Formation and dissociation of protonated cytosine–cytosine base pairs in i-motifs by ab initio quantum chemical calculations

Formation and dissociation mechanisms of C-C＋ base pairs in acidic and alkaline environments are investigated, employing ab initio quantum chemical calculations. Our calculations suggest that, in an acidic environment, a cytosine monomer is first protonated and then dimerized with an unprotonated cytosine monomer to form a C-C＋ base pair; in an alkaline environment, a protonated cytosine dimer is first unprotonated and then dissociated into two cytosine monomers. In addition, the force for detaching a C-C＋ base pair was found to be inversely proportional to the distance between the two cytosine monomers. These results provide a microscopic mechanism to qualitatively explain the experimentally observed reversible formation and dissociation of i-motifs.     

On frequency waves

A new type of wave existing in the frequency domain is deduced and named a frequency wave. For a homogeneous medium, we have obtained the approximate and rigorous solutions of a frequency shift equation for plane radiation under some special, one-sided or two-sided frequency shift conditions.     

The neck linker of kinesin 1 seems optimally designed to approach the largest stepping velocity: a simulation study of an ideal model

The neck linker is widely believed to play a critical role in the hand-over-hand walking of conventional kinesin 1. Experiments have shown that change of the neck linker length will significantly change the stepping velocity of the motor. In this paper, we studied this length effect based on a highly simplified chemically powered ratchet model. In this model, we assume that the chemical steps (ATP hydrolysis, ADP and P(i) release, ATP binding, neck linker docking) are fast enough under conditions far from equilibrium and the mechanical steps (detachment, diffusional search and re-attachment of the free head) are rate-limiting in kinesin walking. According to this model, and regarding the neck linker as a worm-like-chain polypeptide, we can calculate the steady state stepping velocity of the motor for different neck linker lengths. Our results show, under the actual values of binding energy between kinesin head and microtubule (~15k(B)T) and the persistence length of neck linker (~0.5 nm), that there is an optimal neck linker length (~14-16 a.a.) corresponding to the maximal velocity, which implies that the length of the wild-type neck linker (~15 a.a.) might be optimally designed for kinesin 1 to approach the largest stepping velocity.     

The elastic theory of a single DNA molecule

We study the elastic responses of double-(ds) and single-stranded (ss) DNA at external force fields. A double-strand-polymer elastic model is constructed and solved by path integral methods and Monte Carlo simulations to understand the entropic elasticity, cooperative extensibility, and supercoiling property of dsDNA. The good agreement with experiments indicates that short-ranged base-pair stacking interaction is crucial for the stability and the high deformability of dsDNA. Hairpin-coil transition in ssDNA is studied with generating function method. A threshold force is needed to pull the ssDNA hairpin patterns, stabilized by base pairing and base-pair stacking, into random coils. This phase transition is predicted to be of first order for stacking potential higher than some critical level, in accordance with experimental observations.     

Shapes of lipid monolayer domains: Solutions using elliptic functions

Solid lipid monolayer domains surrounded by a fluid phase at an air-water interface exhibit complex shapes. These intriguing shapes can be understood in terms of a competition between line tension and long-range dipole-dipole interaction. The dipolar energy has recently been relevant to a negative line tension and a positive curvature energy at the boundary, and a corresponding shape equation was derived by the variation of the approximated domain energy (Phys. Rev. Lett. 93, 206101 (2004)). Here we further incorporate surface pressure into the shape equation and show that the equation can be analytically solved: the curvature of the domain boundary is exactly obtained as an elliptic function of arc-length. We find that a circular domain can grow into bean-and peach-like domains with pressure, i.e., dipping and cuspidal transitions of circle by compression. The comparison with the experimental observation shows nice agreement.     

Smaller Output Beam Divergence in the Slowly Opened Q-Switch Operation

The mechanism of the slowly opened Q-switch operation was investigated thoroughly. Maximum energy extraction from the resonator could be optimized, and the smallest output beam divergence could be achieved. In this article, we present a detailed analysis that has numerically verified the mode-selection mechanism in the slowly opened Q-switch operation, and the degree of the smaller output laser beam divergence that has been achieved. The mechanism of the slowly opened Q-switch operation is the inherent advantage of the passive saturable absorber in this operation. We can use the maximum energy extraction and the smallest output beam divergence results of the slowly opened Q-switch operation to design and optimize various passive saturable absorbers: plastic dye sheets, LiF:F₂⁻ color center crystals, Cr4⁺: YAG crystals, RG1000 color glass filters, and the single crystal semiconductor saturable absorber wafers that are in developed in our microchip laser systems.     

A new family of supramolecular multiferrocenyl rhomboids:Synthesis,characterization,and their electrochemical behavior

Two novel,supramolecular,multiferrocenyl rhomboids 5 and 6 have been successfully constructed from newly designed 60 ferrocenyl donor precursor 1 via coordination-driven self-assembly.The structures of all multiferrocenyl rhomboids were characterized by multinuclear NMR(¹H and ³¹P),CSI-TOF-MS, and PM6 semi-empirical molecular simulation,and their electrochemical behaviors have been investigated.     

Synthesis and biological evaluation of novel 1, 2, 3-benzotriazin-4-one derivatives as leukotriene A4 hydrolase aminopeptidase inhibitors

A series of novel 1,2,3-benzotriazin-4-one derivatives were designed,synthesized and their inhibitory activities against leulcotriene A_4 hydrolase aminopeptidase in vitro were evaluated.Many compounds showed moderate to good activities at the concentration of 10 μmol/L.Among them,compound Ⅳ-16 exhibited the highest inhibitory activity up to 80.6% with an IC_(50) of 1.30 ± 0.20 μmol/L The compound Ⅳ-16 was also tested the proliferation inhibitory activities in THP1 human AML cell line and its binding model with LTA_4H enzyme by molecular docking was studied.It indicated that 1,2,3-benzotriazin-4-one was a promising scaffold for further study.The relationship between structure and inhibitory activity was also preliminarily discussed.     

A New Probe for Mechanical Testing of Nanostructures in Soft Materials

We report a new application of the optical tweezers, where a harmonically driven oscillating tweezer is combined with the forward light scattering and lock-in amplification techniques, for probing the mechanics of nanostructures in soft materials in a broad frequency range. Model independent dynamic moduli G and G of the material at a localized, sub-micron area can be measured directly from the displacement and the phase shift of the particle in the oscillating trap. The probe particles can be as small as 200nm and the displacement of the particle was in the range of a few nanometers. To illustrate the new methodology, we show the microscopic viscoelastic properties of a transient polymer network in the vicinity of a silica bead.     

Structural and optical properties of ZnS/niobate composites synthesized by exfoliation/self-assembly processing

A new ZnS/niobate composite was first synthesized through two processes: (1) self-assembly of [Ca₂Nb₃O₁₀]_nⁿ⁻ nanosheets in Zn(NH₃)₄²⁺ solution; (2) formation of ZnS/niobate composite by adding Na₂S to the former reacting system. X-ray diffraction (XRD) result shows that the as-prepared ZnS/niobate composite can be indexed to tetrahedral symmetry with a=5.450(2) and c=16.904(7) Å. The uniform distributions of Zn, Ca, Nb, S and O element in the particles were demonstrated by scanning electron microscope (SEM) and energy dispersive spectrometer (EDS). The optical property of the composite was characterized by photoluminescence spectra and UV-vis absorption spectra.