Very Low Frequency Propagation Characteristics Analysis in Coal Mines

Electromagnetic wave penetration coal-rock communication is a significant part for the smart mine communication technology, there are great challenges for electromagnetic wave is rapidly attenuated by factors such as geology and coal seam structure. In order to provide a theory basis for wireless communication technology development in coal rock, based on the Maxwell's equations, this paper establishes a physical model of wireless communication under the conditions of coal seam. To characterize the performance of the electromagnetic wave propagation, we use the Maxwell's equations to derive the exact expression of attenuation coefficient. Also, the parameters of coal and other factors affecting the electromagnetic wave propagation are analyzed and discussed. To further obtain more insights, the attenuation coefficient and skin depth of the very low-frequency (VLF) electromagnetic wave in coal medium with different degrees of metamorphism are studied, as well as the influence of resistivity. This provides scientific theoretical support for the application of VLF communication in coal mines. Finally, our theoretical analyses are verified by computer simulation, and the simulated numerical results show that: 1) The range of frequency of electromagnetic wave suitable for coal medium propagation is 3~3KHz (VLF); 2) The order of the electromagnetic waves attenuation coefficient in coal with different degrees of metamorphism is: anthracite> lignite > fat coal > coking coal > lean coal, and the order of skin depth is: lean coal > coking coal > fat coal> lignite > anthracite; 3) The resistivity of coal has little effect on the attenuation of electromagnetic wave when VLF is used for communication

Systematic Analysis of Survival-Associated Alternative Splicing Signatures in Thyroid Carcinoma

Alternative splicing (AS) is a key mechanism involved in regulating gene expression and is closely related to tumorigenesis. The incidence of thyroid cancer (THCA) has increased during the past decade, and the role of AS in THCA is still unclear. Here, we used TCGA and to generate AS maps in patients with THCA. Univariate analysis revealed 825 AS events related to the survival of THCA. Five prognostic models of AA, AD, AT, ES, and ME events were obtained through lasso and multivariate analyses, and the final prediction model was established by integrating all the AS events in the five prediction models. Kaplan–Meier survival analysis revealed that the overall survival rate of patients in the high-risk group was significantly shorter than that of patients in the low-risk group. The ROC results revealed that the prognostic capabilities of each model at 3, 5, and 8 years were all greater than 0.7, and the final prognostic capabilities of the models were all greater than 0.9. By reviewing other databases and utilizing qPCR, we verified the established THCA gene model. In addition, gene set enrichment analysis showed that abnormal AS events might play key roles in tumor development and progression of THCA by participating in changes in molecular structure, homeostasis of the cell environment and in cell energy. Finally, a splicing correlation network was established to reveal the potential regulatory patterns between the predicted splicing factors and AS event candidates. In summary, AS should be considered an important prognostic indicator of THCA. Our results will help to elucidate the underlying mechanism of AS in the process of THCA tumorigenesis and broaden the prognostic and clinical application of molecular targeted therapy for THCA

Sampling conformational space of intrinsically disordered proteins in explicit solvent: Comparison between well-tempered ensemble approach and solute tempering method

Intrinsically disordered proteins (IDPs) are a class of proteins that expected to be largely unstructured under physiological conditions. Due to their heterogeneous nature, experimental characterization of IDP is challenging. Temperature replica exchange molecular dynamics (T-REMD) is a widely used enhanced sampling method to probe structural characteristics of these proteins. However, its application has been hindered due to its tremendous computational cost, especially when simulating large systems in explicit solvent. Two-methods, parallel tempering well-tempered-ensemble-(PT-WTE) and replica-exchange-with solute tempering (REST), have been proposed to alleviate the computational expense of T-REMD. In this work, we select three different IDP systems to compare the sampling characteristics and efficiencies of the two methods Both the two methods could efficiently sample the conformational space of IDP and yield highly consistent results for all the three IDPs. The efficiencies of the two methods: are compatible, with about 5-6 times better than the plain T-REMD. Besides, the advantages and disadvantages of each method are also discussed. Specially, the PT-WTE method could provide temperature dependent data of the system which could not be achieved by REST, while the REST method could readily be used to a part of the system, which is quite efficient to simulate some biological processes. (C) 2016 Elsevier Inc. All rights reserved.</p

Compromise in competition between free energy and binding effect of intrinsically disordered protein p53 C-terminal domain

The C-terminal domain (CTD) of tumour suppressor p53 is an intrinsically disordered protein which has been shown to be able to bind multiple partner proteins and exercise diverse physiological functions in the cell. In this study, we performed molecular dynamics simulations on the isolated p53 CTD, as well as three regulatory binding complexes to investigate the conformational ensemble of isolated p53 CTD and its dynamic structures when different binding partner present. The results demonstrate that the isolated p53 CTD resembles a molten globule rather than extended structure. It mainly adopts random coil conformations with some tendency to form helical structures, which is consistent with experimental observations. For isolated p53 CTD, the dynamics is exclusively dominated by the intrinsic free energy and the p53 CTD could not folded spontaneously to each binding competent state which is located in high free energy region. However, when the binding partners present, the dynamics of p53 CTD are dominated by two mechanisms, the p53 CTD tending to adopt the structure with minimum free energy as isolate existed and the binding energy from partner protein tending to minimum. Each of them has an extreme tendency and corresponds to a possible characteristic state, the random coil state and each binding competent state. The compromise in competition between these two mechanisms results in alternate realisation of different characteristic states, while the relative strength of each mechanism determines the sampling frequency of each characteristic state.</p

The principle of compromise in competition: exploring stability condition of protein folding

Thermodynamic hypothesis and kinetic stability are currently used to understand protein folding. The former assumes that free energy minimum is the exclusive dominant mechanism in most cases, while the latter shows that some proteins have even lower free energy in intermediate states and their native states are kinetically trapped in the higher free energy region. This article explores the stability condition of protein structures on the basis of our study of complex chemical systems. We believe that separating one from another is not reasonable since they should be coupled, and protein structures should be dominated by at least two mechanisms resulting in different characteristic states. It is concluded that: (1) Structures of proteins are dynamic, showing multiple characteristic states emerging alternately and each dominated by a respective mechanism. (2) Compromise in competition of multiple dominant mechanisms might be the key to understanding the stability of protein structures. (3) The dynamic process of protein folding should be depicted through the time series of both its energetic and structural changes, which is much meaningful and applicable than the free energy landscape

Simulation of coupled folding and binding of an intrinsically disordered protein in explicit solvent with metadynamics

The C-terminal domain of measles virus nucleoprotein is an intrinsically disordered protein that could bind to the X domain (XD) of phosphoprotein P to exert its physiological function. Experiments reveal that the minimal binding unit is a 21-residue alpha-helical molecular recognition element (alpha-MORE-MeV), which adopts a fully helical conformation upon binding to XD. Due to currently limited computing power, direct simulation of this coupled folding and binding process with atomic force field in explicit solvent cannot be achieved. In this work, two advanced sampling methods, metadynamics and parallel tempering, are combined to characterize the free energy surface of this process and investigate the underlying mechanism. Starting from an unbound and partially folded state of alpha-MoRE-MeV, multiple folding and binding events are observed during the simulation and the energy landscape was well estimated. The results demonstrate that the isolated alpha-MORE-MeV resembles a molten globule and rapidly interconverts between random coil and multiple partially helical states in solution. The coupled folding and binding process occurs through the induced fit mechanism, with the residual helical conformations providing the initial binding sites. Upon binding, alpha-MORE-MeV can easily fold into helical conformation without obvious energy barriers. Two mechanisms, namely, the system tending to adopt the structure in which the free energy of isolated alpha-MORE-MeV is the minimum, and the binding energy of alpha-MoRE-MeV to its partner protein XD tending to the minimum, jointly dominate the coupled folding and binding process. With the advanced sampling approach, more IDP systems could be simulated and common mechanisms concerning the coupled folding and binding process could be investigated in the future. (C) 2016 Published by Elsevier Inc.</p

Simulations of flow induced structural transition of the beta-switch region of glycoprotein Ib alpha

Binding of glycoprotein Ib alpha to von Willebrand factor induces platelet adhesion to injured vessel walls and initiates a multistep hemostatic process. It has been hypothesized that the flow condition could induce a loop to beta-sheet conformational change in the beta-switch region of glycoprotein Ib alpha, which regulates it binding to the von Willebrand factor and facilitates the blood clot formation and wound healing. In this work, direct molecular dynamics (MD), flow MD and metadynamics, were employed to investigate the mechanisms of this flow induced conformational transition process. Specifically, the free energy landscape of the whole transition process was drawn by metadynamics with the path collective variable approach. The results reveal that without flow, the free energy landscape has two main basins, including a random loop basin stabilized by large conformational entropy and a partially folded beta-sheet basin. The free energy barrier separating these two basins is relatively high and the beta-switch could not fold from loop to beta-sheet state spontaneously. The fully beta-sheet conformations located in high free energy regions, which are also unstable and gradually unfold into partially folded beta-sheet state with flow. Relatively weak flow could trigger some folding of the beta-switch but could not fold it into fully beta-sheet state. Under strong flow conditions, the beta-switch could readily overcome the high free energy barrier and fold into fully beta-sheet state. (C) 201 5 Elsevier B.V. All rights reserved

Migration Characteristics of Boring Mud in Roadway Floor Anchor Wire Hole and Test in Coal Mine

Given the difficulty in drilling the anchor holes in the roadway floor of the coal mine, the characteristics of slag movement in the process of positive and negative circulation drilling are analyzed. It is concluded that the interaction between the three zones of drilling and slag is the fundamental reason restricting the rapid drilling of the anchor cable hole in the floor, and it is proposed that the pump reverse circulation drilling can effectively prevent the formation of the three zones of drilling and slag. According to the actual situation, the relationship between drilling depth, vacuum degree of the pump, and the velocity of drilling fluid and the volume of drilling slag is obtained. The results show that the pump suction reverse circulation is feasible for the rapid drilling of the anchor hole of the floor. A set of pump suction reverse circulation drilling systems has been developed, and floor anchor wire hole drilling and slag discharge operation at the same time were realized. The field test shows that the effective drilling time of the anchor cable hole in the depth of 5.6 m can be controlled within 30 min, which solves the problem of deep hole drilling in the anchor hole of the bottom plate and purifies the working environment