Study of Endogen Substrates,Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics

Multidrug resistance protein-4 (MRP4) belongs to the ABC transporter superfamily and promotes the transport of xenobiotics including drugs. A non-synonymous single nucleotide polymorphisms (nsSNPs) in the ABCC4 gene can promote changes in the structure and function of MRP4. In this work, the interaction of certain endogen substrates, drug substrates, and inhibitors with wild type-MRP4 (WT-MRP4) and its variants G187W and Y556C were studied to determine differences in the intermolecular interactions and affinity related to SNPs using protein threading modeling, molecular docking, all-atom, coarse grained, and umbrella sampling molecular dynamics simulations (AA-MDS and CG-MDS, respectively). The results showed that the three MRP4 structures had significantly different conformations at given sites, leading to differences in the docking scores (DS) and binding sites of three different groups of molecules. Folic acid (FA) had the highest variation in DS on G187W concerning WT-MRP4. WT-MRP4, G187W, Y556C, and FA had different conformations through 25 ns AA-MD. Umbrella sampling simulations indicated that the Y556C-FA complex was the most stable one with or without ATP. In Y556C, the cyclic adenosine monophosphate (cAMP) and ceefourin-1 binding sites are located out of the entrance of the inner cavity, which suggests that both cAMP and ceefourin-1 may not be transported. The binding site for cAMP and ceefourin-1 is quite similar and the affinity (binding energy) of ceefourin-1 to WT-MRP4, G187W, and Y556C is greater than the affinity of cAMP, which may suggest that ceefourin-1 works as a competitive inhibitor. In conclusion, the nsSNPs G187W and Y556C lead to changes in protein conformation, which modifies the ligand binding site, DS, and binding energy.     

合肥光源高亮度模式Lattice设计

介绍了一组合肥光源新高亮度模式的Lattice. 新的设计维持了储存环上所有元件和光束线位置不变,也没有加入新的元件. 取得了较低发射度. 所有直线节处的垂直方向β函数值都很小，适合插入件的运行. 跟踪计算表明新Lattice具有足够大的动力学孔径用于注入和储存粒子.     

蕴涵代数与BCK代数

系统研究 Fuzzy蕴涵代数与 BCK代数之间的关系 ,给出 MV代数与 BCK代数之间的联系 ,建立正则 FI代数和对合 BCK代数的对偶代数     

Generalized lattice model of liquid state and its relation to Ginzburg–Landau theory

Basic principles of the generalized lattice model of multicomponent condensed systems are formulated. Short-range parts of interatomic interactions are taken into account by means of the geometric constraints method. Long-range parts of the interactions are taken into account in mean field approximation. The expression for Helmholtz free energy is obtained. A system of integral equations for the equilibrium distributions of components is derived. The asymptotic properties of its solutions are investigated. Moment expansion of interatomic interactions and localization of integral terms in free energy is obtained. A Ginzburg–Landau-like functional of free energy is derived.     

A new stochastic method of reconstructing porous media

We present a new stochastic method of reconstructing porous medium from limited morphological information obtained from two-dimensional micro- images of real porous medium. The method is similar to simulated annealing method in the capability of reconstructing both isotropic and anisotropic structures of multi-phase but differs from the latter in that voxels for exchange are not selected completely randomly as their neighborhood will also be checked and this new method is much simpler to implement and program. We applied it to reconstruct real sandstone utilizing morphological information contained in porosity, two-point probability function and linear-path function. Good agreement of those references verifies our developed method’s powerful capability. The existing isolated regions of both pore phase and matrix phase do quite minor harm to their good connectivity. The lattice Boltzmann method (LBM) is used to compute the permeability of the reconstructed system and the results show its good isotropy and conductivity. However, due to the disadvantage of this method that the connectivity of the reconstructed system’s pore space will decrease when porosity becomes small, we suggest the porosity of the system to be reconstructed be no less than 0.2 to ensure its connectivity and conductivity.     

On the counting function of the lattice profile of periodic sequences

The lattice profile analyzes the intrinsic structure of pseudorandom number sequences with applications in Monte Carlo methods and cryptology. In this paper, using the discrete Fourier transform for periodic sequences and the relation between the lattice profile and the linear complexity, we give general formulas for the expected value, variance, and counting function of the lattice profile of periodic sequences with fixed period. Moreover, we determine in a more explicit form the expected value, variance, and counting function of the lattice profile of periodic sequences for special values of the period.     

Au(111)上烷烃硫醇SAMs表面应力的理论研究

应用已建立的关于金属表面吸附层中表面应力的统计热力学理论 ,计算了Au(111)上烷烃硫醇SAMs的表面应力及其与烷烃硫醇链长、吸附覆盖度的定量关系 .计算结果与实验相符 ,较好地解释了Berger等人的实验结果 ,特别是解决了在表面应力符号性质上理论与实验的矛盾 .在表面吸附层应力的多种物理起源中 ,通过底物的分子间作用力有着决定性的贡献 ,揭示了分子的吸附能间接地起着重要作用 .这与阴离子化学吸附体系Cl-/Au(111)的有关研究结果相同 .     

Structural and vibrational properties of dilute GaNxAs1−x(P1−x)

We report a comprehensive analyzes of the Fourier transform infrared (FTIR) absorption and Raman scattering data on the structural and vibrational properties of dilute ternary GaAs_1−xN_x,[GaP_1−xN_x] (x<0.03) alloys grown on GaAs [GaP] by metal organic chemical vapor deposition (MOCVD) and solid source molecular beam epitaxy (MBE). By using realistic total energy and lattice dynamical calculations, the origin of experimentally observed N-induced vibrational features are characterized. Useful information is obtained about the structural stability, vibrational frequencies, lattice relaxations and compositional disorder in GaNAs (GaNP) alloys. At lower composition (x<0.015) most of the N atoms occupy the As [P] sublattice {N_As[N_P]}—they prefer moving out of their substitutional sites to more energetically favorable locations at higher x. Our results for the N-isotopic shifts of local mode frequencies compare favorably well with the existing FTIR data.     

A constructive characterization of the split closure of a mixed integer linear program

Two independent proofs of the polyhedrality of the split closure of mixed integer linear program have been previously presented. Unfortunately neither of these proofs is constructive. In this paper, we present a constructive version of this proof. We also show that split cuts dominate a family of inequalities introduced by Köppe and Weismantel.     

Searching for extensible Korobov rules

Extensible lattice sequences have been proposed and studied in [F.J. Hickernell, H.S. Hong, Computing multivariate normal probabilities using rank-1 lattice sequences, in: G.H. Golub, S.H. Lui, F.T. Luk, R.J. Plemmons (Eds.), Proceedings of the Workshop on Scientific Computing (Hong Kong), Singapore, Springer, Berlin, 1997, pp. 209–215; F.J. Hickernell, H.S. Hong, P. L’Ecuyer, C. Lemieux, Extensible lattice sequences for quasi-Monte Carlo quadrature, SIAM J. Sci. Comput. 22 (2001) 1117–1138; F.J. Hickernell, H.Niederreiter, The existence of good extensible rank-1 lattices, J. Complexity 19 (2003) 286–300]. For the special case of extensible Korobov sequences, parameters can be found in [F.J. Hickernell, H.S. Hong, P. L’Ecuyer, C.Lemieux, Extensible lattice sequences for quasi-Monte Carlo quadrature, SIAM J. Sci. Comput. 22 (2001) 1117–1138]. The searches made to obtain these parameters were based on quality measures that look at several projections of the lattice. Because it is often the case in practice that low-dimensional projections are very important, it is of interest to find parameters for these sequences based on measures that look more closely at these projections. In this paper, we prove the existence of “good” extensible Korobov rules with respect to a quality measure that considers two-dimensional projections. We also report results of experiments made on different problems where the newly obtained parameters compare favorably with those given in [F.J. Hickernell, H.S. Hong, P. L’Ecuyer, C. Lemieux, Extensible lattice sequences for quasi-Monte Carlo quadrature, SIAM J. Sci. Comput. 22 (2001) 1117–1138].