The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions

The effect of the box shape on the dynamic behavior of proteins simulated under periodic boundary conditions is evaluated. In particular, the influence of simulation boxes defined by the near-densest lattice packing (NDLP) in conjunction with rotational constraints is compared to that of standard box types without these constraints. Three different proteins of varying size, shape, and secondary structure content were examined in the study. The statistical significance of differences in RMSD, radius of gyration, solvent-accessible surface, number of hydrogen bonds, and secondary structure content between proteins, box types, and the application or not of rotational constraints has been assessed. Furthermore, the differences in the collective modes for each protein between different boxes and the application or not of rotational constraints have been examined. In total 105 simulations were performed, and the results compared using a three-way multivariate analysis of variance (MANOVA) for properties derived from the trajectories and a three-way univariate analysis of variance (ANOVA) for collective modes. It is shown that application of roto-translational constraints does not have a statistically significant effect on the results obtained from the different simulations. However, the choice of simulation box was found to have a small (5-10%), but statistically significant effect on the behavior of two of the three proteins included in the study.     

Self-affine analysis of protein energy

We study the time series of the total energy of polypeptides and proteins. These time series were generated by molecular dynamics methods and analyzed by applying detrended fluctuation analysis to estimate the long-range power-law correlation, i.e. to measure scaling exponents α. Such exponents were calculated for all systems and their values follow environment conditions, i.e., they are temperature dependent and also, in a continuum medium approach, vary according to the dielectric constants (we simulated ?=2 and ?=80). The procedure was applied to investigate polyalanines, and other realistic models of proteins (Insect Defensin A and Hemoglobin). The present findings exhibit results that are consistent with previous ones obtained by other methodologies.     

一个包含新的Smarandache函数的方程

定义一个新的Smarandache函数(?)(n),并研究一个包含该函数的方程.利用初等方法,给出了一个包含函数(?)(n)的方程的正整数解.方程只有五个正整数解.     

Evaluation of logistics related policies between two different levels of the supply chain network—a case study

This paper will discuss the case study conducted to evaluate a logistics related policy (time between successive collections of commodities) that optimizes the total shifting cost and minimizes the transportation cost by considering the problem as a Dynamic Multi Capacitated Vehicle Routing Problem (DMCVRP). The DMCVRP is formulated and solved for various policies using Mixed Integer Linear Programming (MILP) with an objective to minimize the cost associated with the distance traveled by the vehicles and the cost associated with unutilized capacity in the vehicles. Finally, we approximate the total shifting cost as a single variable function of transportation, inspection and inventory carrying cost, which possesses continuous derivatives at every order with the single variable as time between successive collections and derive the necessary and sufficient conditions in locating the optimum (minimum) total shifting cost.     

Production planning problem with sequence dependent setups as a bilevel programming problem

Each of n products is to be processed on two machines in order to satisfy known demands in each of T periods. Only one product can be processed on each machine at any given time. Each switch from one item to another requires sequence dependent setup time. The objective is to minimize the total setup time and the sum of the costs of production, storage and setup. We consider the problem as a bilevel mixed 0–1 integer programming problem. The objective of the leader is to assign the products to the machines in order to minimize the total sequence dependent setup time, while the objective of the follower is to minimize the production, storage and setup cost of the machine. We develop a heuristics based on tabu search for solving the problem. At the end, some computational results are presented.     

A biobjective method for sample allocation in stratified sampling

The two main and contradicting criteria guiding sampling design are accuracy of estimators and sampling costs. In stratified random sampling, the sample size must be allocated to strata in order to optimize both objectives.     

Symmetric duality for minimax multiobjective variational mixed integer programming problems with partial-invexity

A pair of symmetric dual multiobjective variational mixed integer programs for the polars of arbitrary cones are formulated, which some primal and dual variables are constrained to belong to the set of integers. Under the separability with respect to integer variables and partial-invexity assumptions on the functions involved, we prove the weak, strong, converse and self-duality theorems to related minimax efficient solution. These results include some of available results.     

A dynamic adaptive local search algorithm for the circular packing problem

This paper studies the circular packing problem (CPP) which consists of packing n non-identical circles C_i of known radius r_i, i ∈ N = {1, … , n}, into the smallest containing circle C. The objective is to determine the coordinates (x_i, y_i) of the center of C_i, i ∈ N, as well as the radius r and center (x, y) of C. This problem, which is a variant of the two-dimensional open dimension problem, is solved using a two-step, dynamic, adaptive, local search algorithm. At each iteration, the algorithm identifies the set of potential “best local positions” of a circle C_i, i ∈ N, given the positions of the previously packed circles, and determines for each of these positions the coordinates and radius of the smallest containing circle. The “best local position” minimizes the radius of the current containing circle. That is, every time an additional circle is packed, both the center and the radius of the containing circle are dynamically updated, and the smallest containing circle is known. The experimental results reflect the good performance of the algorithm.     

Using pattern matching for tiling and packing problems

This paper describes a new placement method based on pattern matching for 2D tiling problems. Tiling problem can be considered as a special case of bin packing. In the proposed method, the representation of the figures and the board is based on directional chain codes. Contrary to other works that the area has been used for the board and the figures, the proposed method is based on usage of their boundaries instead. With this representation, consideration of the area has been replaced with that of the exact string matching. With the proposed knowledge representation, rotation and reflection of the figures can be considered easily. The results of a hybrid approach of genetic algorithm and simulated annealing have been shown. This new method, introduces a novel approach for handling and solving a variety of 2D-packing problems.