scholarly journals Liquid-Liquid Phase Transition in Supercooled H2O and D2O: A Path-Integral Computer Simulation Study

Author(s):  
Ali Eltareb ◽  
Gustavo E. Lopez ◽  
Nicolas Giovambattista

Abstract We perform path-integral molecular dynamics (PIMD) and classical MD simulations of H2O and D2O using the q-TIP4P/F water model over a wide range of temperatures and pressures. The density ρ(T), isothermal compressibility κT(T), and self-diffusion coefficients D(T) of H2O and D2O are in excellent agreement with available experimental data; the isobaric heat capacity CP(T) obtained from PIMD and MD simulations agree qualitatively well with the experiments. Some of these thermodynamic properties exhibit anomalous maxima upon isobaric cooling, consistent with recent experiments and with the possibility that H2O and D2O exhibit a liquid-liquid critical point (LLCP) at low temperatures and positive pressures. The data from PIMD/MD for H2O and D2O can be fitted remarkably well using the Two-State-Equation-of-State (TSEOS). Using the TSEOS, we estimate that the LLCP for q-TIP4P/F H2O, from PIMD simulations, is located at Pc = 167±9 MPa, Tc = 159±6 K, and ρc = 1.02±0.01 g/cm3. Isotope substitution effects are important; the LLCP location in q-TIP4P/F D2O is estimated to be Pc = 176 ± 4 MPa, Tc = 177 ± 2 K, and ρc = 1.13±0.01 g/cm3. Interestingly, for the water model studied, differences in the LLCP location from PIMD and MD simulations suggest that nuclear quantum effects (i.e., atoms delocalization) play an important role in the thermodynamics of water around the LLCP (from the MD simulations of q-TIP4P/F water, Pc = 203 ± 4 MPa, Tc = 175 ± 2 K, and ρc = 1.03 ± 0.01 g/cm3). Overall, our results strongly support the LLPT scenario to explain water anomalous behavior, independently of the fundamental differences between classical MD and PIMD techniques. The reported values of Tc for D2O and, particularly, H2O suggest that improved water models are needed for the study of supercooled water.

2007 ◽  
Vol 130 (1) ◽  
pp. 111-116 ◽  
Author(s):  
Artem B. Mamonov ◽  
Rob D. Coalson ◽  
Mark L. Zeidel ◽  
John C. Mathai

Determining the mechanisms of flux through protein channels requires a combination of structural data, permeability measurement, and molecular dynamics (MD) simulations. To further clarify the mechanism of flux through aquaporin 1 (AQP1), osmotic pf (cm3/s/pore) and diffusion pd (cm3/s/pore) permeability coefficients per pore of H2O and D2O in AQP1 were calculated using MD simulations. We then compared the simulation results with experimental measurements of the osmotic AQP1 permeabilities of H2O and D2O. In this manner we evaluated the ability of MD simulations to predict actual flux results. For the MD simulations, the force field parameters of the D2O model were reparameterized from the TIP3P water model to reproduce the experimentally observed difference in the bulk self diffusion constants of H2O vs. D2O. Two MD systems (one for each solvent) were constructed, each containing explicit palmitoyl-oleoyl-phosphatidyl-ethanolamine (POPE) phospholipid molecules, solvent, and AQP1. It was found that the calculated value of pf for D2O is ∼15% smaller than for H2O. Bovine AQP1 was reconstituted into palmitoyl-oleoyl-phosphatidylcholine (POPC) liposomes, and it was found that the measured macroscopic osmotic permeability coefficient Pf (cm/s) of D2O is ∼21% lower than for H2O. The combined computational and experimental results suggest that deuterium oxide permeability through AQP1 is similar to that of water. The slightly lower observed osmotic permeability of D2O compared to H2O in AQP1 is most likely due to the lower self diffusion constant of D2O.


Author(s):  
Nicola Molinari ◽  
Jonathan P. Mailoa ◽  
Boris Kozinsky

We show that strong cation-anion interactions in a wide range of lithium-salt/ionic liquid mixtures result in a negative lithium transference number, using molecular dynamics simulations and rigorous concentrated solution theory. This behavior fundamentally deviates from the one obtained using self-diffusion coefficient analysis and agrees well with experimental electrophoretic NMR measurements, which accounts for ion correlations. We extend these findings to several ionic liquid compositions. We investigate the degree of spatial ionic coordination employing single-linkage cluster analysis, unveiling asymmetrical anion-cation clusters. Additionally, we formulate a way to compute the effective lithium charge that corresponds to and agrees well with electrophoretic measurements and show that lithium effectively carries a negative charge in a remarkably wide range of chemistries and concentrations. The generality of our observation has significant implications for the energy storage community, emphasizing the need to reconsider the potential of these systems as next generation battery electrolytes.<br>


1997 ◽  
Vol 11 (04) ◽  
pp. 129-138 ◽  
Author(s):  
V. Sa-Yakanit ◽  
V. D. Lakhno ◽  
Klaus Haß

The generalized path integral approach is applied to calculate the ground state energy and the effective mass of an electron-plasmon interacting system for a wide range of densities. It is shown that in the self-consistent approximation an abrupt transition between the weak coupling and the strong coupling region of interaction exists. The transition occurs at low electron densities according to a value of 418 for rs, when Wigner crystallization is possible. For densities of real metals, the electron bandwidth is calculated and a comparison with experimental results is given.


2021 ◽  
pp. 1-12
Author(s):  
Haiyan Li ◽  
Zanxia Cao ◽  
Guodong Hu ◽  
Liling Zhao ◽  
Chunling Wang ◽  
...  

BACKGROUND: The ribose-binding protein (RBP) from Escherichia coli is one of the representative structures of periplasmic binding proteins. Binding of ribose at the cleft between two domains causes a conformational change corresponding to a closure of two domains around the ligand. The RBP has been crystallized in the open and closed conformations. OBJECTIVE: With the complex trajectory as a control, our goal was to study the conformation changes induced by the detachment of the ligand, and the results have been revealed from two computational tools, MD simulations and elastic network models. METHODS: Molecular dynamics (MD) simulations were performed to study the conformation changes of RBP starting from the open-apo, closed-holo and closed-apo conformations. RESULTS: The evolution of the domain opening angle θ clearly indicates large structural changes. The simulations indicate that the closed states in the absence of ribose are inclined to transition to the open states and that ribose-free RBP exists in a wide range of conformations. The first three dominant principal motions derived from the closed-apo trajectories, consisting of rotating, bending and twisting motions, account for the major rearrangement of the domains from the closed to the open conformation. CONCLUSIONS: The motions showed a strong one-to-one correspondence with the slowest modes from our previous study of RBP with the anisotropic network model (ANM). The results obtained for RBP contribute to the generalization of robustness for protein domain motion studies using either the ANM or PCA for trajectories obtained from MD.


2007 ◽  
Vol 68 (3) ◽  
pp. 389-393 ◽  
Author(s):  
Guo-Xiang Chen ◽  
Jian-Min Zhang ◽  
Ke-Wei Xu ◽  
Vincent Ji

2021 ◽  
Author(s):  
Y. Sheena Mary ◽  
Y. Shyma Mary ◽  
Razieh Razavi

Abstract In crystal engineering and pharmaceutical chemistry, cocrystals have a wide range of applications. Ethenzamide (EA) is found to form cocrystal with 2-nitrobenzoic acid (NBA). Geometry properties like stability energy, charge distribution, bond length, electronic properties and thermodynamic characteristics have been analyzed. The C-H…O hydrogen bond involves C-H of EA and oxygen of NBA. Configuration with the angle, N3-C4-C5-C6 gives the lowest energy conformation. Partition coefficient value suggests that EA-NBA has pharmaceutics behavior. RMSD values show the simulation’s relative stability and the complexes, remained stable throughout.


Author(s):  
michael kassner

This paper discusses recent developments in creep, over a wide range of temperature, that mqy change our understanding of creep. The five-power law creep exponent (3.5 to 7) has never been explained in fundamental terms. The best the scientific community has done is to develop a natural three power-law creep equation that falls short of rationalizing the higher stress exponents that are typically five. This inability has persisted for many decades. Computational work examining the stress-dependence of the climb rate of edge dislocations we may rationalize the phenomenological creep equations. Harper-Dorn creep, “discovered” over 60 years ago has been immersed in controversy. Some investigators have insisted that a stress exponent of one is reasonable. Others believe that the observation of a stress exponent of one is a consequence of dislocation network frustration. Others believe the stress exponent is artificial due to the inclusion of restoration mechanisms such as dynamic recrystallization or grain growth that is not of any consequence in the five power-law regime. Also, the experiments in the Harper-Dorn regime, which accumulate strain very slowly (sometimes over a year) may not have attained a true steady state. New theories suggest that absence or presence of Harper-Dorn may be a consequence of the initial dislocation density. Novel experimental work suggests that power-law breakdown may be a consequence of a supersaturation of vacancies which increase self-diffusion.


Author(s):  
S. Wu ◽  
P. Angelikopoulos ◽  
C. Papadimitriou ◽  
R. Moser ◽  
P. Koumoutsakos

We present a hierarchical Bayesian framework for the selection of force fields in molecular dynamics (MD) simulations. The framework associates the variability of the optimal parameters of the MD potentials under different environmental conditions with the corresponding variability in experimental data. The high computational cost associated with the hierarchical Bayesian framework is reduced by orders of magnitude through a parallelized Transitional Markov Chain Monte Carlo method combined with the Laplace Asymptotic Approximation. The suitability of the hierarchical approach is demonstrated by performing MD simulations with prescribed parameters to obtain data for transport coefficients under different conditions, which are then used to infer and evaluate the parameters of the MD model. We demonstrate the selection of MD models based on experimental data and verify that the hierarchical model can accurately quantify the uncertainty across experiments; improve the posterior probability density function estimation of the parameters, thus, improve predictions on future experiments; identify the most plausible force field to describe the underlying structure of a given dataset. The framework and associated software are applicable to a wide range of nanoscale simulations associated with experimental data with a hierarchical structure.


1994 ◽  
Vol 49 (3-4) ◽  
pp. 258-264 ◽  
Author(s):  
D. Girlich ◽  
H.-D. Lüdemann ◽  
C. Buttersack ◽  
K. Buchholz

The self diffusion coefficients D of the water molecules and of sucrose have been determined by the pulsed field gradient NMR technique over a wide range of temperatures and concentrations (cmax: 70% w/w suc.). All temperature dependencies can be fitted to a Vogel- Tammann-Fulcher equation. The isothermic concentration dependence of D for the sucrose is given by a simple exponential concentration dependence


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