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 …

I and i

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.

Fast parallel algorithms for short-range molecular dynamics

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

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.

/pdf/quantum-espresso-a-modular-and-open-source-software-project-4t6vlupbeh.pdf

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

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。

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

We have synthesized self-assembled red-colored proton complexes of the aldehyde derivatives of polyaromatic hydrocarbon with strong intermolecular hydrogen bonding. These intermolecularly proton-bonded polyaromatic aldehydes formed as 1-pyrenecarbaldehyde (Py-CHO) reacted with HAuCl(4) to produce [(Py-CHO)(2)H][AuCl(4)] under dry conditions. The formation of [(Py-CHO)(2)H][AuCl(4)] was confirmed by single-crystal structure determination and IR spectral analysis at various temperatures. The compounds are distinctively hydrophobic in nature and are soluble only in a few organic polar solvents. The proton bonds are clearly observed from both the electron density in X-ray analysis and the characteristic IR frequency signature. The proton complex units have an O-H(+)-O distance of the typical Zundel-like cationic hydrogen bond (in which two O atoms share a proton-like H in the midpoint of the short O-O distance of ≈2.4 A). The proton bonds are thermally stable, even over 100 °C, because the complexes are stabilized in layered structures with π-π intermolecular interactions of the polyaromatic hydrocarbon ligands. The IR signatures at around 900, 1200, and 1700 cm(-1) for the Zundel-like proton bond are clearly characterized.

Thermally Stable Intermolecular Proton Bonds in Polyaromatic Aldehyde Crystals

The direct band gap of the conjugated polymer poly(p-phenylenevinylene) (PPV) is calculated in an effective single-band model by means of a renormalization scheme. This model provides a simple computational method for obtaining the band gap of a many-band conjugated π-electron system of long polymers. The calculation shows that, for the existing data for PPV, the present renormalization scheme works well and its results as regards the band energy gap are comparable to those obtained by other approaches including ab initio calculation.

Model calculation of the band energy gap for poly(p-phenylenevinylene)

We report that the {\pi}-electrons of graphene can be spin-polarized to create a phase with a significant spin-orbit gap at the Dirac point (DP) using a graphene-interfaced topological insulator hybrid material. We have grown epitaxial Bi2Te2Se (BTS) films on a chemical vapor deposition (CVD) graphene. We observe two linear surface bands both from the CVD graphene notably flattened and BTS coexisting with their DPs separated by 0.53 eV in the photoemission data measured with synchrotron photons. We further demonstrate that the separation between the two DPs, {\Delta}D-D, can be artificially fine-tuned by adjusting the amount of Cs atoms adsorbed on the graphene to a value as small as {\Delta}D-D = 0.12 eV to find any proximity effect induced by the DPs. Our density functional theory calculation shows a spin-orbit gap of ~20 meV in the {\pi}-band enhanced by three orders of magnitude from that of a pristine graphene, and a concomitant phase transition from a semi-metallic to a quantum spin Hall phase when {\Delta}D-D $\leq$ 0.20 eV. We thus present a practical means of spin-polarizing the {\pi}-band of graphene, which can be pivotal to advance the graphene-based spintronics.

Proximity Effect Induced Electronic Properties of Epitaxial Graphene on Bi2Te2Se

We study the dependence between prime numbers and the real and imaginary parts of the nontrivial zeros of the Riemann zeta function. The Legendre polynomials and the partial derivatives of the Riemann zeta function are used to investigate the above dependence along with the Riemann hypothesis with physical interpretations. A modified zeta function with finite terms is defined as a new implement for the study of the zeta function and its zeros.

https://oasis.postech.ac.kr/bitstream/2014.oak/13128/1/OAIR003902.pdf

Kwang S. Kim

Papers

Thermally Stable Intermolecular Proton Bonds in Polyaromatic Aldehyde Crystals

Model calculation of the band energy gap for poly(p-phenylenevinylene)

Proximity Effect Induced Electronic Properties of Epitaxial Graphene on Bi2Te2Se

Relation between primes and nontrivial zeros in the Riemann hypothesis; Legendre polynomials, modified zeta function and Schrödinger equation

Weak to Strong Hydrogen Bonds