Enhancing ab initio diffusion calculations in materials through Gaussian process regression

Saddle point search schemes are widely used to identify the transition state of different processes, like chemical reactions, surface and bulk diffusion, surface adsorption, and many more. In solid-state materials with relatively large numbers of atoms, the minimum mode following schemes such as dimer are commonly used because they alleviate the calculation of the Hessian on the high-dimensional potential energy surface. Here, we show that the dimer search can be further accelerated by leveraging Gaussian process regression (GPR). The GPR serves as a surrogate model to feed the dimer with the required energy and force input. We test the GPR- accelerated dimer method for predicting the diffusion coefficient of vacancy-mediated self-diffusion in bcc molybdenum and sulfur diffusion in hexagonal molybdenum disulfide. We use a multi-task learning approach that utilizes a shared covariance function between energy and force input, and we show that the multi-task learning significantly improves the performance of the GPR surrogate model compared to previously used learning approaches. Additionally, we demonstrate that a translation-hop sampling approach is necessary to avoid over-fitting the GPR surrogate model to the minimum-mode-following pathway and thus succeeding in locating the saddle point. We show that our method reduces the number of evaluations to a fraction of what a conventional dimer requires.Comment: 13 pages, 8 figures, 1 table, 5 supplemental figures, 2 supplemental tables, 1 supplemental not

Analysis and Evaluation of Traffic Congestion Control Methods in Touristic Metropolis Using Analytical Hierarchy Process (AHP)

One of the most important issues of urban transport management in metropolitan cities is the control of traffic congestion in the central parts of the city or other densely populated areas. Typical ways to control traffic congestion in metropolitan areas are to create a prohibited traffic area, alternate traffic plan (even and odd), and congestion pricing. In this paper, these traffic congestion control methods have been compared and evaluated. The methodology of this research is analytical hierarchy analysis (AHP). Based on the results, the most effective measures for assessing traffic congestion control methods in metropolitan cities were improving traffic conditions, social welfare, reducing environmental pollution and improving the safety of intra-urban travel. The best Traffic congestion control options were also priced for traffic congestion, roaming traffic (odd and odd), and the creation of traffic barriers. The results of analyzes and paired comparisons in analytic hierarchy analysis were also obtained using “Expert choice” software

Creation of potential gene cassette for recombinant protein expression in green microalgal system

Development of efficient strategies and reliable systems for production of recombinant proteins in high quality and quantity to reach the market are gaining more attraction. On the economic side, improvement of the efficiency and cost effectiveness of production process is highly required to be commercially viable. Although many strategies have been theoretically established to increase the level of gene expression in different specific host systems, it is needed to be practically applied. Due to the lack of enough information for expression of recombinant proteins in microalgal systems, the present study aimed at creation of a gene cassette utilizing both upstream (bioinformatics and computational analysis, genetic engineering and molecular biology) and downstream factors (bioprocess engineering) which may have critical roles in gene expression with the emphasis on two microalgae species, Dunaliella salina and Chlamydomonas reinhardtii. As the first step in evaluating the feasibility of molecular farming in microalgae, some of the important upstream factors including matrix attachment regions (MARs), translation initiation sites, signal peptides and gene optimization parameters were studied. An artificial universal MAR sequence was designed and developed considering the MAR specific rules and motifs. To explore the specific translation initiation site, all mRNA sequences in the microalgae D. salina were screened among which the nonredundant mRNAs were selected for bioinformatics analysis. A consensus sequence was finally created to be used in the specific expression vector. For the secretion systems in microalgae D. salina, a screening procedure was carried out to find the specific signal peptides using bioinformatics and in silico tools in DNA, RNA and protein databases. The predicted sequences were then selected for further characterizations and the highest scored predicted signal was embedded in the secretion series of expression vectors. For optimization of the coding sequences, the most important parameters such as the host codon preference, RNA secondary structure, GC and CpG dinucleotides content were taken into consideration. The final expression cassette containing all of the required elements including MAR, signal peptide, translation initiation site, KDEL retention signal, His 6x purification tag, V5 epitope and protease cleavage site was integrated into 25 expression vectors (25 vectors containing different elements). To develop a proprietary series of microalgae specific expression vectors, nine fragments containing the Gateway recombination cassette, optimized genes of interest (2), promoters (2), 5’- UTR, interon, 3’-UTR (2), MARs (2) and pUC18 backbone were amplified using the most high fidelity enzyme available (KAPA). The fragments were successfully assembled in a single recombination reaction through the novel multiple overlap extension PCR (MOE-PCR) technique developed in this study. To assess the efficient transformation techniques for microalgae, three different methods (electroporation, glass beads and PEG-mediated) were used to transform one Dunaliella and three Chlamydomonas strains using the developed expression vectors. Glass bead method with 10 s agitation time, 4% PEG and 300 ng/μL plasmid DNA, as an efficient and simple technique showed the best results despite a drop in viable cells. The use of specific expression vectors resulted in more number and more stable transformants comparing a commercially available vector (pCAMBIA-3301) without the abovementioned optimized elements. The expression cassette containing optimized genetic elements could be delivered into microalgae cells and confer the resistance to the transformants for at least 3 months. For the downstream processes, the culture condition of D. salina was optimized to be used for future studies of the transformants. An experiment was conducted based on response surface methodology (RSM) to realize the reaction of microalgae to different phototrophic conditions including heterotrophic, mixotrophic and phototrophic. It was observed that the higher the amount of supplemented glucose up to 15 g/L, the more glucose utilization, biomass concentration and consequently protein content obtain. The results demonstrated superiority of mixotrophic conditions in constant light in improving the growth of microalgae. This study demonstrated that the upstream factors such as MARs, translation initiation sites and gene optimization along with the optimized transformation systems and downstream processes, could be a potential procedure to be efficiently used in overexpression of recombinant protein production using microalgae as the expression platform. Considering the close relatedness of the studied microalgae and other close species, the proprietary vector series could be generally used in genetic engineering of at least green microalgae

Comparison of drainage bag and chest bottle for pleural drainage

Background: A chest tube is used as a close system for drainage of fluid in the pleural space in trauma patients or after thoracic surgery. A chest bottle used at present is generally made from hard synthetic material with the possibility of breaking. Furthermore, some amounts of sterile solution (normal saline) should be always added into the chest bottle to prevent return of air back into the pleural cavity creating a vacuum and decreasing the mobility of the patient significantly. The purpose of this study was to use a drainage bag which is a new device made from soft and light synthetic materials like those used in urinary bag, so that drainage of fluid and air can be done through the pleural space without any complication related to the use of chest bottle. Materials and Methods: The present study was an interventional clinical trial. Fifty patients were selected among those who had been hospitalized in Hazrat Rasoul Akram Hospital between 2006 and 2007 and chest tubes were placed for them. After obtaining consent for participation in the study, they were divided into two groups (each comprising 25 patients) randomly. Chest bottle and drainage bag were used in groups 1 and 2, respectively. Both groups were compared for severity of chest pain, satisfaction from the device and duration of hospitalization. Results: The study showed the mean pain severity in patients with a drainage bag to be 4.1 units compared to those with chest bottle as 5.4 units. Satisfaction of the patients regarding their ability to move and ease of replacement of the device was 81 in the group with drainage bag and 43 in the group with chest bottle. Mean hospitalization period was 4.8 days in patients with drainage bag and 8.5 days in patients with chest bottles. Conclusion: The present study showed that using drainage bags instead of chest bottles in all patients who have chest tubes, can result in decreased pain, more satisfaction, shorter hospitalization and acceleration of recovery provided that the patients do not need more negative pressure (suction) within the pleural space. © 2007 NRITLD, National Research Institute of Tuberculosis and Lung Disease, Iran

Comparative Evaluation of Clinical and Radiographic Success of MTA and Propolis in Pulpotomy of Primary Molars

Introduction: In this study, the results of using MTA and propolis in the pulpotomy of primary molar teeth are evaluated clinically and radiographically. Methods and Methods: A total of 25 healthy 4 to 8 year old children each having two carious primary molar teeth in one arch, based on inclusion criteria were selected. In each child, random assignment of the pulpotomy medicaments was done as follows: Group I, MTA in one side; Group II, Propolis in another side. All the pulpotomized teeth were evaluated at 3, 6, and 9 month clinically and radiographically, based on the scoring criteria system. Finally data was analyzed using GEE analysis. Results: Results showed that the effects of treatment and time on two scores were tested. Based on the results of this model, the chances of having clinical score 2, versus score 1 are about 2.7 times higher in MTA treatment than in propolis (P=0.001). Similarly, the chance of having a clinical score 2 relative to its one, at 9th month is approximately 6.8 times higher than the 3th month (P=0.000) and at 6th month is approximately 2.8 times higher than the 3th month (P=0.005). The chance of having higher scores of radiographies in treatment of propolis is approximately 6.5 times than that of MTA (P=0.000). Also, the chance of having higher scores of radiographic index at 6th month is approximately 5 times and at 9th month is approximately 27 times more than the 3th month (P=0.00). Conclusions: Based on the results of this experimental study, teeth treated with MTA showed more suitable clinical and radiographic results as compared to propolis at 9 months follow-up.Keywords: Mineral Trioxide Aggregate; Primary Teeth; Propolis; Pulpotom

The free energy of mechanically unstable phases

Phase diagrams provide ‘roadmaps’ to the possible states of matter. Their determination traditionally rests on the assumption that all phases, even unstable ones, have well-defined free energies under all conditions. However, this assumption is commonly violated in condensed phases due to mechanical instabilities. This long-standing problem impedes thermodynamic database development, as pragmatic attempts at solving this problem involve delicate extrapolations that are highly nonunique and that lack an underlying theoretical justification. Here we propose an efficient computational solution to this problem that has a simple interpretation, both as a topological partitioning of atomic configuration space and as a minimally constrained physical system. Our natural scheme smoothly extends the free energy of stable phases, without relying on extrapolation, thus enabling a formal assessment of widely used extrapolation schemes

Phonon-assisted diffusion in bcc phase of titanium and zirconium from first-principles

Diffusion is the underlying mechanism for many complicated materials phenomena, and understanding it is basic to the discovery of novel materials with desired physical and mechanical properties. Certain groups of solid phases, such as the bcc phase of IIIB and IVB metals and their alloys, which are only stable when they reach high enough temperatures and experience anharmonic vibration entropic effects, exhibit "anomalously fast diffusion". However, the underlying reason for the observed extraordinary fast diffusion is poorly understood and due to the existence of harmonic vibration instabilities in these phases the standard models fail to predict their diffusivity. Here, we indicate that the anharmonic phonon-phonon coupling effects can accurately describe the anomalously large macroscopic diffusion coefficients in the bcc phase of IVB metals, and therefore yield a new understanding of the underlying mechanism for diffusion in these phases. We utilize temperature-dependent phonon analysis by combining ab initio molecular dynamics with lattice dynamics calculations to provide a new approach to use the transition state theory beyond the harmonic approximation. We validate the diffusivity predictions for the bcc phase of titanium and zirconium with available experimental measurements, while we show that predictions based on harmonic transition state theory severely underestimates diffusivity in these phases.Comment: 11 pages, 5 figures, supplemental material of 18 pages with 11 figure

Study of Effective Parameters on Stress and Displacement of Axisymmetric Corrugated Diaphragms

Abstract: In this paper, the axisymmetric corrugated diaphragm using finite element method will be discussed, so that half of these diaphragms' cross sections and later the applied pressure will be considered. Following this, using the consequent equations and visual basic software, a computer program will be provided which receives the diaphragms' particulars such as diameter, thickness, pressure and the form of object's cross section as AutoCAD file and then it measures the maximal stress and displacement. Finally, the calculated values will be compared with the experimental values and Theoretical results using the above program and then it will become clear that the results of this research enjoy the acceptable precision. Then, the various parameters which have an influence on the displacement and stress are changed and the results of these changes will be investigated