Conservative allocation models for outbound containers in container terminals

This paper examines location assignment for outbound containers in container terminals. It is an extension to the previous modeling work of Kim et al. (2000) and Zhang et al. (2010). The previous model was an “optimistic” handling way and gave a moderate punishment for placing a lighter container onto the top of a stack already loaded with heavier containers. Considering that the original model neglected the stack height and the state-changing magnitude information when interpreting the punishment parameter and hid too much information about the specific configurations for a given stack representation, we propose two new “conservative” allocation models in this paper. One considers the stack height and the state-changing magnitude information by reinterpreting the punishment parameter and the other further considers the specific configurations for a given stack representation. Solution qualities for the “optimistic” and the two “conservative” allocation models are compared on two performance indicators. The numerical experiments indicate that both the first and second “conservative” allocation models outperform the original model in terms of the two performance indicators. In addition, to overcome computational difficulties encountered by the dynamic programming algorithm for large-scale problems, an approximate dynamic programming algorithm is presented as well.     

The Terminal-Oriented Ship Stowage Planning Problem

The Ship Stowage Planning Problem is the problem of determining the optimal position of containers to be stowed in a containership. In this paper we address the problem considering the objectives of the terminal management that are mainly related to the yard and transport operations. We propose a Binary Integer Program and a two-step heuristic algorithm. An extensive computational experience shows the efficiency and effectiveness of our approach. A classification scheme for stowage planning problems is also provided.     

Application of the VOF method to the sloshing of a fluid in a partially filled cylindrical container

In a previous work we solved numerically the steady-state motion of an ideal fluid that fills a moving cylindrical container with partitions, and were able to compute the equivalent moments of inertia. Here we extend this work in two steps. First we introduce time dependence and then free surfaces, and are able to compute the transient motion of the fluid not filling the container. The main body of the work has to do with the treatment of free surfaces. Our approach is an extention to three dimensions of the volume of fluid method of Hirt and Nichols. The solution algorithm is outlined, and two examples that demonstrate its capability are presented.     

The Cameron-Erd?s conjecture

A subset A of integers is said to be sum-free if a+b∉A for any a,b∈A. Let s(n) be the number of sum-free sets in interval [1,n] of integers. P. Cameron and P. Erd?s conjectured that s(n)=O(2^n/2). We show that for even n and for odd n, where are absolute constants, thereby proving the conjecture.     

Multiscale Virtual Screening Optimization for Shotgun Drug Repurposing Using the CANDO Platform

Drug repurposing, the practice of utilizing existing drugs for novel clinical indications, has tremendous potential for improving human health outcomes and increasing therapeutic development efficiency. The goal of multi-disease multitarget drug repurposing, also known as shotgun drug repurposing, is to develop platforms that assess the therapeutic potential of each existing drug for every clinical indication. Our Computational Analysis of Novel Drug Opportunities (CANDO) platform for shotgun multitarget repurposing implements several pipelines for the large-scale modeling and simulation of interactions between comprehensive libraries of drugs/compounds and protein structures. In these pipelines, each drug is described by an interaction signature that is compared to all other signatures that are subsequently sorted and ranked based on similarity. Pipelines within the platform are benchmarked based on their ability to recover known drugs for all indications in our library, and predictions are generated based on the hypothesis that (novel) drugs with similar signatures may be repurposed for the same indication(s). The drug-protein interactions used to create the drug-proteome signatures may be determined by any screening or docking method, but the primary approach used thus far has been BANDOCK, our in-house bioanalytical or similarity docking protocol. In this study, we calculated drug-proteome interaction signatures using the publicly available molecular docking method Autodock Vina and created hybrid decision tree pipelines that combined our original bio- and chem-informatic approach with the goal of assessing and benchmarking their drug repurposing capabilities and performance. The hybrid decision tree pipeline outperformed the two docking-based pipelines from which it was synthesized, yielding an average indication accuracy of 13.3% at the top10 cutoff (the most stringent), relative to 10.9% and 7.1% for its constituent pipelines, and a random control accuracy of 2.2%. We demonstrate that docking-based virtual screening pipelines have unique performance characteristics and that the CANDO shotgun repurposing paradigm is not dependent on a specific docking method. Our results also provide further evidence that multiple CANDO pipelines can be synthesized to enhance drug repurposing predictive capability relative to their constituent pipelines. Overall, this study indicates that pipelines consisting of varied docking-based signature generation methods can capture unique and useful signals for accurate comparison of drug-proteome interaction signatures, leading to improvements in the benchmarking and predictive performance of the CANDO shotgun drug repurposing platform.     

A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium

Bacteria are increasingly resistant to existing antibiotics, which target a narrow range of pathways. New methods are needed to identify targets, including repositioning targets among distantly related species. We developed a novel combination of systems and structural modeling and bioinformatics to reposition known antibiotics and targets to new species. We applied this approach to Mycoplasma genitalium, a common cause of urethritis. First, we used quantitative metabolic modeling to identify enzymes whose expression affects the cellular growth rate. Second, we searched the literature for inhibitors of homologs of the most fragile enzymes. Next, we used sequence alignment to assess that the binding site is shared by M. genitalium, but not by humans. Lastly, we used molecular docking to verify that the reported inhibitors preferentially interact with M. genitalium proteins over their human homologs. Thymidylate kinase was the top predicted target and piperidinylthymines were the top compounds. Further work is needed to experimentally validate piperidinylthymines. In summary, combined systems and structural modeling is a powerful tool for drug repositioning.     

The multiple container loading cost minimization problem

In the shipping and transportation industry, there are several types of standard containers with different dimensions and different associated costs. In this paper, we examine the multiple container loading cost minimization problem (MCLCMP), where the objective is to load products of various types into containers of various sizes so as to minimize the total cost. We transform the MCLCMP into an extended set cover problem that is formulated using linear integer programming and solve it with a heuristic to generate columns. Experiments on standard bin-packing instances show our approach is superior to prior approaches. Additionally, since the optimal solutions for existing test data is unknown, we propose a technique to generate test data with known optimal solutions for MCLCMP.     

Shunting yard operations: Theoretical aspects and applications

Almost ever since freight has been transported via rail, shunting yards (also called classification or marshaling yards) are operated in order to separate freight trains and reassemble new trains. The efficient use of shunting yards has a deep impact on the efficiency and reliability of rail freight services. Thus, much research on shunting yards has been published, starting from the 1950s. Lately, several publications mostly focusing on the sorting procedures have livened up research on shunting yards. This paper reviews the literature on the operational processes at shunting yards over the last 40 years and discusses the operational challenges of freight transshipment. The approaches are classified according to different sorting strategies which allows an easy access to the models for both, researchers and practitioners. The paper concludes with an overview on future research challenges.     

A comparison of univariate methods for forecasting container throughput volumes

In this paper, six univariate forecasting models for the container throughput volumes in Taiwan’s three major ports are presented. The six univariate models include the classical decomposition model, the trigonometric regression model, the regression model with seasonal dummy variables, the grey model, the hybrid grey model, and the SARIMA model. The purpose of this paper is to search for a model that can provide the most accurate prediction of container throughput. By applying monthly data to these models and comparing the prediction results based on mean absolute error, mean absolute percent error and root mean squared error, we find that in general the classical decomposition model appears to be the best model for forecasting container throughput with seasonal variations. The result of this study may be helpful for predicting the short-term variation in demand for the container throughput of other international ports.