Molecular Docking for Ligand-Receptor Binding Process Based on Heterogeneous Computing

Molecular docking aims to predict possible drug candidates for many diseases, and it is computationally intensive. Particularly, in simulating the ligand-receptor binding process, the binding pocket of the receptor is divided into subcubes, and when the ligand is docked into all cubes, there are many molecular docking tasks, which are extremely time-consuming. In this study, we propose a heterogeneous parallel scheme of molecular docking for the binding process of ligand to receptor to accelerate simulating. The parallel scheme includes two layers of parallelism, a coarse-grained layer of parallelism implemented in the message-passing interface (MPI) and a fine-grained layer of parallelism focused on the graphics processing unit (GPU). At the coarse-grain layer of parallelism, a docking task inside one lattice is assigned to one unique MPI process, and a grouped master-slave mode is used to allocate and schedule the tasks. Meanwhile, at the fine-gained layer of parallelism, GPU accelerators undertake the computationally intensive computing of scoring functions and related conformation spatial transformations in a single docking task. The results of the experiments for the ligand-receptor binding process show that on a multicore server with GPUs the parallel program has achieved a speedup ratio as high as 45 times in flexible docking and as high as 54.5 times in semiflexible docking, and on a distributed memory system, the docking time for flexible docking and that for semiflexible docking gradually decrease as the number of nodes used in the parallel program gradually increases. The scalability of the parallel program is also verified in multiple nodes on a distributed memory system and is approximately linear.

Discrimination of POVMs with rank-one effects

The main goal of this work is to provide an insight into the problem of discrimination of positive operator-valued measures with rank-one effects. It is our intention to study multiple-shot discrimination of such measurements, that is the case when we are able to use to unknown measurement a given number of times. Furthermore, we are interested in comparing two possible discrimination schemes: the parallel and adaptive ones. To this end, we construct a pair of symmetric informationally complete positive operator-valued measures which can be perfectly discriminated in a two-shot adaptive scheme but cannot be distinguished in the parallel scheme. On top of this, we provide an explicit algorithm which allows us to find this adaptive scheme.

A Novel Parallel DTC Segmentation Scheme for Fractional-N Digital PLLs

In this paper, we propose a new parallel segmentation scheme for the digital/time converter (DTC) which is employed in fractional-N digital phase-locked loops (PLLs) to cancel out the quantization error induced by the digital DS modulator. The proposed parallel scheme removes one redundant least-mean square (LMS) gain in compared with the conventional parallel one. Therefore, the design of the system becomes less complicated while guaranteeing a fast convergence speed of the LMS gains and a short DTC time range. The effectiveness of the proposed segmentation scheme is demonstrated via simulations of a digital PLL built at behavioral level and compared to the conventional segmentation schemes.

Development of a PHEV Hybrid Transmission for Low-End MPVs Based on AMT

In order to improve the fuel economy of vehicles, based on the automated mechanical transmission (AMT), a plug-in hybrid electric vehicle (PHEV) hybrid transmission for low-end multi-purpose vehicles (MPVs) is developed. To obtain the statistics of the best-selling models, we took several best-selling models in the Chinese market as the research object to study the relationship between power demand, energy demand, weight, and cost. The power requirements and energy requirements of PHEVs are decoupled. According to the decoupled theory, a single-motor parallel scheme based on the AMT is adopted to develop a PHEV hybrid transmission. In the distribution of engine and motor power, the engine just needs to meet the vehicle’s constant driving power, and the backup power can be provided by the motor, which means we can use an engine with a smaller power rating. The energy of short-distance travel is mainly provided by the motor, which can make full use of the battery, reducing the fuel consumption. The energy of long-distance travel is mainly provided by the engine, which can reduce the need for battery capacity. The working modes of the electrified mechanical transmission (EMT) are proposed, using P3 as the basic working mode and setting the P2 mode at the same time, and the gear ratios are designed. Based on the above basic scheme, two rounds of prototype development and assembling prototype vehicles for testing are carried out for the front-engine-front-drive (FF) layout. The test results show that the vehicle’s economy has been improved compared to the unmodified vehicle, and the fuel-saving rate of 100 kilometers has been achieved at 35.18%. The prototype development and the vehicle matching verify the effectiveness of the new configuration based on AMT.