Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions

A protein energy surface is constructed. Validation is through applications of global energy minimization to surface loops of protein crystal structures. For 9 of 10 predictions, the native backbone conformation is identified correctly. Electrostatic energy is modeled as a pairwise sum of interactions between anisotropic atomic charge densities. Model repulsion energy has a softness similar to that seen in ab initio data. Intrinsic torsional energy is modeled as a sum over pairs of adjacent torsion angles of 2-dimensional Fourier series. Hydrophobic energy is that of a hydration shell model. The remainder of hydration free energy is obtained as the energetic effect of a continuous dielectric medium. Parameters are adjusted to reproduce the following data: a complete set of ab initio energy surfaces, meaning one for each pair of adjacent torsion angles of each blocked amino acid; experimental crystal structures and sublimation energies for nine model compounds; ab initio energies over 1014 conformations of 15 small-molecule dimers; and experimental hydration free energies for 48 model compounds. All ab initio data is at the Hartree–Fock/6–31G* level. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 548–573, 1998     

Conformational searching using a population-based incremental learning algorithm

A new population-based incremental learning algorithm for conformational searching of molecules is presented. This algorithm is particularly effective at determining, by relatively small number of energy minimizations, global energy minima of large flexible molecules. The algorithm is also able to find a large set of low energy conformations of more rigid small molecules. The performance of the algorithm is relation to other algorithm is examined via the test molecules: C(18) H(38) , C(39)H(80) , cycloheptadecane and a set of five drug-like molecules.     

从原子到大分子体系的计算机模拟——计算化学50年

本文综述并修订了从20世纪50年代末至今,我们在计算化学领域所做的一些有意义的工作。序言部分把我们的工作置于当代科学的背景之下。然后我们以一种经典的基准测试体系——一种新的单粒子表象（即替代传统的原子和分子自旋轨道的化学自旋轨道）所构建的氢分子（H2）波函数——作为开始。用Hartree-Fock-Heitler-Lo...     

ON THE ABRUPT CHANGE IN SOUTH ASIAN SUMMER MONSOON CLIMATE AND ITS SYNCHRONISM WITH THE GLOBAL RAPID WARMING

This paper has analysed the major characteristics of long-term variation, of summermonsoon climate in South Asia since 1888. An abrupt enhancement of summer monsoon inthe 1920s and its synchronism with the global rapid warming have been detected by theMann-Kendall Rank Statistic test. Based on diagnostic analysis on the atmospheric circulationover the monsoon region and the thermal conditions of both ocean and land during theperiod of abrupt change, it is found that the warming over land was stronger and earlierthan that over the ocean, which would enhance the land-sea thermal contrast and thereforebe favorable to the development of monsoon low and the disturbance in the monsoon flow.This may be a direct factor for the abrupt enhancement of summer monsoon.     

A generalized preimage theorem in global analysis

The concept of locally fine point and generalized regular value of a C¹ map between Banach spaces were carried over C¹ map between Banach manifolds. Hence the preimage theorem, a principle constructing Banach manifolds in global analysis, is generalized.     

DYNAMICS OF A NONLINEAR NON-AUTONOMOUS n-PATCHES PREDATOR-PREY DISPERSION-DELAY MODEL

In this paper,a nonlinear nonautonomous predator-prey dispersion model with continuous distributed delay is studied,where all parameters are time-dependent.In this system consisting of n-patches the prey species can disperse among n-patches,but the predator species is confined to one patch and cannot disperse.It is proved that the system is uniformly persistent under any dispersion rate effect.Furthermore,some sufficient conditions are established for the existence of a unique almost periodic solution of the system.The example shows that the criteria in the paper are new,general and easily verifiable.     

Global Existence for a Parabolic-hyperbolic Free Boundary Problem Modelling Tumor Growth

In this paper we study a free boundary problem modelling tumor growth, proposed by A. Friedman in 2004. This free boundary problem involves a nonlinear second-order parabolic equation describing the diffusion of nutrient in the tumor, and three nonlinear first-order hyperbolic equations describing the evolution of proliferative cells, quiescent cells and dead cells, respectively. By applying Lp theory of parabolic equations, the characteristic theory of hyperbolic equations, and the Banach fixed point theorem, we prove that this problem has a unique global classical solution.     

Exponential synchronization of complex networks with nonidentical time-delayed dynamical nodes

In this Letter, exponential synchronization of a complex network with nonidentical time-delayed dynamical nodes is considered. Two effective control schemes are proposed to drive the network to synchronize globally exponentially onto any smooth goal dynamics. By applying open-loop control to all nodes and adding some intermittent controllers to partial nodes, some simple criteria for exponential synchronization of such network are established. Meanwhile, a pinning scheme deciding which nodes need to be pinned and a simply approximate formula for estimating the least number of pinned nodes are also provided. By introducing impulsive effects to the open-loop controlled network, another synchronization scheme is developed for the network with nonidentical time-delayed dynamical nodes, and an estimate of the upper bound of impulsive intervals ensuring global exponential stability of the synchronization process is also given. Numerical simulations are presented finally to demonstrate the effectiveness of the theoretical results.     

A smoothing method for mathematical programs with equilibrium constraints

Received May 3, 1996 / Revised version received November 19, 1997 Published online January 20, 1999     

Experimental artefacts in 2D-MAS exchange experiments: non-uniform mixing time within a single 2D run

The practical realization of rotor-synchronized mixing-times in 2D-MAS exchange experiments without the need for a special hardware is reviewed; its consequence for the ‘true mixing time' of the experiment is discussed. We demonstrate influences on experimental rate constants derived from such experiments as well as on the appearance of the 2D-MAS spectra, taken at short mixing times.