Entropic Description of Gas Hydrate Ice-Liquid Equilibrium via Enhanced Sampling of Coexisting Phases

Małolepsza, Edyta; Kim, Jaegil; Keyes, T.

doi:10.1103/physrevlett.114.170601

Cited by 13 publications

(28 citation statements)

References 28 publications

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“…Statistical temperatures, T S ( H ), obtained from the gREM and ST-WHAM for melting and freezing of the 32-lipid explicit solvent bilayer, are shown in Figure . As mentioned above, − even with gREM sampling, hysteresis for strong transitions cannot be avoided with this small system and our computational resources, nor can it be in experiment . Freezing does not lead to the perfect equilibrium low-enthalpy gel phase within available CPU time, so T S for freezing cannot yield the equilibrium transition temperature, T eq .…”

Section: Resultsmentioning

confidence: 95%

“…Thus, we employ an enhanced sampling algorithm based on generalized ensembles, using H as the control parameter, the gREM, specifically the isobaric MD version that was implemented by our group in LAMMPS and is further described in our recent papers. − The gREM has been contributed to the LAMMPS distribution and is available in the latest release as fix grem .…”

Section: Methodsmentioning

confidence: 99%

“…If the barrier between the phases is high enough, hysteresis between freezing and melting may be observed, despite the enhanced sampling. − Similarly, if the barrier between coexisting states with distinct topographies“subphases”is high enough, some of them may still be inaccessible. Thus, the gREM is not a complete solution to the problem of sampling at phase transitions in all cases, but the basic ideas still apply and always provide new insights and computational approaches.…”

Section: Methodsmentioning

confidence: 99%

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Enhanced Sampling of Phase Transitions in Coarse-Grained Lipid Bilayers

Stelter

Keyes

2017

J. Phys. Chem. B

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Freezing and melting of dipalmitoylphosphatidylcholine (DPPC) bilayers are simulated in both the explicit (Wet) and implicit solvent (Dry) coarse-grained MARTINI force fields with enhanced sampling, via the isobaric, molecular dynamics version of the generalized replica exchange method (gREM). Phase transitions are described with the entropic viewpoint, based upon the statistical temperature as a function of enthalpy, T(H) = 1/(dS(H)/dH), where S is the configurational entropy. Bilayer thickness, area per lipid, and the second-rank order parameter (P2) are calculated vs temperature in the transition range. In a 32-lipid Wet MARTINI system, transitions in the lipid and water subsystems are strongly coupled, giving rise to considerable structure in T(H) and the need to specify the state of the water when reporting a lipid transition temperature. For gel lipid + liquid water → fluid lipid + liquid water, we find 292.4 K. The small system is influenced by finite-size effects, but it is argued that the entropic approach is well suited to revealing them, which will be particularly relevant for studies of finite nanosystems where there is no thermodynamic limit. In a 390-lipid Dry MARTINI system, two-dimensional analogues of the topographies of coexisting states ("subphases") seen in pure fluids are found. They are not seen in the 32-lipid Wet or Dry system, but the Dry lipids show a new type of state with gel in one leaflet and tilted gel in the other. Dry bilayer transition temperatures are 333.3 K (390 lipids) and 338 K (32 lipids), indicating that the 32-lipid system is not too small for a qualitative study of the transition. Physical arguments are given for Dry lipid system size dependence and for the difference between Wet and Dry systems.

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Section: Resultsmentioning

confidence: 95%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Enhanced Sampling of Phase Transitions in Coarse-Grained Lipid Bilayers

Stelter

Keyes

2017

J. Phys. Chem. B

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“…In addition to RH, temperature, pressure, net layer charge, substitution location, and interlayer cation have been documented to affect the hydration process of MMT and other clay phases. − The influence of these variables on clay mineral hydration has been the focus of numerous molecular simulation studies of bulk clay models, as detailed previously. − The stepwise swelling process of clays due to interlayer hydration and expansion likely occurs as a series of rare events at time scales outside the scope of standard molecular dynamics (MD) simulation methods. Enhanced sampling methods − have been used in MD simulations of other rare events, including ion adsorption–desorption, − nucleation, − bulk solution properties, , and hydration of layered materials. , However, to our knowledge such methods have not been used to determine the free-energy profile of clay swelling.…”

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confidence: 99%

Revealing Transition States during the Hydration of Clay Minerals

Criscenti

Greathouse

2019

J. Phys. Chem. Lett.

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A molecular-scale understanding of the transition between hydration states in clay minerals remains a challenging problem because of the very fast stepwise swelling process observed from X-ray diffraction (XRD) experiments. XRD profile modeling assumes the coexistence of multiple hydration states in a clay sample to fit the experimental XRD pattern obtained under humid conditions. While XRD profile modeling provides a macroscopic understanding of the heterogeneous hydration structure of clay minerals, a microscopic model of the transition between hydration states is still missing. Here, for the first time, we use molecular dynamics simulation to investigate the transition states between a dry interlayer, one-layer hydrate, and two-layer hydrate. We find that the hydrogen bonds that form across the interlayer at the clay particle edge make an important contribution to the energy barrier to interlayer hydration, especially for initial hydration.

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“…The isobaric extension of gREM was proposed by Małolepsza and Keyes. [26][27][28][29] In this extension, the enthalpy H is used instead of the potential energy E, which is employed in the canonical case (to be exact, H refers to the sum of E and the product of pressure and volume). The effective temperature for each replica is introduced with respect to H, and owing to the use of H, gREM is appropriate for simulating constantpressure ensembles.…”

Section: Introductionmentioning

confidence: 99%

Simulating the nematic-isotropic phase transition of liquid crystal model via generalized replica-exchange method

Takemoto,

Ishii,

Washizu

et al. 2021

Preprint

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The nematic-isotropic (NI) phase transition of 4-cyano-4'-pentylbiphenyl (5CB) was simulated using the generalized replica-exchange method (gREM) based on molecular dynamics simulations. The effective temperature is introduced in gREM, allowing the enhanced sampling of configurations in the unstable region, which is intrinsic to the first-order phase transition. The sampling performance was analyzed with different system sizes and compared with that of the temperature replica-exchange method (tREM). It was observed that gREM is capable of sampling configurations at sufficient replica-exchange acceptance ratios even around the NI transition temperature. A bimodal distribution of the order parameter at the transition region was found, which is in agreement with the mean-field theory. In contrast, tREM is ineffective around the transition temperature owing to the potential energy gap between the nematic and isotropic phases.

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Entropic Description of Gas Hydrate Ice-Liquid Equilibrium via Enhanced Sampling of Coexisting Phases

Cited by 13 publications

References 28 publications

Enhanced Sampling of Phase Transitions in Coarse-Grained Lipid Bilayers

Enhanced Sampling of Phase Transitions in Coarse-Grained Lipid Bilayers

Revealing Transition States during the Hydration of Clay Minerals

Simulating the nematic-isotropic phase transition of liquid crystal model via generalized replica-exchange method

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