Assembling hydrodynamic cloaks to conceal complex objects from drag

Transformation hydrodynamics and the corresponding metamaterials have been proposed as a means to exclude the drag force acting on an object. Here, we report a strategy to deploy the hydrodynamic cloaks in a more practical manner by assembling different-shaped cloaking parts. Our strategy is to first model a square-shaped cloak and a carpet cloak and then combine them to conceal a more complex-shaped space in the three-dimensional hydrodynamic flow. With the derivation of transformation hydrodynamics, the coordinate transformations for each hydrodynamic cloaking are demonstrated with the calculated viscosity tensors. The pressure and velocity fields of the square, triangular (carpet), and exemplary three-dimensional house-shaped cloaks are numerically simulated, thus showing a cloaking effect and reduced drag. This study suggests an efficient way of cloaking complex architectures from fluid-dynamic forces.     

predForm-Site: Formylation site prediction by incorporating multiple features and resolving data imbalance

Formylation is one of the newly discovered post-translational modifications in lysine residue which is responsible for different kinds of diseases. In this work, a novel predictor, named predForm-Site, has been developed to predict formylation sites with higher accuracy. We have integrated multiple sequence features for developing a more informative representation of formylation sites. Moreover, decision function of the underlying classifier have been optimized on skewed formylation dataset during prediction model training for prediction quality improvement. On the dataset used by LFPred and Formator predictor, predForm-Site achieved 99.5% sensitivity, 99.8% specificity and 99.8% overall accuracy with AUC of 0.999 in the jackknife test. In the independent test, it has also achieved more than 97% sensitivity and 99% specificity. Similarly, in benchmarking with recent method CKSAAP_FormSite, the proposed predictor significantly outperformed in all the measures, particularly sensitivity by around 20%, specificity by nearly 30% and overall accuracy by more than 22%. These experimental results show that the proposed predForm-Site can be used as a complementary tool for the fast exploration of formylation sites. For convenience of the scientific community, predForm-Site has been deployed as an online tool, accessible at http://103.99.176.239:8080/predForm-Site.     

Scaffold-based molecular design with a graph generative model

Searching for new molecules in areas like drug discovery often starts from the core structures of known molecules. Such a method has called for a strategy of designing derivative compounds retaining a particular scaffold as a substructure. On this account, our present work proposes a graph generative model that targets its use in scaffold-based molecular design. Our model accepts a molecular scaffold as input and extends it by sequentially adding atoms and bonds. The generated molecules are then guaranteed to contain the scaffold with certainty, and their properties can be controlled by conditioning the generation process on desired properties. The learned rule of extending molecules can well generalize to arbitrary kinds of scaffolds, including those unseen during learning. In the conditional generation of molecules, our model can simultaneously control multiple chemical properties despite the search space constrained by fixing the substructure. As a demonstration, we applied our model to designing inhibitors of the epidermal growth factor receptor and show that our model can employ a simple semi-supervised extension to broaden its applicability to situations where only a small amount of data is available.

We propose a scaffold-based graph generative model for designing novel drug candidates that include the desired scaffold as a substructure.     

Sparse non-negative matrix factorizations for ultrasound factor analysis

Factor analysis is a powerful tool used for the analysis of dynamic studies. One of the major drawbacks of Factor Analysis of Dynamic Structures (FADS) is that the solution is not mathematically unique when only non-negativity constraints are used to determine factors and factor coefficients. In this paper, we introduce a novel method to correct FADS solutions by constructing and minimizing a new objective function. The method is improved from non-negative matrix factorizations (NMFs) algorithm by adding a sparse constraint that penalizes multiple components in the images of the factor coefficients. The technique is tested on computer simulations, and a patient ultrasound liver study. The results show that the method works well in comparison to the truth in computer simulations and to region of interest (ROI) measurements in the experimental studies.     

Persistence of oxidation state III of gold in thione coordination

Ligands N,N'-tetramethylthiourea and 2-mercapto-1-methyl-imidazole form stable Au(III) complexes [AuCl₃(N,N'-tetramethylthiourea)] (1) and [AuCl₃(2-mercapto-1-methyl-imidazole)] (2) instead of reducing the Au(III) metal center into Au(I), which would be typical for the attachment of sulfur donors. Compounds 1 and 2 were characterized by spectroscopic methods and by X-ray crystallography. The spectroscopic details were explained by simulation of the UV-Vis spectra via the TD-DFT method. Additionally, computational DFT studies were performed in order to find the reason for the unusual oxidation state in the crystalline materials. The preference for Au(III) can be explained via various weak intra- and intermolecular interactions present in the solid state structures. The nature of the interactions was further investigated by topological charge density analysis via the QTAIM method.     

How the expanded crowd-funding mechanism of some southern rural areas in China affects cooperative behaviors in threshold public goods game

The pursuit of high cooperation rates in public goods games has attracted many researchers. However, few researchers attach much weight to the influence of emotions on decision-making, especially on public goods games. From ancient to modern times, publishing the list of cooperators to stimulate cooperation has been a common phenomenon in some southern rural areas in China. Actually, the published list can influence individuals’ behaviors by affecting their emotions. Here we extend the method of publishing the list and optimize it by adding a lobbyist mechanism. Through numerical simulations, we find that the role of lobbyists can not be ignored unless the synergy factor is larger than a certain value. Additionally, we find that publishing the list certainly has a great effect on individual’s cooperative behavior. But whether to publish the list or not and how to publish the list depend on the situation.     

Pattern formation and control of spatiotemporal chaos in a reaction diffusion prey–predator system supplying additional food

Spatiotemporal dynamics of a predator–prey system in presence of spatial diffusion is investigated in presence of additional food exists for predators. Conditions for stability of Hopf as well as Turing patterns in a spatial domain are determined by making use of the linear stability analysis. Impact of additional food is clear from these conditions. Numerical simulation results are presented in order to validate the analytical findings. Finally numerical simulations are carried out around the steady state under zero flux boundary conditions. With the help of numerical simulations, the different types of spatial patterns (including stationary spatial pattern, oscillatory pattern, and spatiotemporal chaos) are identified in this diffusive predator–prey system in presence of additional food, depending on the quantity, quality of the additional food and the spatial domain and other parameters of the model. The key observation is that spatiotemporal chaos can be controlled supplying suitable additional food to predator. These investigations may be useful to understand complex spatiotemporal dynamics of population dynamical models in presence of additional food.     

Quantum Windowed Fourier Transform and its Application to Quantum Signal Processing

International Journal of Theoretical Physics - In classical information processing, the windowed Fourier transform (WFT), or short-time Fourier transform, which is a variant of the Fourier...