12783
Jianbin Fang, Ana Lucia Varbanescu, Baldomero Imbernon, Jose M. Cecilia, Horacio Perez-Sanchez
Currently, medical research for the discovery of new drugs is increasingly using Virtual Screening (VS) methods. In these methods, the calculation of the non-bonded interactions, such as electrostatic or van der Waals, plays an important role, representing up to 80% of the total execution time. These are computationally intensive operations, and massively parallel in nature, […]
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Anuj V. Prakash, Anwesha Chaudhury, Rohit Ramachandran
Computer-aided modeling and simulation are a crucial step in developing, integrating, and optimizing unit operations and subsequently the entire processes in the chemical/pharmaceutical industry. This study details two methods of reducing the computational time to solve complex process models, namely, the population balance model which given the source terms can be very computationally intensive. Population […]
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Anuj V. Prakash, Anwesha Chaudhury, Rohit Ramachandran
Computer-aided modeling and simulation is a crucial step in developing, integrating and optimizing unit operations and subsequently entire processes, in the chemical/pharmaceutical industry. This study details two methods of reducing the computational time to solve complex process models, namely the population balance model which given the source terms can be very computationally intensive. Population balance […]
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Martin Simonsen, Mikael H. Christensen, Rene Thomsen, Christian N. S. Pedersen
The objective in molecular docking is to determine the best binding mode of two molecules in silico. A common application of molecular docking is in drug discovery where a large number of ligands are docked into a protein to identify potential drug candidates. This is a computationally intensive problem especially if the flexibility of the […]
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Timothy J Rudge, Paul J Steiner, Andrew Phillips, Jim Haseloff
Microbial biofilms are complex, self-organized communities of bacteria, which employ physiological cooperation and spatial organization to increase both their metabolic efficiency and their resistance to changes in their local environment. These properties make biofilms an attractive target for engineering, particularly for the production of chemicals such as pharmaceutical ingredients or biofuels, with the potential to […]
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Michael Krone, Sebastian Grottel, Thomas Ertl
Molecular Dynamics simulations are an essential tool for many applications. The simulation of large molecules – like proteins – over long trajectories is of high importance e. g. for pharmaceutical, biochemical and medical research. For analyzing these data sets interactive visualization plays a crucial role as details of the interactions of molecules are often affected […]
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Gines D. Guerrero, Horacio Perez-Sanchez, Wolfgang Wenzel, Jose M. Cecilia, Jose M. Garcia
In this work we discuss the benefits of using massively parallel architectures for the optimization of Virtual Screening methods. We empirically demonstrate that GPUs are well suited architecture for the acceleration of non-bonded interaction kernels, obtaining up to a 260 times sustained speedup compared to its sequential counterpart version.
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M.N. Osman, R. Abdullah, N. AbdulRashid
Ribonucleic acid (RNA) plays a fundamental and important role in cellular life forms and their function is directly related to their structure. RNA secondary structure prediction is a significant area of study for many scientists seeking insights into potential drug interactions or innovative new treatment methodologies. Predicting structure can overcome many issues related with physical […]
Li Liu, Xiaofeng Liu, Jiayu Gong, Hualiang Jiang, Honglin Li
All-atom normal mode analysis (NMA) is an efficient way to predict the collective motions in a given macromolecule, which is essential for the understanding of protein biological function and drug design. However, the calculations are limited in time scale mainly because the required diagonalization of the Hessian matrix by Householder-QR transformation is a computationally exhausting […]
Charles A. Radeke, Benjamin J. Glasser, Johannes G. Khinast
Granular flows are extremely important for the pharmaceutical and chemical industry, as well as for other scientific areas. Thus, the understanding of the impact of particle size and related effects on the mean, as well as on the fluctuating flow field, in granular flows is critical for design and optimization of powder processing operations. We […]

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