Levy Constrained Search in Fock Space: An Alternative Approach to Noninteger Electron NumberSCI北大核心CSCD

By extending the Levy wavefunction constrained search to Fock Space,one can define a wavefunction constrained search for electron densities in systems having noninteger number of electrons.For pure-state v-representable densities,the results are equivalent to what one would obtain with the zero-temperature grand canonical ensemble.In other cases,the wavefunction constrained search in Fock space presents an upper bound to the grand canonical ensemble functional.One advantage of the Fock-space wavefunction constrained search functional over the zero-temperature grand-canonical ensemble constrained search functional is that certain specific excited states(i.e.,those that are not ground-statev-representable) are the stationary points of the Fock-space functional.However,a potential disadvantage of the Fock-space constrained search functional is that it is not convex.     

Optimisation of a flow injection system with electrochemical detection using the desirability function: Application to the determination of hydroquinone in cosmetics

A procedure is proposed in which the determination of hydroquinone using a flow injection system with electrochemical detection is described. Size and coefficient of variation of the signal are optimised by a desirability function and a central composite design. The robustness of the optimum reached in the optimisation step is evaluated by means a Plackett-Burman design. The optimised FIA system is able to determine hydroquinone with a minimum detectable net concentration of 10 μg l⁻¹ with a false positive probability of 0.05 and a false negative probability less than 0.05. In samples of bleaching cream, the proposed procedure has a recovery of 102.2% with standard deviation of 4.4% and a relative error of 6.2%.     

Rigid-body dynamics in the isothermal-isobaric ensemble: a test on the accuracy and computational efficiency

We have developed a time-reversible rigid-body (rRB) molecular dynamics algorithm in the isothermal-isobaric (NPT) ensemble. The algorithm is an extension of rigid-body dynamics [Matubayasi and Nakahara, J Chem Phys 1999, 110, 3291] to the NPT ensemble on the basis of non-Hamiltonian statistical mechanics [Martyna, G. J. et al., J Chem Phys 1994, 101, 4177]. A series of MD simulations of water as well as fully hydrated lipid bilayer systems have been undertaken to investigate the accuracy and efficiency of the algorithm. The rRB algorithm was shown to be superior to the state-of-the-art constraint-dynamics algorithm SHAKE/RATTLE/ROLL, with respect to computational efficiency. However, it was revealed that both algorithms produced accurate trajectories of molecules in the NPT as well as NVT ensembles, as long as a reasonably short time step was used. A couple of multiple time-step (MTS) integration schemes were also examined. The advantage of the rRB algorithm for computational efficiency increased when the MD simulation was carried out using MTS on parallel processing computer systems; total computer time for MTS-MD of a lipid bilayer using 64 processors was reduced by about 40% using rRB instead of SHAKE/RATTLE/ROLL.     

Simple algorithm for isothermal-isobaric molecular dynamics

We review principles of non-Hamiltonian statistical mechanics and present a new set of equations and integration algorithm for isothermal-isobaric dynamics. The chief advantage of the present scheme is that it is somewhat simpler than previous methods. We perform numerical simulations to test the accuracy of the algorithm and compare its stability to that of a "gold standard," a symplectic integrator for Hamiltonian dynamics of the same system. The stability of the isothermal-isobaric algorithm is comparable to the stability of the symplectic integrator.     

TargetATPsite: A template‐free method for ATP‐binding sites prediction with residue evolution image sparse representation and classifier ensemble

Understanding the interactions between proteins and ligands is critical for protein function annotations and drug discovery. We report a new sequence‐based template‐free predictor (TargetATPsite) to identify the Adenosine‐5′‐triphosphate (ATP) binding sites with machine‐learning approaches. Two steps are implemented in TargetATPsite: binding residues and pockets predictions, respectively. To predict the binding residues, a novel image sparse representation technique is proposed to encode residue evolution information treated as the input features. An ensemble classifier constructed based on support vector machines (SVM) from multiple random under‐samplings is used as the prediction model, which is effective for dealing with imbalance phenomenon between the positive and negative training samples. Compared with the existing ATP‐specific sequence‐based predictors, TargetATPsite is featured by the second step of possessing the capability of further identifying the binding pockets from the predicted binding residues through a spatial clustering algorithm. Experimental results on three benchmark datasets demonstrate the efficacy of TargetATPsite. © 2013 Wiley Periodicals, Inc.     

Orbital Energy Order and the Through Bond Interaction in Homonuclear Diatomic Molecules

The homonuclear diatomic molecules are the simplest systems having both the σ framework and the lone pair orbitals n_a and _b for investigating their through space and through bond interaction. The striking orbital energy order n_g～ n_a+ n_b > n_n ～ n_a - n_b has been accounted for by the through bond interaction. However, when the p-content in the lone pair orbitals n_a and n_b decreases, one may have the reverse orbital energy order: n_g < n_g. A reverse orbital energy order has been found in F₂ and Cl₂, whose n_a and n_b are almost pure s-type atomic orbitals. The reverse order also occurs in molecule N₂ when the internuclear distance is larger man 1.5 Å. It is also found that the detail through space and through bond interaction and the eventual orbital energy order for n_g and n_u can be accounted for by the Fock operator within the localized molecular orbital space.     

多壁碳纳米管储氢的物理吸附特性

The physisorption of hydrogen stored in armchair multi-walled carbon nanotubes (MWCNTs) is simulated by the grand canonical Monte Carlo (GCMC) method on the condition of 10 MPa at normalt emperature. Hydrogen-hydrogen and hydrogen-carbon interactions are both modeled with Lennard-Jones potential. The hydrogen storage in double-walled carbon-nanotubes (DWCNTs) has been investigated on the condition that the internal or external radius is changed while the other radius remains constant. The results show that hydrogen molecules are mostly absorbed near the tube walls, and the hydrogens to rage capacityisim proved effectively when the difference between the internal radius and the external radius increases from 0.34 to 0.61 or 0.88 nm. Its simple theoretic explanation also is given. Further more, the capacity of hydrogen physisorbed in there-walled carbon nanotubes (TWCNTs) is calculated when the wall-wall distance is 0.34, 0.61 and 0.88 nm respectively. Then its hydrogen storage capacity is compared with that of single-walled carbon nanotubes (SWCNTs) and DWCNTs, and it is discovered that the capacity of hydrogen physisorbed in MWCNTs decreases as the number of wall increases.     

甲硫醇和氢原子反应的从头算直接动力学

利用双水平直接动力学方法对反应CH3SH+H的微观机理和动力学性质进行了理论研究.对于此反应的三个反应通道,即—SH和—CH3基团上的两个氢提取通道及一个取代通道,在MP2/6-311+G(d,p)水平上优化得到了各稳定点的结构及振动频率,并在G3(MP2)水平上进行了单点能量计算以获得更精确的能量信息;在此基础上运用结合小曲率隧道效应校正的变分过渡态理论(CVT/SCT)计算了各反应通道在220-1000 K温度区间的速率常数.计算结果表明提取—SH基团上H的反应通道R1在整个反应温度区间都是主要通道,而随着温度的升高,低温下的次要反应通道——取代通道R3变得越来越重要,并且在高温下将成为一个竞争的反应通道;提取—CH3基团上H的反应通道(R2)由于具有较高的反应能垒,因而,其对总反应速率常数的贡献可以忽略.计算得到的总反应速率常数与已有的实验值符合得很好,进而我们预测了该反应在220-1000 K温度范围内速率常数的表达式为:k=5.00×10-18T2.39exp(-119.81/T),为将来的实验研究提供参考.