Duck-Soo Kim

We carried out the near-field optical imaging of isolated and dimerized gold nanocubes to directly investigate the strong coupling between two adjacent nanoparticles. The high-resolution (approximately 10 nm) local field maps (intensities and phases) of self-assembled nanocube dimers reveal antisymmetric plasmon modes that are starkly different from a simple superposition of two monomeric dipole plasmons, which is fully reproduced by the electrodynamics simulations. The result decisively proves

In this article, an enhanced version of GalaxyDock protein-ligand docking program is introduced. GalaxyDock performs conformational space annealing (CSA) global optimization to find the optimal binding pose of a ligand both in the rigid-receptor mode and the flexible-receptor mode. Binding pose prediction has been improved compared to the earlier version by the efficient generation of high-quality initial conformations for CSA using a predocking method based on a beta-complex derived from the Vo

3D printing, also called additive manufacturing, has been increasingly popular and printing efficiency has become more critical. To print artifacts faster with less material, thus leading to lighter and cheaper printed products, various types of void structureshave been designed and engineered inside of shape models. In this paper, we present a novel method for generating support-free elliptic hollowing for 3D shapes which can entirely avoid additional supporting structures. To achieve this, we

A computer program has been developed for analyzing the three-dimensional, steady conservation equations for transport phenomena in a slab continuous casting process with Electromagnetic Brake (EMBr) to investigate the effect of EMBr on the turbulent melt-flow, temperature fields, and macroscopic solidification of the molten metal. The enthalpy-porosity relation was employed to suppress the velocity within a mushy region. A revised low-Reynolds number k–ε turbulence model was used to consider th

The proximity and topology among particles are often the most important factor for understanding the spatial structure of particles. Reasoning the morphological structure of molecules and reconstructing a surface from a point set are examples where proximity among particles is important. Traditionally, the Voronoi diagram of points, the power diagram, the Delaunay triangulation, and the regular triangulation, etc. have been used for understanding proximity among particles. In this paper, we pres

A 0.3–1.4 GHz all-digital phase locked loop (ADPLL) with an adaptive loop gain controller (ALGC), a 1/8-resolution fractional divider and a frequency search block is presented. The ALGC reduces the nonlinearity of the bang-bang phase-frequency detector (BBPFD), reducing output jitter. The fractional divider partially compensates for the large input phase error caused by fractional-N frequency synthesis. A fast frequency search unit using the false position method achieves frequency lock in 6 ite

Quasi-triangulation is the dual structure of the Voronoi diagram of spheres, and it has been used as a convenient and powerful geometric construct for representing the proximity among spherical particles with different radii. In this paper, we present the formalism of the quasi-triangulation based on a quasi-world model and define primitive query operators called quasi-operators for correct and efficient topology traversal on the quasi-triangulation. Algorithms for the quasi-operators are also p

Molecular cavities, which include voids and channels, are critical for molecular function. We present a webserver, BetaCavityWeb, which computes these cavities for a given molecular structure and a given spherical probe, and reports their geometrical properties: volume, boundary area, buried area, etc. The server's algorithms are based on the Voronoi diagram of atoms and its derivative construct: the beta-complex. The correctness of the computed result and computational efficiency are both mathe