Isochore evolution

Galtier N. and Mouchiroud D. (1998) Isochore evolution in mammals a human-like ancestral structure. Genetics 150 1577-1584. 

Propellant properties pertinent to the problem are density p gas evolution Vg (cm /g), and isochoric flame temperature Ty. From the above, we know the volumes of the vessels Vq and Vi = We also know the masses of the propellants mo and w, = The volume of gas evolved Irom the propellant at standard temperature and pressure (STP) is... 

Cartesian coordinates for all nuclei of particle), the isochoric dynamical evolution of the Af-particle system follows the Newtonian equations of motion ... 

Figure 6. Evolution of isochors in the P - 7 phase diagram for the core softened potential with third critical point in metastable region. Cl - gas + liquid, C2 - LDL + LIDL, and C3 - HDL + VHDL critical points. Red lines (online) are coexistence curves. Blue curves (online) are isochors. Critical point location na = 0.0064, Xa = 0.1189, ya =0.0998 nc2 = 0.1423, Xc2 = 0.3856, yc2 = 0.33 Ties = 0.07487, xcs = 0.2398, yes = 0.6856. Model parameter set a = 6.962, bh =2.094, Ur/Ua=3, b,=7.0686.

The initial state of the simulations consisted of RDX perfect crystals using simulation cells containing 8 molecules (one unit cell, 168 atoms) and 3D periodic conditions. After relaxing the atomic positions at each density with low temperature MD, we studied the time evolution of the system at the desired temperature with isothermal isochoric (NVT ensemble) MD simulations (using a Berendsen thermostat the relaxation time-scale associated with the coupling between the thermostat and the atomistic system was 200 femtoseconds). 

Using the definition of H/X, the isochoric constraint may then be expressed in terms of the time evolution of the system pressure as the hydrogen is absorbed or desorbed during the th step according to the kinetics of the sample ... 

Figure 16. Orientational dynamics of the ellipsoids of revolution in the 50 50 binary mixture (N = 256) at several temperatures along the isochor at density p = 0.8. (a) Time evolution of the single-particle second-rank orientational time correlation function in a log-log plot. Temperature decreases from left to right (4.997 >T> 0.498). (b) Time dependence of the OKE signal in a log-log plot at temperatures T = 0.574,0.550,0.529, and 0.498. The continuous lines are linear fits, showing the power law decay. Temperature decreases from top to bottom across the linear regime. (Reproduced from Ref. 126.)...

Figure 22. Potential energy landscape explored by the model calamitic system GB(3, 5, 2, 1) (N = 256) as the system makes a transit through mesophases upon cooling, (a) Temperature dependence of the average inherent structure energy per particle, (< /s), along three isochors at densities p = 0.31,0.32, and 0.33. (b) Evolution of the average second-rank orientational order parameter S with temperature both for the inherent structures (filled) and for the instantaneous configurations (opaque). (Reproduced from Ref. 144.)...

Figure 26. Characterization of the inherent structures for the model calamitic system GB(3,5,2, 1) ( = 256). (a) Parallel radial distribution function g (/ ) for the inherent structures at all temperatures considered along the isochor at density p = 0.32. Note that the curves for the highest five temperatures are nearly superposed on each other. For others, the amplitude of the peaks gradually increases as the temperature drops, (b) Evolution of the 6-fold bond orientational order parameter 4>6 for the inherent stmctures with temperature at three densities. (Reproduced from Ref. 144.)...

Figure 12,2. A. Scheme of negative selection in the conservative mode of evolution. Isochores (solid lines) that drift beyond the GC thresholds indicated by the broken lines are counterselected. B. Scheme of negative and positive selection in the transitional or shifting mode of genomes evolution. Isochores (solid lines) with decreasing GC levels are counterselected, whereas those with increasing GC levels are selected for. (From...

Bernardi G. (1993a). The vertebrate genome isochores and evolution. Mol. Biol. Evol. 10 186-204. 

Eyre-Walker A. (1999) Evidence of selection on silent site base composition in mammals potential implications for the evolution of isochores and junk DNA. Genetics 152 675-683. 

Eyre-Walker A. and Hurst L.D. (2001). The evolution of isochores. Nature Rev. Genet. 2 549-555. 

Fryxell K.J. and Zuckerkandl E. (2000). Cytosine deamination plays a primary role in the evolution of mammalian isochores. Mol. Biol. Evol. 17 1371-1383. 

Lercher M., Smith N.G.C, Eyre-Walker A., Hurst L. (2002). The evolution of isochores evidence from SNP frequency distributions. Genetics 162 1805-1810. 

Fig. 9.3 a Three- and b two-dimensional liquid/cry stal coexistence curves (black lines). The dashed lines indicate the isochoric and isocoordinate transition pressure (stress). The red lines indicate pathways around the coexistence curve around which key properties are determined. In both figures the inset shows the evolution of the mean coordination numbers about the respective pathways. In both (a) and (b) the blue curves show the scaled gaussian core coexistence curves [93, 94]... 

The isochoric simulations for pure silica were conducted for fixed density values ranging between 2.97 and 4.2 g cm and for a temperature of 3000 K. The evolution of pressure as a function of density is given... 

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