Water PMF for predicting the properties of water molecules in protein binding site

Water is an important component in living systems and deserves better understanding in chemistry and biology. However, due to the difficulty of investigating the water functions in protein structures, it is usually ignored in computational modeling, especially in the field of computer‐aided drug design. Here, using the potential of mean forces (PMFs) approach, we constructed a water PMF (wPMF) based on 3946 non‐redundant high resolution crystal structures. The extracted wPMF potential was first used to investigate the structure pattern of water and analyze the residue hydrophilicity. Then, the relationship between wPMF score and the B factor value of crystal waters was studied. It was found that wPMF agrees well with some previously reported experimental observations. In addition, the wPMF score was also tested in parallel with 3D‐RISM to measure the ability of retrieving experimentally observed waters, and showed comparable performance but with much less computational cost. In the end, we proposed a grid‐based clustering scheme together with a distance weighted wPMF score to further extend wPMF to predict the potential hydration sites of protein structure. From the test, this approach can predict the hydration site at the accuracy about 80% when the calculated score lower than ?4.0. It also allows the assessment of whether or not a given water molecule should be targeted for displacement in ligand design. Overall, the wPMF presented here provides an optional solution to many water related computational modeling problems, some of which can be highly valuable as part of a rational drug design strategy. © 2012 Wiley Periodicals, Inc.     

Study on the activity and mechanism of skimmianine against human non-small cell lung cancer

The present research was to investigate the effects of skimmianine (SK) in four non-small cell lung cancer (NSCLC) cells. We found that SK can significantly inhibit the growth of NSCLC cells and markedly induce apoptosis in NSCLC cells. The effects of growth inhibition and apoptosis induction were in a concentration–response relationship and caspase-dependent manner.     

显式模拟类橡胶材料Mullins效应滞回圈

通过显式、直接的方法提出一个多轴可压缩应变能函数,用来模拟类橡胶材料在加载——卸载作用下,由于Mullins效应而产生的应力——应变滞回圈. 本文的创新点在于将表征能量耗散的变量引入到应变能函数.新的弹性势具有以下两个特点:第一,在加载情况下,新引入的变量不会对弹性势产生任何影响,因此,只要给出合适的形函数显式表达,3个基准实验,包括单轴拉伸和压缩,等双轴拉伸和压缩,以及平面应变,都可精确模拟;第二,新引入的变量在卸载情况下将被激活.在不同的卸载应力下,变量将发生改变,从而影响弹性势,使其最终产生不同的应力——应变关系卸载曲线,与对应的加载曲线共同构成应力——应变滞回圈.通过对Mullins效应实验数据进行分析和研究,得出了卸载形函数在不同卸载应力下变化的规律,并预测不同卸载应力下的应力——应变关系.最后,我们将得到精确匹配实验数据的数值模拟结果,从而证明本文方法不仅可以精确匹配至少3个基准实验,还可以模拟和预测类橡胶材料在加载——卸载作用下由于Mullins效应而产生的滞回圈.      

Implicit–explicit schemes for nonlinear nonlocal equations with a gradient flow structure in one space dimension

Nonlinear convection–diffusion equations with nonlocal flux and possibly degenerate diffusion arise in various contexts including interacting gases, porous media flows, and collective behavior in biology. Their numerical solution by an explicit finite difference method is costly due to the necessity of discretizing a local spatial convolution for each evaluation of the convective numerical flux, and due to the disadvantageous Courant–Friedrichs–Lewy (CFL) condition incurred by the diffusion term. Based on explicit schemes for such models devised in the study of Carrillo et al. a second‐order implicit–explicit Runge–Kutta (IMEX‐RK) method can be formulated. This method avoids the restrictive time step limitation of explicit schemes since the diffusion term is handled implicitly, but entails the necessity to solve nonlinear algebraic systems in every time step. It is proven that this method is well defined. Numerical experiments illustrate that for fine discretizations it is more efficient in terms of reduction of error versus central processing unit time than the original explicit method. One of the test cases is given by a strongly degenerate parabolic, nonlocal equation modeling aggregation in study of Betancourt et al. This model can be transformed to a local partial differential equation that can be solved numerically easily to generate a reference solution for the IMEX‐RK method, but is limited to one space dimension.     

Corrigendum on ‘investigation on molecular interaction studies of binary mixture of Dehpa and Petrofin at 298.15 K’

Expressions of Redlich–Kister (RK) excess function using polynomials on difference of molar composition are used. Calculated values of excess properties from experimental values are well presented in some curves as a function of mole fraction (x₂) of the second pure component of the studied binary liquid mixture. Nevertheless, the authors presented values of adjustable parameters, not for the polynomial of the popular RK equation (i.e. vs. x₂–x₁), but for globally the excess property Y^E as an overall three degree polynomial on (x₂) including implicitly the molar fraction product (x₁·x₂) in their nonlinear regression, which can then induces some readers to probable confusion.