Assessment of free energy predictors for ligand binding to a methyllysine histone code reader

Methyllysine histone code readers constitute a new promising group of potential drug targets. For instance, L3MBTL1, a malignant brain tumor (MBT) protein, selectively binds mono- and di-methyllysine epigenetic marks (KMe, KMe(2) ) that eventually results in the negative regulation of multiple genes through the E2F/Rb oncogenic pathway. There is a pressing need in potent and selective small-molecule probes that would enable further target validation and might become therapeutic leads. Such an endeavor would require efficient tools to assess the free energy of protein-ligand binding. However, due to an unparalleled function of the MBT binding pocket (i.e., selective binding to KMe/KMe(2) ) and because of its distinctive structure representing a small aromatic "cage," an accurate assessment of its binding affinity to a ligand appears to be a challenging task. Here, we report a comparative analysis of computationally affordable affinity predictors applied to a set of seven small-molecule ligands interacting with L3MBTL1. The analysis deals with novel ligands and targets, but applies widespread computational approaches and intuitive comparison metrics that makes this study compatible with and incremental to earlier large scale accounts on the efficiency of affinity predictors. Ultimately, this study has revealed three top performers, far ahead of the other techniques, including two scoring functions, PMF04 and PLP, along with a simulation-based method MM-PB/SA. We discuss why some methods may perform better than others on this target class, the limits of their application, as well as how the efficiency of the most CPU-demanding techniques could be optimized.     

Linearity-preserving flux correction and convergence acceleration for constrained Galerkin schemes

This paper is concerned with the development of general-purpose algebraic flux correction schemes for continuous (linear and multilinear) finite elements. In order to enforce the discrete maximum principle (DMP), we modify the standard Galerkin discretization of a scalar transport equation by adding diffusive and antidiffusive fluxes. The result is a nonlinear algebraic system satisfying the DMP constraint. An estimate based on variational gradient recovery leads to a linearity-preserving limiter for the difference between the function values at two neighboring nodes. A fully multidimensional version of this scheme is obtained by taking the sum of local bounds and constraining the total flux. This new approach to algebraic flux correction provides a unified treatment of stationary and time-dependent problems. Moreover, the same algorithm is used to limit convective fluxes, anisotropic diffusion operators, and the antidiffusive part of the consistent mass matrix.The nonlinear algebraic system associated with the constrained Galerkin scheme is solved using fixed-point defect correction or a nonlinear SSOR method. A dramatic improvement of nonlinear convergence rates is achieved with the technique known as Anderson acceleration (or Anderson mixing). It blends a number of last iterates in a GMRES fashion, which results in a Broyden-like quasi-Newton update. The numerical behavior of the proposed algorithms is illustrated by a grid convergence study for convection-dominated transport problems and anisotropic diffusion equations in 2D.     

Space-domain lock-in amplifier based on a liquid-crystal spatial light modulator

We present a two-dimensional (2D) spatial lock-in amplifier that provides a contrast ratio of more than 10,000:1 for transmitted and blocked intensity patterns using a conventional liquid-crystal spatial light modulator. The device is based on spatial-domain modulation-demodulation of intensity patterns under coherent imaging conditions. The operation of the 2D lock-in amplifier is illustrated by implementing Young's double-slit arrangement for measurements of the mutual coherence between individual emitters of a 2D phase-coupled array of vertical cavity surface emitting lasers.     

Electron photodetachment from aqueous anions. 3. Dynamics of Geminate pairs derived from photoexcitation of mono- vs polyatomic anions

Photostimulated electron detachment from aqueous inorganic anions is the simplest example of solvent-mediated electron transfer reaction. As such, this photoreaction became the subject of many ultrafast studies. Most of these studied focused on the behavior of halide anions, in particular, iodide, that is readily accessible in the UV. In this study, we contrast the behavior of these halide anions with that of small polyatomic anions, such as pseudohalide anions (e.g., HS(-)) and common polyvalent anions (e.g., SO(3)(2-)). Geminate recombination dynamics of hydrated electrons generated by 200 nm photoexcitation of aqueous anions (I(-), Br(-), OH(-), HS(-), CNS(-), CO(3)(2-), SO(3)(2-), and Fe(CN)(6)(4-)) have been studied. Prompt quantum yields for the formation of solvated, thermalized electrons and quantum yields for free electrons were determined. Pump-probe kinetics for 200 nm photoexcitation were compared with kinetics obtained at lower photoexcitation energy (225 or 242 nm) for the same anions, where possible. Free diffusion and mean force potential models of geminate recombination dynamics were used to analyze these kinetics. These analyses suggest that for polyatomic anions (including all polyvalent anions studied) the initial electron distribution has a broad component, even at relatively low photoexcitation energy. There seems to be no well-defined threshold energy below which the broadening of this electron distribution does not occur, as is the case for halide anions. The constancy of (near-unity) prompt quantum yields vs the excitation energy as the latter is scanned across the lowest charge-transfer-to-solvent band of the anion is observed for halide anions but not for other anions: the prompt quantum yields are considerably less than unity and depend strongly on the excitation energy. Our study suggests that halide anions are in the class of their own; electron photodetachment from polyatomic, especially polyvalent, anions exhibits qualitatively different behavior.     

Self-organized hierarchical ZnS/SiO(2) nanowire heterostructures

Novel hierarchical heterostructures formed by wrapping ZnS nanowires with highly dense SiO(2) nanowires were successfully synthesized by a vapor-liquid-solid process. The as-synthesized products were characterized using X-ray diffraction, scanning electron microscopy and transmission electron microscopy equipped with an energy-dispersive X-ray spectrometer. Studies indicate that a typical hierarchical ZnS/SiO(2) heterostructure consists of a single-crystalline ZnS nanowire (core) with diameter gradually decreasing from several hundred nanometers to 20 nm and adjacent amorphous SiO(2) nanowires (branches) with diameters of about 20 nm. A possible growth mechanism was also proposed for the growth of the hierarchical heterostructures.     

Synthesis and interface structures of zinc sulfide sheathed zinc-cadmium nanowire heterojunctions

Zinc sulfide (ZnS) sheathed zinc (Zn)-cadmium (Cd) nanowire heterojunctions have been prepared by thermal evaporating of ZnS and CdS powders in a vertical induction furnace at 1200 degrees C. Studies found that both the Zn and Cd subnanowires, within a single nanoheterojunction, are single-crystallines with the growth directions perpendicular to the [210] plane, whereas the sheathed ZnS is polycrystalline with a thickness of ca. 5 nm. The Zn/Cd interface structure in the ZnS sheathed Zn-Cd nanowire heterojunctions was thoroughly experimentally studied by high-resolution transmission electron microscopy and theoretically studied using a near-coincidence site lattice (NCSL) concept. The results show that the Cd and Zn have a crystalline orientation relationship as [0001]Zn//[0001]Cd, (10(-)10)Zn//(10(-)10)Cd, (01(-)10)Zn//(01(-)10)Cd, and ((-)1100)Zn//((-)1100)Cd.     

SnO2 nanoparticle-functionalized boron nitride nanotubes

Boron nitride nanotubes (BNNTs) were synthesized by a carbon-free chemical vapor deposition method using boron and metal oxide as reactants. Then SnO(2) nanoparticles were functionalized on them via a simple wet chemistry method. Detailed transmission electron microscopy (TEM) observations reveal that SnO(2) nanoparticles may cover the tube surface or be encapsulated in tube channels. The lattice distances of both BNNT and SnO(2) have been changed due to the strong interactions between them. The band gap energy of SnO(2) particles is found enlarged due to the size effect and interaction with BNNTs.