has been hampered by a spurious wave reflection problem at the atomistic-continuum interface. This problem is mainly caused by the difference in material descriptions between the atomistic and continuum models, which results in a mismatch in phonon dispersion relations. In this work, we introduce a new method based on atomistic dynamics of lattice coupled with a concurrent atomistic-continuum method to enable a full phonon representation in the continuum description. This then permits the passage of short-wavelength, high-frequency phonon waves from the atomistic to continuum regions. The benchmark examples presented in this work demonstrate that the new scheme enables the passage of all allowable phonons through the atomistic-continuum interface; it also preserves the wave coherency and energy conservation after phonons transport across multiple atomistic-continuum interfaces. This work is the first step towards developing a concurrent atomistic-continuum simulation tool for non-equilibrium phonon-mediated thermal transport in materials with microstructural complexity

Nucleosome Structure Incorporated Histone Acetylation Site Prediction in \u3ci\u3eArabidopsis thaliana\u3c/i\u3e

Background Acetylation is a crucial post-translational modification for histones, and plays a key role in gene expression regulation. Due to limited data and lack of a clear acetylation consensus sequence, a few researches have focused on prediction of lysine acetylation sites. Several systematic prediction studies have been conducted for human and yeast, but less for Arabidopsis thaliana. Results Concerning the insufficient observation on acetylation site, we analyzed contributions of the peptide-alignment-based distance definition and 3D structure factors in acetylation prediction. We found that traditional structure contributes little to acetylation site prediction. Identified acetylation sites of histones in Arabidopsis thaliana are conserved and cross predictable with that of human by peptide based methods. However, the predicted specificity is overestimated, because of the existence of non-observed acetylable site. Here, by performing a complete exploration on the factors that affect the acetylability of lysines in histones, we focused on the relative position of lysine at nucleosome level, and defined a new structure feature to promote the performance in predicting the acetylability of all the histone lysines in A. thaliana. Conclusion We found a new spacial correlated acetylation factor, and defined a ε-N spacial location based feature, which contains five core spacial ellipsoid wired areas. By incorporating the new feature, the performance of predicting the acetylability of all the histone lysines in A. Thaliana was promoted, in which the previous mispredicted acetylable lysines were corrected by comparing to the peptide-based prediction

Exploring virus relationships based on virus-host protein-protein interaction network

<p>Abstract</p> <p>Background</p> <p>Currently, several systems have been proposed to classify viruses and indicate the relationships between different ones, though each system has its limitations because of the complexity of viral origins and their rapid evolution rate. We hereby propose a new method to explore the relationships between different viruses.</p> <p>Method</p> <p>A new method, which is based on the virus-host protein-protein interaction network, is proposed in this paper to categorize viruses. The distances between 114 human viruses, including 48 HIV-1 and HIV-2 viruses, are estimated according to the protein-protein interaction network between these viruses and humans.</p> <p>Conclusions/significance</p> <p>The results demonstrated that our method can disclose not only relationships consistent with the taxonomic results of currently used systems of classification but also the potential relationships that the current virus classification systems have not revealed. Moreover, the method points to a new direction where the functional relationships between viruses and hosts can be used to explore the virus relationships on a systematic level.</p

Salt Tolerance of Sego SupremeTM Plants

Sego SupremeTM is a designated plant breeding and introduction program at the Utah State University Botanical Center and the Center for Water Efficient Landscaping. This plant selection program introduces native and adapted plants to the arid West for aesthetic landscaping and water conservation. The plants are evaluated for characteristics such as color, flowering, ease of propagation, market demand, disease/pest resistance, and drought tolerance. However, salt tolerance has not been considered during the evaluation processes. Four Sego SupremeTM plants [Aquilegia barnebyi (oil shale columbine), Clematis fruticosa (Mongolian gold clematis), Epilobium septentrionale (northern willowherb), and Tetraneuris acaulis var. arizonica (Arizona four-nerve daisy)] were evaluated for salt tolerance in a greenhouse. Uniform plants were irrigated weekly with a nutrient solution at an electrical conductivity (EC) of 1.25 dS·m−1 as control or a saline solution at an EC of 2.5, 5.0, 7.5, or 10.0 dS·m−1 for 8 weeks. After 8 weeks of irrigation, A. barnebyi irrigated with saline solution at an EC of 5.0 dS·m−1 had slight foliar salt damage with an average visual score of 3.7 (0 = dead; 5 = excellent), and more than 50% of the plants were dead when irrigated with saline solutions at an EC of 7.5 and 10.0 dS·m−1. However, C. fruticosa, E. septentrionale, and T. acaulis had no or minimal foliar salt damage with visual scores of 4.2, 4.1, and 4.3, respectively, when irrigated with saline solution at an EC of 10.0 dS·m−1. As the salinity levels of treatment solutions increased, plant height, leaf area, and shoot dry weight of C. fruticosa and T. acaulis decreased linearly; plant height of A. barnebyi and E. septentrionale also declined linearly, but their leaf area and shoot dry weight decreased quadratically. Compared with the control, the shoot dry weights of A. barnebyi, C. fruticosa, E. septentrionale, and T. acaulis decreased by 71.3%, 56.3%, 69.7%, and 48.1%, respectively, when irrigated with saline solution at an EC of 10.0 dS·m−1. Aquilegia barnebyi and C. fruticosa did not bloom during the experiment at all treatments. Elevated salinity reduced the number of flowers in E. septentrionale and T. acaulis. Elevated salinity also reduced the number of shoots in all four species. Among the four species, sodium (Na+) and chloride (Cl–) concentration increased the most in A. barnebyi by 53 and 48 times, respectively, when irrigated with saline solution at an EC of 10.0 dS·m−1. In this study, C. fruticosa and T. acaulis had minimal foliar salt damage and less reduction in shoot dry weight, indicating that they are more tolerant to salinity. Epilobium septentrionale was moderately tolerant to saline solution irrigation with less foliar damage, although it had more reduction in shoot dry weight. On the other hand, A. barnebyi was the least tolerant with severe foliar damage, more reduction in shoot dry weight, and a greater concentration of Na+ and Cl–

Mass segmentation using a combined method for cancer detection

<p>Abstract</p> <p>Background</p> <p>Breast cancer is one of the leading causes of cancer death for women all over the world and mammography is thought of as one of the main tools for early detection of breast cancer. In order to detect the breast cancer, computer aided technology has been introduced. In computer aided cancer detection, the detection and segmentation of mass are very important. The shape of mass can be used as one of the factors to determine whether the mass is malignant or benign. However, many of the current methods are semi-automatic. In this paper, we investigate fully automatic segmentation method.</p> <p>Results</p> <p>In this paper, a new mass segmentation algorithm is proposed. In the proposed algorithm, a fully automatic marker-controlled watershed transform is proposed to segment the mass region roughly, and then a level set is used to refine the segmentation. For over-segmentation caused by watershed, we also investigated different noise reduction technologies. Images from DDSM were used in the experiments and the results show that the new algorithm can improve the accuracy of mass segmentation.</p> <p>Conclusions</p> <p>The new algorithm combines the advantages of both methods. The combination of the watershed based segmentation and level set method can improve the efficiency of the segmentation. Besides, the introduction of noise reduction technologies can reduce over-segmentation.</p

Phonon Thermal Transport Through Tilt Grain Boundaries in Strontium Titanate

In this work, we perform nonequilibrium molecular dynamics simulations to study phonon scattering at two tilt grain boundaries (GBs) in SrTiO3. Mode-wise energy transmission coefficients are obtained based on phonon wave-packet dynamics simulations. The Kapitza conductance is then quantified using a lattice dynamics approach. The obtained results of the Kapitza conductance of both GBs compare well with those obtained by the direct method, except for the temperature dependence. Contrary to common belief, the results of this work show that the optical modes in SrTiO3 contribute significantly to phonon thermal transport, accounting for over 50% of the Kapitza conductance. To understand the effect of the GB structural disorder on phonon transport, we compare the local phonon density of states of the atoms in the GB region with that in the single crystalline grain region. Our results show that the excess vibrational modes introduced by the structural disorder do not have a significant effect on phonon scattering at the GBs, but the absence of certain modes in the GB region appears to be responsible for phonon reflections at GBs. This work has also demonstrated phonon mode conversion and simultaneous generation of new modes. Some of the new modes have the same frequency as the initial wave packet, while some have the same wave vector but lower frequencies