Biomedical subjects

Jing Kong

Publications and source records attributed to Jing Kong.

At least 19 recordsLinked to original sources

PubMed2006

Dual-basis second-order Moller-Plesset perturbation theory: A reduced-cost reference for correlation calculations.

The resolution-of-the-identity (RI) approximation has placed the onus of the cost of a second-order Moller-Plesset (MP2) calculation on the underlying self-consistent field (SCF) calculation for many moderately sized molecules. A dual-basis approach to the SCF calculation, based on previous methods demonstrated for density functional theory, is combined with RI-MP2 calculations, and small basis subsets for cc-pVTZ, cc-pVQZ, and 6-311++G(3df,3pd) are presented. These subsets provide time savings of greater than 90%, with negligible errors in absolute and relative energies, compared to the associated full-basis counterpart. The method is tested with a series of rotational barriers, relative conformational energies of alanine tetrapeptides, as well as the full G3/99 molecular set. RI-MP2 calculations on alanine octapeptides (40 heavy atoms, 3460 basis functions), using cc-pVQZ, are presented. Results improve upon previous methods that diagonalize the virtual space separately.

Journal Article↗

PubMed2006

Advances in methods and algorithms in a modern quantum chemistry program package.

Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.

Algorithms↗

PubMed2006

Generating suspended single-walled carbon nanotubes across a large surface area via patterning self-assembled catalyst-containing block copolymer thin films.

Using self-assembled block copolymers as templates, catalytically active nanostructures with controlled size and space have been produced. A self-assembled polystyrene-b-polyferrocenylsilane thin film and monolayer of surface micelles of cobalt-complexed polystyrene-b-poly(2-vinylpyridine) are fully compatible with novolac-based conventional photoresists. Combining bottom-up self-assembly of catalyst-containing block copolymers with top-down microfabrication processing, plateaus covered with arrays of catalytically active nanostructures have been generated. Spatially selective growth of suspended single-walled carbon nanotubes over a large surface area has been achieved. Greatly enhanced Raman signals have been detected from the suspended tubes. This facile method of creating highly ordered catalyst nanostructures on top of posts enables the rational synthesis of suspended carbon nanotubes, thus facilitating the study of CNT properties by optical methods and enabling the fabrication of devices based on suspended CNTs.

Letter↗

PubMed2006

Electrochemistry at single-walled carbon nanotubes: the role of band structure and quantum capacitance.

We present a theoretical description of the kinetics of electrochemical charge transfer at single-walled carbon nanotube (SWNT) electrodes, explicitly taking into account the SWNT electronic band structure. SWNTs have a distinct and low density of electronic states (DOS), as expressed by a small value of the quantum capacitance. We show that this greatly affects the alignment and occupation of electronic states in voltammetric experiments and thus the electrode kinetics. We model electrochemistry at metallic and semiconducting SWNTs as well as at graphene by applying the Gerischer-Marcus model of electron transfer kinetics. We predict that the semiconducting or metallic SWNT band structure and its distinct van Hove singularities can be resolved in voltammetry, in a manner analogous to scanning tunneling spectroscopy. Consequently, SWNTs of different atomic structure yield different rate constants due to structure-dependent variations in the DOS. Interestingly, the rate of charge transfer does not necessarily vanish in the band gap of a semiconducting SWNT, due to significant contributions from states which are a few k(B)T away from the Fermi level. The combination of a nanometer critical dimension and the distinct band structure makes SWNTs a model system for studying the effect of the electronic structure of the electrode on electrochemical charge transfer.

Journal Article↗

PubMed2006

Efficient computation of the exchange-correlation contribution in the density functional theory through multiresolution.

A new algorithm is presented to improve the efficiency of the computation of exchange-correlation contributions, a major time-consuming step in a density functional theory (DFT) calculation. The new method, called multiresolution exchange correlation (mrXC), takes advantage of the variation in resolution among the Gaussian basis functions and shifts the calculation associated with low-resolution (smooth) basis function pairs to an even-spaced cubic grid. The cubic grid is much less dense in the vicinity of the nuclei than the atom-centered grid and the computation on the former is shown to be much more efficient than on the latter. MrXC does not alter the formalism of the current standard algorithm based on the atom-centered grid (ACG), but instead employs two fast and accurate transformations between the ACG and the cubic grid. Preliminary results with local density approximation have shown that mrXC yields three to five times improvement in efficiency with negligible error. The extension to DFT functionals with generalized gradient approximation is also briefly discussed.

Algorithms↗

PubMed2006

Expression of pituitary adenylate cyclase-activating polypeptide 1 and 2 receptor mRNA in gallbladder tissue of patients with gallstone or gallbladder polyps.

AIM: To detect the expression of pituitary adenylate cyclase-activating polypeptide receptor 1 (VPCAP1-R)and VPCAP2-R mRNA in gallbladder tissues of patients with gallstone or gallbladder polyps. METHODS: The expression of VPCAP1-R and VPCAP2-R mRNA in gallbladder tissues was detected in 25 patients with gallstone,8 patients with gallbladder polyps and 7 donors of liver transplantation by reverse transcription polymerase chain reaction (RT-PCR). RESULTS: The VPCAP2-R mRNA expression level in the control group (1.09+/-0.58) was lower than that in the gallbladder polyp group (1.64+/-0.56) and the gallstone group (1.55+/-0.45) (P<0.05) while the VPCAP1-R mRNA expression level in the control group (1.15+/-0.23) was not apparently different from that in the gallbladder polyp group (1.28+/-0.56) and the gallstone group (1.27+/-0.38). CONCLUSION: The abnormal expression of VPCAP2-R mRNA in gallbladder tissue may play a role in the formation of gallbladder stone and gallbladder polyps.

Adult↗

PubMed2006

[Study on relationship between HBV post-transcriptional regulatory element and response to IFN-alpha by using a reporter gene luciferase].

AIM: To identify the function of HBV post-transcriptional regulatory element(HPRE) in response to IFN-alpha by using the reporter gene luciferase (LUC). METHODS: The gene encoding LUC was obtained by PCR from the vector pGEM-luc and then cloned into the eukaryotic expression vector pcDNA3.0. The HPRE, HPREalphabeta(1) and HPREbeta(1)beta(2) fragments were amplified by PCR from HBV genome and then cloned into the recombinant vector pcDNA3.0-luc. These constructed plasmids were transfected into the human hepatoma cell line HepG2. The expression of LUC before and after the addition of IFN-alpha was detected by LUC assay system. RESULTS: The DNA sequencing analysis showed that the recombinant plasmids pcDNA3.0-luc, pcDNA3.0-luc-HPRE, pcDNA3.0-luc-HP-REalphabeta(1) and pcDNA3.0-luc-HPREbeta(1)beta(2) were successfully constructed. The results of LUC detection assay showed that HPRE, HPREalphabeta(1) and HPREbeta(1)beta(2) could enhance the expression of LUC before the addition of IFN-alpha. When IFN-alpha was added, only the fragment of HPRE, HPREbeta(1)beta(2) could significantly reduce the expression of LUC, but the expression of LUC was not influenced by HPREalphabeta(1). CONCLUSION: The functional element beta(2) of HPRE plays a more important part in response to IFN-alpha than the element alpha and beta(1), which may be valuable for further research on mechanisms of IFN-alpha therapy in HBV infection and function of HPRE binding protein.

Animals↗

PubMed2006

[Study on the coinfection of Hantavirus and Orientia tsutsugamushi in tissue cell culture].

OBJECTIVE: To investigate the possibility of Hantavirus (HV) and Orientia tsutsugamushi (Ot) coinfection in their hosts. METHODS: HV and Ot were used to infect Vero E6 cells cultured in vitro singly, simultaneously or successively. Genes of HV and Ot were identified in different generation cells with RT-PCR. RESULTS: Five experiment groups of infected Vero E6 cells were tested, the results were as follows: HV and Ot were both positive in infected Vero E6 cells passaged 2 times and the positive rate increased following the passaged times in HV and Ot infection groups, simultaneously or successively. However, in the groups which were infected with HV and Ot separately, the gene of HV or Ot could be detected in infected Vero E6 cells passaged only once and the positive rate increased following the times of the passaged. The positive rate was higher in the singly infected groups than in those infected simultaneously or successively. CONCLUSION: Coinfection of HV and Ot did exist in the hosts while HV and Ot could inhibit each other in the initial infection stage.

Animals↗

PubMed2005

Substrate-induced Raman frequency variation for single-walled carbon nanotubes.

We report on the monotonic Raman frequency shift and intensity variation when a laser spot moves along the same single-walled carbon nanotube (SWNT) for both the radial-breathing mode (RBM) and the G-band. Our substrates are Si wafers coated with thermal oxide, and trenches with widths of 1-80 mum are etched in the SiO2 by photolithography and reactive ion etching. SWNTs are grown by chemical vapor deposition and lie on top of the SiO2 and across the trenches. When the laser spot moves from the middle of the trench to the SiO2 region along the nanotube, we observe a clear upshift in the RBM and G-band frequencies and a decrease of intensity. The effect is more significant with large ( approximately 2 nm) diameter nanotubes and appears to be chirality dependent. These studies provide important information about environmental effects on single-walled carbon nanotube resonant Raman spectroscopy.

Journal Article↗

PubMed2005

A beta-galactose-specific lectin isolated from the marine worm Chaetopterus variopedatus possesses anti-HIV-1 activity.

A 30 kDa beta-galactose-specific lectin named CVL was isolated from the polychaete marine worm Chaetopterus variopedatus (Annelida) and its anti-HIV-1 activity in vitro was determined. Results showed that CVL inhibited cytopathic effect induced by HIV-1 and the production of viral p24 antigen. The EC(50) values were 0.0043 and 0.057 microM, respectively. Time-of-addition analysis of anti-HIV-1 activity indicated its action was at the early stage of virus replication. CVL could blocked the cell-to-cell fusion process of HIV infected and uninfected cells with an EC(50) of 0.073 microM. The inhibition of HIV-1 entry into host cells was demonstrated by using fluorescence-based real-time quantify PCR. At CVL concentration of 0.33 microM and 0.07 microM, 86% and 21% virus attachment were blocked, respectively. The anti-HIV-1 action of CVL might relate to blockade of HIV-1 entry into cells.

Animals↗

PubMed2005

[Effects of different drugs on the sphincter of Oddi motility: study with choledochoscope manometry].

OBJECTIVE: This study assessed the effects of narcotic analgesics, nitrates drugs, somatostatin analogues on human sphincter of Oddi motility and the antagonistic effects of nitrates drugs and anticholinergic agents against morphine measured by choledochoscope manometry. METHODS: 157 patients who had a T tube after cholecystectomy and choledochotomy were assessed by choledochoscope manometry. They were randomly divided into 5 groups. Sphincter of Oddi basal pressure (SOBP), amplitude (SOCA), frequency of contractions (SOF), duration of contractions (SOD), duodenal pressure (DP), common bile duct pressure (CBDP) were scored and analyzed. RESULTS: SOBP, SOCA and SOF increased after injection of morphine and Ap-237, CBDP increased after intramuscular administered morphine. No apparent change occurred after intramuscularly administered pethidine. SOBP and SOCA decreased after tramadol. After intravenous administration of stilamin in a dose of 250 microg/h, SOCA increased. After administration stilamin of 500 microg/h dose, SOCA and SOBP declined. After intravenous administration of sandostatin, CBDP increased obviously. BPOS and SOCA decreased significantly after administration of isosorbide dinitrate (ISDN) and glyceryl trinitrate (GTN), SOBP reduced evidently after application of pentaerythritol tetranitrate (PTN). SOBP, SOCA, SOF and CBDP increased evidently after injection of morphine. After associated application of ISDN and GTN, the four indications above decreased. As to associated application with PTN, SOCA and SOF decreased. After associated application of anisodamine or atropine, SOCA, SOBP declined, after injected buscopan, SOCA, SOBP, SOF all declined. CONCLUSION: The regular dose of morphine and Ap-237 shows excitatory effect on the sphincter of Oddi motility. Tramadol shows inhibitory effect on the sphincter of Oddi. The regular dose of pethidine and sandostatin shows no apparent effect on the sphincter of Oddi. Stilamin in low dose shows excitated effect on the sphincter of Oddi. Nitrates drugs show inhibited effects on SO motility. Nitrates drugs and anticholinergic agents can antagonize the excitated effect of morphine.

Adult↗

PubMed2005

Nitroester drug's effects and their antagonistic effects against morphine on human sphincter of Oddi motility.

AIM: To evaluate the effects of nitroester drugs on human sphincter of Oddi (SO) motility and their antagonistic effects against morphine which shows excitatory effect on Oddi's sphincter motility. METHODS: The effects of these drugs on SO were evaluated by means of choledochofiberoscopy manometry. A total of 67 patients having T-tubes after cholecystectomy and choledochotomy were involved in the study, they were randomly divided into glyceryl trinitrate (GTN) group, isosorbide dinitrate (ISDN) group, pentaerythritol tetranitrate (PTN) group, morphine associated with GTN group, morphine associated with ISDN group and morphine associated with PTN group. Basal pressure of Oddi's sphincter (BPOS), amplitude of phasic contractions (SOCA), frequency of phasic contractions (SOF), duration of phasic contractions (SOD), duodenal pressure (DP) and common bile duct pressure (CBDP) were scored and analyzed. Morphine was given intramuscularly while nitroester drugs were applied sublingually. RESULTS: BPOS and SOCA decreased significantly after administration of ISDN and GTN, BPOS reduced from 10.95+/-7.49 mmHg to 5.92+/-4.04 mmHg (P<0.05) evidently after application of PTN. BPOS increased from 7.37+/-5.58 mmHg to 16.60+/-13.87 mmHg, SOCA increased from 54.09+/-38.37 mmHg to 100.70+/-43.51 mmHg, SOF increased from 7.15+/-3.20 mmHg to 10.38+/-2.93 mmHg and CBDP increased 3.75+/-1.95 mmHg to 10.49+/-8.21 mmHg (P<0.01) evidently after injection of morphine. After associated application of ISDN and GTN, the four indications above decreased obviously. As for application associated with PTN, SOCA and SOF decreased separately from 100.64+/-44.99 mmHg to 66.17+/-35.88 mmHg and from 10.70+/-2.76 mmHg to 9.04+/-1.71 mmHg (P<0.05) markedly. CONCLUSION: The regular dose of GTN, ISDN and PTN showed inhibitory effect on SO motility, morphine showed excitatory effect on SO while GTN, ISDN and PTN could antagonize the effect of morphine. Among the three nitroester drugs, the effect of ISDN on SO was most significant.

Adult↗

PubMed2005

Orbital Kondo effect in carbon nanotubes.

Progress in the fabrication of nanometre-scale electronic devices is opening new opportunities to uncover deeper aspects of the Kondo effect--a characteristic phenomenon in the physics of strongly correlated electrons. Artificial single-impurity Kondo systems have been realized in various nanostructures, including semiconductor quantum dots, carbon nanotubes and individual molecules. The Kondo effect is usually regarded as a spin-related phenomenon, namely the coherent exchange of the spin between a localized state and a Fermi sea of delocalized electrons. In principle, however, the role of the spin could be replaced by other degrees of freedom, such as an orbital quantum number. Here we show that the unique electronic structure of carbon nanotubes enables the observation of a purely orbital Kondo effect. We use a magnetic field to tune spin-polarized states into orbital degeneracy and conclude that the orbital quantum number is conserved during tunnelling. When orbital and spin degeneracies are present simultaneously, we observe a strongly enhanced Kondo effect, with a multiple splitting of the Kondo resonance at finite field and predicted to obey a so-called SU4 symmetry.

Journal Article↗

PubMed2005

Fast and accurate Coulomb calculation with Gaussian functions.

Coulomb interaction is one of the major time-consuming components in a density functional theory (DFT) calculation. In the last decade, dramatic progresses have been made to improve the efficiency of Coulomb calculation, including continuous fast multipole method (CFMM) and J-engine method, all developed first inside Q-Chem. The most recent development is the advent of Fourier transform Coulomb method developed by Fusti-Molnar and Pulay, and an improved version of the method has been recently implemented in Q-Chem. It replaces the least efficient part of the previous Coulomb methods with an accurate numerical integration scheme that scales in O(N2) instead of O(N4) with the basis size. The result is a much smaller slope in the linear scaling with respect to the molecular size and we will demonstrate through a series of benchmark calculations that it speeds up the calculation of Coulomb energy by several folds over the efficient existing code, i.e., the combination of CFMM and J-engine, without loss of accuracy. Furthermore, we will show that it is complementary to the latter and together the three methods offer the best performance for Coulomb part of DFT calculations, making the DFT calculations affordable for very large systems involving thousands of basis functions.

Journal Article↗

PubMed2005

Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31G*/AMBER potential.

A combined DFT quantum mechanical and AMBER molecular mechanical potential (QM/MM) is presented for use in molecular modeling and molecular simulations of large biological systems. In our approach we evaluate Lennard-Jones parameters describing the interaction between the quantum mechanical (QM) part of a system, which is described at the B3LYP/6-31+G* level of theory, and the molecular mechanical (MM) part of the system, described by the AMBER force field. The Lennard-Jones parameters for this potential are obtained by calculating hydrogen bond energies and hydrogen bond geometries for a large set of bimolecular systems, in which one hydrogen bond monomer is described quantum mechanically and the other is treated molecular mechanically. We have investigated more than 100 different bimolecular systems, finding very good agreement between hydrogen bond energies and geometries obtained from the combined QM/MM calculations and results obtained at the QM level of theory, especially with respect to geometry. Therefore, based on the Lennard-Jones parameters obtained in our study, we anticipate that the B3LYP/6-31+G*/AMBER potential will be a precise tool to explore intermolecular interactions inside a protein environment.

Acetamides↗

PubMed2005

Individual single-walled carbon nanotubes as nanoelectrodes for electrochemistry.

We demonstrate the use of individual single-walled carbon nanotubes (SWNTs) as nanoelectrodes for electrochemistry. SWNTs were contacted by nanolithography, and cyclic voltammetry was performed in aqueous solutions. Interestingly, metallic and semiconducting SWNTs yielded similar steady-state voltammetric curves. We clarify this behavior through a model that considers the electronic structure of the SWNTs. Interfacial electron transfer to the SWNTs is observed to be very fast but can nonetheless be resolved due to the nanometer critical dimension of SWNTs. These studies demonstrate the potential of using a SWNT as a model carbon nanoelectrode for electrochemistry.

Journal Article↗

PubMed2005

Effects of somatostatin analogues on human sphincter of Oddi pressure.

BACKGROUND: Somatostatin, a neuropeptide and hormone, exists in the biliary tract of several species. The effects of somatostatin and its analogues on the sphincter of Oddi motility have been controversial. The aim of this study was to observe the action of stilamin and sandostatin on the sphincter of Oddi via choledochofiberscope manometry. METHODS: Twenty patients who had had "T" duct after cholecystectomy and choledochotomy were divided into 2 groups randomly: stilamin and sandostatin. They were subjected to manometry via a choledochofiberscope through the "T" duct tract. The following data recorded included duodenal pressure (DP), sphincter of Oddi basal pressure (SOBP), sphincter of Oddi contractive amplitude (SOCA), frequency of the sphincter of Oddi (SOF), duration of the sphincter of Oddi, and the common bile duct pressure (CBDP). RESULTS: After intravenous administration of stilamin at a dose of 250 microg/h, the mean SOCA increased from 89.18(26.50) to 128.57(54.21) mmHg (P<0.05). After the administration of stilamin at a dose of 500 microg/h the mean SOCA declined to 92.18(42.81) mmHg (P<0.05), and mean SOBP declined from 17.63(13.36) to 8.16(4.01) mmHg (P<0.05). Although SOF had declined from 9.25(2.45) to 7.46(1.52) n/min, it was not significantly influenced. After intravenous administration of sandostatin at a dose of 100 microg, the mean CBDP increased obviously. CONCLUSIONS: Intravenous administration of stilamin at a dose of 250 microg/h stimulates the motility of the sphincter of Oddi whereas the injection of stilamin at a dose of 500 microg/h inhibits its motility. Intravenous injection of sandostatin of 100 mug has no effect on the sphincter of Oddi.

Adult↗

PubMed2004

Effects of narcotic analgesic drugs on human Oddi's sphincter motility.

AIM: To assess the effects of intramuscular analgesics (morphine, Ap-237, pethidine and tramadol) on human Oddi's sphincter motility with choledochoscope manometry. METHODS: A total of 70 patients having T tubes after cholecystectomy and choledochotomy were assessed by choledochoscope manometry. They were randomly divided into morphine group, Ap-237 group, pethidine group and tramadol group. Basal pressure of Oddi's sphincter (BPOS), amplitude of phasic contractions (SOCA), frequency of phasic contractions (SOF), duration of phasic contractions(SOD), duodenal pressure (DP) and common bile duct pressure (CBDP) were scored and analyzed. All narcotic analgesic drugs were administered intramuscularly. RESULTS: Levels of BPOS, SOCA and SOF were increased after injection of morphine and Ap-237 (P<0.05), level of CBDP was increased from 4.97+/-3.87 mmHg to 8.62+/-7.43 mmHg (10 min later) and 7.32+/-5.95 mmHg (20 min later) after injection of morphine (P<0.01). No apparent change occurred after intramuscular injection of pethidine. Level of BPOS was increased from 7.01+/-5.50 mmHg to 2.87+/-2.78 mmHg 10 min after injection of tramadol and SOCA was decreased from 63.34+/-35.29 mmHg to 45.90+/-27.86 mmHg (10 min later,P<0.05) and 35.97+/-24.30 (20 min later,P<0.01) after administration of tramadol. CONCLUSION: All these findings indicate that Oddi's sphincter manometry via choledochoscope is a practical and new way to study the dynamics of Oddi' s sphincter. The regular dose of morphine and Ap-237 could increase BPOS, SOF and SOCA. Morphine could increase the level of CBDP, demonstrating an excitatory effect on the sphincter of Oddi. Pethidine had no effect on Oddi's sphincter motility. Tramadol shows an inhibitory effect on the motility of the sphincter of Oddi and decreases levels of BPOS and SOCA.

Adult↗