Evaluation of Poisson solvation models using a hybrid explicit/implicit solvent method

Implicit solvent methods have become popular tools in the field of protein dynamics simulations, yet evaluation of their validity has been primarily limited to comparisons with experimental and theoretical data for small molecules. In this paper, we use a recently developed hybrid explicit/implicit solvent methodology to evaluate the accuracy of several Poisson-based implicit solvent models. Specifically, we focus on the calculation of electrostatic solvation free energies of various fixed conformations for two proteins. We show that, among various dielectric boundary definitions, the Lee-Richards molecular surface has the best agreement with hybrid solvent results. Furthermore, certain modifications of the molecular surface Poisson protocol provide varied results. For instance, simple modifications of atomic radii on charged residues generally improve absolute errors but do not significantly reduce relative errors among conformations. On the other hand, using a water-probe radius of 1.0 A, as opposed to the standard value of 1.4 A, to generate the molecular surface, moderately improves both absolute and relative results.     

Total internal reflection-based biochip utilizing a polymer-filled cavity with a micromirror sidewall

A total internal reflection (TIR)-based biochip utilizing a polymer-filled cavity with a micromirror sidewall has been designed and fabricated. The implementation of the micromirror sidewall cavity facilitates precise alignment of the excitation light beam into the system. The incident angle of illumination can be easily modified by selecting polymers of different indices of refraction while optical losses are minimized. The design enables the hybrid, vertical integration of a laser diode and a CCD camera, resulting in a compact optical system. Brownian motion of fluorescent microspheres and real-time photobleaching of rhodamine 6G molecules is demonstrated. The proposed TIR-based chip simplifies current TIR optical configurations and could potentially be used as an optical-microfluidic platform for an integrated lab-on-a-chip microsystem.     

Numerical computations of integrals over paths on Riemann surfaces of genusN

This paper is a continuation of work by Forest and Lee [1,2]. In [1,2] it was proved that the function theory of periodic soliton solutions occurs on the Riemann surfaces ? of genusN, where the integrals over paths on ? play the most fundamental role. In this paper a numerical method is developed to evaluate these integrals. Predisely, the aim is to develop a computational code for integrals of the form $$\int\limits_\gamma {f(z)\frac{{dz}}{{R(z)}}, or} \int\limits_\gamma {f(z)R(z)dz,} $$ wheref(z) is any single-valued analytic function on the complex planeC, andR(z) is a two-valued function onC of the form $$R^2 (z) = \prod\limits_{k = 1}^{2N + \delta } {(z - z_0 (k)), \delta = 0 or 1,} $$ where {z ₀(k),1≤k≤2N+δ} are distinct complex numbers which play the role of the branch points of the Riemann surface ? = {(z, R(z))} of genusN?1+δ. The integral path γ is continuous on ?. The numerical code is developed in “Mathematica” [3].