RNAGCN: RNA tertiary structure assessment with a graph convolutional network

RNAs play crucial and versatile roles in cellular biochemical reactions. Since experimental approaches of determining their three-dimensional (3D) structures are costly and less efficient, it is greatly advantageous to develop computational methods to predict RNA 3D structures. For these methods, designing a model or scoring function for structure quality assessment is an essential step but this step poses challenges. In this study, we designed and trained a deep learning model to tackle this problem. The model was based on a graph convolutional network (GCN) and named RNAGCN. The model provided a natural way of representing RNA structures, avoided complex algorithms to preserve atomic rotational equivalence, and was capable of extracting features automatically out of structural patterns. Testing results on two datasets convincingly demonstrated that RNAGCN performs similarly to or better than four leading scoring functions. Our approach provides an alternative way of RNA tertiary structure assessment and may facilitate RNA structure predictions. RNAGCN can be downloaded from https://gitee.com/dcw-RNAGCN/rnagcn.     

Optimization of heterogeneous Catalyst-assisted fatty acid methyl esters biodiesel production from Soybean oil with different Machine learning methods

There is a growing attention to the bio and renewable energies due to fast depletion of fossil fuels as well as the global warming problem. Here, we developed a modeling and simulation method by means of artificial intelligence (AI) for prediction of the bioenergy production from vegetable bean oil. AI methods are well known for prediction of complex and nonlinear process. Three distinct Adaptive Boosted models including Huber regression, LASSO, and Support Vector Regression (SVR) as well as artificial neural network (ANN) were applied in this study to predict actual yield of Fatty acid methyl esters (FAME) production. All boosted utilizing the Adaptive boosting algorithm. The important influencing parameters on the biodiesel production such as the catalyst loading (CAO/Ag, wt%) and methanol to oil (Soybean oil) molar ratio were selected as the input variables of models while the yield of FAME production was selected as output. Model hyper-parameters were tuned to maintain generality while improving prediction accuracy. The models were evaluated using three distinct metrics Mean Absolute Error (MAE), Root Mean Square Error (RMSE), and R². Error rates of 8.16780E-01, 4.43895E-01, 2.06692E + 00, and 3.92713 E-01 were obtained with the MAE metric for boosted Huber, SVR, LASSO and ANN models. On the other hand, the RMSE error of these models were about 1.092E-02, 1.015E-02, 2.669E-02, and 1.01174E-02, respectively. Finally, the R-square score were calculated for boosted Huber, boosted SVR, and boosted LASSO as 0.976, 0.990, 0.872, and 0.99702, respectively. Therefore, it can be concluded that although the boosted SVR and ANN models were better models for prediction of process efficiency in terms of error, but all algorithms had high accuracy. The optimum yield of 83.77% and 81.60% for biodiesel production were observed at optimum operating values from boosted SVR and ANN models, respectively.     

Theoretical study of (e,2e) triple differential cross sections of pyrimidine and tetrahydrofurfuryl alcohol molecules using multi-center distorted-wave method

We report theoretical studies of electron impact triple differential cross sections of two bio-molecules,pyrimidine and tetrahydrofurfuryl alcohol,in the coplanar asymmetric kinematic conditions with the impact energy of 250 eV and ejected electron energy of 20 eV at three scattering angles of-5°,-10°,and-15°.Present multi-center distorted-wave method well describes the experimental data,which was obtained by performing(e,2e)experiment.The calculations show that the secondary electron produced by the primary impact electron is strongly influenced by the molecular ionic multi-center potential,which must be considered when the low energy electron interacts with DNA analogues.     

Generalized Jacobi spectral Galerkin method for fractional pantograph differential equation

This work is concerned with the extension of the Jacobi spectral Galerkin method to a class of nonlinear fractional pantograph differential equations. First, the fractional differential equation is converted to a nonlinear Volterra integral equation with weakly singular kernel. Second, we analyze the existence and uniqueness of solutions for the obtained integral equation. Then, the Galerkin method is used for solving the equivalent integral equation. The error estimates for the proposed method are also investigated. Finally, illustrative examples are presented to confirm our theoretical analysis.