Simulation of Droplet Trains in Microfluidic Networks

In this work we show that in a microfluidic network and in low Reynolds numbers a system can be irreversible because of hysteresis effects.The network, which is employed in our simulations, is taken from recent experiments. The network consists of one loop connected to input and output pipes. A train of droplets enter the system at a uniform rate, but they may leave it in different patterns, e.g. periodic or even chaotic. The out put pattern depends on the time interval among the incoming droplets as well as the network geometry and for some parameters the system is not reversible

Comparison of the thermodynamic integration and free energy perturbation in the computing alchemical free energy difference

On an atomistic scale, free energy calculations are important for our understanding of biological processes, which provides an insight to grasp the various mechanisms. Over the years, many computational methods have been developed to calculate free energy differences such as geometrical (e.g. umbrella sampling) and alchemical methods. In this work, we present alchemical-free energy methods, thermodynamic integration (TI) and free energy perturbation (FEP), to investigate polarization effect of paclitaxel drug. Then, we have compared our simulation studies using TI, FEP, and Hamiltonian replica exchange FEP from the perspective of computational cost and accuracy