DNA origami structures such as nanotubes, due to their diverse and extensive applications including drug delivery, are highly regarded. The issue of stability and protection of DNA origami nanotubes against environmental changes is a significant and noteworthy challenge. In this paper, the stability of DNA origami nanotubes in the presence of positively charged protein cargo and negatively charged protein cargo inside them has been investigated at different temperatures using molecular dynamics simulation. To obtain quantitative results, specific points on each helix of the DNA origami nanotube have been considered at three sections: the beginning, the middle, and the end of the nanotubes. Then, the distance between each adjacent pair of helices has been calculated as an average over a specific period of time. The results indicate that the presence of a positive cargo increases the stability, while the presence of a negative cargo decreases the stability of the DNA origami nanotube. Consequently, positive protein cargo can be utilized as a tool to protect DNA origami nanotubes against environmental thermal stresses. This finding could be crucial in the design of nanotubes as drug carriers.

Introduction: Human Serum Albumin is one of the most important proteins in blood that can bind a wide range of components and different drugs such as Warfarin. Therefore, studying human serum albumin is very significant in pharmacology. In this research, dynamic behavior of residues of Warfain binding site of human serum albumin was investigated. Method: First, three-dimensional format of human serum albumin (PDB ID: 4G04) was downloaded from RCSB. Then, using GROMACS package, molecular dynamics simulation has been done on chain A of crystallography structure during 30ns. Results: RMSD analysis on residues of binding site showed that Arginines 186 and 218 have wide fluctuations in their RMSD plot. Also, Lysines 185 and 190 have nearly wide fluctuations of RMSD; however, these fluctuations were less than Arginine's. Other residues such as Glycine 189 have few fluctuations. Fluctuations in RMSD have direct relationship with accessible surface area of the residues. Conclusion: The results show that Warfarin binding site in human serum albumin can have various conformational situations because of the dynamics of its residues. This can be important in drug design. Overall, according to the results of this study, residues are divided into 3 categories. Among them, Tryptophan 214, that is one of the most important residues according to different studies, was placed in the category of residues with the least mobility.

Obesity, a lipid metabolic disorder characterized by excess fat deposition in the adipose tissue, is among the leading top global health challenges. The only Food and Drug Agency (FDA) approved drug (Orlistat®) for its treatment has shown some adverse effects. To find new compounds that may be more effective or with less adverse effects compared to Orlistat®. Catechin and chlorogenic acid were computationally studied using molecular docking and validated with molecular dynamics simulation techniques. The ADMET and drug-likeliness evaluation of the two compounds was carried out in silico. The binding affinities, structural stability, and flexibility vis-a-vis root-mean-square deviation (RMSD) and root-mean-square fluctuations (RMSF) plots, hydrogen bonding, and surface area analysis of the two compounds were compared to the Orlistat®. It was found that the selected two compounds passed Lipinski’s rule of 5 and other parameters expected of a drug. In addition, both catechin and chlorogenic acid exhibited good docking scores, better fit and molecular interactions, good structural stability, and flexibility compared to Orlistat®.

A model was designed according to NRC (2001) equations, which simulates growth of preruminant calves based on three different indexes (Energy, Apparently digestible protein and mean of them). Results showed that the best estimation of calves weight in different ages was based on energy index (RMSD=7.251). Also model estimations of calves weight were generally greater than observations, so there were positive MBE values with RMSD=11.549, 16.705 and 7.251 respectively for mean index, apparently digestible protein and energy. Daily weight gain estimation according to energy index was lower than observed data, so MBE value was negative (RMSD=0.250). About the other two indexes (Apparently digestible protein and mean index), results showed that model estimations were greater than observations with positive MBE values (RMSD=0.241 and 0.307 respectively). Model made an over estimation about dry matter intake with positive MBE value (RMSD=0.666). According to model estimation trends, this model is a start point for designing a complex model. With respect to correct determination of observations trend, it seems a suitable model.

Recently, optimization methods have been extensively applied in phase equilibrium calculations. Among these methods, Genetic Algorithm (GA) can be used to calculate the interaction parameters of activity coefficient models in equilibrium systems. In this study, based on the genetic algorithm, the interaction parameters of 5 activity coefficient models (2-suffix Margules, 3-suffix Margules, Wilson, NRTL and UNIQUAC) have been calculated for 20 ternary extraction systems (water + carboxylic acids + organic solvents) including 126 tie-lines. The values of binary interaction parameters of these models along with the root mean square deviations (RMSD) are reported. The mean values of RMSD of the systems in the order of the mentioned models have been calculated 0. 0298, 0. 0067, 0. 0114, 0. 0025 and 0. 0052, respectively. The results show that all models except 2-suffix Margules model have relatively good accuracy. By comparing the RMSD values in literature and the values determined by GA for NRTL and UNIQUAC models, the RMSD values of the models improved from 0. 0124 and 0. 0181 to 0. 0025 and 0. 0052, respectively.

A 100-ns MD simulation of the apo-protein and compound A protein complex was carried out using RMSD and RMSF evaluations to investigate the stability of the tested complex with regards to the HDAC-2 target site. The apoprotein (C𝛼) showed a significant RMSD value of 0.90 Å throughout the simulation period with no major fluctuation, showing the conformational stability of the apo-protein structure. In addition, the compound A/protein complex displayed stability during the simulation period with an RMSD value of 1.6 Å, suggesting a low chance of compound escape from the target pocket with no fluctuation.

Soil moisture is a key variable in determinant terrestrial systems for water and energy exchanges between the earth's surface and the atmosphere. In this study, the soil moisture data of SMAP satellite at different times and land uses were validated through four indices of correlation coefficient, root mean square error, unbiased root mean square error, and mean difference in 2017. For this purpose, Simineh-Zarineh basin located in the south and southeast of Urmia Lake, which is the largest sub-basin of the Urmia Lake basin, was investigated. The total study area is about 1762500 hectares. The spatial and temporal resolution of the SMAP satellite is 9 square kilometers and three days. Therefore, 287 ground points on a grid were selected for sampling in the study area. The results showed that the SMAP satellite data with ground observation data on December 3 and April 3 had a maximum RMSD value of 0. 25 to 0. 35 cm3 cm-3. The results revealed that the soil moisture data of SMAP satellite with RMSD values between 0. 18 to 0. 33 cm3 cm-3 and ubRMSE between 0. 17 to 0. 33 cm3 cm-3 show better performances correspond to ground data. The highest correlations and the lowest RMSD value were observed in July 3rd and September 13th, respectively. The lowest RMSD and the highest correlation for dryland was observed on April 3rd. In July 3rd the highest correlation was observed in all land uses, and among them the highest correlation was observed in dryland.

Recently, optimization methods have been extensively applied in phase equilibrium calculations. Among these methods, Particle Swarm Optimization (PSO) can be used to calculate the interaction parameters of activity coefficient models in equilibrium systems. In this study, based on the particle swarm optimization, the interaction parameters of 5 activity coefficient models (2-suffix Margules, 3-suffix Margules, Wilson, NRTL and UNIQUAC) have been calculated for 20 ternary extraction systems (water + carboxylic acids + organic solvents) including 126 tie-lines. The values of binary interaction parameters of these models along with the root mean square deviations (RMSD) are reported. The mean values of RMSD of the systems in the order of the mentioned models have been calculated 0. 0294, 0. 0041, 0. 0114, 0. 0016 and 0. 0034, respectively. The results show that all models except 2-suffix Margules model have relatively good accuracy. By comparing the RMSD values in literature and the values determined by PSO for NRTL and UNIQUAC models, the RMSD values of the models improved from 0. 0124 and 0. 0181 to 0. 0016 and 0. 0034, respectively.

Introduction: Surface soil moisture is one of the most important variables in the hydrological cycle, and plays a key role in scientific and practical applications such as hydrological modelling, weather forecasting, climate change studies and water resources managements. Microwave radiometry at low frequencies (1.4GHz) is an established technique for estimating global surface soil moisture with a suitable accuracy. …

Aim and background: Pathological studies have suggested that formation of fibrous plaques and accumulated masses of amyloid beta peptides in central nervous system is one of the causes to Alzheimer’s disease. Since these diseases depend on conformational structure of protein, we investigate initial conformational changes of Ab (1-42) and Ab (1-40 by molecular dynamic simulations in this paper.Materials and methods: The solution NMR structures of Ab (1-42) and Ab (1-40) (protein data bank: 1IYT 1& BA4) was chosen as a template for comparative modeling. All simulations and data analysis were performed by GROMACS program with the united-atom protein force field. The final sampling simulations were 20-ns MD simulations, 310K and constant pressure (1 bar).Results: The results of RMSD, radius of gyration and solvent accessible surface area showed that structural changes, flexibility and the propensity to aggregation of Ab (1-42) is more than Ab (1-40).Conclusions: The solvent accessible surface area show the hydrophobicity interaction have important role in aggregation and creation of deformed structures. Our data showed that Ab (1-42) have critical role in the development of Alzheimer’s disease.