01431nas a2200157 4500008004100000022001400041245008300055210006900138260007300207300001200280490000800292520082000300100002501120700001501145856011301160 2011 eng d a0009-261400aEarly stages of unwinding of zwitterionic alpha-helical homopolymeric peptides0 aEarly stages of unwinding of zwitterionic alphahelical homopolym aPO BOX 211, 1000 AE AMSTERDAM, NETHERLANDSbELSEVIER SCIENCE BVcOCT a330-3350 v5143 a

Unwinding mechanisms of helices of the zwitterionic polyalanine, polyleucine, and polylysine were studied using classical molecular dynamics simulation at 300 K temperature. Interestingly the helices of polyalanine and polyleucine start to unwind from the terminals, which is further relayed to the middle of the chain with time. Polylysine helix also starts to unwind from the terminals of the alpha-helical chain but the unwinding is not relayed to the middle. The reason behind this observation is investigated whether the presence of -NH(2) groups in the side chain of polylysine is influencing the unwinding. Two competitive mechanisms, fluctuation of the terminal residues and exchange of H-bonds between residues and water trigger the process of unwinding. (C) 2011 Elsevier B. V. All rights reserved.

1 aPandey, Prithvi, Raj1 aRoy, Sudip uhttp://library.ncl.res.in/content/early-stages-unwinding-zwitterionic-alpha-helical-homopolymeric-peptides-001938nas a2200157 4500008004100000022001400041245011500055210006900170260012500239300001100364490000800375520123400383100002001617700001501637856012801652 2013 eng d a0021-960600aEvidence and characterization of dynamic heterogeneity in binary mixtures of phosphoric acid and benzimidazole0 aEvidence and characterization of dynamic heterogeneity in binary aCIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USAbAMER INST PHYSICScOCT a1547010 v1393 a

We report here anomalous diffusions of components in mixtures of monomer of polybenzimidazole, i.e., 2-phenyl-1H, 1'H-5,5'-bibenzo[d] imidazole (BI) and phosphoric acid (PA) from molecular dynamics simulations. We have observed initial drop and further increase in self-diffusion constant for both monomer molecule (BI) and PA with gradual increase in PA concentration. The origin of such anomalous diffusion is identified in this work, which happens to be the presence of dynamic heterogeneity in each component of the binary mixture. We characterized microscopic picture of dynamical heterogeneity by finding correlation between dynamical heterogeneity and structural arrangement among the components of the binary system. Different types of H-bonding arrangements in the BI-PA systems at different concentration of PA are observed. The stability of the H-bonded network consisting of different types of H-bonds between BI and PA in the system has been studied by calculating the lifetime of various H-bonds. The results indicate that there are fast and slow moving PA molecules in the mixtures because of coexistence of different types of hydrogen bonds among the components of the mixture. (C) 2013 AIP Publishing LLC.

1 aPahari, Swagata1 aRoy, Sudip uhttp://library.ncl.res.in/content/evidence-and-characterization-dynamic-heterogeneity-binary-mixtures-phosphoric-acid-and-001550nas a2200157 4500008004100000022001400041245007600055210006900131260009100200300002600291490000600317520092900323100002201252700001501274856010301289 2014 eng d a1932-620300aEffect of gold nanoparticle on structure and fluidity of lipid membrane0 aEffect of gold nanoparticle on structure and fluidity of lipid m a1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USAbPUBLIC LIBRARY SCIENCEcDEC aArticle No. : e1141520 v93 a

This paper deals with the effect of different size gold nanoparticles on the fluidity of lipid membrane at different regions of the bilayer. To investigate this, we have considered significantly large bilayer leaflets and incorporated only one nanoparticle each time, which was subjected to all atomistic molecular dynamics simulations. We have observed that, lipid molecules located near to the gold nanoparticle interact directly with it, which results in deformation of lipid structure and slower dynamics of lipid molecules. However, lipid molecules far away from the interaction site of the nanoparticle get perturbed, which gives rise to increase in local ordering of the lipid domains and decrease in fluidity. The bilayer thickness and area per head group in this region also get altered. Similar trend, but with different magnitude is also observed when different size nanoparticle interact with the bilayer.

1 aMhashal, Anil, R.1 aRoy, Sudip uhttp://library.ncl.res.in/content/effect-gold-nanoparticle-structure-and-fluidity-lipid-membrane-000639nas a2200157 4500008004100000245014500041210006900186260000800255300001200263490000800275100002200283700001800305700001500323700001900338856012400357 2016 eng d00aEffect of polyvinylpyrrolidone at methane hydrate-liquid water interface. application in flow assurance and natural gas hydrate exploitation0 aEffect of polyvinylpyrrolidone at methane hydrateliquid water in cDEC a613-6220 v1861 aChoudhary, Nilesh1 aDas, Subhadip1 aRoy, Sudip1 aKumar, Rajnish uhttp://library.ncl.res.in/content/effect-polyvinylpyrrolidone-methane-hydrate-liquid-water-interface-application-flow-101312nas a2200169 4500008004100000245008400041210006900125260000800194300001000202490000800212520073000220100003300950700002500983700001901008700001501027856010001042 2017 eng d00aEffect of shape of protrusions and roughness on the hydrophilicity of a surface0 aEffect of shape of protrusions and roughness on the hydrophilici cOCT a34-390 v6583 aWe have investigated wetting of model rough surfaces made up of hydrophilic triangular and hexagonal pillars (protrusions). The surface roughnesses are altered by varying the area of the rough surface, the height of the pillars, and the surface interactions to the water. We have established a correlation between structure i.e., the shape of a pillar, which actually depends on the number of edges (due to shape), and the wetting phenomena. We have found that surface with higher number of edges repels water at lower roughness value. We explain the correlation by analyzing the variation of interactions energy components and density profiles of water on the structured surfaces. (C) 2017 Elsevier B.V. All rights reserved.1 aChowdhury, Sheelan, Sengupta1 aPandey, Prithvi, Raj1 aKumar, Rajnish1 aRoy, Sudip uhttp://library.ncl.res.in/content/effect-shape-protrusions-and-roughness-hydrophilicity-surface01513nas a2200193 4500008004100000022001400041245010500055210006900160260000800229300001400237490000800251520082700259100002201086700002401108700001501132700002301147700001901170856013001189 2018 eng d a1520-610600aEffect of sodium dodecyl sulfate surfactant on methane hydrate formation: a molecular dynamics study0 aEffect of sodium dodecyl sulfate surfactant on methane hydrate f cJUN a6536-65420 v1223 a

In experimental studies, it has been observed that the presence of sodium dodecyl sulfate (SDS) significantly increases the kinetics of hydrate formation and the final water-to-hydrate conversion ratio. In this study, we intend to understand the molecular mechanism behind the effect of SDS on the formation of methane hydrate through molecular dynamics simulation. Hydrate formation conditions similar to that of laboratory experiments were chosen to study hydrate growth kinetics in 1 wt % SDS solution. We also investigate the effect of interactions with isolated SDS molecules on methane hydrate growth. It was observed that the hydrophobic tail part of the SDS molecule favorably interacts with the growing hydrate surface and may occupy the partial hydrate cages while the head groups remain exposed to water.

1 aChoudhary, Nilesh1 aHande, Vrushali, R.1 aRoy, Sudip1 aChakrabarty, Suman1 aKumar, Rajnish uhttp://library.ncl.res.in/content/effect-sodium-dodecyl-sulfate-surfactant-methane-hydrate-formation-molecular-dynamics-study