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DICP Biomolecular Simulation Theory Research Results Published on the Cover of Theoretical Computational Chemistry Core Magazine
  English.dicp.cas.cn    Posted:2016-02-24    From:Group1106

With the development and improvement of a variety of experimental techniques, more and more complex structures of biological molecules have been parsed so that the microscopic mechanism of complex biological phenomena gained unprecedented information in atomic resolution. However, the current biomolecular simulation methods of most are limited to traditional, all-atom model with fixed point charge based on the quantum mechanics but also with a certain gap in the description of large biomolecules the calculation speed is very slow. The rapid development of computer hardwareprovides a strong support for studying the relationship between the structure and function of biological macromolecules with high precision theories.

In order to study and answer the microscopic mechanism of large protein molecule machines, due to limitations in computer speed, conventional coarse-grained molecular models ignore the calculation accuracy while pursuingfor speed calculation, such a model may be useful for large-scale self-assembly, but cannot be used in the description of molecular function of the microscopic mechanism aspect, Guohui’s group since 2009 first proposed the new coarse-grained molecular model of balanced development speed and accuracy (GBEMP) internationally, the model was validated based on the solvent for organic molecules, amino acids and complete protein, nucleotide molecules, nucleic acids, and a series of biological membrane phospholipid molecules and associated systems. A series of research papers have been published in international core journals in theoretical chemistry field. Most recently, our work on the establishment and validation of new nucleic coarse-grained model was chosen as the cover of theoretical computational chemistry highest impact factor journal J. Chem. Theory Comp.'s.



DICP Biomolecular Simulation Theory Research Results Published on the Cover of Theoretical Computational Chemistry Core Magazine (Photo by LI Guohui)


For some biological phenomena, descriptions of the interaction between molecules is critical, full-atom molecular field polarization is recently developed, and attracted considerable attention for precision molecular model internationally. Multi-pole pitch describes the inherent electrostatic characteristics and induced dipole polarization effects that can be described by AMOEBA force field. However, in conventional molecular dynamics with old computer hardware the simulation speed is very slow using polarizable force field, and cannot be cooperated with enhanced sampling simulation for complex biological phenomena, resulting in the limited applications of high-precision force fields. Guohui group recently used the latest GPU hardware to achieve efficient operation using this polarizable force field molecular dynamics simulation program cooperating with enhanced sampling technology, making the precision of molecular dynamics simulation of force field 5-10 times faster. Results were published as a partial cover of the core theoretical magazine J.Comp. Chem. http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1096-987X/homepage/AdvSampVI.html (Text/Photo by LI Guohui)







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