Efficient first-principles simulation of noncontact atomic force microscopy for structural analysis

We propose an efficient scheme to simulate noncontact atomic force microscopy images by using first-principles self-consistent potential from the sample as input without explicit modeling of the atomic force microscopy tip. Our method is applied to various types of semiconductor surfaces including Si(111)-(7x7), TiO2(110)-(1x1), Ag/Si(111)-(sqrt[3]xsqrt[3])R30 degrees, and Ge/Si(105)-(1x2) surfaces. We obtain good agreement with experimental results and previous theoretical studies, and our method can aid in identifying different structural models for surface reconstruction.

American ginseng berry juice intake reduces blood glucose and body weight in ob/ob mice

Diabetes is a serious chronic metabolic disease and has a significant impact on patients' lives and the health care system. We previously observed that the organic solvent extract of American ginseng berry possessed significant antidiabetic effects in obese diabetic ob/ob mice after intraperitoneal injection. If American ginseng berry is useful as a dietary supplement, simple preparation and oral intake would be a convenient, safe, and practical means for consumers. In this study, the simply prepared berry juice was first analyzed using high-performance liquid chromatography, and then administered orally in the ob/ob mice. The animals received daily berry juice 0.6 mL/kg or vehicle for 10 consecutive days. The results indicated that oral juice administration significantly lowered fasting blood glucose levels, and this effect continued for at least 10 d after cessation of the treatment. Data from intraperitoneal glucose tolerance test demonstrated that there was a notable improvement in glucose tolerance in the juice treated group. In addition, the berry juice significantly reduced body weight. Our data suggest that ginseng berry juice, as a dietary supplement, may have functional efficacy in consumers with diabetes.

Simultaneous identification of Bulbus Fritillariae cirrhosae using PCR-RFLP analysis

Bulbus Fritillariae (BF) is the most commonly used antitussive herb in China. There are nine species of Fritillaria recorded as the drug BF in the Chinese Pharmacopoeia. Bulbus Fritillariae cirrhosae (BF cirrhosae) is a group that includes four species of BF; these four species come from wild sources with higher efficiency and lower toxicity compared to the other five species of BF. Due to reasons of carelessness and reduced costs, the other five species are often sold as BF cirrhosae. Analysis through appearance, microscopic and chemical techniques has limitations. Identifying botanical resources is a primary step in the standardization of herbal medicine. In the present article, the internal transcribed spacer 1 (ITS1) regions of the nuclear ribosomal DNA (nrDNA) of nine species and one variety of Fritillaria genus have been sequenced. A mutation site in the ITS1 region among BF cirrhosae and other species of BF has been found and can be recognized by the restriction endonuclease SmaI. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the nuclear ribosomal ITS1 region was used to differentiate BF cirrhosae from other species of BF and is a successful method in distinguishing the subgroups.

Oxidation Pattern of Small Silicon Oxide Clusters: Structures and Stability of Si6On (n = 1−12)

We have performed systematic ab initio calculations to study the structures and stability of Si(6)O(n)() clusters (n = 1-12) in order to understand the oxidation process in silicon systems. Our calculation results show that oxidation pattern of the small silicon cluster, with continuous addition of O atoms, extends from one side to the entire Si cluster. Si atoms are found to be separated from the pure Si cluster one-by-one by insertion of oxygen into the Si-O bonds. From fragmentation energy analyses, it is found that the Si-rich clusters usually dissociate into a smaller pure Si clusters (Si(5), Si(4), Si(3), or Si(2)), plus oxide fragments such as SiO, Si(2)O(2), Si(3)O(3), Si(3)O(4), and Si(4)O(5). We have also studied the structures of the ionic Si(6)O(n)(+/-) (n = 1-12) clusters and found that most of ionic clusters have different lowest-energy structures in comparison with the neutral clusters. Our calculation results suggest that transformation Si(6)O(n)+(a) + O --> Si(6)O(n+1)+(a) should be easier.

Quantum size effect on the diffusion barriers and growth morphology of Pb/Si(111)

An intriguing growth morphology of Pb islands on a Si(111) surface is observed in our STM experiments: the growth of a Pb layer on Pb islands with unstable heights starts from the periphery and moves towards the center, while the nucleation of the next layer on stable Pb islands starts away from the periphery. Using first-principles total energy calculations, we have studied the diffusion barriers of Pb adatoms on a freestanding Pb(111) film as a function of film thickness. The diffusion barriers are found to be very low (<60 meV), and a bi-layer oscillation due to the quantum size effect (QSE) is observed, with a lower barrier on the odd-layered, relatively unstable Pb films. The diffusion barrier difference between the odd- and even-layered film is as large as 40 meV. The observed unusual growth can be attributed to this big difference in the diffusion barriers due to QSE.

Molecule intrinsic minimal basis sets. II. Bonding analyses for Si4H6 and Si2 to Si10

The method, introduced in the preceding paper, for recasting molecular self-consistent field (SCF) or density functional theory (DFT) orbitals in terms of intrinsic minimal bases of quasiatomic orbitals, which differ only little from the optimal free-atom minimal-basis orbitals, is used to elucidate the bonding in several silicon clusters. The applications show that the quasiatomic orbitals deviate from the minimal-basis SCF orbitals of the free atoms by only very small deformations and that the latter arise mainly from bonded neighbor atoms. The Mulliken population analysis in terms of the quasiatomic minimal-basis orbitals leads to a quantum mechanical interpretation of small-ring strain in terms of antibonding encroachments of localized molecular-orbitals and identifies the origin of the bond-stretch isomerization in Si4H6. In the virtual SCF/DFT orbital space, the method places the qualitative notion of virtual valence orbitals on a firm basis and provides an unambiguous ab initio identification of the frontier orbitals.

Molecule intrinsic minimal basis sets. I. Exact resolution of ab initio optimized molecular orbitals in terms of deformed atomic minimal-basis orbitals

A method is presented for expressing the occupied self-consistent-field (SCF) orbitals of a molecule exactly in terms of chemically deformed atomic minimal-basis-set orbitals that deviate as little as possible from free-atom SCF minimal-basis orbitals. The molecular orbitals referred to are the exact SCF orbitals, the free-atom orbitals referred to are the exact atomic SCF orbitals, and the formulation of the deformed "quasiatomic minimal-basis-sets" is independent of the calculational atomic orbital basis used. The resulting resolution of molecular orbitals in terms of quasiatomic minimal basis set orbitals is therefore intrinsic to the exact molecular wave functions. The deformations are analyzed in terms of interatomic contributions. The Mulliken population analysis is formulated in terms of the quasiatomic minimal-basis orbitals. In the virtual SCF orbital space the method leads to a quantitative ab initio formulation of the qualitative model of virtual valence orbitals, which are useful for calculating electron correlation and the interpretation of reactions. The method is applicable to Kohn-Sham density functional theory orbitals and is easily generalized to valence MCSCF orbitals.

Ganoderma lucidum extract inhibits proliferation of SW 480 human colorectal cancer cells

AIM

Ganoderma lucidum is a commonly used Chinese herb and an important ingredient in traditional Chinese medicine herbal formulations for immune dysfunction related illnesses. The effects of this medicinal mushroom on human colorectal cancer cells have not yet been evaluated. In this study, we investigated the effects of Ganoderma lucidum extract using SW 480 human colorectal cancer cell line.

MATERIALS AND METHODS

Two different fractions of Ganoderma lucidum extract, i.e., a fraction containing mainly polysaccharides (GLE-1), and a triterpenoid fraction without polysaccharides (GLE-2) were analyzed. Their antiproliferative activity was evaluated by cell proliferation assay and 3H-thymidine incorporation assay. Scavenging effects of DPPH radical were assessed using ESR-spectroscopy.

RESULTS

Our data showed that both GLE-1 and GLE-2 significantly inhibited the proliferation of SW 480 cells. The inhibitory effect of GLE-2 was much stronger than that of GLE-1. GLE-1 inhibited DNA synthesis in the cells and reduced the formation of DPPH radicals.

CONCLUSION

Ganoderma lucidum extract inhibits proliferation of human colorectal cancer cells and possesses antioxidant properties.

Structure and stability of oxygen adsorption on Si(n) (n = 5-10) clusters

The structures, binding energies, and electronic properties of one oxygen atom (O) and two oxygen atoms (2O) adsorption on silicon clusters Si(n) with n ranging from 5 to 10 are studied systematically by ab initio calculations. Twelve stable structures are obtained, two of which are in agreement with those reported in previous literature and the others are new structures that have not been proposed before. Further investigations on the fragmentations of Si(n)O and Si(n)O2 (n = 5-10) clusters indicate that the pathways Si(n)O --> Si(n-1) + SiO and Si(n)O2 --> Si(n-2) + Si2O2 are most favorable from thermodynamic viewpoint. Among the studied silicon oxide clusters, Si8O, Si9O, Si5O2 and Si8O2 correspond to large adsorption energies of silicon clusters with respect to O or 2O, while Si8O, with the smallest dissociation energy, has a tendency to separate into Si7 + SiO. Using the recently developed quasi-atomic minimal-basis-orbital method, we have also calculated the unsaturated valences of the neutral Si(n) clusters. Our calculation results show that the Si atoms which have the largest unsaturated valences are more attractive to O atom. Placing O atom right around the Si atoms with the largest unsaturated valences usually leads to stable structures of the silicon oxide clusters.

Diffusion, coalescence, and reconstruction of vacancy defects in graphene layers

Diffusion, coalescence, and reconstruction of vacancy defects in graphene layers are investigated by tight-binding molecular dynamics (TBMD) simulations and by first principles total energy calculations. It is observed in the TBMD simulations that two single vacancies coalesce into a 5-8-5 double vacancy at the temperature of 3000 K, and it is further reconstructed into a new defect structure, the 555-777 defect, by the Stone-Wales type transformation at higher temperatures. First principles calculations confirm that the 555-777 defect is energetically much more stable than two separated single vacancies, and the energy of the 555-777 defect is also slightly lower than that of the 5-8-5 double vacancy. In TBMD simulation, it is also found that the four single vacancies reconstruct into two collective 555-777 defects which is the unit for the hexagonal haeckelite structure proposed by Terrones et al. [Phys. Rev. Lett. 84, 1716 (2000)].

Potential Energy Surfaces of SimOn Cluster Formation and Isomerization

The reaction paths for formation and isomerization of a set of silica SimOn (m = 2,3, n = 1-5) nanoclusters have been investigated using second-order perturbation theory (MP2) with the 6-31G(d) basis set. The MP2/6-31G(d) calculations have predicted singlet ground states for all clusters excluding Si3O2. The total energies of the most important points on the potential energy surfaces (PES) have been determined using the completely renormalized (CR) singles and doubles coupled cluster method including perturbative triples, CR-CCSD(T) with the cc-pVTZ basis set. Although transition states have been located for many isomerization reactions, only for Si3O3 and Si3O4 have some transition states been found for the formation of a cluster from the separated reactants. In all other cases, the process of formation of SimOn clusters appears to proceed without potential energy barriers.

Ab initio molecular dynamics simulation of liquid Al88Si12 alloys

First-principles molecular dynamics simulations are carried out to study the structures, dynamics, and electronic properties of liquid Al88Si12 in the temperature ranging from 898 to 1298 K. The temperature dependence of static structure factors, pair correlation functions, and electronic density-of-states are investigated. The structural properties obtained from the simulations are in good agreement with the x-ray diffraction experimental results.

Effect of chain connectivity on the structure of Lennard-Jones liquid and its implicationon statistical potentials for protein folding

Statistical contact potentials and bead-spring models have been widely used for computational studies of protein folding. However, there has been speculation that systematic error may arise in the contact energy calculations when the statistical potentials are deduced under the assumption that the chain connectivity in proteins can be ignored. To address this issue, we have performed molecular-dynamics simulations to study the structure and dynamics of a simple liquid system in which the beads are either connected or unconnected with springs. Results from the present study provide useful information for assessing the accuracy of the statistical potentials for protein structure simulations.

Heat-induced transformation of nanodiamond into a tube-shaped fullerene: a molecular dynamics simulation

Heat-induced structural transformation in nanodiamond of diameter approximately 1.4 nm is investigated by tight-binding molecular dynamics simulations using the environment-dependent tight-binding carbon potential. The nanodiamond is found to transform into a tube-shaped fullerene via annealing. Three interesting mechanisms for promoting inner carbon atoms of the nanodiamond into the surface carbon atoms of the tubular structure are observed. The "flow-out" mechanism prevails at temperatures lower than 2500 K and the "direct adsorption" and "push-out" mechanisms are observed at higher temperatures.

Pharmacological and behavioral analysis of the effects of some bivalent ligand-based monoamine reuptake inhibitors

Novel piperidine-based bivalent ligands were prepared in enantiomerically pure form and evaluated for their ability to inhibit reuptake of dopamine (DA), serotonin (5-HT), and norepinephrine (NE) into rat brain nerve endings (synaptosomes). In this study, we have succeeded in using (1) the length of the linking chain connecting the two piperidine-based monomer units and (2) the absolute configuration of the piperidine monomer as a means to tailor activity and selectivity at the three monoamine transporters tested. In this series, the bivalent ligand 16, comprised of two (+)-trans-piperidine units linked by a pentamethylene spacer, exhibits a combination of high DA transporter (DAT) and 5-HT transporter (SERT) activity (K(i) = 39 nM and 7 nM, respectively). Piperidine 16 is capable of reducing cocaine's locomotor effects in mice while not having any effect on locomotion when tested alone. Additionally, compound 16 (1-10 mg/kg) does not substitute for cocaine in drug discrimination studies in rats. However, the analogous bivalent ligand 15 comprised of two (-)-trans-piperidine units, which is SERT selective, was less effective in antagonizing cocaine's locomotor stimulant activity. The piperidine-based bivalent inhibitors described herein constitute a new class of monoamine reuptake inhibitors that exhibit varying levels of monoamine transporter activity and selectivity, and these ligands may serve as lead candidates in the discovery of new therapeutics to treat a range of neurological disorders including cocaine addiction.