Supercomputers for biomedicine and pharmacology
Bio-help from technicians
Intel told about the results of the joint scientific program with MIPTGeorgy Pulyaevsky, "Expert Online"
And it becomes doubly pleasant when their joint projects of various institutions and corporations are literally right next door.
Today Intel and the Moscow Institute of Physics and Technology (MIPT) summed up the results of the work of the laboratory of supercomputer technologies for biomedicine, pharmacology and small structures I-SCALARE (Intel super computer applications laboratory for advanced research) for three years.
This laboratory on the basis of MIPT was established in 2010 as part of a grant from the Ministry of Education and Science of the Russian Federation with the participation of employees of the Institute and Intel Corporation. The laboratory is managed by Dr. Vladimir Pentkovsky, a well-known developer of software and hardware architectures, an honored Intel researcher. The main activity of the laboratory is the development of problem-oriented architectures of computing systems for biomedicine, pharmacology and small-sized structures.
Several applied computational tasks related to the modeling of viruses, cell membranes, as well as the interaction of proteins and external fields with cell membranes were selected as "targets". All of them, on the one hand, have great practical value, and on the other hand, they cannot be solved on the available computing resources and require new approaches to cluster architecture. An innovative and energy-efficient supercomputer based on high-performance Intel Xeon E5-2690 server processors, developed and installed by specialists of the RSK Group of companies, is used to conduct a wide range of research within the framework of the laboratory's activities. The use of older models of Intel Xeon E5-2600 family processors has become possible thanks to the use of advanced liquid cooling technology underlying the RSC Tornado architecture.
The peak performance of the supercomputer at the moment is 83.14 TFLOPS with an area of less than 4 sq. m. The cluster consists of two computing racks containing a total of 224 computing nodes based on Intel S2600JF server boards and two Intel Xeon E5-2690 processors in each (total 448 processors, 3584 cores). At the same time, a large amount of RAM per node is supported – 64 GB, which totals 14.3 TB of RAM for the entire system. The communication network is based on the high-speed Infiniband QDR interface.
The expansion of the computing cluster was carried out in three stages, and at each of them the architecture of the computing system was created by its own laboratory group responsible for developing software and analytical models of future computing complexes with subsequent study of their performance on applications solving problems of molecular dynamics. At the moment, laboratory specialists are successfully modeling systems that are 10 times higher than the capacity of the installed cluster, that is, with a performance of up to 830 TFLOPS, using Wind River Simics, Intel VTune Amplifier, as well as technologies developed in the laboratory.
Thus, a group led by Professor Roman Efremov from the Institute of Bioorganic Chemistry of the Russian Academy of Sciences uses a computing cluster at MIPT to study the structure and dynamics of protein-membrane systems and design a new class of antimicrobial compounds based on natural lantibiotics – (performers A. Chugunov, D. Nolde, D. Pyrkova, A. Polyansky). During the development of this project, calculations and modeling, microsecond trajectories of molecular dynamics (MD) of the target of antibiotic action – lipid-II molecules – in the bacterial membrane were obtained.
(Lantibiotics are polypeptides synthesized by harmless bacteria and have a wide spectrum of action against pathogenic microorganisms – VM.)
The modernization of the supercomputer made it possible to conduct more large–scale computational experiments, increasing the size of the systems by 10 times, and the duration of the trajectories of molecular dynamics by 20 times. Scientists conducted a detailed simulation of the interaction of lantibiotics with lipid-II in the membrane and for the first time found that the target molecule (lipid-II) creates a specific pattern in the bacterial membrane that is effectively recognized by designed "traps" - potential antibiotics. As a result of such studies, an atomistic "trap-target" binding model was proposed – the basis for further rational design of new antibiotics. These results were achieved by analyzing large (up to 2.2x10 5 atoms) systems on long (up to 1 microsecond) trajectories of molecular dynamics.
Also, thanks to the significant computing capabilities of the I-SCALARE laboratory cluster, a group headed by academician Nikolai Zefirov and a leading researcher, PhD Vladimir Palyulin, managed to carry out pioneering work in two areas – modeling of the flavivirus shell (performers D. Osolodkin, E. Dueva) and the molecular dynamics of the most important neuroreceptor NMDA (E. Radchenko, D. Karlov).
The idea of the flavivirus shell modeling subproject is to apply the molecular dynamics method to systems containing tens of millions of atoms. Flaviviruses are enveloped viruses that cause diseases such as tick–borne encephalitis and West Nile and Dengue fever. The process of penetration of flaviviruses into a human cell is associated with a significant structural rearrangement of the envelope proteins. One of the tasks of the laboratory is to simulate this process on a full-atomic scale. Modeling systems of this size using modern computing tools is still extremely burdensome, but next-generation computers should be able to work with them adequately. To date, the molecular dynamics of the membrane of a virus particle consisting of 1.5 million atoms has been simulated on the supercomputer of the I-SCALARE laboratory. Based on modeling of virus envelope proteins, substances with antiviral activity against tick-borne encephalitis virus have been proposed (biological tests were conducted at the M.P. Chumakov Institute of Poliomyelitis and Viral Encephalitis of the Russian Academy of Medical Sciences).
In addition to these remarkable and important scientific discoveries, it is worth noting that the I-SCALARE laboratory carries out not only scientific, but also educational activities. Its employees have developed a training course on the use of simulators for modeling various computing systems. In addition, scientific seminars are regularly held in the laboratory, and Vladimir Pentkovsky became the supervisor of several graduate students and students of MIPT.
"Intel Corporation actively cooperates with Russian universities in the field of scientific research. In particular, Intel is the base organization for the Faculty of Radio Engineering and Cybernetics at MIPT, and the joint project to create the I-SCALARE laboratory with allocated state funding has become a logical continuation of our cooperation," summed up Kamil Isaev, General Director of Research and Development at Intel Corporation in Russia. –Thanks to the joint activities of the staff of MIPT, Intel, RSC and Russian scientists, the laboratory has achieved significant results in the field of research and development of software and hardware architectures and solutions to biomedicopharmaceutical problems over three years of work."
Portal "Eternal youth" http://vechnayamolodost.ru17.12.2012