Biomedical subjects

C Z Wang

Publications and source records attributed to C Z Wang.

At least 19 recordsLinked to original sources

PubMed2006

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.

Journal Article↗

PubMed2006

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.

Journal Article↗

PubMed2006

Dynamics of the trimeric AcrB transporter protein inferred from a B-factor analysis of the crystal structure.

The Escherichia coli AcrB multidrug transporter recognizes a wide range of toxic chemicals and actively extrudes them from cells. The molecular basis of multidrug transport in AcrB remains unknown. Herein, we describe normal mode analyses to study important regions for drug recognition and extrusion in this transporter. Based on the X-ray structure of AcrB, an elastic network model has been able to correct errors arising from crystal imperfection in the experimental B-factors. The results allow us to understand the functional dynamics of this membrane protein. It is expected that this technique can be applied to other membrane proteins with known structures.

Crystallography↗

PubMed2006

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.

Cell Division↗

PubMed2005

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)].

Journal Article↗

PubMed2005

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.

Adsorption↗

PubMed2005

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.

Journal Article↗

PubMed2005

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.

Journal Article↗

PubMed2004

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.

Base Sequence↗

PubMed2004

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.

Journal Article↗

PubMed2004

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.

Journal Article↗

PubMed2003

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.

Journal Article↗

PubMed2001

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.

Animals↗

PubMed2001

[Effect of Tripterygium wilfordii on Th1, Th2 cytokines production in asthma patients].

OBJECTIVE: To observe the effect of Tripterygium wilfordii on Th1, Th2 cytokines in asthma patients for further study on the therapeutic mechanism. METHODS: Twelve patients of middle or severe asthma were treated by Tripterygium polyglucoside 40 mg or 60 mg daily for 4 weeks. Blood of patients was colleted before and after treatment for serum and peripherol blood mononuclear cells (PBMC) preparation. The prepared PBMCs were stimulted in vitro with Concanavalin A (ConA) for 6 hrs and followed by culturing with Triptolide for 24 hrs and then the supernatant was collected. The concentration of interleukin-2(IL-2), -4(IL-4), -5(IL-5) and interferon-gamma(IFN-gamma) in serum and in the supernatant were detected by enzyme-linked immunosorbent assay (ELISA). RESULTS: Serum levels of IL-2, IL-4 and IL-5 of patients decreased significantly after treatment of Tripterygium polyglucoside (P < 0.01), but IFN-gamma level was under the detection sensitivity both before and after treatment. Triptolide could inhibit PBMC to secrete IL-2, IL-4 and IL-5 in vitro (P < 0.01), but IFN-gamma was also under the detection sensitivity. CONCLUSION: The marked inhibition of Th2 cytokine expression by Tripterygium was the important mechanism of it in treating asthma. But the fact that Tripterygium also showed inhibition on Th1 cytokine indicated that the inhibition of Tripterygium on Th2 and Th1 cytokines was non-specific.

Adult↗

PubMed2000

Unique dynamic appearance of a Ge-Si ad-dimer on Si(001).

We carry out a comparative study of the energetics and dynamics of Si-Si, Ge-Ge, and Ge-Si ad-dimers on top of a dimer row in the Si(001) surface, using first-principles calculations. The dynamic appearance of a Ge-Si dimer is distinctively different from that of a Si-Si or Ge-Ge dimer, providing a unique way for its identification by scanning tunneling microscopy (STM). Its "rocking" motion, observed in STM, actually reflects a 180 degrees rotation of the dimer, involving a piecewise-rotation mechanism. The calculated energy barrier of 0.74 eV is in good agreement with the experimental value of 0.82 eV.

Journal Article↗

PubMed2000

The Na+-driven Cl-/HCO3- exchanger. Cloning, tissue distribution, and functional characterization.

The Na(+)-driven Cl(-)/HCO(3)(-) exchanger is an important regulator of intracellular pH in various cells, but its molecular basis has not been determined. We show here the primary structure, tissue distribution, and functional characterization of Na(+)-driven chloride/bicarbonate exchanger (designated NCBE) cloned from the insulin-secreting cell line MIN6 cDNA library. The NCBE protein consists of 1088 amino acids having 74, 72, and 55% amino acid identity to the human skeletal muscle, rat smooth muscle, and human kidney sodium bicarbonate cotransporter, respectively. The protein has 10 putative membrane-spanning regions. NCBE mRNA is expressed at high levels in the brain and the mouse insulinoma cell line MIN6 and at low levels in the pituitary, testis, kidney, and ileum. Functional analyses of the NCBE protein expressed in Xenopus laevis oocytes and HEK293 cells demonstrate that it transports extracellular Na(+) and HCO(3)(-) into cells in exchange for intracellular Cl(-) and H(+), thus raising the intracellular pH. Thus, we conclude that NCBE is a Na(+)-driven Cl(-)/HCO(3)(-) exchanger that regulates intracellular pH in native cells.

Animals↗

PubMed2000

Laser-induced graphitization on a diamond (111) surface.

We report an atomistic simulation study of laser-induced graphitization on the diamond (111) surface. Our simulation results show that the diamond to graphite transition occurs along different pathways depending on the length of the laser pulse being used. Under nanosecond or longer laser pulses, graphitization propagates vertically into bulk layers, leading to the formation of diamond-graphite interfaces after the laser treatment. By contrast, with femtosecond (0.2-0.5 ps) laser pulses, graphitization of the surface occurs layer by layer, resulting in a clean diamond surface after the ablation. This atomistic picture provides an explanation of recent experimental observations.

Journal Article↗

PubMed2000

The interactions between soybean trypsin inhibitor and delta-endotoxin of Bacillus thuringiensis in Helicoverpa armigera larva.

No significant difference in larval mortality was observed when a sublethal dose of Bacillus thuringiensis (Bt) var. kurstaki HD-1 crystal was supplemented with soybean trypsin inhibitor (STI) in the artificial diet fed to Helicoverpa armigera in the laboratory, but supplementing a nonlethal dose of crystal with STI in the diet led to a pronounced reduction of larval growth. This concentration of crystal and two lower concentrations of STI alone had no significant effects on larval growth. The results of substrate-gel electrophoresis demonstrated that the proteases in the H. armigera midgut fluid responsible for the degradation of protoxin consisted of at least four proteases with molecular weights of 71, 49, 36, and 30 kDa. All four proteases could utilize casein also as the substrate. When larvae were fed with STI or Bt + STI, the proteolytic activities of the 49-kDa enzyme disappeared, and the activities of the other three enzymes were reduced. Enzyme assays also indicated that feeding larvae with diets containing Bt, STI, or Bt + STI significantly decreased the specific activities of larval general proteases and the trypsin-like enzyme. The protein concentration of midgut fluid was elevated, especially in the larvae fed on the diets containing STI and Bt + STI. Both in vitro and in vivo studies showed that the degradation of protoxin and toxin could be inhibited by soybean trypsin inhibitors, but when the incubation time was prolonged, the protoxin could be degraded completely, while the degradation of toxin was inhibited further. This suggested that the retention time of toxins in the larval midgut was extended and synergism between insecticidal crystal protein and soybean trypsin inhibitor occurred, which showed as the inhibition of H. armigera larval growth.

Animals↗