Informal traders lock horns with the formal milk industry: the role of research in pro-poor dairy policy shift in Kenya

A polarizable atomic multipole-based force field for the membrane bilayer models 1,2-dioleoyl-phosphocholine (DOPC) and 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE) has been developed. The force field adopts the same framework as the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) model, in which the charge distribution of each atom is represented by the permanent atomic monopole, dipole and quadrupole moments. Many-body polarization including the inter- and intra-molecular polarization is modelled in a consistent manner with distributed atomic polarizabilities. The van der Waals parameters were first transferred from existing AMOEBA parameters for small organic molecules and then optimised by fitting to ab initio intermolecular interaction energies between models and a water molecule. Molecular dynamics simulations of the two aqueous DOPC and POPE membrane bilayer systems, consisting of 72 model molecules, were then carried out to validate the force field parameters. Membrane width, area per lipid, volume per lipid, deuterium order parameters, electron density profile, etc. were consistent with experimental values

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Polarizable force field development for lipids and their efficient applications in membrane proteins

Polarizable force fields have been developed due to the intrinsic problem of additive force fields in modeling electrostatic interactions. Because of the capability to accurately describe the behavior of systems with significant changes in their electrostatic environments, polarizable force fields might be a decent tool to study membrane-related systems, such as lipid bilayers, though not so much progresses have been made. In this overview article we described the developments of a variety of polarizable force fields, including the corresponding theories, benchmark examples, and more specifically we were focused on the applications on lipid membranes. (C) 2017 John Wiley & Sons, Lt

Free Energy Simulations with the AMOEBA Polarizable Force Field and Metadynamics on GPU Platform

The free energy calculation library PLUMED has been incorporated into the OpenMM simulation toolkit, with the purpose to perform enhanced sampling MD simulations using the AMOEBA polarizable force field on GPU platform. Two examples, (I) the free energy profile of water pair separation (II) alanine dipeptide dihedral angle free energy surface in explicit solvent, are provided here to demonstrate the accuracy and efficiency of our implementation. The converged free energy profiles could be obtained within an affordable MD simulation time when the AMOEBA polarizable force field is employed. Moreover, the free energy surfaces estimated using the AMOEBA polarizable force field are in agreement with those calculated from experimental data and ab initio methods. Hence, the implementation in this work is reliable and would be utilized to study more complicated biological phenomena in both an accurate and efficient way. (C) 2015 Wiley Periodicals, Inc

A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids

In all of the classical force fields, electrostatic interaction is simply treated and explicit electronic polarizability is neglected. The condensed-phase polarization, relative to the gas-phase charge distributions, is commonly accounted for in an average way by increasing the atomic charges, which remain fixed throughout simulations. Based on the lipid polarizable force field DMPC and following the same framework as Atomic Multipole Optimized Energetics for BiomoleculAr (AMOEBA) simulation, the present effort expands the force field to new anionic lipid models, in which the new lipids contain DMPG and POPS. The parameters are compatible with the AMOEBA force field, which includes water, ions, proteins, etc. The charge distribution of each atom is represented by the permanent atomic monopole, dipole and quadrupole moments, which are derived from the ab initio gas phase calculations. Many-body polarization including the inter- and intramolecular polarization is modeled in a consistent manner with distributed atomic polarizabilities. Molecular dynamics simulations of the two aqueous DMPG and POPS membrane bilayer systems, consisting of 72 lipids with water molecules, were then carried out to validate the force field parameters. Membrane width, area per lipid, volume per lipid, deuterium order parameters, electron density profile, electrostatic potential difference between the center of the bilayer and water are all calculated, and compared with limited experimental data

Introducing Improved Transformer to Land Cover Classification Using Multispectral LiDAR Point Clouds

The use of Transformer-based networks has been proposed for the processing of general point clouds. However, there has been little research related to multispectral LiDAR point clouds that contain both spatial coordinate information and multi-wavelength intensity information. In this paper, we propose networks for multispectral LiDAR point cloud point-by-point classification based on an improved Transformer. Specifically, considering the sparseness of different regions of multispectral LiDAR point clouds, we add a bias to the Transformer to improve its ability to capture local information and construct an easy-to-implement multispectral LiDAR point cloud Transformer (MPT) classification network. The MPT network achieves 78.49% mIoU, 94.55% OA, 84.46% F1, and 0.92 Kappa on the multispectral LiDAR point cloud testing dataset. To further extract the topological relationships between points, we present a standardization set abstraction (SSA) module, which includes the global point information while considering the relationships among the local points. Based on the SSA module, we propose an advanced version called MPT+ for the point-by-point classification of multispectral LiDAR point clouds. The MPT+ network achieves 82.94% mIoU, 95.62% OA, 88.42% F1, and 0.94 Kappa on the same testing dataset. Compared with seven point-based deep learning algorithms, our proposed MPT+ achieves state-of-the-art results for several evaluation metrics

Integrating Multiple Accelerated Molecular Dynamics To Improve Accuracy of Free Energy Calculations

Accelerated Molecular Dynamics (aMD) is a promising enhanced sampling method to explore the conformational space of biomolecules. However, the large statistical noise in reweighting limits its accuracy to recover the original free energy profile. In this work, we propose an Integrated accelerated Molecule Dynamics (IaMD) method by integrating a series of aMD subterms with different acceleration parameters to improve the sampling efficiency and maintain the reweighting accuracy simultaneously. We use Alanine Dipeptide and three fast-folded proteins (Chignolin, Trp-cage, and Villin Headpiece) as the test objects to compare our IaMD method with aMD systematically. These case studies indicate that the statistical noise of IaMD in reweighting for free energy profiles is much smaller than that of aMD at the same level of acceleration and simulation time. To achieve the same accuracy as IaMD, aMD requires 1-3 orders of magnitude longer simulation time, depending on the complexity of the simulated system and the level of acceleration. Our method also outperforms aMD in controlling systematic error caused by the disappearance of the low-energy conformations when high acceleration parameters are used in alVID simulations for fast-folded proteins. Furthermore, the performance comparison between IaMD and the Integrated Tempering Sampling (ITS) in the case of Alanine Dipeptide demonstrates that IaMD possesses a better ability to control the potential energy region of sampling

Numerical Simulation of Rock Uniaxial Compressive Strength and Deformation Failure Law under Different Size Conditions

Rock engineering occupies an important position in the 21st century. In the face of rock engineering disasters, we are only looking for the essential problems through experiments on rocks, but rock experiments cannot be realized in large numbers, so the article uses numerical simulation software RFPA (Realistic Failure Process Analysis) 2D Basic to simulate rock under different size conditions numerically. In this paper, a rock model with a diameter of 50 mm is used for simulation research. Meanwhile, five calculation models of height-to-diameter ratios of 1.0, 1.5, 2.0, 2.5, and 3 are used. Through simulation calculation, we find that the rock model failure is more than complicated when the value of the height-to-diameter ratio is exceedingly low (1), but as the height-to-diameter ratio increases, the failure mode will become simpler. The stress-concentrated failure will be in the form of axial failure. When the height-to-diameter ratio increases (1.5–2), other damage cracks appear on the basis of axial cleavage failure. As the height-to-diameter ratio continues to increase (about 2.5), only shear failure occurs. When the height-to-diameter ratio reaches a relatively high level (3), there will be both axial rip and other damage. When the height-to-diameter ratio is oversize, there will be both axial rip failure and end damage

The Impact of the Allocation of Facilities on Reducing Carbon Emissions from a Green Container Terminal Perspective

The main contribution of this paper is to quantify the impact of the allocation of facilities, including the number of facilities and the fuels adopted by facilities, on carbon emissions. In order to deal with the complex queuing network of container terminals, a simulation model is established with the changing of the number of and the fuel adopted by facilities as inputs. Firstly, the operation process and complex queuing network of container terminals are described to explain why simulation technology needs to be used. Then, various simulation experiments based on a container terminal in Algeria are designed and carried out. Finally, the carbon emissions from facilities and ships at berth and inside container terminals, and the total carbon emissions inside container terminals, are obtained and analyzed. Results show that the emissions from facilities are only a small fraction of the total emissions of container terminals. Improving the number of trucks and yard cranes can help reduce carbon emissions, but when the number continues to rise, the emissions are decreased very slightly. The results obtained and proposed method can be applied to build a green container terminal, which can also be used for similar problems

A Method for Determining the Required Power Capacity of an On-Shore Power System Considering Uncertainties of Arriving Ships

The contribution of this paper is to provide a method for determining the required power capacity of an on-shore power system (OPS) considering the stochastic nature of arriving ships. In order to cope with such complicated and stochastic operation processes in container terminals, simulation models are established with arrival intervals of ships ranging from 1 to 100 h as inputs. Firstly, the mobile pattern of OPS adopted in the container terminal is introduced. Then, patterns of arriving ships are analyzed to explain why a simulation method is necessary. Next, a series of simulation experiments based on a container terminal in China are constructed and carried out. Finally, the required power capacity of an OPS under different arrival intervals is given when considering all berthed ships using an OPS. Besides, with the consideration of reducing environmental impact of ships at different levels, the required power capacity is provided with different proportions of arriving ships using an OPS. The results obtained, and the proposed method can be used to provide references for government policy making and green container terminal construction