A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations

We study how the results of molecular dynamics (MD) simulations are affected by various choices during the setup, e.g., the starting velocities, the solvation, the location of protons, the conformation of His, Asn, and Gln residues, the protonation and titration of His residues, and the treatment of alternative conformations. We estimate the binding affinity of ligands to four proteins calculated with the MM/GBSA method (molecular mechanics combined with a generalized Born and surface area solvation energy). For avidin and T4 lysozyme, all variations gave similar results within 2 kJ/mol. For factor Xa, differences in the solvation or in the selection of alternative conformations gave results that are significantly different from those of the other approaches by 4-6 kJ/mol, whereas for galectin-3, changes in the conformations, rotations, and protonation gave results that differed by 10 kJ/mol, but only if residues close to the binding site were modified. This shows that the results of MM/GBSA calculations are reasonably reproducible even if the MD simulations are set up with different software. Moreover, we show that the sampling of phase space can be enhanced by solvating the systems with different equilibrated water boxes, in addition to the common use of different starting velocities. If different conformations are available in the crystal structure, they should also be employed to enhance the sampling. Protonation, ionization, and conformations of Asn, Gln, and His may also be used to enhance sampling, but great effort should be spent to obtain as reliable predictions as possible close to the active site.     

Strong pressure-energy correlations in van der Waals liquids

Strong correlations between equilibrium fluctuations of the configurational parts of pressure and energy are found in computer simulations of the Lennard-Jones liquid and other simple liquids, but not for hydrogen-bonding liquids such as methanol and water. The correlations that are present also in the crystal and glass phases reflect an effective inverse power-law repulsive potential dominating fluctuations, even at zero and slightly negative pressure. In experimental data for supercritical argon, the correlations are found to be approximately 96%. Consequences for viscous liquid dynamics are discussed.     

Oscillation and decay of particle current due to a quench and dephasing in an interacting fermionic system

We study the response of a particle current to dissipative dephasing in an interacting, few body fermionic lattice system. The particles are prepared in the many-body interacting ground state in presence of an artificial magnetic gauge field, which is subsequently quenched to zero. The initial current decays non-trivially in the dissipative environment and we explore the emerging dynamics, time scales and their dependence on the various system parameters.     

二维传声器阵列测量技术及其对飞机进场着陆过程噪声的实验研究

发展了一种由111个传声器组成的M维平面传声器阵列测量技术,111个传声器在平面阵列中的位置应用随机优化的方法确定,从而保证平面传声器阵列在感兴趣的测量频率范围内具有理想的性能,并应用数值模拟的方法检验了平面传声器阵列的频谱特性.应用此平面传声器阵列对当前流行的民用客机进场着陆过程中飞机噪声源进行了测量分析,实验结果表明应用此项技术可以辨别出在飞机表面上所有重要的噪声源,并可获得全尺寸飞机机体重要噪声源的详细的频谱特性、指向特性和声级变化.     

Small-Molecule Diffusion in Semicrystalline Polymers as Revealed by Experimental and Simulation Studies

Summary: Diffusion of n-hexane in poly(ethylene-co-1-hexene)s with 15–75 wt.% crystallinity was studied by desorption experiments analyzing data using the Fickian equations with a concentration dependent diffusivity. The effect of the impenetrable crystalline phase on the penetrant diffusivity (D) is described by D = D_a/(τβ), where D_a is the diffusivity of the amorphous polymer, τ is the geometrical impedance factor and β is a factor describing the constraining effect of the crystals on the non-crystalline phase. For a polymer with 75 wt.% crystallinity, τβ varied markedly with penetrant concentration (v_1a) in the penetrable phase: 1000 (v_1a = 0) and 10 (v_1a = 0.15). This penetrant-uptake had no effect on the gross crystal morphology, i.e. β must be strongly dependent on v_1a. Samples saturated in n-hexane exhibited a penetrant-induced loosening of the interfacial structure, as revealed by an increase in crystal density that require an increased mobility in the interfacial component and by a decrease in the intensity of the asymmetric X-ray scattering associated with the interfacial component. The geometrical impedance factor has been modelled by mimicking spherulite growth and τ was obtained as the ratio of the diffusivities of the fully amorphous and semicrystalline systems. The maximum τ obtained from these simulations is ca. ten, which suggests that β in the systems with v_1a = 0.15 takes values close to unity. The simulations showed that the geometrical impedance factor is insensitive to the ratio of the crystal width and the crystal thickness. A free path length scaling parameter characteristic of the amorphous phase correlated with τ.     

Fluorenyl based syndiotactic specific metallocene catalysts structural features,origin of syndiospecificity

The stereochemistry of propylene insertion/propagation reactions with a variety of C_s symmetric fluorenyl- containing single site catalysts is discussed. Our recent results indicate that independent of the chemical composition of the ancillary ligand fragments, or nature of the transition metal, active sites with local C_s symmetry and enantiotopic coordination positions behave syndioselectively in the general context of chain migratory insertion mechanism. Perfect bilateral symmetry neither exists nor is required in these processes. In this context the mechanism of syndiospecific polymerization is revisited by taking into account the structural characteristics and catalytic behavior of the original metallocene based (η⁵-C₅H₄-CMe₂-η⁵-C₁₃H₈) MCl₂/ MAO; M = Zr ( 1 ), Hf ( 2 ) catalyst systems and new syndiotactic specific systems including (η⁵-C₅H₄-CPh2-η5-3,6-di-tBut-C₁₃H₆)ZrCl₂ ( 3 ), η¹,η⁵-(μMe₂Si)(3,6-di-tBut-Flu)(t-ButN)MCl₂/ MAO; M =Ti ( 4 ), Zr ( 5 ) and η¹,η⁵-(μMe₂Si)(2,7-di-tBut-Flu)(t-ButN)MCl₂/ MAO; M = Ti ( 6 ), Zr ( 7 ).