Tramp Ship Scheduling Problem with Berth Allocation Considerations and Time-dependent Constraints

This work presents a model for the Tramp Ship Scheduling problem including berth allocation considerations, motivated by a real case of a shipping company. The aim is to determine the travel schedule for each vessel considering multiple docking and multiple time windows at the berths. This work is innovative due to the consideration of both spatial and temporal attributes during the scheduling process. The resulting model is formulated as a mixed-integer linear programming problem, and a heuristic method to deal with multiple vessel schedules is also presented. Numerical experimentation is performed to highlight the benefits of the proposed approach and the applicability of the heuristic. Conclusions and recommendations for further research are provided.Comment: 16 pages, 3 figures, 5 tables, proceedings paper of Mexican International Conference on Artificial Intelligence (MICAI) 201

SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution

BACKGROUND: General protein evolution models help determine the baseline expectations for the evolution of sequences, and they have been extensively useful in sequence analysis and for the computer simulation of artificial sequence data sets. RESULTS: We have developed a new method of simulating protein sequence evolution, including insertion and deletion (indel) events in addition to amino-acid substitutions. The simulation generates both the simulated sequence family and a true sequence alignment that captures the evolutionary relationships between amino acids from different sequences. Our statistical model for indel evolution is based on the empirical indel distribution determined by Qian and Goldstein. We have parameterized this distribution so that it applies to sequences diverged by varying evolutionary times and generalized it to provide flexibility in simulation conditions. Our method uses a Monte-Carlo simulation strategy, and has been implemented in a C++ program named Simprot. CONCLUSION: Simprot will be useful for testing methods of analysis of protein sequence families particularly alignment methods, phylogenetic tree building, detection of recombination and horizontal gene transfer, and homology detection, where knowing the true course of sequence evolution is essential

Creep characterisation of Inconel 718 lattice metamaterials manufactured by laser powder bed fusion

Lattice metamaterials manufactured by laser powder bed fusion (LPBF) are limited by their performance for critical applications. LPBF materials have microstructural or macroscale anomalies, such as suboptimal grain size, morphology, and lack of fusion. This results in LPBF metamaterials performance degradation for various mechanical properties, such as creep, which has seldom been researched. To understand the creep behavior of LPBF Inconel 718, body-centered cubic metamaterials are fabricated for creep test at 650 °C. Kachanov's damage modeling is used to predict the creep performance of the metamaterials under different loading conditions. Microstructural characterization is performed with scanning electron microscopy to identify critical microstructure defects affecting the failure mechanisms and creep behaviors of the metamaterials. It is shown in the results that the loading conditions affect the fracture process of the metamaterials owing to different failure mechanisms. In the simulation and test results, the logarithmic decline in creep life is shown when loading increases; also, logarithmic increase in the creep life is shown when relative density increases

Preference of Small Molecules for Local Minimum Conformations when Binding to Proteins

It is well known that small molecules (ligands) do not necessarily adopt their lowest potential energy conformations when binding to proteins. Analyses of protein-bound ligand crystal structures have reportedly shown that many of them do not even adopt the conformations at local minima of their potential energy surfaces (local minimum conformations). The results of these analyses raise a concern regarding the validity of virtual screening methods that use ligands in local minimum conformations. Here we report a normal-mode-analysis (NMA) study of 100 crystal structures of protein-bound ligands. Our data show that the energy minimization of a ligand alone does not automatically stop at a local minimum conformation if the minimum of the potential energy surface is shallow, thus leading to the folding of the ligand. Furthermore, our data show that all 100 ligand conformations in their protein-bound ligand crystal structures are nearly identical to their local minimum conformations obtained from NMA-monitored energy minimization, suggesting that ligands prefer to adopt local minimum conformations when binding to proteins. These results both support virtual screening methods that use ligands in local minimum conformations and caution about possible adverse effect of excessive energy minimization when generating a database of ligand conformations for virtual screening

Normal-Mode-Analysis–Monitored Energy Minimization Procedure for Generating Small–Molecule Bound Conformations

The energy minimization of a small molecule alone does not automatically stop at a local minimum of the potential energy surface of the molecule if the minimum is shallow, thus leading to folding of the molecule and consequently hampering the generation of the bound conformation of a guest in the absence of its host. This questions the practicality of virtual screening methods that use conformations at local minima of their potential energy surfaces (local minimum conformations) as potential bound conformations. Here we report a normal-mode-analysis–monitored energy minimization (NEM) procedure that generates local minimum conformations as potential bound conformations. Of 22 selected guest–host complex crystal structures with guest structures possessing up to four rotatable bonds, all complexes were reproduced, with guest mass–weighted root mean square deviations of <1.0 Å, through docking with the NEM–generated guest local minimum conformations. An analysis of the potential energies of these local minimum conformations showed that 22 (100%), 18 (82%), 16 (73%), and 12 (55%) of the 22 guest bound conformations in the crystal structures had conformational strain energies of less than or equal to 3.8, 2.0, 0.6, and 0.0 kcal/mol, respectively. These results suggest that (1) the NEM procedure can generate small–molecule bound conformations, and (2) guests adopt low-strain–energy conformations for complexation, thus supporting the virtual screening methods that use local minimum conformations

Individual freedom versus collective responsibility: too many rights make a wrong?

Individuals might reasonably expect the freedom to make their own decisions regarding their health. However, what happens when an individual's wishes conflict with what is in that individual's best interests? How far should an individual's rights be restricted for his or her own benefit? Similarly, what limitations should be placed on an individual's behaviour when that person's wishes go against what is good for the population in general? Here we discuss the issues that can arise when the rights of individuals conflict with individual and population benefits in relation to infectious diseases

A pilot study to evaluate the application of a generic protein standard panel for quality control of biomarker detection technologies

<p>Abstract</p> <p>Background</p> <p>Protein biomarker studies are currently hampered by a lack of measurement standards to demonstrate quality, reliability and comparability across multiple assay platforms. This is especially pertinent for immunoassays where multiple formats for detecting target analytes are commonly used.</p> <p>Findings</p> <p>In this pilot study a generic panel of six non-human protein standards (50 - 10^7 pg/mL) of varying abundance was prepared as a quality control (QC) material. Simulated "normal" and "diseased" panels of proteins were prepared in pooled human plasma and incorporated into immunoassays using the Meso Scale Discovery^®(MSD^®) platform to illustrate reliable detection of the component proteins. The protein panel was also evaluated as a spike-in material for a model immunoassay involving detection of ovarian cancer biomarkers within individual human plasma samples. Our selected platform could discriminate between two panels of the proteins exhibiting small differences in abundance. Across distinct experiments, all component proteins exhibited reproducible signal outputs in pooled human plasma. When individual donor samples were used, half the proteins produced signals independent of matrix effects. These proteins may serve as a generic indicator of platform reliability.</p> <p>Each of the remaining proteins exhibit differential signals across the distinct samples, indicative of sample matrix effects, with the three proteins following the same trend. This subset of proteins may be useful for characterising the degree of matrix effects associated with the sample which may impact on the reliability of quantifying target diagnostic biomarkers.</p> <p>Conclusions</p> <p>We have demonstrated the potential utility of this panel of standards to act as a generic QC tool for evaluating the reproducibility of the platform for protein biomarker detection independent of serum matrix effects.</p