Template-Based Structure Prediction and Classification of Transcription Factors in \u3ci\u3eArabidopsis thaliana\u3c/i\u3e

Transcription factors (TFs) play important roles in plants. However, there is no systematic study of their structures and functions of most TFs in plants. Here, we performed template-based structure prediction for all TFs in Arabidopsis thaliana, with their full-length sequences as well as C-terminal and N-terminal regions. A total of 2,918 model structures were obtained with a high confidence score. We find that TF families employ only a smaller number of templates for DNA-binding domains (DBD) but a diverse number of templates for transcription regulatory domains (TRD). Although TF families are classified according to DBD, their sizes have a significant correlation with the number of unique non-DNA-binding templates employed in the family (Pearson correlation coefficient of 0.74). That is, the size of TF family is related to its functional diversity. Network analysis reveals new connections between TF families based on shared TRD or DBD templates; 81% TF families share DBD and 67% share TRD templates. Two large fully connected family clusters in this network are observed along with 69 island families. In addition, 25 genes with unknown functions are found to be DNA-binding and/or TF factors according to predicted structures. This work provides a global view of the classification of TFs based on their DBD or TRD templates, and hence, a deeper understanding of DNA-binding and regulatory functions from structural perspective. All structural models of TFs are deposited in the online database for public usage at http://sysbio.unl.edu/AthTF

Template-Based Structure Prediction and Classification of Transcription Factors in \u3ci\u3eArabidopsis thaliana\u3c/i\u3e

Transcription factors (TFs) play important roles in plants. However, there is no systematic study of their structures and functions of most TFs in plants. Here, we performed template-based structure prediction for all TFs in Arabidopsis thaliana, with their full-length sequences as well as C-terminal and N-terminal regions. A total of 2,918 model structures were obtained with a high confidence score. We find that TF families employ only a smaller number of templates for DNA-binding domains (DBD) but a diverse number of templates for transcription regulatory domains (TRD). Although TF families are classified according to DBD, their sizes have a significant correlation with the number of unique non-DNA-binding templates employed in the family (Pearson correlation coefficient of 0.74). That is, the size of TF family is related to its functional diversity. Network analysis reveals new connections between TF families based on shared TRD or DBD templates; 81% TF families share DBD and 67% share TRD templates. Two large fully connected family clusters in this network are observed along with 69 island families. In addition, 25 genes with unknown functions are found to be DNA-binding and/or TF factors according to predicted structures. This work provides a global view of the classification of TFs based on their DBD or TRD templates, and hence, a deeper understanding of DNA-binding and regulatory functions from structural perspective. All structural models of TFs are deposited in the online database for public usage at http://sysbio.unl.edu/AthTF

Effect analysis of non-condensable gases on superheated steam flow in vertical single-tubing steam injection pipes based on the real gas equation of state and the transient heat transfer model in formation

Abstract Huge amount of efforts were done on saturated steam flow in wellbores with relatively little work on superheated multi-component thermal fluid (SMTF) flow in wellbores. In this paper, based on the continuity, energy and momentum balance equations, a flow model in the vertical wellbores is proposed. Then, coupled with the real gas model and transient heat flow model in formation, a comprehensive model is established for estimating thermophysical properties of SMTF in wellbores. Results show that (a) the effect of mass content of non-condensing gases on temperature profiles is negligible. The enthalpy of SMTF decreases rapidly with increasing of mass content of non-condensing gases. (b) When the injection rate is small, heat loss is the main factor on temperature drop, while when the injection rate is large enough, pressure drop becomes the dominant factor on temperature drop. (c) The two components of non-condensing gases and superheated steam in SMTF have a relatively independent mechanism of enhanced oil recovery, which should be selected based on the unique characteristics of each reservoir

Effect of gaseous CO2 on superheated steam flow in wells

In this paper, a novel model is proposed for estimating pressure and temperature in wellbores when CO2 and superheated steam (SHS) are co-injected. Firstly, a model comprised of mass, energy and momentum conservation equations are developed. Then, Coupled with real gas model and heat transfer model in formation, a comprehensive model is established. The mass, momentum and energy balance equations are solved simultaneously with finite difference method on space and the iteration method. Finally, sensitivity analysis is conducted. Results show that (a). In order to obtain a higher superheat degree, a higher injection temperature and a lower mass fraction of CO2 are suggested. (b). Superheat degree decreases with increasing injection pressure or with increasing mass fraction of CO2. (c). Superheat degree increases with increasing mass flow rate. (d). Superheat degree decreases with increasing mass fraction of CO2

New analytical equations for productivity estimation of the cyclic CO2-assisted steam stimulation process considering the non-Newtonian percolation characteristics

Abstract The research course in the estimation of productivity of cyclic steam stimulation wells can be divided into three stages: (a) the mobility of heavy oil in the cold area is neglected, (b) the mobility of heavy oil in the cold area is considered—however, it is Newtonian fluid seepage, and (c) it is conserved as non-Newtonian fluid seepage in the cold area. However, the distribution of the value of starting pressure gradient in the heated area where heavy oil is still non-Newtonian fluid is neglected. In this paper, a new model is developed for productivity estimation of cyclic steam stimulation wells with consideration of the non-Newtonian fluid flow behaviors in the heated area where the temperature is higher than the turning point. New percolation equations are developed based on the new proposed concept of “the transition region” in the heated area. The results show that: (1) when the non-Newtonian fluid characteristic is neglected, the predicted results from the new model match the results from the numerical simulator perfectly, and (2) in oil field, the non-Newtonian fluid characteristic cannot be neglected. When the non-Newtonian fluid characteristic is considered in the model, the average oil production in each cycle can match the filed data better than Yang et al.’s model. This new model laid a basic reference for oil companies and researchers involved in the area when they are designing the well pattern, spacing or estimating the productivity of oil wells

The heat and mass transfer characteristics of superheated steam in horizontal wells with toe-point injection technique

Abstract Little efforts were done on the heat and mass transfer characteristics of superheated steam (SHS) flow in the horizontal wellbores. In this paper, a novel numerical model is presented to analyze the heat and mass transfer characteristics of SHS in horizontal wellbores with toe-point injection technique. Firstly, with consideration of heat exchange between inner tubing (IT) and annuli, a pipe flow model of SHS flow in IT and annuli is developed with energy and momentum balance equations. Secondly, coupled with the transient heat transfer model in oil layer, a comprehensive mathematical model for predicting distributions of pressure and temperature of SHS in IT and annuli is established. Then, type curves are obtained with numerical methods and iteration technique, and sensitivity analysis is conducted. The results show that (1). The decrease in SHS temperature in annuli caused by heat and mass transfer to oil layer is offset by heat absorbtion from SHS in IT. (2). SHS temperature in both IT and annuli increases with the increase in injection pressure. (3). IT heat loss rate decreases with the increases in injection pressure. (4). Increasing pressure can improve development effect

Effect of critical thickness on nanoconfined water fluidity: review, communication, and inspiration

Abstract It is crucial to precisely estimate the water transport behaviors in shale formation. However, the present study on this subject is quite limited. A comprehensive literature review is conducted and some improvements are proposed. In this paper, an improved model is proposed to investigate the flow of water in nanopores of shale formation. First, a quadratic equation is proposed to build the relationship between water viscosity and contact angle. Then, the effect of critical thickness on water transport behaviors is discussed. Results show that: (a) the flow enhancement is smaller than 1 when the contact angle is smaller than 100° due to energy barrier induced by strong hydrophilicity of the nanopore wall; (b) the flow enhancement becomes infinite when the contact angle is approaching 180°; and (c) the flow enhancement increases with decreasing of critical thickness, especially for hydrophilic nanopores (the contact angle is smaller than 120°) and nanopores with a relatively small diameter (smaller than 50 nm)

Effect of physical heating on productivity of cyclic superheated steam stimulation wells

Abstract Previous works have focused on the single factor analysis of the effects of chemical reactions of superheated steam with oil and rock minerals on the oil well productivity. However, the relationship between the factors and the contributions to productivity is still unknown. In this paper, the contribution of physical heating of superheated steam to well productivity is studied with the numerical method. Results show that: (a) the heat in the area has a very limited increase when the temperature of superheated steam continues to increase. (b) At the starting stage, the oil is heated to a higher temperature and the mobility is increased. The elastic energy becomes the dominant factor controlling the productivity of the oil well in the following stage. (c) The chemical reactions of superheated steam with oil and rock minerals are the dominant factors contributing to the productivity

Analytical model for pressure and rate analysis of multi-fractured horizontal wells in tight gas reservoirs

Abstract Multi-fractured horizontal wells (MFHWs) are effective for developing unconventional reservoirs. A complex fracture network around the well and hydraulic fractures form during fracturing. Hydraulic fractures and fracture network are sensitive to the effective stress. However, most existing models do not consider the effects of stress sensitivity. In this study, a new analytical model was established for an MFHW in tight gas reservoirs based on the trilinear flow model. Fractal porosity and permeability were employed to describe the heterogeneous distribution of the complex fracture network. The stress sensitivity of fractures was also considered in the model. Pedrosa substitution and perturbation method were applied to eliminate the nonlinearity of the model. Analytical solutions in the Laplace domain were obtained using Laplace transformation. The model was then validated and applied. Finally, sensitivity analyses of pressure and rate were discussed. The presented model provides a new approach to estimate the effect of fracturing. It can also be utilized to recognize formation properties and forecast the dynamics of pressure and the production of tight gas reservoirs

An analytical equation for oil transport in nanopores of oil shale considering viscosity distribution

Abstract Huge amount of works was done on modeling of gas transport in nanopores (both organic and inorganic) of shale formation. However, the study on oil transport behaviors is quite limited. Based on the study on water transport in carbon nanotubes, an analytical model is developed for oil transport in nanopores of shale formation. The new model takes the effect of oil–wall interaction on the oil viscosity in the adsorption region into consideration. Results show that: (1) the oil–wall interaction on oil viscosity in the adsorption region plays an important role in oil transport behaviors and cannot be neglected; (2) when the critical thickness is smaller than 1 nm, the volume flux increases slowly with increasing contact angle; (3) when the critical thickness increases to 2 nm, the volume flux increases rapidly to infinity when the contact angle is larger than 140°