Computer simulation of dynamical anomalies in stretched water

Netz, Paulo Augusto; Starr, Francis W.; Barbosa, Márcia C.; Stanley, H. Eugene

doi:10.1590/s0103-97332004000100004

Cited by 7 publications

(4 citation statements)

References 55 publications

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“…Simulations have also shown that the rotational diffusion and relaxation times are lower in the hydration layer of small peptides, proteins and cells compared to the bulk [44]. In this studies, the evolution of the orientational relaxation time, integrated over the rotational auto-correlation function, is proportional to the translational diffusion coefficient [45,46].…”

Section: Resultsmentioning

confidence: 76%

Role of the hydrophobic and hydrophilic sites in the dynamic crossover of the protein-hydration water

Köhler

Barbosa

Silva

et al. 2017

Physica A: Statistical Mechanics and its Applications

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h i g h l i g h t s• The water diffusion near the protein surface is lower than in bulk.• A crossover in the diffusion of the hydration water is observed.• The crossover happens at different temperatures for hydrophilic and hydrophobic sites. g r a p h i c a l a b s t r a c t a b s t r a c t Molecular dynamics simulations were performed to study the water structure and dynamics in the hydration shell of the globular TS-Kappa protein. The results show that for a wide range of temperatures the diffusion coefficient of water near the protein surface is lower than in bulk. A crossover in the diffusion behavior of hydration water is observed at different temperatures for hydrophilic and hydrophobic vicinities. We have found a correlation between the crossover in the hydrophilic case and the protein dynamical transition. An explanation in terms of the competition between water-water water-protein H-bond formation is provided based on H-bond network analysis.

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Section: Resultsmentioning

confidence: 76%

Role of the hydrophobic and hydrophilic sites in the dynamic crossover of the protein-hydration water

Köhler

Barbosa

Silva

et al. 2017

Physica A: Statistical Mechanics and its Applications

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“…The thermophysical properties investigated in this work include pressure ( P ), potential energy ( U ), residual isochoric heat capacity ( C V ,res ), viscosity (η), and diffusion coefficient ( D self ). Previous molecular simulation studies have investigated the thermophysical properties of stretched homogeneous water at similar conditions, − and comparisons are made here to these earlier studies. To our knowledge, the thermophysical properties of two-phase bubbly water have not been investigated previously.…”

Section: Introductionmentioning

confidence: 90%

Molecular Simulations Probing the Thermophysical Properties of Homogeneously Stretched and Bubbly Water Systems

et al. 2019

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Molecular simulations in the canonical ensemble were performed to probe a variety of thermophysical properties of both homogeneously stretched and bubbly water systems at a temperature of 298 K. Two types of water models, the four-site TIP4P/2005 model and the coarse-grained single-site mW model, were investigated. Simulations for the computationally efficient mW model were carried out using cubic simulation boxes with linear dimensions of 4, 8, 16, and 32 nm, whereas 4, 6, and 8 nm boxes were considered for the TIP4P/2005 model. Various thermophysical properties, including pressure (P), potential energy (U), residual isochoric heat capacity (C V,res ), viscosity (η), and self-diffusion coefficient (D self ), were calculated for densities ranging from 800 kg/m 3 to the saturated liquid density (ρ sat ). Following two simulation protocols starting either from a homogeneous configuration or from a heterogeneous configuration with a single spherical cavity, spinodal cavitation (SC) and bubble collapse (BC) points were located separately. This behavior of a fluid in a box of fixed volume is analogous to the hysteresis observed for adsorption−desorption isotherms of a subcritical fluid in a mesoporous adsorbent. As the system size is increased, both BC and SC points are shifted to larger densities. In terms of thermophysical properties, qualitatively similar trends are observed for the mW and TIP4P/2005 models. As the system approaches the SC point from ρ sat , P decreases to a large negative value, U, C V,res , and η increase, and D self decreases. Upon cavitation, the system undergoes a relaxation as signaled by step changes in these properties. In the heterogeneous (bubbly) region, a decrease in the density leads to relatively slower increases in P and U and a slow decrease in η, but C V,res does not exhibit significant changes, whereas a significant decrease in D self is observed only for the mW model and boxes larger than 8 nm. For the system sizes investigated here, the thermophysical properties at a given density cannot be simply estimated from a linear combination of the corresponding properties taken from the saturated liquid and vapor phases. For the bubbly phases, the Young−Laplace relation is found to hold well, whereas the Stokes−Einstein relation is not obeyed.

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“…The density of the system increases about 15% when the system goes from ambient pressure to 500 MPa. It is known that this increase in density leads to a substantial increase of the average coordination number of water 22 , and also to an increase in the diffusion coefficient at low temperatures 23 , but at high temperatures the effect of the pressure on the diffusion coefficient is the opposite. Indeed, when the high pressure is applied, the diffusion coefficient of water and methanol (data not shown) decrease by about 40% and 50%, respectively.…”

Section: Coordination and Excess Coordination Numbersmentioning

confidence: 99%

Why does high pressure destroy co-non-solvency of PNIPAm in aqueous methanol?

et al. 2015

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It is well known that poly(N-isopropylacrylamide) (PNIPAm) exhibits an interesting, yet puzzling, phenomenon of co-non-solvency. Co-non-solvency occurs when two competing good solvents for PNIPAm, such as water and alcohol, are mixed together. As a result, the same PNIPAm collapses within intermediate mixing ratios. This complex conformational transition is driven by preferential binding of methanol with PNIPAm. Interestingly, co-non-solvency can be destroyed when applying high hydrostatic pressures. In this work, using a large scale molecular dynamics simulation employing high pressures, we propose a microscopic picture behind the suppression of co-non-solvency phenomenon. Based on thermodynamic and structural analysis, our results suggest that the preferential binding of methanol with PNIPAm gets partially lost at high pressures, making the background fluid reasonably homogeneous for the polymer. This is consistent with the hypothesis that the co-non-solvency phenomenon is driven by preferential binding and is not based on depletion effects.

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Computer simulation of dynamical anomalies in stretched water

Abstract: In this work, we describe how the anomalous diffusivity is related to the structural anomalies. For this purpose, we study how the thermodynamics and the dynamics of low-temperature water are affected by the decrease of the density.

Cited by 7 publications

References 55 publications

Role of the hydrophobic and hydrophilic sites in the dynamic crossover of the protein-hydration water

Role of the hydrophobic and hydrophilic sites in the dynamic crossover of the protein-hydration water

Molecular Simulations Probing the Thermophysical Properties of Homogeneously Stretched and Bubbly Water Systems

Why does high pressure destroy co-non-solvency of PNIPAm in aqueous methanol?

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