Microscopic pathways of transition from low-density to high-density amorphous phase of water.

In recent years, much attention has been devoted to understanding the pathways of phase transition between two equilibrium condensed phases (such as liquids and solids). However, the microscopic pathways of transition involving non-equilibrium, non-diffusive amorphous (glassy) phases still remain poorly understood. In this work, we have employed computer simulations, persistence homology (a tool rooted in topological data analysis), and machine learning to probe the microscopic pathway of pressure-induced non-equilibrium transition between the low- and high-density amorphous (LDA and HDA, respectively) ice phases of the TIP4P/2005 and ST2 water models. Using persistence homology and machine learning, we introduced a new order parameter that unambiguously identifies the LDA- and HDA-like local environments. The LDA phase transitions continuously and collectively into the corresponding HDA phase via a pre-ordered intermediate phase during the isothermal compression. The local order parameter susceptibilities show a maximum near the transition pressure (P*)-suggesting maximum structural heterogeneities near P*. The HDA-like clusters are structurally ramified and spatially delocalized inside the LDA phase near the transition pressure. We also found manifestations of the first-order low-density to high-density liquid transition in the sharpness of the order parameter change during the LDA to HDA transition. We further investigated the (geometrical) structures and topologies of the LDA and HDA ices formed via different protocols and also studied the dependence of the (microscopic) pathway of phase transition on the protocol followed to prepare the initial LDA phase. Finally, the method adopted here to study the phase transition pathways is not restricted to the system under consideration and provides a robust way of probing phase transition pathways involving any two condensed phases at both equilibrium and out-of-equilibrium conditions.

Binding order of substrate and cofactor in sulfonamide monooxygenase during sulfa drug degradation: in silico studies.

For decades, sulfonamide antibiotics have been used across industries such as agriculture and animal husbandry. However, the use and inadvertent misuse of these antibiotics have resulted in the advent of sulfonamide-drug-resistant strains due to antibiotic pollution. Enzymatic bioremediation of antibiotics remains a potential emerging solution to combat antibiotic pollution. Here, we propose an enzymatic model for the degradation of sulfonamides by Microbacterium sp. We have employed a multi-pronged computational strategy involving - protein structure modelling, ligand docking and molecular dynamics simulations to decipher a plausible binding order for the enzymatic degradation of sulfonamides by the bacterial sulfonamide monooxygenase, SulX. Our results enable us to predict that this degradation is achieved through the sequential binding of the antibiotic sulfonamide followed by the reduced flavin cofactor FMNH2, thereby laying the computational foundation for further advancements in enzyme-mediated degradation of the antibiotic. We also provide a list of experiments which may be performed to verify and follow-up on our in-silico studies.Communicated by Ramaswamy H. Sarma.