In this paper, a new solvation model is proposed for simulations of biomolecules in aqueous solutions that combines the strengths of explicit and implicit solvent representations. Solute molecules are placed in a spherical cavity filled with explicit water, thus providing microscopic detail where it is most needed. Solvent outside of the cavity is modeled as a dielectric continuum whose effect on the solute is treated through the reaction field corrections. With this explicit/implicit model, the electrostatic potential represents a solute molecule in an infinite bath of solvent, thus avoiding unphysical interactions between periodic images of the solute commonly used in the lattice-sum explicit solvent simulations. For improved computational efficiency, our model employs an accurate and efficient multiple-image charge method to compute reaction fields together with the fast multipole method for the direct Coulomb interactions. To minimize the surface effects, periodic boundary conditions are employed for nonelectrostatic interactions. The proposed model is applied to study liquid water. The effect of model parameters, which include the size of the cavity, the number of image charges used to compute reaction field, and the thickness of the buffer layer, is investigated in comparison with the particle-mesh Ewald simulations as a reference. An optimal set of parameters is obtained that allows for a faithful representation of many structural, dielectric, and dynamic properties of the simulated water, while maintaining manageable computational cost. With controlled and adjustable accuracy of the multiple-image charge representation of the reaction field, it is concluded that the employed model achieves convergence with only one image charge in the case of pure water. Future applications to pKa calculations, conformational sampling of solvated biomolecules and electrolyte solutions are briefly discussed.
A big challenge for nonlinear optical (NLO) materials is the application in high power lasers, which needs the simultaneous occurrence of large second harmonic generation (SHG) and high laser induced damage threshold (LIDT). Herein we report the preparation of a new Ga2Se3 phase, which shows the SHG intensities of around 2.3 times and the LIDT of around 16.7 times those of AgGaS2 (AGS), respectively. In addition, its IR transparent window ca. 0.59–25 μm is also significantly wider than that of AGS (ca. 0.48–≈11.4 μm). The occurrence of the strong SHG responses and good phase‐matching indicate that the structure of the new Ga2Se3 phase can only be non‐centrosymmetric and have a lower symmetry than the cubic γ‐phase. The observed excellent SHG and phase‐matching properties are consistent with our diffraction experiments and can be well explained by using the orthorhombic models obtained through our high throughput simulations.
Second order accurate elliptic solvers using Cartesian grids are presented for three dimensional interface problems in which the coefficients, the source term, the solution and its normal flux may be discontinuous across an interface. One of our methods is designed for general interface problems with variable but discontinuous coefficient. The scheme preserves the discrete maximum principle using constrained optimization techniques. An algebraic multigrid solver is applied to solve the discrete system. The second method is designed for interface problems with piecewise constant coefficient. The method is based on the fast immersed interface method and a fast 3D Poisson solver. The second method has been modified to solve Helmholtz/Poisson equations on irregular domains. An application of our method to an inverse interface problem of shape identification is also presented. In this application, the level set method is applied to find the unknown surface iteratively.
An unusual room-temperature light sensitivity was realized in a polyoxometalate-based hybrid material due to cooperative multicomponent molecular charge-transfer interactions taking place in this material, mainly among POMs, NDIs, and other molecules. The functional π-acidic NDI linkers and POM clusters in the discussed hybrid material were individually designed as photosensors and electron reservoirs. To propose a photo-induced charge-transfer mechanism, EPR, XPS, UV-Vis and computational studies were carried out, and indicated the presence of active charge-transfer interactions among several of the components.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.