Research Description: 

Dan Mermelstein, alum as of June, 2018, completed his dissertation titled Improvements and Applications of Alchemical Free Energy, Constant pH and Accelerated Molecular Dynamics Calculations in the AMBER Molecular Dynamics Suite. 

While I have been supported by this NIH training grant, I have successfully implemented GPU based AFE calculations in AMBER. We have achieved a performance boost of over 360X compared to the existing CPU implementation in AMBER, without sacrificing accuracy. This has code has already facilitated the high-throughput rational design of drugs for a wide variety of diseases in the pharmaceutical industry as well as academic labs, directly improving human life and society.

Graduate Program: 
Chemistry and Biochemistry