MolADI: A Web Server for Automatic Analysis of Protein–Small Molecule Dynamic Interactions

Protein–ligand interaction analysis is important for drug discovery and rational protein design. The existing online tools adopt only a single conformation of the complex structure for calculating and displaying the interactions, whereas both protein residues and ligand molecules are flexible to some extent. The interactions evolved with time in the trajectories are of greater interest. MolADI is a user-friendly online tool which analyzes the protein–ligand interactions in detail for either a single structure or a trajectory. Interactions can be viewed easily with both 2D graphs and 3D representations. MolADI is available as a web application.     

Applying robust multibit watermarks to digital images

The current work is focusing on the implementation of a robust multibit watermarking algorithm for digital images, which is based on an innovative spread spectrum technique analysis. The paper presents the watermark embedding and detection algorithms, which use both wavelets and the Discrete Cosine Transform and analyzes the arising issues.     

On the bifurcation analysis of a food web of four species

This paper is concerned with bifurcations of equilibria and the chaotic dynamics of a food web containing a bottom prey X, two competing predators Y and Z on X, and a super-predator W only on Y. Conditions for the existence of all equilibria and the stability properties of most equilibria are derived. A two-dimensional bifurcation diagram with the aid of a numerical method for identifying bifurcation curves is constructed to show the bifurcations of equilibria. We prove that the dynamical system possesses a line segment of degenerate steady states for the parameter values on a bifurcation line in the bifurcation diagram. Numerical simulations show that these degenerate steady states can help to switch the stabilities between two far away equilibria when the system crosses this bifurcation line. Some observations concerned with chaotic dynamics are also made via numerical simulations. Different routes to chaos are found in the system. Relevant calculations of Lyapunov exponents and power spectra are included to support the chaotic properties.     

STOCHASTICITY NEAR RESONANCES IN A KIND OF NEAR-INTEGRABLE HAMILTONIAN SYSTEMS BASED ON SMALE HORSESHOES

In this paper, a method is developed to detect the appearance of stochasticity in a kind of near-integrable Hamiltonian system with two time-scales. One is fast and the other slow. The stochasticity is showed to be chaos in the sense of Smale horseshoes actually.A stochastic web is discovered in our example, by use of the results obtained in this paper.     

Molecular property diagnostic suite (MPDS): Development of disease-specific open source web portals for drug discovery$

Abstract

Molecular property diagnostic suite (MPDS) is a Galaxy-based open source drug discovery and development platform. MPDS web portals are designed for several diseases, such as tuberculosis, diabetes mellitus, and other metabolic disorders, specifically aimed to evaluate and estimate the drug-likeness of a given molecule. MPDS consists of three modules, namely data libraries, data processing, and data analysis tools which are configured and interconnected to assist drug discovery for specific diseases. The data library module encompasses vast information on chemical space, wherein the MPDS compound library comprises 110.31 million unique molecules generated from public domain databases. Every molecule is assigned with a unique ID and card, which provides complete information for the molecule. Some of the modules in the MPDS are specific to the diseases, while others are non-specific. Importantly, a suitably altered protocol can be effectively generated for another disease-specific MPDS web portal by modifying some of the modules. Thus, the MPDS suite of web portals shows great promise to emerge as disease-specific portals of great value, integrating chemoinformatics, bioinformatics, molecular modelling, and structure- and analogue-based drug discovery approaches.     

Phytoplankton Temporal Strategies Increase Entropy Production in a Marine Food Web Model

We develop a trait-based model founded on the hypothesis that biological systems evolve and organize to maximize entropy production by dissipating chemical and electromagnetic free energy over longer time scales than abiotic processes by implementing temporal strategies. A marine food web consisting of phytoplankton, bacteria, and consumer functional groups is used to explore how temporal strategies, or the lack thereof, change entropy production in a shallow pond that receives a continuous flow of reduced organic carbon plus inorganic nitrogen and illumination from solar radiation with diel and seasonal dynamics. Results show that a temporal strategy that employs an explicit circadian clock produces more entropy than a passive strategy that uses internal carbon storage or a balanced growth strategy that requires phytoplankton to grow with fixed stoichiometry. When the community is forced to operate at high specific growth rates near 2 d⁻¹, the optimization-guided model selects for phytoplankton ecotypes that exhibit complementary for winter versus summer environmental conditions to increase entropy production. We also present a new type of trait-based modeling where trait values are determined by maximizing entropy production rather than by random selection.     

基于Rough集的Web页面信息的提取模型及页面近似度比较

将Rough集理论应用于web信息提取模型,从而将结构含糊的Web资源,转换成了结构化信息,并以“法律”关键词搜索的Web网页为例,量化在特定标签属性上进行全文搜索的结果页面与关键词之间的近似程度。     

考虑梗腋影响的波形钢腹板组合箱梁剪力滞效应研究

考虑梗腋在波形钢腹板组合箱梁剪力滞效应的影响,通过剪力流公式定义了考虑梗腋影响的修正系数,运用变分法得到对应的微分方程,然后求出简支波形钢腹板组合箱梁在集中荷载作用下的剪力滞系数计算公式,采用数值模拟进行对比验证。最后通过调整梗腋尺寸参数,研究梗腋形状变化对剪力滞效应的影响。结果表明,考虑梗腋影响后的理论计算结果与有限元结果吻合较好;波形钢腹板组合箱梁的剪力滞效应现象随着梗腋影响系数的增大而减小;考虑梗腋影响的波形钢腹板组合箱梁剪力滞系数较未考虑情况大幅度降低,在集中荷载下剪力滞效应系数减小约10%;当梗腋宽度与上翼板宽度的比值大于0.5时,对剪力滞效应的影响变化较小,梗腋高度为其宽度的0.16~0.19倍时对剪力滞效应影响最大。     

Origin of Piezoelectricity in an Electrospun Poly(vinylidene fluoride‐trifluoroethylene) Nanofiber Web‐Based Nanogenerator and Nano‐Pressure Sensor

A single stage electrospinning process can give rise to preferentially oriented induced dipoles in poly(vinylidene fluoride‐trifluoroethylene) [P(VDF‐TrFE)] nanofibers. The piezoelectricity of as‐electrospun P(VDF‐TrFE) nanofiber webs opens up new possibilities for their use as a flexible nanogenerators and nano‐pressure sensors. In this work, the origin of the piezoelectricity has been spotlighted by randomization of the induced dipoles at the Curie temperature and analyzed by polarized FT‐IR spectroscopic techniques as well as by detecting the piezoelectric signal from a nano‐pressure sensor.

     

The stochastic web on a spherical surface generated by simple, 3-dimensional rotational transformations

It is shown that the stochastic web (or chaotic web) on the surface of a sphere can be generated by a simple, 3-dimentional rotational map, constructed by three rotational angles about each coordinate axis: x-axis, y-axis and z-axis. It is remarkable that the rotational angles in our model do not need to be complicated functions of the coordinates. As a matter of fact, the stochastic web is found when our map only consists of one simple functional rotational angle and two constant rotational angles, under certain resonance conditions. The trajectories are computed and the 3-dimentional plots of the stochastic web on the spherical surface are also presented.