Exploring bacterial biofilms with NAMD, a highly scalable parallel code for complex molecular simulations

Bacterial biofilms are highly complex structures. We are more and more recognizing that bacterial biofilms are predominant forms of the bacterial existence against the planktonic one. Under certain circumstances, bacteria starts to build biofilm and forms 3D structure, so called extracellular matrix. Hulled within this matrix, bacteria becomes more prone to host defense mechanisms and most antibiotics, thus expressing considerably higher virulence and antibiotic resistance than its planktonic form. Because of their importance, numerous researchers investigated bacterial biofilms in the last decades, using numerous methods, like electron microscopy, mass spectroscopy and nuclear magnetic resonance. However, neither of these methods is able to reveal an exact structure of extracellular matrix. Exploring dynamics of extracellular matrix is even more complex, and out of the reach for known analysis methods. For these reasons, there is a need for more effective method, and this could be computer driven simulation. In order to check if it could be a method of choice, we estimated the computational resources needed to simulate the bacterial biofilm. We found that possibility of performing this simulation in the reasonable time on fastest supercomputers today does not exists, and will not be available until at least 2028. For this reason, we explored possibilities of running NAMD based bacterial biofilms simulations on Cloud, and landed with the same conclusion. Besides, we found that for both approaches NAMD has to extend its scalability from about current 500.000 cores to many millions of cores in the future.