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

Analysis of interspecies adherence of oral bacteria using a membrane binding assay coupled with polymerase chain reaction-denaturing gradient gel electrophoresis profiling.

Information on co-adherence of different oral bacterial species is important for understanding interspecies interactions within oral microbial community. Current knowledge on this topic is heavily based on pariwise coaggregation of known, cultivable species. In this study, we employed a membrane binding assay coupled with polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) to systematically analyze the co-adherence profiles of oral bacterial species, and achieved a more profound knowledge beyond pairwise coaggregation. Two oral bacterial species were selected to serve as "bait": Fusobacterium nucleatum (F. nucleatum) whose ability to adhere to a multitude of oral bacterial species has been extensively studied for pairwise interactions and Streptococcus mutans (S. mutans) whose interacting partners are largely unknown. To enable screening of interacting partner species within bacterial mixtures, cells of the "bait" oral bacterium were immobilized on nitrocellulose membranes which were washed and blocked to prevent unspecific binding. The "prey" bacterial mixtures (including known species or natural saliva samples) were added, unbound cells were washed off after the incubation period and the remaining cells were eluted using 0.2 mol x L(-1) glycine. Genomic DNA was extracted, subjected to 16S rRNA PCR amplification and separation of the resulting PCR products by DGGE. Selected bands were recovered from the gel, sequenced and identified via Nucleotide BLAST searches against different databases. While few bacterial species bound to S. mutans, consistent with previous findings F. nucleatum adhered to a variety of bacterial species including uncultivable and uncharacterized ones. This new approach can more effectively analyze the co-adherence profiles of oral bacteria, and could facilitate the systematic study of interbacterial binding of oral microbial species

C2G2: Controllable Co-speech Gesture Generation with Latent Diffusion Model

Co-speech gesture generation is crucial for automatic digital avatar animation. However, existing methods suffer from issues such as unstable training and temporal inconsistency, particularly in generating high-fidelity and comprehensive gestures. Additionally, these methods lack effective control over speaker identity and temporal editing of the generated gestures. Focusing on capturing temporal latent information and applying practical controlling, we propose a Controllable Co-speech Gesture Generation framework, named C2G2. Specifically, we propose a two-stage temporal dependency enhancement strategy motivated by latent diffusion models. We further introduce two key features to C2G2, namely a speaker-specific decoder to generate speaker-related real-length skeletons and a repainting strategy for flexible gesture generation/editing. Extensive experiments on benchmark gesture datasets verify the effectiveness of our proposed C2G2 compared with several state-of-the-art baselines. The link of the project demo page can be found at https://c2g2-gesture.github.io/c2_gestureComment: 12 pages, 6 figures, 7 table

Flowtable-Free Routing for Data Center Networks: A Software-Defined Approach

The paradigm shift toward SDN has exhibited the following trends: (1) relying on a centralized and more powerful controller to make intelligent decisions, and (2) allowing a set of relatively dumb switches to route packets. Therefore, efficiently looking up the flowtables in forwarding switches to guarantee low latency becomes a critical issue. In this paper, following the similar paradigm, we propose a new routing scheme called KeySet which is flowtable-free and enables constant-time switching at the forwarding switches. Instead of looking up long flowtables, KeySet relies on a residual system to quickly calculate routing paths. A switch only needs to do simple modular arithmetics to obtain a packet's forwarding output port. Moreover, KeySet has a nice fault- tolerant capability because in many cases the controller does not need to update flowtables at switches when a failure occurs. We validate KeySet through extensive simulations by using general as well as Facebook fat-tree topologies. The results show that the KeySet outperforms the KeyFlow scheme [1] by at least 25% in terms of the length of the forwarding label. Moreover, we show that KeySet is very efficient when applied to fat-trees

Characteristics of emission from laser-induced plasma of metallic compounds in gaseous condition : The effects of gas pressure and laser pulse energy

Low pressure laser-induced breakdown spectroscopy was employed to measure mercury, strontium, and cesium under different conditions. Mercury was measured in detail to discuss the effects of pressure, laser pulse energy, delay time, and buffer gas. The continuum emission from plasma reduced dramatically to enhance signal to background ratio due to the change of influence of electron impact ionization process when reducing pressure and decreasing laser pulse energy to some extent. The comparison of mercuric chloride and mercury, as well as strontium and cesium measurements, demonstrates the enhancement of detection ability for trace species measurement using low pressure laser-induced breakdown spectroscopy