02321nas a2200181   4500008004100000022001400041245014200055210006900197260000900266300001100275490000800286520163300294100002001927700002201947700002301969700001901992856012802011       2020                        eng d  a0167-732200aMorphology and dynamics of self-assembled structures in mixed surfactant systems (SDS plus CAPB) in the context of methane hydrate growth0 aMorphology and dynamics of selfassembled structures in mixed sur  cDEC   a1142960 v3193 a<p>Presence of small dosages of surfactants in the aqueous phase has been reported to enhance the rate of gas hydrate (clathrate) formation. In this work, using extensive atomistic molecular dynamics (MD) simulations, we have investigated how SDS (surfactant) aggregates in the presence/absence of CAPB (co-surfactant) at ambient conditions (temperature 298 K and pressure 1 bar) and at hydrate forming conditions (temperature 275 K and pressure 50 bar) resulting in altered growth kinetics of methane hydrate. We observe that SDS forms aggregates of different sizes and shapes depending on the thermodynamic condition starting from random distributions of the surfactants. In the presence of the CAPB co-surfactant, tightly packed mixed aggregates are formed. Using various structural order parameters, we demonstrate that shape of the aggregates deviates from spherical as well as cylindrical symmetry. During the aggregation process in presence of methane, the methane molecules get absorbed into the aggregates, enhance the aggregation kinetics and provide structural flexibility to the aggregates. This result is partly in agreement with previous experimental observations that SDS (with or without a co-surfactant) may form micelle-like structures under hydrate forming conditions and that methane gets absorbed by these aggregates leading to enhanced solubility of methane in the aqueous phase. Further, we have investigated the dynamics of shape fluctuations of the aggregates and observed that several distinct relaxation timescales exist in these heterogenous systems. (C) 2020 Elsevier B.V. All rights reserved.</p>
1 aHande, Vrushali1 aChoudhary, Nilesh1 aChakrabarty, Suman1 aKumar, Rajnish  uhttps://library.ncl.res.in/content/morphology-and-dynamics-self-assembled-structures-mixed-surfactant-systems-sds-plus-capb02771nas a2200157   4500008004100000022001400041245012700055210006900182260000800251300001400259490000600273520216100279100002002440700002302460856013002483       2022                        eng d  a2470-134300aSize-dependent order-disorder crossover in hydrophobic hydration: comparison between spherical solutes and linear alcohols0 aSizedependent orderdisorder crossover in hydrophobic hydration c  cJAN  a2671-26780 v73 a<p>
	Theory and computer simulation studies have predicted that water molecules around hydrophobic molecules should undergo an order-disorder transition with increasing solute size around a 1 nm length scale. Some theories predict the formation of a clathrate-like ordered structure around smaller hydrophobic solutes (&lt;1 nm) and the formation of disordered vapor-liquid interfaces around larger solutes (&gt;1 nm) and surfaces. Experimental validation of these predictions has often been elusive and contradictory. High-resolution Raman spectroscopy has detected that water around small hydrophobic solutes shows a signature similar to that of bulk water at lower temperature (increased ordering and a stronger hydrogen-bonded network). Similarly, water around larger solutes shows an increasing population of dangling OH bonds very similar to higher temperature bulk water. Thus, the solute size dependence of the structure and dynamics of water around hydrophobic molecules seems to have an analogy with the temperature dependence in bulk water. In this work, using atomistic classical molecular dynamics (MD) simulations, we have systematically investigated this aspect and characterized this interesting analogy. Structural order parameters including the tetrahedral order parameter (Q), hydrogen bond distribution, and vibrational power spectrum highlight this similarity. However, in contrast to the experimental observations, we do not observe any length-dependent crossover for linear hydrophobic alcohols (n-alkanols) using classical MD simulations. This is in agreement with earlier findings that linear alkane chains do not demonstrate the length-dependent order-disorder transition due to the presence of a sub-nanometer length scale along the cross section of the chain. Moreover, the collapsed state of linear hydrocarbon chains is not significantly populated for smaller chains (number of carbons below 20). In the context of our computational results, we raise several pertinent questions related to the sensitivity of various structural and dynamical parameters toward capturing these complex phenomena of hydrophobic hydration.</p>
1 aHande, Vrushali1 aChakrabarty, Suman  uhttps://library.ncl.res.in/content/size-dependent-order-disorder-crossover-hydrophobic-hydration-comparison-between-spherical02171nas a2200193   4500008004100000022001400041245007900055210006900134260000800203300001200211490000700223520154000230100002201770700001801792700002001810700002001830700002001850856010701870       2024                        eng d  a1549-959600aImproved protein dynamics and hydration in the martini3 coarse-grain model0 aImproved protein dynamics and hydration in the martini3 coarsegr  cJAN  a837-8500 v643 a<p>
	The Martini coarse-grain force-field has emerged as an important framework to probe cellular processes at experimentally relevant time- and length-scales. However, the recently developed version, the Martini3 force-field with the implemented Go model (Martini3Go), as well as previous variants of the Martini model have not been benchmarked and rigorously tested for globular proteins. In this study, we consider three globular proteins, ubiquitin, lysozyme, and cofilin, and compare protein dynamics and hydration with observables from experiments and all-atom simulations. We show that the Martini3Go model is able to accurately model the structural and dynamic features of small globular proteins. Overall, the structural integrity of the proteins is maintained, as validated by contact maps, radii of gyration (Rg), and SAXS profiles. The chemical shifts predicted from the ensemble sampled in the simulations are consistent with the experimental data. Further, a good match is observed in the protein-water interaction energetics, and the hydration levels of the residues are similar to atomistic simulations. However, the protein-water interaction dynamics is not accurately represented and appears to depend on the protein structural complexity, residue specificity, and water dynamics. Our work is a step toward testing and assessing the Martini3Go model and provides insights into future efforts to refine Martini models with improved solvation effects and better correspondence to the underlying all-atom systems.</p>
1 aKharche, Shalmali1 aYadav, Manjul1 aHande, Vrushali1 aPrakash, Shikha1 aSengupta, Durba  uhttps://library.ncl.res.in/content/improved-protein-dynamics-and-hydration-martini3-coarse-grain-model