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Comparison of the primary damage states in iron and nickel by molecular dynamics simulations
Kwon, J.,Kim, W.,Hong, J. -H. GORDON & BREACH / HARWOOD ACADEMIC PUBLISHING 2006 RADIATION EFFECTS AND DEFECTS IN SOLIDS Vol.161 No.4
<P> A displacement cascade formation in bcc-Fe and fcc-Ni has been investigated by using molecular dynamics (MD) simulations and improved many-body interatomic potentials. To assure the statistical validity of the calculation, multiple simulations are required at identical conditions. Six cascade simulations were run in the following two cases, with simulation energies of 3.5 keV at 100 K and 4.1 keV at 570 K. The cascade simulations for bcc-Fe were carried out by using the MOLDY code and the interatomic potentials developed by Finnis and Sinclair, whereas those for fcc-Ni were conducted by using the MDCASK code and the embedded-atom method potentials. The MD calculations demonstrate that the atomic configurations of the primary damage state are similar in Fe and Ni. However, the bcc-Fe displacement cascade produced more residual defects than the fcc-Ni cascade. In addition, various sizes of interstitial clusters are observed in Ni. As these parameters have important implications for the assessment of a radiation damage to materials, we derived the primary damage parameters for a future use in the kinetic models.</P>
FlexE ensemble docking approach to virtual screening for CDK2 inhibitors
Kim, J.,Park, J. G.,Chong, Y. GORDON & BREACH SCIENCE PUBLISHERS 2007 MOLECULAR SIMULATION Vol.33 No.8
<P> In spite of a proven potential and effectiveness of FlexE in docking flexible ligands into an ensemble of protein structures, FlexE has rarely been successful in virtual screening situations. In this study, we constructed cyclin-dependent kinase 2 (CDK2) ensemble structures which have exactly the same backbone conformations as 1AQ1 but differ only at the side chain torsion angles of the key amino acid (Lys33, Phe80, Lys89 and Asp145) residues: the torsion angles observed in the 17 CDK2 crystal structures were adapted to represent conformational flexibility. FlexE ensemble docking protocol then completely samples the full conformational fields generated by combination of torsions of the four amino acids in the ATP binding site. Virtual screening for CDK2 inhibitors by using the FlexE ensemble docking of a database composed of 48,703 inactives and 82 actives showed significant enrichment factor (EF = 18.5), and successfully identified 71 actives among the top 132 ligands (53.8%) ranked by total energy scores. Moreover, total energy scoring followed by visual inspection filtered-off non-specific binders among the highly-ranked ligands to increase the ratio of actives-to-inactives to 71:13 at the top 5% of the virtual screening solutions.</P>
A phase-field modeling of void swelling in the Austenitic stainless steel
Chang, Kunok,Lee, Gyeong-Geun,Kwon, Junhyun GORDON & BREACH / HARWOOD ACADEMIC PUBLISHING 2016 RADIATION EFFECTS AND DEFECTS IN SOLIDS Vol.171 No.3
<P>Two-dimensional phase-field simulations of void swelling in the Austenitic stainless steel were performed for irradiated materials. A numerical model was established for void swelling with an implementation of the elasticity effect, and we examined the roles of the applied stress and grain boundary sink strength and Frenkel defect recombination in determining the void swelling rate. The obtained results were compared with the existing experimental observations.</P>
Docking and 3-D QSAR studies of dual PDE4-PDE7 inhibitors
Kang, N. S.,Jhon, D. J.,Song, J. H.,Yoo, S. -E. GORDON & BREACH SCIENCE PUBLISHERS 2007 MOLECULAR SIMULATION Vol.33 No.14
<P> Small dual-specificity molecules inhibiting PDE4 and PDE7 can be used to treat inflammatory diseases. To design and synthesize dual PDE4 and PDE7 inhibitors, we carried out the target-based docking and the 3D QSAR study using CoMFA. Three compounds were synthesized. We predicted their inhibitory activities using our 3D QSAR model and tested their activities against PDE4 and PDE7 in vitro.</P>
Study on the hydrolysis mechanism of phosphodiesterase 4 using molecular dynamics simulations
Kang, N. S.,Chae, C. H.,Yoo, S.-E. GORDON & BREACH SCIENCE PUBLISHERS 2006 MOLECULAR SIMULATION Vol.32 No.5
<P>We carried out NPT molecular dynamics simulations in an explicit solvent to better understand the mechanism of cyclic adenosine monophosphates (cAMP) hydrolysis by phosphodiesterase 4 (PDE4) enzyme on atomic details and to obtain information on the dynamics characteristic of the catalytic domains of PDE4. In analyzing the water hydrogen-bond network around the active site, we also showed the importance of water in drug–protein interactions. In addition, we reported the characteristics of the hydration pattern and the dynamic distance distribution around the interesting residues. The results indicated that Asp318 plays the role of a general base that can activate water molecule for nucleophilic attack on cAMP. As expected, His160 plays the role of a proton donor for cAMP.</P>