Related papers: When does TMAO fold a polymer chain and urea unfol…
To understand the mechanism of trimethylamine N-oxide (TMAO) induced stabilization of folded protein states, we systematically investigated the action of TMAO on several model dipeptides (Leucine, L2, Serine, S2, Glutamine, Q2, Lysine, K2,…
Elucidation of possible pathways between folded (native) and unfolded states of a protein is a challenging task, as the intermediates are often hard to detect. Here we alter the solvent environment in a controlled manner by choosing two…
Urea, a polar molecule with a large dipole moment, not only destabilizes the folded RNA structures, but can also enhance the folding rates of large ribozymes. Unlike the mechanism of urea-induced unfolding of proteins, which is well…
Urea titration of RNA by urea is an effective approach to investigate the forces stabilizing this biologically important molecule. We used all atom molecular dynamics simulations using two urea force fields and two RNA constructs to…
Understanding the molecular mechanism by which denaturants modulate protein structure remains a central challenge in protein biophysics. In this work, molecular dynamics simulations were employed to investigate the effects of urea on the…
Enhanced stabilisation of protein structures via the presence of inert excipients is a key mechanism adopted both by physiological systems and in biotechnological applications. While the intrinsic stability of proteins is ultimately fixed…
Urea denatures proteins due to its strong tendency to dehydrate the first solvation shell via urea-residue preferential binding. However, even after extensive experimental and computational investigations, the influence of urea on the…
Urea at sufficiently high concentration unfolds the secondary structure of proteins leading to denaturation. In contrast, Choline Chloride (ChCl) and urea, in 1:2 molar ratio form a deep eutectic mixture, a liquid at room temperature and…
Despite the success of reverse osmosis (RO) for water purification, the molecular-level physico-chemical processes of contaminant rejection are not well understood. Here we carry out NEMD simulations on a model polyamide RO membrane to…
We introduce a polymer model where the transition from swollen to compact configurations is due to interactions between the monomers and the solvent. These interactions are the origin of the effective attractive interactions between…
Here we report the linear viscoelastic properties of amorphous poly(tetramethylene oxide) (PTMO), which is one of the key components in synthesizing segmented polyurethane (PU) elastomers. The temperature and molecular weight dependent…
We explore the implications of the conservation law(s) and the corresponding "continuity equation(s)", resulting from the coupling between the positional and the orientational order in main-chain polymer nematics, by showing that the…
The disruption of protein structures by denaturants like urea is well studied, though its molecular mechanisms remain unclear. Using Molecular Dynamics (MD) simulations, we investigated how urea affects the structural stability of Bovine…
In order to understand the nuclei which develop during the course of protein folding and unfolding, we examine phase segregation of a single heteropolymer chain which occurs in equilibrium. These segregated conformations are characterized…
We investigate conformations and dynamics of a polymer considering its monomers to be active Brownian particles. This active polymer shows very intriguing physical behavior which is absent in an active Rouse chain. The chain initially…
The mechanism of cold- and pressure-denaturation are matter of debate. Some models propose that when denaturation occurs more hydrogen bonds between the molecules of hydration water are formed. Other models identify the cause in the density…
Polyamide membranes, such as nanofiltration (NF) and reverse osmosis (RO) membranes, are widely used for water desalination and purification. However, the mechanisms of solute transport and solute rejection due to charge interactions remain…
This study investigates the electrochemical behavior and decomposition pathways of four monomers, namely PMC, PMC-OH, PeMC-OH, and DEO-EA, which are potential candidates for polymer electrolytes in solid-state batteries. Density functional…
The Angstrom-scale transport characteristics of water and six different solutes, methanol, ethanol, 2-propanol, urea, Na+, and Cl-, were studied for a polyamide reverse osmosis (RO) membrane, FT-30, using non-equilibrium molecular dynamics…
The interactions of a protein, its phase behavior, and ultimately, its ability to function, are all influenced by the interactions between the protein and its hydration waters. Here we study proteins with a variety of sizes, shapes,…