Loudi, China

Hunan University of Humanities, Science and Technology (simplified Chinese: 湖南人文科技学院; traditional Chinese: 湖南人文科技學院; pinyin: Húnán Rénwén Kējì Xuéyuàn), established in 1978, is a state-owned provincial university of higher education approved by the Chinese Ministry of Education. It is located in Loudi, a newly built city in central Hunan province, China . Wikipedia.


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Wu C.,Hunan University of Humanities, Science and Technology
Molecular Simulation | Year: 2010

This work presents the first molecular dynamics simulation of poly(propylene imine) (PPI) dendrimer in explicit water under various pH conditions. The sizes, shapes, surfaces/volumes and density profiles of the PPI dendrimer are analysed. The PPI dendrimer essentially approaches the perfect sphere under all pH conditions, and higher pH leads to more globular structure. The radius of gyration, solvent-accessible surface area (SASA) and solvent-excluded volume (SEV) are all found to increase significantly from high pH to neutral pH and to level thereafter until low pH, which illustrate the dramatic changes in the whole conformation of the dendrimer. These behaviours of the PPI dendrimer quite differ from those of polyamidoamine [Liu, et al. J. Am. Chem. Soc. 2009, 131, 2798-2799], which can be explained by the favourable interactions arising from the additional amide groups. The density profiles have also been calculated to confirm the shifts of density and back-folding of terminals and penetrations of water. © 2011 Taylor & Francis.


Wu C.,Hunan University of Humanities, Science and Technology
Journal of Molecular Modeling | Year: 2014

The chain tacticity of a polymer is a key influence on its structure and dynamics, which ultimately determine its properties. While they have great potential to elucidate the influence of chain tacticity, all-atom molecular simulations are often restricted to short chains and small systems. In thiswork, two typical stereoregular poly(methyl methacrylate) melts were investigated via multiscale simulations. To improve computational efficiency, systematic coarse-graining was first performed. While the coarse-grained molecular dynamics simulations were able to show the effects of tacticity on intramolecular structure and intermolecular interactions, they were not able to reproduce the exact structural distribution or even the effects of tacticity on the dynamics. An alternative reverse-mapping scheme was therefore developed specifically to treat chain configurations in a direct geometric way. The backmapped all-atomistic simulations were found to accurately reproduce the microscopic features of the polymers. Since the effects of tacticity are rather subtle and therefore difficult to discern, this multiscale simulation scheme is a very important method of investigating complex high molecular weight polymer systems. © Springer-Verlag 2014.


Wu C.,Hunan University of Humanities, Science and Technology
Polymer | Year: 2010

An aqueous poly(vinyl alcohol) (PVA) model has been extensively studied by using the molecular dynamics (MD) simulation method. The employed molecular and force field models are validated against the available data in the literature. In particular, the glass transition temperature (T g) is determined from the specific volume versus temperature, which compares well with the experimental observations. The diffusion coefficients of water (H 2O) through the PVA matrix follow the Arrhenius equations at both temperature regions separated by T g, indicating the existence of free and bound water defined by hydrogen bonds (HBs). It has also been confirmed that HBs occur between PVA and H 2O, between PVA and PVA, between H 2O and H 2O, and all of them play the key roles in the glass transition. The local dynamics suggested by the decorrelations of various bond vectors can be well described by the Williams-Landel-Ferry (WLF) equation. This work demonstrates the cooperative behavior of PVA and H 2O which is responsible for the glass transition of the whole binary system. © 2010 Elsevier Ltd.


Wu C.,Hunan University of Humanities, Science and Technology
Journal of Physical Chemistry B | Year: 2011

Stepwise cooling molecular dynamics (MD) simulations have been carried out on the bulk and film models for poly(ethylene oxide) (PEO) to understand glass transition of amorphous polymer films. Three types of properties-density, energy, and dynamics-are computed and plotted against the temperature for the two systems. It has been confirmed that all these properties can reveal glass transition in both PEO bulk and film systems. All the determined glass transition temperatures (Tg's) drop in the same order of magnitude to the experimental data available. Among various methods, the Tg's obtained from the density and energy data are close to each other if the same space regions are defined, which can suggest the same free volume theory, and dynamic Tg's obtained from mean-squared displacements (MSDs) are highest, which can suggest the kinetic theory for structural relaxation. Consistently, all these Tg's obtained using different methods show that the Tg's of PEO film are lower than those of PEO bulk. The free surface layers of polymer films dictate this offset. © 2011 American Chemical Society.


Wu C.,Hunan University of Humanities, Science and Technology
Journal of Polymer Science, Part B: Polymer Physics | Year: 2011

Position restrained (PR) molecular dynamics (MD) simulations were carried out on the bulk models for the two composite systems including epoxy monomers and carbon nanotube (CNT). The pair energies and the radial distribution functions (RDFs) were computed to evaluate the relative strength of the epoxy monomers binding to the CNT. It is found that the aromatic amine binds more strongly to the CNT than does the aliphatic amine. A vivid view indicates the aromatic rings tend to form π-stacking with the CNT, and the compounds with aromatic rings prefer to wrap the CNT. These simulated results are in good agreement with those obtained previously from the vacuum models. This work demonstrates that curing agents affect the interactions between epoxy resin and CNT. Other comparisons of relative binding strength of epoxy monomers also depend upon the temperature. Further analyses suggest that the aliphatic amine exhibits more strong interactions with epoxy resin than does the aromatic amine, mainly due to the presence of hydrogen bonds (HBs) between them. Thus, the ultimate performance of epoxy-CNT polymer nanocomposites should be affected by the two reverse interactions. © 2011 Wiley Periodicals, Inc.


Wu C.,Hunan University of Humanities, Science and Technology
Macromolecules | Year: 2013

A new computationally inexpensive scheme has been developed for deriving coarse-grained (CG) potentials of stereoregular polymers. In this scheme, from the constraint-distance stochastic dynamics (SD) simulations of trimer/trimer pairs in a vacuum, the nonbonded CG potentials are first parametrized by the conditional reversible work (CRW) method, which are then used to optimize the bonded CG potentials by the iterative Boltzmann inversion (IBI) method against the SD simulations of single-oligomer chains in a vacuum. This method is exemplarily applied to two technically important polymer blends composed of either isotactic or syndiotactic poly(methyl methacrylate) (iPMMA, sPMMA) and isotactic poly(vinyl chloride) (iPVC). Based on the molecular dynamics (MD) simulations with the so-derived CG potentials, detailed analyses on structural and energy properties suggest that the two studied mixtures are homogeneous. More critically, our simulations yield that sPMMA is more miscible with iPVC than is iPMMA, which reproduces the known experimental trends. From the dynamics analyses, the CG simulations also exhibit very high computational efficiency. Therefore, the so-developed CG scheme holds great promise in multiscale simulations of complex polymer systems. © 2013 American Chemical Society.


Wu C.,Hunan University of Humanities, Science and Technology
Journal of Polymer Science, Part B: Polymer Physics | Year: 2015

The stereoregular poly(methyl methacrylate)/poly(-vinyl chloride) blends with a wide formulation range are extensively simulated using the coarse-grained (CG) molecular dynamics (MD) method. To improve the representability, the bonded CG potentials are re-parameterized against the atomistic simulated melt systems whereas the nonbonded CG potentials are adopted as developed in our previous work. Based on the CG potentials, the MD simulations reproduce all the local distributions of pure systems and the miscibility of mixed systems. Moreover, the global conformational properties are also closer to the target ones than those obtained using the previous CG potentials. The changes in density and volume upon mixing are computed together with the energies of mixing. They are all negative over the entire composition range and indicate stronger intermolecular interactions between distinct components than those between identical components. In particular, it is found that upon mixing the changes in density are insensible to chain tacticity but the changes in volume and the energies of mixing do, which quantitatively confirms that both inter-molecular interactions and free-volumes mainly contribute to the observed phase behaviors. Such models and methods reported herein can be used to quickly optimize formulations of polymer blends. © 2014 Wiley Periodicals, Inc.


Ding C.,Hunan University of Humanities, Science and Technology
International Journal of Theoretical Physics | Year: 2014

In the frame of Hamilton-Jacobi method, the back-reactions of the radiating particles together with the total entropy change of the whole system are investigated. The emission probability from this process is found to be equivalent to the null geodesic method. However its physical picture is more clear: the negative energy one of a virtual particle pair is absorbed by the black hole, resulting in the temperature, electric potential and angular velocity increase; then the black hole amount of heat, electric charge and angular momentum can spontaneously transfer to the positive energy particle; when obtaining enough energy, it can escape away to infinity, visible to distant observers. And this method can be applied to any sort of horizons and particles without a specific choice of (regular-across-the-horizon) coordinates. © 2013 Springer Science+Business Media New York.


Chen H.,Central South University | Chen H.,Hunan University of Humanities, Science and Technology | Zhang Z.,Central South University
BMC Medical Genomics | Year: 2013

Background: The identification of microRNA-disease associations is critical for understanding the molecular mechanisms of diseases. However, experimental determination of associations between microRNAs and diseases remains challenging. Meanwhile, target diseases need to be revealed for some new microRNAs without any known target disease association information as new microRNAs are discovered each year. Therefore, computational methods for microRNA-disease association prediction have gained a lot of research interest. Methods. Herein, based on the assumption that functionally related microRNAs tend to be associated with phenotypically similar diseases, three inference methods were presented for microRNA-disease association prediction, namely MBSI (microRNA-based similarity inference), PBSI (phenotype-based similarity inference) and NetCBI (network-consistency-based inference). Global network similarity measure was used in the three methods to predict new microRNA-disease associations. Results. We tested the three methods on 242 known microRNA-disease associations by leave-one-out cross-validation for prediction evaluation, and achieved AUC values of 74.83%, 54.02% and 80.66%, respectively. The best-performed method NetCBI was then chosen for novel microRNA-disease association prediction. Some associations strongly predicted by NetCBI were confirmed by the publicly accessible databases, which indicated the usefulness of this method. The newly predicted associations were publicly released to facilitate future studies. Moreover, NetCBI was especially applicable to predicting target diseases for microRNAs whose target association information was not available. Conclusions: The encouraging results suggest that our method NetCBI can not only provide help in identifying novel microRNA-disease associations but also guide biological experiments for scientific research. © 2013 Chen and Zhang; licensee BioMed Central Ltd.


Chen H.,Central South University | Chen H.,Hunan University of Humanities, Science and Technology | Zhang Z.,Central South University
PLoS ONE | Year: 2013

Computational prediction of interactions between drugs and their target proteins is of great importance for drug discovery and design. The difficulties of developing computational methods for the prediction of such potential interactions lie in the rarity of known drug-protein interactions and no experimentally verified negative drug-target interaction sample. Furthermore, target proteins need also to be predicted for some new drugs without any known target interaction information. In this paper, a semi-supervised learning method NetCBP is presented to address this problem by using labeled and unlabeled interaction information. Assuming coherent interactions between the drugs ranked by their relevance to a query drug, and the target proteins ranked by their relevance to the hidden target proteins of the query drug, we formulate a learning framework maximizing the rank coherence with respect to the known drug-target interactions. When applied to four classes of important drug-target interaction networks, our method improves previous methods in terms of cross-validation and some strongly predicted interactions are confirmed by the publicly accessible drug target databases, which indicates the usefulness of our method. Finally, a comprehensive prediction of drug-target interactions enables us to suggest many new potential drug-target interactions for further studies. © 2013 Chen, Zhang.

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