Kwang S. Kim

Bio: Kwang S. Kim is an academic researcher from Ulsan National Institute of Science and Technology. The author has contributed to research in topics: Ab initio & Graphene. The author has an hindex of 97, co-authored 642 publications receiving 62053 citations. Previous affiliations of Kwang S. Kim include Asia Pacific Center for Theoretical Physics & IBM.

Ab initio study of the structures, energetics, and spectra of Aquazinc(II)

Abstract: By using extensive ab initio calculations including electron correlation, we have studied the structures, thermodynamic quantities, and spectra of hydrated zinc ions [Zn(H2O)n2+ (n = 1−6)]. Various conformers for n = n1 + n2 (where n1 and n2 are the numbers of water molecules in the first and second hydration shells, respectively) were investigated along with their thermodynamic quantities. The entropy effect was found to be important for the stabilities. At 0 K, the most stable structures for n = 5 and 6 are 5 + 0 and 6 + 0, respectively. However, at room temperature, both 4 + 1 and 5 + 0 seem to be almost equally populated in the case of n = 5, while 6 + 0 is the most populated in the case of n = 6. The predicted successive binding energies for the addition of each water molecule to the zinc ion are reported. The vibrational frequency shifts, depending on the number of water molecules, were investigated along with the frequency characteristics, depending on the presence/absence of outer-shell water mole...

Selective fluorescent detection of RNA in living cells by using imidazolium-based cyclophane.

Abstract: A water-soluble imidazolium-based fluorescent chemosensor senses RNA selectively through fluorescence enhancement over other biologically relevant biomolecules in aqueous solution at physiological pH 7.4. Fluorescence image detection of RNA in living cells such as onion cells, HeLa cells, and animal model cells was successfully demonstrated which displays a chelation-enhanced fluorescence effect. These affinities can be attributed to the strong electrostatic (C–H)+···A– ionic H-bonding and the aromatic moiety driven π-stacking of imidazolium-based cyclophane with the size-complementary major groove of RNA.

Water dimer to pentamer with an excess electron: Ab initio study

Abstract: We have studied the electronic structures, energetics, electron vertical detachment energies (VDEs), and O–H vibrational spectra of various conformers of water clusters with an excess electron [e+(H2O)n, n=2–5] or anionic water clusters [(H2O)n−] using comprehensive ab initio calculations. As noted in our preliminary work [J. Kim et al., Phys. Rev. A 59, 930 (1999)], the structure of the water dimer anion is characterized to be linear-like (slightly towards the cis conformer) but very floppy with large wide-ranging zero point vibration motion at 0 K. The lowest energy structures of the water trimer to pentamer anion are all cyclic with very small VDEs (< 0.05 eV). However, these cyclic structures which are metastable are prone to become the neutral species by releasing an excess electron because the transition barriers seem to be very small. Thus, observation of such cyclic structures would not be feasible. On the other hand, a linear water trimer structure which is 0.8 kcal/mol higher in energy than the ...

Role of Lewis Acid(AlCl3)−Aromatic Ring Interactions in Friedel−Craft's Reaction: An ab Initio Study

Abstract: Electrophilic aromatic substitution reactions, which are highly exemplified by the widely used Friedel-Craft's reaction, have been extensively studied using theoretical and experimental techniques. A number of elegant mechanisms have been proposed for the Friedel-Craft's reaction till date. In all the proposed mechanisms, the role of the Lewis acid has been limited to the generation of the electrophile, which subsequently attacks the aromatic system to form either a π or a σ complex. A recent experimental report on the reaction of CO with benzene in zeolite catalysts intrigued us because the presence or absence of AlCl3 was found to govern the reaction product. These clearly indicated that AlCl3 has an additional role in the reaction. We probed this role theoretically by performing high-level ab initio calculations on two model systems C6H6−BCl3 and C6H6−AlCl3. Our results clearly indicate that one of the benzene carbon tends to become highly nucleophilic, thereby facilitating an attack by an incipient el...

Carbon nanotube, graphene, nanowire, and molecule-based electron and spin transport phenomena using the nonequilibrium Green's function method at the level of first principles theory.

Abstract: Based on density functional theory, we have developed a program code to investigate the electron transport characteristics for a variety of nanometer scaled devices in the presence of an external bias voltage. We employed basis sets comprised of linear combinations of numerical type atomic orbitals, particularly focusing on k-point sampling for the realistic modeling of the bulk electrode. The scheme coupled with the matrix version of the nonequilibrium Green's function method enables calculation of the transmission coefficients at a given energy and voltage in a self-consistent manner as well as the corresponding current-voltage (I-V) characteristics. This scheme has advantages because it is applicable to large systems, easily transportable to different types of quantum chemistry packages, and extendable to time-dependent phenomena or inelastic scatterings. It has been applied to diverse types of practical electronic devices such as carbon nanotubes, graphene nanoribbons, metallic nanowires, and molecular electronic devices. The quantum conductance phenomena for systems involving quantum point contacts and I-V curves for a single molecule in contact with metal electrodes using the k-point sampling method are described.

I and i

Abstract: There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality. Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials

Abstract: QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。