THE ISOSPIN DEPENDENCE OF THE NUCLEAR PHASE TRANSITION NEAR THE CRITICAL POINT

The experimental results reveal the isospin dependence of the nuclear phase transition in terms of the Landau Free Energy description of critical phenomena. Near the critical point, different ratios of the neutron to proton concentrations lead to different critical points for the phase transition which is analogous to the phase transitions in He-4-He-3 liquid mixtures. The antisymmetrized molecular dynamics (AMD) and GEMINI models calculations were also performed and the results will be discussed as well.

Computational study on the addition of HCN to methanimine catalyzed by formamidine and formamide

In this paper, we have carried out a theoretical study on the addition of HCN to methanimine with formamidine or formamide using second-order Moller-Plesset perturbation (MP2) method with 6-31 + G(d,p) basis sets. At MP2 level. a high-energy, intermediate has been located for each pathway. The addition of HCN to methanimine with formamidine has the lowest free energy barrier according to the calculations at MP2 level. (C) 2004 Elsevier B.V. All rights reserved.

Lattice Boltzmann study of hydrodynamic effects in lamellar ordering process of two-dimensional quenched block copolymers

By incorporating self-consistent field theory with lattice Boltzmann method, a model for polymer melts is proposed. Compared with models based on Ginzburg-Landau free energy, our model does not employ phenomenological free energies to describe systems and can consider the chain topological details of polymers. We use this model to study the effects of hydrodynamic interactions on the dynamics of microphase separation for block copolymers. In the early stage of phase separation, an exponential growth predicted by Cahn-Hilliard treatment is found. Simulation results also show that the effect of hydrodynamic interactions can be neglected in the early stage.

Studies on coarsening of microdomains in binary polymer mixtures by Lattice Boltzmann methods

An improved free energy approach Lattice Boltzmann model(LBM) is proposed by introducing a forcing term instead of the pressure tensor. This model can reach the proper thermodynamic equilibrium after enough simulation time. On the basis of this model, the phase separation in binary polymer mixtures is studied by applying a Flory-Huggins-type free energy. The numerical results show good agreement with the analytic coexistence curve. This model can also be used to study the coarsening of microdomains in binary polymer mixtures at the early and intermediate stages.

STUDY OF COARSENING OF MICRODOMAINS IN BLOCK COPOLYMERS BY LATTICE BOLTZMANN METHODS

In order to understand the coarsening of microdomains in symmetric diblock copolymers at the late stage, a model for block copolymers is proposed. By incorporating the self consistent field theory with the free energy approach Lattice Boltzmann model, hydrodynamic interactions can be considered. Compared with models based on Ginzburg-Landau free energy, this model does not employ phenomenological free energies to describe systems. The model is verified by comparing the simulation results obtained using this method with those of a dynamical version of the self consistent mean field theory. After that,the growth exponents of the characteristic domain size for symmetric block copolymers at late stage are studied. It is found that the viscosity of the system affects the growth exponents greatly, although the growth exponents are all less than 1/3 Furthermore, the relations between the growth exponent, the interaction parameter and the chain length are studied.

Optimal specificity and function for flexible biomolecular recognition

Biomolecular associations often accompanied by large conformational changes, sometimes folding and unfolding. By exploring an exactly solvable model, we constructed the free energy landscape and established a general framework for studying the biomolecular flexible binding process. We derived an optimal criterion for the specificity and function for flexible biomolecular binding where the binding and conformational folding are coupled.

Crystallization behavior of poly(epsilon-caprolactone) in poly(epsilon-caprolactone) and poly(vinyl methyl ether) mixtures

The morphological development and crystallization behavior of poly(epsilon-caprolactone) (PCL) in miscible mixtures of PCL and poly(vinyl methyl ether) (PVME) were investigated by optical microscopy as a function of the mixture composition and crystallization temperature. The results indicated that the degree of crystallinity of PCL was independent of the mixture composition upon melt crystallization because the glass-transition temperatures of the mixtures were much lower than the crystallization temperature of PCL. The radii of the PCL spherulites increased linearly with time at crystallization temperatures ranging from 42 to 49 degrees C. The isothermal growth rates of PCL spherulites decreased with the amount of the amorphous PVME components in the mixtures. Accounting for the miscibility of PCL/PVME mixtures, the radial growth rates of PCL spherulites were well described by a kinetic equation involving the Flory-Huggins interaction parameter and the free energy for the nuclei formation in such a way that the theoretical calculations were in good agreement with the experimental data. From the analysis of the equilibrium melting point depression, the interaction energy density of the PVME/PCL system was calculated to be -3.95 J/cm(3).

Optimal specificity and function for flexible biomolecular recognition

Biomolecular associations often accompanied by large conformational changes, sometimes folding and unfolding. By exploring an exactly solvable model, we constructed the free energy landscape and established a general framework for studying the biomolecular flexible binding process. We derived an optimal criterion for the specificity and function for flexible biomolecular binding where the binding and conformational folding are coupled.

Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding

We show that diffusion can play an important role in protein-folding kinetics. We explicitly calculate the diffusion coefficient of protein folding in a lattice model. We found that diffusion typically is configuration- or reaction coordinate-dependent. The diffusion coefficient is found to be decreasing with respect to the progression of folding toward the native state, which is caused by the collapse to a compact state constraining the configurational space for exploration. The configuration- or position-dependent diffusion coefficient has a significant contribution to the kinetics in addition to the thermodynamic free-energy barrier. It effectively changes (increases in this case) the kinetic barrier height as well as the position of the corresponding transition state and therefore modifies the folding kinetic rates as well as the kinetic routes. The resulting folding time, by considering both kinetic diffusion and the thermodynamic folding free-energy profile, thus is slower than the estimation from the thermodynamic free-energy barrier with constant diffusion but is consistent with the results from kinetic simulations. The configuration- or coordinate-dependent diffusion is especially important with respect to fast folding, when there is a small or no free-energy barrier and kinetics is controlled by diffusion.Including the configurational dependence will challenge the transition state theory of protein folding.

Energetic basis of molecular recognition in a DNA aptamer

The thermal stability and ligand binding properties of the L-argininamide-binding DNA aptamer (5'-GATCGAAACGTAGCGCCTTCGATC3') were studied by spectroscopic and calorimetric methods. Differential calorimetric studies showed that the uncomplexed aptamer melted in a two-state reaction with a melting temperature T-m = 50.2 +/- 0.2 degrees C and a folding enthalpy Delta H degrees(fold) = -49.0 +/- 2.1 kcal mol(-1). These values agree with values of T-m = 49.6 degrees C and Delta H degrees(fold) = -51.2 kcal mol(-1) predicted for a simple hairpin structure. Melting of the uncomplexed aptamer was dependent upon salt concentration, but independent of strand concentration. The T of aptamer melting was found to increase as L-argininamide concentrations increased. Analysis of circular dichroism titration data using a single-site binding model resulted in the determination of a binding free energy Delta G degrees(bind) = -5.1 kcal mol(-1). Isothermal titration calorimetry studies revealed an exothermic binding reaction with Delta H degrees(bind) = -8.7 kcal mol(-1). Combination of enthalpy and free energy produce ail unfavorable entropy of -T Delta S degrees = +3.6 kcal mol(-1). A molar heat capacity change of -116 cal mol(-1) K-1 was determined from calorimetric measurements at four temperatures over the range of 15-40 degrees C. Molecular dynamics simulations were used to explore the structures of the unligated and ligated aptamer structures.

Daunomycin binding to detergent micelles: A model system for evaluating the hydrophobic contribution to drug-DNA interactions

The interaction of daunomycin with sodium dodecyl sulfate and Triton X-100 micelles was investigated as a model for the hydrophobic contribution to the free energy of DNA intercalation reactions. Measurements of visible absorbance, fluorescence lifetime, steady-state fluorescence emission intensity, and fluorescence anisotropy indicate that the anthraquinone ring partitions into the hydrophobic micelle interior. Fluorescence quenching experiments using both steady-state and lifetime measurements demonstrate reduced accessibility of daunomycin in sodium dodecyl sulfate micelles to the anionic quencher iodide and to the neutral quencher acrylamide. Quenching of daunomycin fluorescence by iodide in Triton X-100 micelles was similar to that seen with free daunomycin. Studies of the energetics of the interaction of daunomycin with micelles by fluorescence and absorbance titration methods and by isothermal titration calorimetry in the presence of excess micelles revealed that association with sodium dodecyl sulfate and Triton X-100 micelles is driven by a large negative enthalpy. Association of the drug with both types of micelles also has a favorable entropic contribution, which is larger in magnitude for Triton X-100 micelles than for sodium dodecyl sulfate micelles.

Influence of shear on polypropylene crystallization kinetics

Isothermal crystallization kinetics under shear in the melt of iPP was investigated by optical microscopy. It appears that shearing from 200 to the crystallization temperatures enhanced the kinetics, but the shear effect was not obvious if the melt of iPP was sheared only at 200. The experiment results show that relaxation plays an important role during crystallization, and that spherulite growth rates increased with shear rates and were governed by relaxation. The effect of flow on the crystallization kinetics can be understood by considering that the increase of the degree of order due to flow results is an effective change of the melt free energy. The Laurizen-Hoffman theory and the DE-IAA model were used to describe the shear-induced crystallization kinetics of iPP excellently.

Crystallization kinetics in shearing-induced oriented and stretched poly(ethylene oxide)

Isothermal crystallization kinetics in the melting of poly(ethylene oxide) (PEO) were investigated as a function of the shear rate and crystallization temperature by optical microscopy. The radial growth rates of the spherulites are described by a kinetics equation including shearing and relaxation combined effects and the free energy for the formation of a secondary crystal nucleus. The free-energy difference between the liquid and crystalline phases increased slightly with rising shearing rates. The experimental findings showed that the influence of the relaxation of PEO, which is related to the shear-induced orientation and stretch in a PEO melt, on the rate of crystallization predominated over the influence of the shearing. This indicated that the relaxation of PEO should be more important so that the growth rates increase with shearing, but it was nearly independent of the shear rate within the measured experimental range.

Enthalpy/entropy compensation: Influence of DNA flanking sequence on the binding of 7-amino actinomycin D to its primary binding site in short DNA duplexes

The effect of the context of the flanking sequence on ligand binding to DNA oligonucleotides that contain consensus binding sites was investigated for the binding of the intercalator 7-amino actinomycin D. Seven self-complementary DNA oligomers each containing a centrally located primary binding site, 5'-A-G-C-T-3', flanked on either side by the sequences (AT)(n) or (AA)(n) (with n = 2, 3, 4) and AA(AT)(2), were studied. For different flanking sequences, (AA)(n)-series or (AT)(n)-series, differential fluorescence enhancements of the ligand due to binding were observed. Thermodynamic studies indicated that the flanking sequences not only affected DNA stability and secondary structure but also modulated ligand binding to the primary binding site. The magnitude of the ligand binding affinity to the primary site was inversely related to the sequence dependent stability. The enthalpy of ligand binding was directly measured by isothermal titration calorimetry, and this made it possible to parse the binding free energy into its energetic and entropic terms.

Crystallization behaviors of n-nonadecane in confined space: Observation of metastable phase induced by surface freezing

Crystallization and phase transition behaviors of n-nonadecane in microcapsules with a diameter of about 5 mu m were studied with the combination of differential scanning calorimetry ( DSC) and synchrotron radiation X-ray diffraction ( XRD). As evident from the DSC measurement, a surface freezing monolayer, which is formed in the microcapsules before the bulk crystallization, induces a novel metastable rotator phase ( RII), which has not been reported anywhere else. We argue that the existence of the surface freezing monolayer decreases the nucleating potential barrier of the RII phase and induces its appearance, while the lower free energy in the confined geometry turns the transient RII phase to a " long- lived" metastable phase.