Добірка наукової літератури з теми "Multicale molecular simulations"
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Статті в журналах з теми "Multicale molecular simulations"
Javan Nikkhah, Sousa, Elsi Turunen, Anneli Lepo, Tapio Ala-Nissila, and Maria Sammalkorpi. "Multicore Assemblies from Three-Component Linear Homo-Copolymer Systems: A Coarse-Grained Modeling Study." Polymers 13, no. 13 (June 30, 2021): 2193. http://dx.doi.org/10.3390/polym13132193.
Повний текст джерелаNg, Kam, Vladimir Nazarov, Sergey Kuchinsky, Aramais Zakharian, and Ming-Jun Li. "Analysis of Crosstalk in Multicore Fibers: Statistical Distributions and Analytical Expressions." Photonics 10, no. 2 (February 7, 2023): 174. http://dx.doi.org/10.3390/photonics10020174.
Повний текст джерелаPeng, Liu, Manaschai Kunaseth, Hikmet Dursun, Ken-ichi Nomura, Weiqiang Wang, Rajiv K. Kalia, Aiichiro Nakano, and Priya Vashishta. "Exploiting hierarchical parallelisms for molecular dynamics simulation on multicore clusters." Journal of Supercomputing 57, no. 1 (February 3, 2011): 20–33. http://dx.doi.org/10.1007/s11227-011-0560-1.
Повний текст джерелаQiu, Yang. "Partial-Failure Segregated Spectrum Assignment for Multicast Traffic in Flex-Grid Optical Networks." Photonics 9, no. 7 (July 12, 2022): 488. http://dx.doi.org/10.3390/photonics9070488.
Повний текст джерелаLi, Jiamin, Lingling Chen, Pengcheng Zhu, Dongming Wang, and Xiaohu You. "Satellite-Assisted Cell-Free Massive MIMO Systems with Multi-Group Multicast." Sensors 21, no. 18 (September 16, 2021): 6222. http://dx.doi.org/10.3390/s21186222.
Повний текст джерелаAl-hussaniy, Hany Akeel. "The development of molecular docking and molecular dynamics and their application in the field of chemistry and computer simulation." Journal of medical pharmaceutical and allied sciences 12, no. 1 (January 31, 2023): 5552–62. http://dx.doi.org/10.55522/jmpas.v12i1.4137.
Повний текст джерелаGuo, Xiaojin, Liying Sang, and Huanlin Liu. "Minimization Number of Network-Coded Links Based on Improved Adaptive Genetic Algorithm for Multi-source Optical Networks." Journal of Optical Communications 40, no. 3 (July 26, 2019): 205–12. http://dx.doi.org/10.1515/joc-2017-0030.
Повний текст джерелаMartin, Richard L., Prabhat, David D. Donofrio, James A. Sethian, and Maciej Haranczyk. "Accelerating analysis of void space in porous materials on multicore and GPU platforms." International Journal of High Performance Computing Applications 26, no. 4 (February 5, 2012): 347–57. http://dx.doi.org/10.1177/1094342011431591.
Повний текст джерелаGalbraith, Madeline, Federico Bocci, and José N. Onuchic. "Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway." PLOS Computational Biology 18, no. 7 (July 21, 2022): e1010306. http://dx.doi.org/10.1371/journal.pcbi.1010306.
Повний текст джерелаAldinucci, Marco, Cristina Calcagno, Mario Coppo, Ferruccio Damiani, Maurizio Drocco, Eva Sciacca, Salvatore Spinella, Massimo Torquati, and Angelo Troina. "On Designing Multicore-Aware Simulators for Systems Biology Endowed with OnLine Statistics." BioMed Research International 2014 (2014): 1–14. http://dx.doi.org/10.1155/2014/207041.
Повний текст джерелаДисертації з теми "Multicale molecular simulations"
Bidoggia, Silvia. "Mixed-monolayer protected gold nanoparticles for applications in medicine." Doctoral thesis, Università degli studi di Trieste, 2013. http://hdl.handle.net/10077/8573.
Повний текст джерелаIn the last years, gold nanoparticles (AuNPs) protected by an organic shell of ligands have received a large interest for applications in the biomedical field in particular for diagnosis, imaging and therapy. This class of nanomaterials is largely used because of the easy of synthesis with different core sizes and shapes and controlled dispersion. Moreover, NPs can be protected by a large variety of organic compounds, with different functionalities and to allow the linkage of drugs and biomolecules. The nature of the ligand is responsible of the solubility of the NPs and could be also tuned in order to have NPs soluble in water and in the biological environment. Additionally, at least gold is no toxic, biocompatible and could be easily released from the body. The present thesis is focused on three projects. The first one deals with the study of the morphology of gold nanoparticles coated by a mixture of hydrogenated and fluorinated ligands which solubility in water is favored by the presence of PEG chains. Few years ago, our research group has shown that mixtures of these hydrogenated and fluorinated ligands, forming the monolayer of gold nanoparticles, phase-segregate in separated domains because of the reciprocal immiscibility of the two chains. During this thesis, we wanted to investigate more deeply the organization of such monolayers and in particular, to understand the shape and the size of these domains. In collaboration with the group of Prof. S. Pricl and Prof. M. Fermeglia of the University of Trieste, in silico experiments have been performed in order to predict the size and the shape of these domains. Moreover, we have studied how the shape and the size of these domains is influenced by the ratio between the two thiols, the size of the core and the difference in length between the two ligands. The obtained results were supported by further ESR experiments performed by Prof. Lucarini of the University of Bologna. ESR experiments have allowed us to estimate the value of the affinity constants of the probe for the fluorinated and hydrogenated domains of the monolayer and to establish that mixed monolayers have chemical and physical properties that cannot be predicted by simply knowing the properties of homoligand monolayers. The results that have been reported in a recent publication on ACS Nano are presented in Chapter 3. The second project of this PhD thesis is based on the synthesis and characterization of water soluble gold nanoparticles coated by different ratios of charged hydrogenated ligands and commercially available fluorinated ligands. Some of these nanoparticles, with an average core diameter between 3 and 4 nm, have been used for preliminary investigations in vitro. In particular, cell membrane permeation and the cellular toxicity have been evaluated. These experiments have been performed in collaboration with the group of Prof. Stellacci in IFOM-IEO, Milan. Preliminary results are described in Chapter 4. The last part of this PhD project is focused on the synthesis and characterization of NPs coated by mixtures of commercially available fluorinated and hydrogenated thiols. These NPs present the advantages over those described in Chapter 3 and Chapter 4 because they are suited for a direct “visualization” by STM experiments and may help us in understanding the rules governing the organization of mixtures of fluorinated and hydrogenated ligands on a curved surface. The choice to synthesize NPs without charged groups is dictated by the limitations of STM technique. In Chapter 5 synthetic aspects and preliminary STM results would be presented.
XXV Ciclo
1983
Khan, MD Ashfaquzzaman. "Scalable molecular dynamics simulation using FPGAs and multicore processors." Thesis, Boston University, 2013. https://hdl.handle.net/2144/12792.
Повний текст джерелаWhile Molecular Dynamics Simulation (MD) uses a large fraction of the world's High Performance Compute cycles, the modeling of many physical phenomena remains far out of reach. Improving the cost-effectiveness of MD has therefore received much attention, especially in using accelerators or modifying the computation itself. While both approaches have demonstrated great potential, scalability has emerged as a critical common challenge. The goal of this research is to study this issue and develop MD solutions that not only achieve substantial acceleration but also remain scalable. In the first part of this research, we focus on Discrete Molecular Dynamics Simulation (DMD)., which achieves high performance by simplifying the underlying computation by converting it into a Discrete Event Simulation (DES). In addition to the inherent serial nature of DES, causality issues make DMD a notorious target for parallelization. We propose a parallel version of DMD that, unlike any previous work, uses task decomposition and efficient synchronization and achieves more than 8.5x speed-up for 3D physical systems on a 12 core processor, with potential for further strong scaling. The second part of this research focuses on FPGA acceleration of timestep-driven MD. We first enhance an existing FPGA kernel to take advantage of the Block RAM architecture of FPGAs. This results in a 50% improvement in speed-up, without sacrificing simulation quality. We then parallelize the design targeting multiple on-board FPGA cores. We combine this with software pipelining and careful load distribution at the application level to achieve a 3.37x speedup over its CPU counterpart. In the third part we create a framework that integrates the FPGA accelerator into a prominent MD package called NAMD. This framework allows users to switch between the actual accelerator and a simulated version, and provides a means to study different characteristics, such as the communication pattern, of such an accelerated system. Using this framework, we identify the drawbacks of the current FPGA kernel and provide guidelines for future designs. In addition, the integrated design achieves 2.22x speed-up over a quad-core CPU, making it the first ever FPCA-accelerated full-parallel MD package to achieve a positive end-to-end speed-up.
Частини книг з теми "Multicale molecular simulations"
Swat, Maciej H., Susan D. Hester, Ariel I. Balter, Randy W. Heiland, Benjamin L. Zaitlen, and James A. Glazier. "Multicell Simulations of Development and Disease Using the CompuCell3D Simulation Environment." In Methods in Molecular Biology, 361–428. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-59745-525-1_13.
Повний текст джерелаChau, Nguyen Hai. "Parallelization of the Fast Multipole Method for Molecular Dynamics Simulations on Multicore Computers." In Advanced Computational Methods for Knowledge Engineering, 209–24. Heidelberg: Springer International Publishing, 2013. http://dx.doi.org/10.1007/978-3-319-00293-4_16.
Повний текст джерела