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Atomistic Analysis of Myoglobin Mechanical Unfolding
HE Erbin, LUO Zhirong, ZHU Liuhua
CHINESE JOURNAL OF COMPUTATIONAL PHYSICS    2020, 37 (2): 205-211.   DOI: 10.19596/j.cnki.1001-246x.8009
Abstract348)   HTML0)    PDF (9473KB)(1338)      
Myoglobin, which exists widely in skeletal muscle of vertebrates, plays crucial roles in life processes. Its proper folding depends on the binding of heme. In this paper, we report an atomistic and statistical analysis of force-induced unfolding of myoglobin with and without heme binding. It shows that heme is responsible for not only its biological functions, but also its unfolding dynamics. The unfolding pathway of myoglobin without heme binding involve an intermediate configuration. More importantly, it shows that intermediate state in force-induced unfolding process is different from that in chemical denaturant, which leads to the discovery of new intermediate configurations. Our results are in good agreement with related experimental observations and provide significant insight into general mechanisms of myoglobin unfolding.
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Phase Field Modeling of Columnar Grain Growth:Effect of Second-Phase Particles
LUO Zhirong, GAO Yingjun, MAO Hong, LU Chengjian, HUANG Shiye
CHINESE JOURNAL OF COMPUTATIONAL PHYSICS    2016, 33 (3): 367-373.  
Abstract421)   HTML5)    PDF (2450KB)(1206)      
In a moving hot zone model with uniform temperature and an infinite temperature gradient under directional annealing, effect of second-phase particles (SPPs) on growth of columnar grain microstructure in polycrystalline materials was studied with phase field method. It shows that SPPs inhibit formation of columnar grain structure and inhibitory effect increases with increasing volume fraction of SPPs and decreasing size of SPPs. Effect of SPPs on final grain radius follows Zener relation under condition of directional annealing. Volume fraction of SPPs and their dispersive distribution at grain boundaries in materials should be reduced as far as possible to obtain better columnar grain structures during directional annealing.
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Phase-Field-Crystal Modeling of Microcrack Propagation and Branching in Ductile Materials
GAO Yingjun, LUO Zhirong, DENG Qianqian, HUANG Lilin, LIN Kui
CHINESE JOURNAL OF COMPUTATIONAL PHYSICS    2014, 31 (4): 471-478.  
Abstract610)      PDF (2210KB)(1788)      
Morphology of microcrack propagation and crack branching of single crystal ductile materials under tensile are simulated with phase-field-crystal method. It shows that shape of notch has a strong effect on crack propagation. With uniaxial tension crack propagation appears if only strain reaches a critical value. With biaxial tension a crack branches if only strain reaches a critical value. Temperature parameter takes significant effects on crack propagation. The smaller the temperature parameter is (the temperature is higher), the faster the cracks propagate and the more the crack branches are. It is observed that free energy of system decreases with time and decreases faster after crack starts to branch. During crack propagation, disconnectedly isolated cavities around the main cracks can be found and these defects become new cracks. They grow up along a line and become a branching crack. Simulated results are in agreement with other simulations and experimental results.
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Nano-twin Structure Simulation with Phase Field Crystal Method
GAO Yingjun, WANG Jiangfan, LUO Zhirong, LU Qianghua, LIU Yao
CHINESE JOURNAL OF COMPUTATIONAL PHYSICS    2013, 30 (4): 577-581.  
Abstract324)      PDF (1229KB)(2181)      
Two-mode phase-field-crystal (PFC) method is used to simulate coherent boundary of nano-twins.It shows that atomic arrangement in coherent twin-grain boundary is not in good order as sphere grains grow and run into each other to form dislocations.Atomic arrangement in coherent twin-grain boundary as band-shape grains colliding each other is more tidy.For designing and controlling numbers of atomic layer in nano-twins,PFC model can be used to realize manipulation for coherent nano-twins structure.It is significant for guiding experiment and revealing nano-twins structure and properties.
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