Calculating the equation of state parameters and predicting the spinodal curve of isotactic polypropylene/poly(ethylene-co-octene) blend by molecular dynamics simulations combined with Sanchez-Lacombe lattice fluid theory

Molecular dynamics simulations are adopted to calculate the equation of state characteristic parameters P*, rho*, and T* of isotactic polypropylene (iPP) and poly(ethylene-co-octene) (PEOC), which can be further used in the Sanchez-Lacombe lattice fluid theory (SLLFT) to describe the respective physical properties. The calculated T* is a function of the temperature, which was also found in the literature. To solve this problem, we propose a Boltzmann fitting of the data and obtain T* at the high-temperature limit. With these characteristic parameters, the pressure-volume-temperature (PVT) data of iPP and PEOC are predicted by the SLLFT equation of state. To justify the correctness of our results, we also obtain the PVT data for iPP and PEOC by experiments. Good agreement is found between the two sets of data. By integrating the Euler-Lagrange equation and the Cahn-Hilliard relation, we predict the density profiles and the surface tensions for iPP and PEOC, respectively. Furthermore, a recursive method is proposed to obtain the characteristic interaction energy parameter between iPP and PEOC. This method, which does not require fitting to the experimental phase equilibrium data, suggests an alternative way to predict the phase diagrams that are not easily obtained in experiments.

Diffusion and single molecule dynamics on biomolecular interface binding energy landscape

We propose a new approach to study the diffusion dynamics on biomolecular interface binding energy landscape. The resulting mean first passage time (MFPT) has 'U'curve dependence on the temperature. It is shown that the large specificity ratio of gap to roughness of the underlying binding energy landscape not only guarantees the thermodynamic stability and the specificity [P.A. Rejto, G.M. Verkhivker, in: Proc. Natl. Acad. Sci. 93 (1996) 8945; C.J. Tsai, S. Kumar, B. Ma, R. Nussinov, Protein Sci. 8 (1999) 1181; G.A. Papoian, P.G. Wolynes, Biopolymers 68 (2003) 333; J. Wang, G.M. Verkhivker, Phys. Rev. Lett. 90 (2003) 198101] but also the kinetic accessibility. The complex kinetics and the associated fluctuations reflecting the structures of the binding energy landscape emerge upon temperature changes. The theory suggests a way of connecting the models/simulations with single molecule experiments by analysing the kinetic trajectories.

Temperature dependence of the distribution of the first passage time: Results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G

More than 22 000 folding kinetic simulations were performed to study the temperature dependence of the distribution of first passage time (FPT) for the folding of an all-atom Go-like model of the second beta-hairpin fragment of protein G. We find that the mean FPT (MFPT) for folding has a U (or V)-shaped dependence on the temperature with a minimum at a characteristic optimal folding temperature T-opt*. The optimal folding temperature T-opt* is located between the thermodynamic folding transition temperature and the solidification temperature based on the Lindemann criterion for the solid. Both the T-opt* and the MFPT decrease when the energy bias gap against nonnative contacts increases. The high-order moments are nearly constant when the temperature is higher than T-opt* and start to diverge when the temperature is lower than T-opt*. The distribution of FPT is close to a log-normal-like distribution at T* greater than or equal to T-opt*. At even lower temperatures, the distribution starts to develop long power-law-like tails, indicating the non-self-averaging intermittent behavior of the folding dynamics. It is demonstrated that the distribution of FPT can also be calculated reliably from the derivative of the fraction not folded (or fraction folded), a measurable quantity by routine ensemble-averaged experimental techniques at dilute protein concentrations.