Biomedical subjects

Qian Shu Li

Publications and source records attributed to Qian Shu Li.

15 recordsLinked to original sources

PubMed2006

Critical threshold of noise-induced energy transduction in molecular machinery system.

Responses of energy transduction of molecular machinery to random perturbation were investigated at the conditions where the system stayed near the bifurcation point. It was found that noise-induced oscillation (NIO) could occur. But how far from bifurcation point could one get the admissible region of NIO? We proposed and demonstrated numerically that there existed a critical threshold of NIO for each fixed noise intensity. Furthermore, it was found that noise intensity was a key factor for the determination of critical threshold. Finally, the detailed bifurcation diagram depending on noise intensity was replotted.

Journal Article↗

PubMed2006

Enhancement and sustainment of internal stochastic resonance in unidirectional coupled neural system.

In this study, the collective dynamical behavior of two unidirectionally, linearly coupled neurons was investigated. Our investigation illustrates that, depending on the coupling strength, the internal stochastic resonance (ISR) effect observed in one of the two neurons could be amplified or sustained by the other. The amplification of ISR is enhanced as the coupling strength is increased from 0. However, when the coupling strength is increased above a certain level, the amplification of ISR is reduced, implicating that there exists an optimal coupling strength for the information flow between two neurons. As the coupling strength is increased further, i.e., above the critical level, synchronization of the two subsystems is achieved, yet the two subsystems exhibit the same magnitude response to the external noise, suggesting that the information transmission among coupled subunits could not be improved by further enhancing their coupling strength. And similar phenomena could also be obtained for the nonidentical case.

Journal Article↗

PubMed2005

Direct dynamics study on the hydrogen abstraction reaction CH2O + HO2 --> CHO + H2O2.

We present a direct ab initio dynamics study on the hydrogen abstraction reaction CH2O + HO2 --> CHO + H2O2, which is predicted to have four possible reaction channels caused by different attacking orientations of HO2 radical to CH2O. The structures and frequencies at the stationary points and the points along the minimum energy paths (MEPs) of the four reaction channels are calculated at the B3LYP/cc-pVTZ level of theory. Energetic information of stationary points and the points along the MEPs is further refined by means of some single-point multilevel energy calculations (HL). The rate constants of these channels are calculated using the improved canonical variational transition-state theory with the small-curvature tunneling correction (ICVT/SCT) method. The calculated results show that, in the whole temperature range, the more favorable reaction channels are Channels 1 and 3. The total ICVT/SCT rate constants of the four channels at the HL//B3LYP/cc-pVTZ level of theory are in good agreement with the available experiment data over the measured temperature ranges, and the corresponding three-parameter expression is k(ICVT/SCT) = 3.13 x 10(-20) T(2.70) exp(-11.52/RT) cm3 mole(-1) s(-1) in the temperature range of 250-3000 K. Additionally, the flexibility of the dihedral angle of H2O2 is also discussed to explain the different experimental values.

Journal Article↗

PubMed2005

Density functional theoretical study of a series of binary azides M(N3)n (n = 3, 4).

Geometrical structures of a series of binary azides M(N3)n (M = elements in groups 3 and 13 (n = 3) and in groups 4 and 14 (n = 4)) were investigated at the B3LYP/6-311+G level of theory. Our calculations found that binary group 3 triazides M(N3)3 (M = Sc, Y, La) and binary group 4 tetraazides M(N3)4 (M = Ti, Zr, Hf) turn out to be stable with all frequencies real having a similar linear M-N-NN structural feature, as previously reported for M(N3)4 (M = Ti, Zr, Hf). However, binary azides of group 13 M(N3)3 (M = B, Al, Ga, In, Tl) and group 14 elements M(N3)4 (C, Si, Ge, Sn, Pb) with bent M-N-NN bond angles differ obviously from binary group 3 and 4 azides in geometrical structure. These facts are mainly explained by the difference in electronic density overlap between the central atom and the alpha-N atoms of the azido groups. Two lone-pair electrons on the sp hybridization alpha-N atoms in the binary group 3 and 4 azides donate electron density into two empty d orbitals of the central transition metal atom and a pair of valence bonding electrons, resulting in the alpha-N atoms acting as a tridentate ligand. The sp2 hybridization alpha-N atoms of the binary group 13 and 14 azides only give one valence electron to form one valence bonding electron pair acting virtually as monodentate donors.

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PubMed2005

Turing pattern formation in coupled reaction-diffusion system with distributed delays.

Turing pattern formation in coupled two-layer system with distributed delayed is investigated. Numerical simulations prove that, when the coupling is weak, it can apparently accelerate the formation process and enhance the spatial amplitude of the pattern. When it is strong, it will prolong the formation process or even inhibit the pattern and turn the whole system into bulk oscillatory state by its influence on the transient oscillatory state. If the coupling covers only part of the system, Turing pattern can be prominently oriented according to the shape of the coupling area at tiny coupling strength. However, if the coupling is too strong, the Turing pattern may also be destroyed. This means that in coupled systems, the delay effect in the cross-layer signal transfer may significantly influence the spatial character and/or the evolution dynamics in Turing pattern formation, even to destroy the pattern. This work is of practical significance in the study of Turing pattern in biosystems, where bilayer membranes or multilayer tissues are often found.

Chemistry, Physical↗

PubMed2005

The reaction of the aminoboranylidene-iminoborane isomerization: a CASSCF direct dynamics study.

The barrier and the potential-energy surface of the isomerization from aminoboranylidene (BNH2) to iminoborane (HBNH) have been studied using complete active space self-consistent field (CASSCF) with the 6-31 + G(d, p) basis set and higher-level energy methods. The rate constants of the isomerization reaction are reported by employing the direct ab initio dynamics method. The geometries of all the stationary points were optimized using the B3LYP and CCSD methods with the cc-pVTZ and cc-pVQZ basis sets. The information along the intrinsic reaction coordinate (IRC) was also calculated at the CASSCF/6-31 + G (d,p) level of theory. The energies were refined at the G3, G3MP2, G3MP2B3, CBS-Q, CBS-QB3, and two high-level (HL) methods based on the geometries optimized using CASSCF/6-31 + G(d,p). The rate constants were evaluated using conventional transition-state theory (TST), canonical variational transition-state theory (CVT), and canonical variational transition-state theory with small curvature tunneling correction (CVT/SCT) and conventional transition-state theory with Eckart tunneling correction (TST/Eckart). According to the calculated results, we conclude that the tunneling effect is very important to this isomerization reaction.

Boranes↗

PubMed2004

Direct ab initio dynamics studies of the hydrogen abstraction reactions of hydrogen atom with n-propyl radical and isopropyl radical.

The kinetics of the hydrogen abstraction reactions of hydrogen atom with n-propyl radical and isopropyl radical were studied using the direct ab initio dynamics approach. BHandHLYP/cc-pVDZ method was employed to optimize the geometries of stationary points as well as the points on the minimum energy path (MEP). The energies of all the points for the two reactions were further refined at the QCISD(T)/cc-pVTZ level of theory. No barrier was found at the QCISD(T)/cc-pVTZ//BHandHLYP/cc-pVDZ level of theory for both reactions. The forward and reverse rate constants were evaluated with both canonical variational transition state theory (CVT) and microcanonical variational transition state theory (mu VT) in the temperature range of 300-2,500 K. The fitted three-parameter Arrhenius expression of the calculated CVT rate constants at the QCISD(T)/cc-pVTZ//BHandHLYP/cc-pVDZ level of theory are k(CVT) (n-C3H7) = 1.68 x 10(-14) T(0.84) e((319.5/T)) cm3 molecule(-1) s(-1) and k(CVT) (iso-C3H7)=4.99 x 10(-14) T(0.90) e((159.5/T)) cm3 molecule(-1) s(-1) for reactions of n-C3H7 + H and iso-C3H7 + H, respectively, which are in good agreement with available literature data. The variational effects were analysed.

Alkenes↗

PubMed2004

Direct ab initio dynamics study on the rate constants and kinetics isotope effects of CH(3)O+H-->CH(2)O+H(2) reaction.

We present a direct ab initio dynamics study of thermal rate constants of the hydrogen abstraction reaction of CH(3)O+H-->CH(2)O+H(2). The unrestricted Becke's half-and-half hybrid functional using the Lee-Yang-Parr correlation functional with Dunning's correlation consistent polarized valence double-zeta basis set, the unrestricted quadratic configuration interaction calculation including single and double substitutions with Dunning's correlation consistent polarized valence double-zeta basis set, and the unrestricted quadratic configuration interaction calculation including single and double substitutions with a triples contribution with Dunning's correlation consistent polarized valence triple-zeta basis set methods were employed to optimize the structures and to calculate frequencies for all stationary points. Minimum energy paths were obtained by the unrestricted Becke's half-and-half hybrid functional using the Lee-Yang-Parr correlation functional and the unrestricted quadratic configuration interaction calculation including single and double substitutions with the same Dunning's correlation consistent polarized valence double-zeta basis set levels of theory. No barrier is found at the unrestricted Becke's half-and-half hybrid functional using the Lee-Yang-Parr correlation functional with Dunning's correlation consistent polarized valence double-zeta basis set level of theory in contrast to a small barrier of 1.43 kcal mol(-1) at the unrestricted quadratic configuration interaction calculation including single and double substitutions with Dunning's correlation consistent polarized valence double-zeta basis set level of theory. In particular, the barrier vanishes as the energies along the minimum energy path MEP are refined at the unrestricted quadratic configuration interaction calculation including single and double substitutions with a triples contribution with Dunning's correlation consistent polarized valence triple-zeta basis set level of theory. Smaller barriers of 0.47 and 0.17 kcal mol(-1) were obtained at the unrestricted quadratic configuration interaction calculation including single and double substitutions with a triples contribution with Dunning's correlation consistent polarized valence triple-zeta basis set and the unrestricted quadratic configuration interaction calculation including single and double substitutions with a triples contribution with Dunning's correlation consistent polarized valence triple-zeta basis set based on the geometries at the unrestricted quadratic configuration interaction calculation including single and double substitutions with Dunning's correlation consistent polarized valence triple-zeta basis set levels of theory, respectively. The forward rate constants are evaluated with the canonical variational transition state theory in the temperature range of 300-2500 K. The calculated forward rate constants at the unrestricted quadratic configuration interaction calculation including single and double substitutions with a triples contribution with Dunning's correlation consistent polarized valence triple-zeta basis set based on the geometries at the unrestricted quadratic configuration interaction calculation including single and double substitutions with Dunning's correlation consistent polarized valence double-zeta basis set level of theory are in good agreement with the available experimental data. The kinetic isotope effects are estimated.

Journal Article↗

PubMed2004

Controlling of explicit internal signal stochastic resonance by external signal.

Explicit internal signal stochastic resonance (EISSR) is investigated in a model of energy transduction of molecular machinery when noise is added to the region of oscillation in the presence of external signal (ES). It is found that EISSR could be controlled, i.e., enhanced or suppressed by adjusting frequency (omega(e)) and amplitude (A) of ES, and that there exits an optimal frequency for ES, which makes EISSR strength reach the maximum. Meanwhile, a critical amplitude (A(c)) is found, which is a threshold of occurrence of EISSR. Finally, the difference and similarity between EISSR and IISSR (implicit internal signal stochastic resonance) are discussed.

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PubMed2004

Control of Turing pattern by weak spatial perturbation.

The control of Turing pattern formation by weak spatial perturbation is investigated. The weak spatial perturbation added before Turing pattern stabilization is found to show prominent spatial orientation effect. The control process of perturbation to Turing patterns is tracked. The effect of perturbation factors, such as amplitude and imposing time are also discussed.

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PubMed2004

Internal stochastic resonance under two-parameter modulation in intercellular calcium ion oscillations.

Internal stochastic resonance (ISR) in a model of intercellular calcium ion oscillations is investigated under the modulation of two parameters, viz., degree of extracellular stimulation (beta) and leak rate (k(f)). ISR can occur when either beta or k(f) is subjected to a noise. Internal stochastic biresonance (ISBR) can occur when noise is added to the two parameters simultaneously. The distance to the bifurcation point is found to be able to enhance or suppress the ISBR, and to affect the number of peaks of ISR.

Journal Article↗

PubMed2004

Control of Turing pattern formation by delayed feedback.

The effect of the global delayed feedback technique on Turing pattern formation is investigated in the modified Lengyel-Epstein two-variable model. Feedback intensity, delay time, and feedback-imposing time (the period of time that feedback is present in the system) are all found to be of significant influence on Turing pattern formation time. Under appropriate parameter settings, delayed feedback could suppress or induce the Turing pattern if the feedback intensity is strong enough.

Journal Article↗

PubMed2004

Internal stochastic resonance in two coupled liquid membrane oscillators.

Internal stochastic resonance (ISR) is investigated in two coupled liquid membrane oscillators when only one oscillator is subjected to environmental noise in the absence of an external signal. Comparing the responses of both subsystems, it is found that enhancement or suppression of ISR for each oscillator depends on the coupling strength, that synchronization of the two oscillators can occur only at strong coupling strength, and that ISR without tuning can also occur under certain conditions in the above-mentioned models.

Journal Article↗

PubMed2004

A dual-level ab initio and hybrid density functional theory dynamics study on the unimolecular decomposition reaction C2H5O-->CH2O + CH3.

We present a direct ab initio and hybrid density functional theory dynamics study of the thermal rate constants of the unimolecular decomposition reaction of C2H5O-->CH2O + CH3 at a high-pressure limit. MPW1K/6-31+G(d,p), MP2/6-31+G(d,p), and MP2(full)/6-31G(d) methods were employed to optimize the geometries of all stationary points and to calculate the minimum energy path (MEP). The energies of all the stationary points were refined at a series of multicoefficient and multilevel methods. Among all methods, the QCISD(T)/aug-cc-pVTZ energies are in good agreement with the available experimental data. The rate constants were evaluated based on the energetics from the QCISD(T)/aug-cc-pVTZ//MPW1K/6-31+G(d,p) level of theory using both microcanonical variational transition state theory (microVT) and RRKM theory with the Eckart tunneling correction in the temperature range of 300-2500 K. The calculated rate constants at the QCISD(T)/aug-cc-pVTZ/MPW1K/6-31+G(d,p) level of theory are in good consistent with experimental data. The fitted three-parameter Arrhenius expression from the microVT/Eckart rate constants in the temperature range 200-2500 K is k = 2.52 x 10(12)T(0.41)e(-8894.0/T) s(-1). The falloff curves of pressure-dependent rate constants are performed using master-equation method within the temperature range of 391-471 K. The calculated results are in good agreement with the available experimental data.

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PubMed2003

Structures and stability of N13+ and N13- clusters.

The structures and stabilities of eleven N13+ and N13- isomers have been investigated with second-order Moller-Plesset (MP2) and density functional theory (DFT) methods. Five N13+ isomers and six N13- isomers are all reasonable local minima on their potential energy hypersurfaces. The most stable N13+ cation is structure C-2 with C2v symmetry, which contains a pentazole ring and two N4 open chains. It is different from those of the N7+ and N9+ clusters, but similar to the N11+ cluster. Meanwhile, the most stable N13- structure A-2 is composed of a pentazole ring and a six-membered ring connected by two nitrogen atoms. It is not only different from those of the N7- and N9- clusters, but also from the N11- cluster. The decomposition pathways of structures C-2 and A-2 were investigated at the B3LYP/(aug)-cc-pVDZ level. From the barrier heights of the structures C-2 and A-2 decomposition processes, it is suggested that C-2 is difficult to observe experimentally and A-2 may be observed as a short-lived species.

Cations↗