• Advances in nano research
• /
• v.1 no.3
• /
• pp.133-151
• /
• 2013

The availability of advanced nanotechnological methodologies (experimental and theoretical) has widened the investigation of biological/organic matter in interaction with substrates. Minerals are good candidates as substrates because they may present a wide variety of physico-chemical properties and surface nanostructures that can be used to actively condense and manipulate the biomolecules. Scanning Probe Microscopy (SPM) is one of the best suited techniques used to investigate at a single molecule level the surface interactions. In addition, the recent availability of high performance computing has increased the possibility to study quantum mechanically the interaction phenomena extending the number of atoms involved in the simulation. In the present paper, firstly we will briefly introduce new SPM technological developments and applications to investigate mineral surfaces and mineral-biomolecule interaction, then we will present results on the specific RNA-mineral interaction and recent basics and applicative achievements in the field of the interactions between other fundamental biological molecules and mineral surfaces from both an experimental and theoretical point of view.

• Proceeding of EDISON Challenge
• /
• 2013.04a
• /
• pp.294-298
• /
• 2013

A FeRh alloy is a well-known efficient magnetocaloric material and some experimental and theoretical studies of bulk FeRh have been reported already by several groups. In this study we report first-principles calculations on magnetic properties of different thickness FeRh thin films in order to investigate the possibility to enhance further the magnetocaloric efficiency. We used two methods of a Vienna Ab-initio Simulation Package (VASP) code and SIESTA package. We found that the FeRh thin films have quite different magnetic properties from the bulk when the thickness is thinner than 6-atomic-layers. While bulk FeRh has a G-type antiferromagnetic(AFM) state, thin films which are thinner than 6-atomic-layers have an A-type AFM state or a ferromagnetic (FM) state. We will discuss possibility of magnetic phase transitions of the FeRh thin films in the view point of a magnetocaloric effect. And we found 4-, 5-, 6-layers films with Fe surface and 7-layers film with Rh surface are FM and they have relatively small magnetocrystalline anisotropy (MCA) energy about less than 70 meV. The small MCA energy leads to reduction of the strength of magnetic field in operating a magnetic refrigerator.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
• /
• 2005.07a
• /
• pp.172-173
• /
• 2005

The electronic state of ZnO doped with Y was calculated using the density functional theory. In this study, the program used for the calculation on theoretical structures of ZnO and doped ZnO was Vienna Ab-initio Simulation Package (VASP), which is a sort of pseudo potential method. The detail of electronic structure was obtained by the descrite variational $X\alpha$ (DV-$X\alpha$) method, which is a sort of molecular orbital full potential method. The optimized crystal structures obtained by calculations were compared to the measured structure. The density of state and energy levels of dopant elements was shown and discussed in association with optical properties.

• Bulletin of the Korean Chemical Society
• /
• v.14 no.4
• /
• pp.491-496
• /
• 1993

A class A ${\beta}$-lactamase from Staphylococcus aureus PC1 complexed with 3R,5R-clavulanate is studied. The starting geometry for the computation is the crystal structure of the ${\beta}$-lactamase. Docking of the clavulanate to the enzyme is done exploiting the requirements of electrostatic and shape complementarity between the enzyme and clavulanate. This structure is then hydrated by water molecules and refined by energy minimization and short molecular dynamics simulation. In the energy refined structure of this complex, the carboxyl group of the clavulanate is hydrogen bonded to Lys-234, and the the carbonyl carbon atom of the clavulanate is adjacent to the $O_{\gamma}$ of Ser-70. It is found that a crystallographic water molecule initially located at the oxyanion hole, which is formed by the two -NH group of Ser-70 and Gln-237, is replaced by the carbonyl oxygen atom of the 3R,5R-clavulanate after docking and energy reginement. The crystallographic water molecules are proved to be important in ligand binding. Glu-166 residue is found to be repulsive to the binding of clavulanate, which is in agreement with experimental observation. Arg-244 residue is found to be important to the binding of clavulanate as well as to interaction with C2 side chain of the clavulanate. The electron density redistribution of the clavulanate on binding to the ${\beta}$-lactamase in studied by an ab initio quantum-mechanical calculation. A significant redistribution of electron density of the clavulanate is induced by the enzyme, toward the enzyme, toward the transition state of the enzymatic reaction.

• Genomics & Informatics
• /
• v.21 no.3
• /
• pp.41.1-41.11
• /
• 2023

The Dengue virus M protein is a 75 amino acid polypeptide with two helical transmembranes (TM). The TM domain oligomerizes to form an ion channel, facilitating viral release from the host cells. The M protein has a critical role in the virus entry and life cycle, making it a potent drug target. The oligomerization of the monomeric protein was studied using ab initio modeling and molecular dynamics simulation in an implicit membrane environment. The representative structures obtained showed pentamer as the most stable oligomeric state, resembling an ion channel. Glutamic acid, threonine, serine, tryptophan, alanine, isoleucine form the pore-lining residues of the pentameric channel, conferring an overall negative charge to the channel with approximate length of 51.9 Å. Residue interaction analysis for M protein shows that Ala94, Leu95, Ser112, Glu124, and Phe155 are the central hub residues representing the physicochemical interactions between domains. The virtual screening with 165 different ion channel inhibitors from the ion channel library shows monovalent ion channel blockers, namely lumacaftor, glipizide, gliquidone, glisoxepide, and azelnidipine to be the inhibitors with high docking scores. Understanding the three-dimensional structure of M protein will help design therapeutics and vaccines for Dengue infection.

• Journal of Photoscience
• /
• v.9 no.2
• /
• pp.51-54
• /
• 2002

We propose a novel mechanism (Twist Sharing Mechanism) for the cis-trans photoisomerization of rhodopsin, based on the molecular dynamics (MD) simulation study. New things devised in our simulations are (1) the adoption of Mt. Fuji potentials in the excited state for twisting of the three bonds C9=C10, C11=C12 and C13=14 which are modeled using the detailed ab initio quantum chemical calculations and (2) to use the rhodopsin structure which was resolved recently by the X-ray crystallographic study. As a result, we found the followings: Due to the intramolecular steric hindrance between 20-methyl and 10-H in the retinal chromophore, the C12-C13 and C10-C11 bonds are considerably twisted counterclockwise in rhodopsin, allowing only counterclockwise rotation of the C11 =C12 in the excited state. The movement of 19-methyl in rhodopsin is blocked by the surrounding three amino acids, Thr 118, Met 207 and Tyr 268, prohibiting the rotation of C9=C10. As a result only all-trans form of the chromophore is obtainable as a photoproduct. At the 90$^{\circ}$ twisting of C11=C12 in the course of photoisomerization, twisting energies of the other bonds amount to about 20 kcal/mol. If the transition state for the thermal isomerization is assumed to be similar to this structure, the activation energy for the thermal isomerization around C11=C12'in rhodopsin is elevated by about 20 kcal/mol and the thermal isomerization rate is decelerated by 10$\^$-14/ times than that of the retinal chromophore in solution, protecting photosignal from the thermal noise.

• Proceedings of the Korean Vacuum Society Conference
• /
• 2014.02a
• /
• pp.185.2-185.2
• /
• 2014

We have studied the atomic and electronic structure of graphene nanoribbons (GNRs) on a hexagonal boron nitride (h-BN) sheet with intercalated atoms using first-principles calculations. The h-BN sheet is an insulator with the band gap about 6 eV and then it may a good candidate as a supporting dielectric substrate for graphene-based nanodevices. Especially, the h-BN sheet has the similar bond structure as graphene with a slightly longer lattice constant. For the computation, we use the Vienna ab initio simulation package (VASP). The generalized gradient approximation (GGA) in the form of the PBE-type parameterization is employed. The ions are described via the projector augmented wave potentials, and the cutoff energy for the plane-wave basis is set to 400 eV. To include weak van der Waals (vdW) interactions, we adopt the Grimme's DFT-D2 vdW correction based on a semi-empirical GGA-type theory. Our calculations reveal that the localized states appear at the zigzag edge of the GNR on the h-BN sheet due to the flat band of the zigzag edge at the Fermi level and the localized states rapidly decay into the bulk. The open-edged graphene with a large corrugation allows some space between graphene and h-BN sheet. Therefore, atoms or molecules can be intercalated between them. We have considered various types of atoms for intercalation. The atoms are initially placed at the edge of the GNR or inserted in between GNR and h-BN sheet to find the effect of intercalated atoms on the atomic and electronic structure of graphene. We find that the impurity atoms at the edge of GNR are more stable than in between GNR and h-BN sheet for all cases considered. The nickel atom has the lowest energy difference of ~0.2 eV, which means that it is relatively easy to intercalate the Ni atom in this structure. Finally, the magnetic properties of intercalated atoms between GNR and h-BN sheet are investigated.

• Journal of the Korean Magnetics Society
• /
• v.25 no.4
• /
• pp.101-105
• /
• 2015

Recent theoretical calculations predicted that a system composed exclusively of 3d transition metals without 4d/5d transition metals or rare earth metals can have strong perpendicular magnetocrystalline anisotropy (MCA) if Fe and Ni layers are arranged appropriately. They considered only Fe-terminated surfaces, noting that Fe/MgO(001) and CoFeB/MgO(001) show strong perpendicular MCA. In this paper, we investigate magnetism and MCA of Ni/Fe(001) surface where Ni layer is positioned at the surface, by using complementarily the first principles calculational methods of Vienna Ab-initio Simulation Package (VASP) and Full-potential Linearized Augmented Plane Wave (FLAPW) method. Comparing results of magnetism and MCA obtained by VASP with the results by FLAPW method, we find the VASP results do not show big difference from results by FLAPW method. Magnetic moments of Fe and Ni are enhanced due to strong hybridization between Fe and Ni bands. MCA of Ni/Fe(001) is parallel to the surface, which implies the surface termination plays a crucial role in determining MCA of a system.

• Journal of Electrochemical Science and Technology
• /
• v.2 no.3
• /
• pp.146-151
• /
• 2011

The formation of Li-Si-O phases, $Li_4SiO_4$ and $Li_2SiO_3$ from the starting materials SiO and $Li_2O$ are analyzed using Vienna Ab-initio Simulation (VASP) package and the total energies of Li-Si-O compounds are evaluated using Projector Augmented Wave (PAW) method and correlated the structural characteristics of the binary system SiO-$Li_2O$ with experimental data from electrochemical method. Despite $Li_2SiO_3$ becomes stable phase by virtue of lowest formation energy calculated through VASP, the experimental method shows presence of $Li_4SiO_4$ as the only product formed when SiO and $Li_2O$ reacts during slow heating to reach $550^{\circ}C$ and found no evidence for the formation of $Li_2SiO_3$. Also, higher density of $Li_4SiO_4$(2.42 g $ml^{-1}$) compared to the compositional mixture $1SiO_2-2Li_2O$ (2.226 g $ml^{-1}$) and better cycle capacity observed through experiment proves that $Li_4SiO_4$ as the most stable anode supported by better cycleabilityfor lithium ion battery remains as paradox from the point of view of VASP calculations.