Dynamic transition pressure induced

AokI M I and Tsumuraya K 1997 Ab initio molecular-dynamics study of pressure-induced glass-to-crystal transitions In the sodium system Pbys. Rev. B 56 2962-8... 

Just as one may wish to specify the temperature in a molecular dynamics simulation, so may be desired to maintain the system at a constant pressure. This enables the behavior of the system to be explored as a function of the pressure, enabling one to study phenomer such as the onset of pressure-induced phase transitions. Many experimental measuremen are made under conditions of constant temperature and pressure, and so simulations in tl isothermal-isobaric ensemble are most directly relevant to experimental data. Certai structural rearrangements may be achieved more easily in an isobaric simulation than i a simulation at constant volume. Constant pressure conditions may also be importai when the number of particles in the system changes (as in some of the test particle methoc for calculating free energies and chemical potentials see Section 8.9). 

McHale JM, Auroux A, Perrotta AJ, Navrotsky A (1997) Surface energies and thermodynamic phase stability in nanocrystalline aluminas. Science 277 788-791 Molteni C, Martonak R, Parrinello M (2001) First principles molecular dynamics simulations of pressure-induced stiuctural transformations in silicon clusters. J Chem Phys 114 5358-5365 Murray CB, Norris DJ, Bawendi MG (1993) Synthesis and characterization of nearly monodisperse CdE (E = S, Se, Te) semiconductor nanocrystallites. J Am Chem Soc 115 8706-8715 Onodera A (1972) Kinetics of polymorphic transitions of cadmium chalcogenides under high pressure. Rev Phys Chem Japan 41 1... 

The potential of Eq. (1) with parameters determined in Refs. [10, 11] was thoroughly tested in computer simulations of silica polymorphs. In Ref. [10], the structural parameters and bulk modulus of cc-quartz, a-cristobalite, coesite, and stishovite obtained from molecular dynamics computer simulations were found to be in good agreement with the experimental data. The a to / structural phase transition of quartz at 850 K ha.s also been successfully reproduced [12]. The vibrational properties computed with the same potential for these four polymorphs of crystalline silica only approximately reproduce the experimental data [9]. Even better results were reported in Ref. [5] where parameters of the two-body potential Eq. (1) were taken from Ref. [11]. It was found that the calculated static structures of silica polymorphs are in excellent agreement with experiments. In particular, with the pressure - volume equation of state for a -quartz, cristobalite, and stishovite, the pressure-induced amorphization transformation in a -quartz and the thermally induced a — j3 transformation in cristobalite are well reproduced by the model. However, the calculated vibrational spectra were only in fair agreement with experiments. 

One question that needs to be addressed is why are the activation volumes of pericyclic cycloadditions smaller (more negative) than those of the corresponding stepwise reactions involving diradical intermediates In the past it was assumed that the simultaneous formation of two new n bonds in a pericyclic [4 - - 2] cycloaddition leads to a larger contraction of volume than the formation of one bond in the stepwise process. The interpretation presented [28] is limited by the scope of Eyring transition state theory where the activation volume is related to the transition state volume, as mentioned above, and does not incorporate dynamic effects related to pressure-induced changes in viscosity [41]. An extensive discussion of reaction rates in highly viscous solvents can be found in Chapter 3. 

Kingma, K., Meade, C., Hemley, R.J., Mao, H.-H., and Veblen, D.R. (1993) Mi-crostructural observations of a-quartz amorphization. Science, 259, 666-669. Chaplot, S.L., and Sikka, S.K. (1993) Molecular-dynamics simulation of pressure induced crystalline-to-amorphous transition in some corner-linked polyhedral compounds, Phys. Rev., B47, 5710-5715. 

Compression Radial compression was studied via a combined molecular dynamics and density functional theory-based nonequilibrium Green s function approach (Wu et al. 2004). Reversible pressure-induced metal-to-semiconductor transitions of armchair SWNTs were predicted suggesting that SWNTs maybe used as miniature sensitive pressure detectors (Mehrez et al. 2005 Wu et al. 2004). 

This picture agrees with the available experimental analysis of the effect of hydration on lysozyme dynamics [473, 508-510, 512, 513]. Namely, internal dynamics of lysozyme molecule is restored when it is covered by some minimal amount of hydration water. Note that correlation between the percolation transition of water and pressure-induced dynamic transition of protein molecules was also observed in simulations of crystalline Snase [612]. 

In dilute aqueous solutions, biomolecules are completely covered by water molecules. The structure of water near a boundary essentially differs from the structure of bulk water (see Sections 2 and 5). Specific water structure is seen in one or two water layers near hydrophilic surfaces, whereas the rest of liquid water is bulk-like. This is also the case for the surfaces of biomolecules, which allow consideration of hydration water as a separate subsystem. Conformational transitions and aggregation of biomolecules occur in dilute solution due to variations of temperature and/or pressure and due to additions of some cosolvents. It is natural to expect that these biologically important processes are related to the changes in the state of hydration water shell. First, we consider the effect of heating on the state of hydration water shell and on the properties of biomolecules. Then, we discuss the dynamic transition of biomolecules and pressure-induced denaturation in relation with the liquid-liquid transitions of hydration water. 

Hiickel calculations have been employed extensively in other approaches such as the angular overlap model and the method of moments developed by Burdett and coworkers. Stabilities of crystal structures, pressure- and temperature-induced transitions, dynamical pathways in reactions and other phenomena have been analysed using angular overlap models. Thus, the electronic control of rutile structures and the stability of the defect structure of NbO have been examined (Burdett, 1985 Burdett Mitchell, 1993). In the case of NbO, the structure is stable at involving the formation... 

Clear evidence of L-L transitions has been found only in /-Si modeled by the SW potential [269]. Sastry and Angell [288] performed MD simulations of supercooled /-Si using the SW potential. After cooling at ambient pressure, the liquid (HDL) was transformed to LDL at 1060 K. The Nc in LDL is almost 4, and the diffusivity is low compared with that in HDL. The structural properties of LDL, such as g(r) and Nc, are very close to those of LDA, which indicates that this HDL-LDL transition is a manifestation of the multiple amorphous forms (LDA and HDA) of Si. McMillan et al. [264] and Morishita [289] have also found structural fluctuations between LDL-like and HDL-like forms in their MD calculations for /-Si at 1100 K. Morishita has demonstrated that such a structural fluctuation induces spatial and temporal dynamical heterogeneity, and this heterogeneity accounts for the non-Debye relaxation process that becomes noticeable in the supercooled state [289]. 

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