Molecular Dynamics Simulation of Macromolecules Using Graphics Processing Unit

Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In recent years, graphics processing unit (GPU) provides unprecedented computational power for scientific applications. Many MD algorithms suit with the multithread nature of GPU. In this paper, MD algorithms for macromolecular systems that run entirely on GPU are presented. Compared to the MD simulation with free software GROMACS on a single CPU core, our codes achieve about 10 times speed-up on a single GPU. For validation, we have performed MD simulations of polymer crystallization on GPU, and the results observed perfectly agree with computations on CPU. Therefore, our single GPU codes have already provided an inexpensive alternative for macromolecular simulations on traditional CPU clusters and they can also be used as a basis to develop parallel GPU programs to further speedup the computations.Comment: 21 pages, 16 figure

Investigation of nonlinear flame response to dual-frequency disturbances

The two-way interaction between the unsteady flame heat release rate and acoustic waves can lead to combustion instability within combustors. To understand and quantify the flame response to oncoming acoustic waves, previous studies have typically considered the flame dynamic response to pure tone forcing and assumed a dynamically linear or weakly nonlinear response. In this study, the introduction of excitation with two distinct frequencies denoted $St_1$ and $St_2$ is considered, including the effect of excitation amplitude in order to gain more insight into the nature of flame nonlinearities and these associated with combustion instabilities. Corresponding results are obtained by combining a low-order asymptotic analysis (up to third order in normalised excitation amplitude) with numerical methods based on the model framework of the $G$-equation. The influence paths of the disturbance at $St_2$ on the flame dynamic response at $St_1$ are studied in detail. Due to the flame propagating forward normally to itself (named flame kinematic restoration), the perturbation at $St_2$ acts together with that at $St_1$ to induce a third-order nonlinear interaction in the flame kinematics, impressively suppressing the spatial wrinkling of the flame at $St_1$. Additionally, introducing the perturbation at $St_2$ alters the effective flame displacement speed, which is responsible for the calculation of the flame heat release rate and further affects the global response at $St_1$. Taking into account the above two factors, the nonlinear response of the flame at $St_1$ is completely quantified and the corresponding characteristics are clearly interpreted

Proteomic Analysis of the Hepatopancreas of Chinese Mitten Crabs (Eriocheir sinensis) Fed With a Linoleic Acid or α-Linolenic Acid Diet

As representatives of n-6 and n-3 fatty acids, many studies have analyzed the use of soybean oil and linseed oil rich in linoleic acid (18:2n-6, LA) and α-linolenic acid (18:3n-3, LNA) as better substitutes for fish oil. In aquatic animals, different dietary ratios of LA and LNA could have significant effects on growth, lipid metabolism, immune response, and reproduction. To assess the nutritive value of these two fatty acids in Chinese mitten crab (Eriocheir sinensis), we performed transcriptome analysis and label-free quantification proteomic analysis of the hepatopancreas from mitten crabs fed with LA or LNA diet. Parallel reaction monitoring was used to confirm the reliability of the proteomic analysis. A total of 186 proteins were differentially expressed with fold change ≥1.5 or ≤0.666. Among the 186 proteins, 116 were upregulated and 70 were downregulated in the LA than LNA. Most of these proteins participate in cellular process and metabolism process and have molecular functions such as binding and catalytic activity; the cellular component of these proteins are cell, cell part, membrane, and membrane part. A total of 18 proteins were identified to be related to lipid, carbohydrate, and protein metabolism, and they mainly participate in digestive enzyme activities, fatty acid transport, and glycolysis. Our results provide new insights for further investigation into the replacement of fish oil from mitten crabs with vegetable oils and enable us to better understand the different roles and nutrition value of LA and LNA in mitten crabs

Air travel demand forecasting based on big data: A struggle against public anxiety

It is of great significance to accurately grasp the demand for air travel to promote the revival of long-distance travel and alleviate public anxiety. The main purpose of this study is to build a high-precision air travel demand forecasting framework by introducing effective Internet data. In the age of big data, passengers before traveling often look for reference groups in search engines and make travel decisions under their informational influence. The big data generated based on these behaviors can reflect the overall passenger psychology and travel demand. Therefore, based on big data mining technology, this study designed a strict dual data preprocessing method and an ensemble forecasting framework, introduced search engine data into the air travel demand forecasting process, and conducted empirical research based on the dataset composed of air travel volume of Shanghai Pudong International Airport. The results show that effective search engine data is helpful to air travel demand forecasting. This research provides a theoretical basis for the application of big data mining technology and data spatial information in air travel demand forecasting and tourism management, and provides a new idea for alleviating public anxiety

Spatiotemporal Distribution of Eutrophication in Lake Tai as Affected by Wind

One common hypothesis is that wind can affect concentrations of nutrients (i.e., nitrogen and phosphorus) and chlorophyll-a (Chl-a) in shallow lakes. However, the tests of this hypothesis have yet to be conclusive in existing literature. The objective of this study was to use long-term data to examine how wind direction and wind speed affect the spatiotemporal variations of total nitrogen (TN), total phosphorus (TP) and Chl-a in Lake Tai, a typical shallow lake located in east China. The results indicated that the concentrations of nutrients and Chl-a tended to decrease from the northwest to the southeast of Lake Tai, with the highest concentrations in the two leeward bays (namely Meiliang Bay and Zhushan Bay) in the northwestern part of the lake. In addition to possible artificial reasons (e.g., wastewater discharge), the prevalent southeastward winds in warm seasons (i.e., spring and summer) and northwestward winds in cool seasons (i.e., fall and winter) might be the major natural factor for such a northwest-southeast decreasing spatial pattern. For the lake as a whole, the concentrations of TN, TP and Chl-a were highest for a wind speed between 2.1 and 3.2 m·s-1, which can be attributed to the idea that the wind-induced drifting and mixing effects might be dominant in the bays while the wind-induced drifting and resuspension effects could be more important in the other parts of the lake. Given that the water depth of the bays was relatively larger than that of the other parts, the drifting and mixing effects were likely dominant in the bays, as indicated by the negative relationships between the ratios of wind speed to lake depth, which can be a surrogate for the vertical distribution of wind-induced shear stress and the TN, TP and Chl-a concentration. Moreover, the decreasing temporal trend of wind speed in combination with the ongoing anthropogenic activities will likely increase the challenge for dealing with the eutrophication problem of Lake Tai. © 2017 by the authors

Research on Government-Enterprise Regulation of Online Car-Hailing Based on Differential Game

In the Internet era, with the widespread application of digital technology, the way people travel has changed. Compared with traditional taxis, more and more people prefer to choose online car-hailing. The rapid development of the online car-hailing industry has solved the problem of taxi-hailing to a certain extent, but it has also brought some new problems. To change the dilemma of the online car-hailing industry, it is necessary to strengthen the regulation of the online car-hailing industry. In this study, we consider the regulatory system composed of a local government and an enterprise and use the differential game to study the regulation of online car-hailing. In the Nash non-cooperative game, Stackelberg master–slave game, and cooperative game, we, respectively, investigate the indicators, such as the optimal regulatory effort of the government, the optimal regulatory effort of the enterprise, the optimal benefit function of the government, the optimal benefit function of the enterprise, the optimal benefit function of the system, the optimal trajectory of the service quality level for the enterprise, and the optimal trajectory of the goodwill for the enterprise. Moreover, we analyze the corresponding conclusions through examples. We obtained some important results. (i) In the Stackelberg master–slave game, the optimal ratio of the local government subsidy to the enterprise's regulatory cost is only related to the benefit distribution coefficient and has nothing to do with other factors. Moreover, when the benefit distribution coefficient is >1/3, the local government is willing to share the regulatory cost of the enterprise. Otherwise, the local government refuses to share the regulatory cost of the enterprise. (ii) Compared with the Nash non-cooperative game, the optimal regulatory effort of the local government remains unchanged in the Stackelberg master–slave game, but the optimal benefit of the local government increases. Moreover, when the benefit distribution coefficient is >1/3, both the optimal regulatory effort and the optimal benefit of the enterprise increase. (iii) Compared with the Stackelberg master–slave game, in the cooperative game, the optimal regulatory effort of both government and enterprise increases, and the system's optimal benefit also increases. (iv) From the Nash non-cooperative game to the Stackelberg master–slave game and then to the cooperative game when the benefit distribution coefficient is >1/3, the service quality level and goodwill of the enterprise all increase

The circular economy in China: Achievements, challenges and potential implications for decarbonisation

China's wide-ranging circular economy (CE) efforts have been studied multiple times from a range of perspectives. Synthesizing the relevant literature, this paper provides a critical reflection on the transition to a CE in China. Key factors for China's success in shifting towards a CE are seen in multi-level indicators and upscaling niches. This paper makes a novel contribution on limitations to progress, based on emerging evidence on CE projects that fail to sustain. Enriched by experts feedback, this paper critically addresses future challenges to a deep transition resulting from implementation gaps between early majorities and mass markets and coordination challenges arising through regional and sectoral differences. In light of China's commitments to climate neutrality by 2060, such challenges are considered serious. Based on feasible policy learning, the paper however proposes synergies between the CE and decarbonisation driven by efficiency improvements, comprehensive core indicators, upscaling and urban policies as trigger for deeper transformations. Finally the paper undertakes broader reflections and an outlook on evidence-orientated policy learning for a CE and decarbonisation in China

Identification of Cassava MicroRNAs under Abiotic Stress

Edwardsiella ictaluri (E. ictaluri) is one of the main bacterial pathogens in catfish which has caused serious economic loss to yellow catfish (Pelteobagrus fulvidraco) in China. In our previous work, we demonstrated that CypA was up-regulated at the early stage of E. ictaluri infection in yellow catfish and displayed strong chemotactic activity for leukocytes in vitro. However, the effect of CypA on E. ictaluri is unknown in vivo. Therefore, two homozygous transgenic zebrafish lines expressing yellow catfish CypA (TG-CypA-1 and TG-CypA-2) were generated. After challenged with E. ictaluri at a dose of 1.0 x 10(4) CFU per adult fish, both two transgenic lines exhibited a higher resistance to bacterial infection than the wildtype zebrafish. Herein, CypA gene in E. ictalurichallenged yellow catfish was screened for presence of polymorphisms by sequencing and six single nucleotide polymorphisms (SNPs) were identified. SNP association analysis revealed that 528T/C SNP in the first intron was significantly different in disease-susceptible and-resistant groups, which was confirmed in two independent populations of yellow catfish. Moreover, the relative expression of CypA in the resistant group (CC genotype in 528T/C SNP) was significantly higher than that in the susceptible group (TT genotype in 528T/C SNP) in different immune organs of yellow catfish including spleen, head kidney, body kidney and liver. Our results reveal the potential function of CypA in host defense to bacterial infection and suggest the SNP marker in CypA gene associated with the resistance to E. ictaluri may facilitate the selective breeding of disease-resistant yellow catfish in the future