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Molecular dynamics calculations have been used to study structural relaxation and dynamical correlations near the glass transition in the system [Ca(N0 3 h]o.4 [KN0 3 ]o.6' As in a typical molten salt, the overall structure is determined by charge ordering. However, the radial distribution function for Ca 2 + ions is unusual in that even at high temperatures it shows a split first peak due to specific spatial correlations of the cations with the nitrate anions. Structural relaxation that accompanies cooling of the system has been characterized with the aid of the van Hove real-space correlation functions G s (r,t) for the constituent atoms (Ca, K, N, 0). The relaxation of the incoherent structure factor Fs (k,t), with a wave vector k near the peak of the static structure factor, has been investigated as a function of temperature. The results clearly reveal both the a and /3 relaxation processes; the former can be well represented by a master curve with a stretched exponential shape. An analysis of the susceptibility, which agrees qualitatively with neutron spin-echo data, suggests that the glass transition for the model occurs around 400 K. The relatively small discrepancy with the experimental transition temperature derived from neutron scattering data (366 K) is likely related to inadequacies in the model employed for the interionic interactions. The functions C1(t) and C 2 (t) , which describe the reorientational relaxation of the threefold symmetry axes of the nitrate ions, are shown to exhibit a scaling behavior analogous to that of the structure factor. In the region of the glass transition, where translational diffusion has essentially stopped, the nitrate ions continue to flip predominantly about their twofold axes

Serial Generalized Ensemble Simulations of Biomolecules with Self-Consistent Determination of Weights

Serial generalized ensemble simulations, such as simulated tempering, enhance phase space sampling through non-Boltzmann weighting protocols. The most critical aspect of these methods with respect to the popular replica exchange schemes is the difficulty in determining the weight factors which enter the criterion for accepting replica transitions between different ensembles. Recently, a method, called BAR-SGE, was proposed for estimating optimal weight factors by resorting to a self-consistent procedure applied during the simulation (<i>J. Chem. Theory Comput.</i> <b>2010</b>, <i>6</i>, 1935–1950). Calculations on model systems have shown that BAR-SGE outperforms other approaches proposed for determining optimal weights in serial generalized ensemble simulations. However, extensive tests on real systems and on convergence features with respect to the replica exchange method are lacking. Here, we report on a thorough analysis of BAR-SGE by performing molecular dynamics simulations of a solvated alanine dipeptide, a system often used as a benchmark to test new computational methodologies, and comparing results to the replica exchange method. To this aim, we have supplemented the ORAC program, a FORTRAN suite for molecular dynamics simulations (<i>J. Comput. Chem.</i> <b>2010</b>, <i>31</i>, 1106–1116), with several variants of the BAR-SGE technique. An illustration of the specific BAR-SGE algorithms implemented in the ORAC program is also provided

Conformational Landscape of N-Glycosylated Peptides Detecting Autoantibodies in Multiple Sclerosis, Revealed by Hamiltonian Replica Exchange

Synthetic N-glycosylated CSF114­(Glc) and related peptides were proved to be able to recognize specific and high-affinity autoantibodies circulating in blood of relapsing-remitting multiple sclerosis (MS) patients and correlating with disease activity. The effect of these peptides has been linked to the β-turn structure around the minimal epitope Asn­(Glc). In this work we performed Hamiltonian replica exchange molecular dynamics simulations on the central heptapeptide fragment of a CSF114­(Glc)-derived peptide in water and in a water/hexafluoroacetone mixture, confirming a significant incidence of β-turn structures in both solvents. The structural similarity of the glycosylated and unglycosylated forms in all environments proves that the conformation of the heptapeptide is only marginally affected by the presence of the sugar. Moreover, the presence of a significant amount of bioactive hairpin-like conformations in the water environment suggests a possible use not only in the diagnosis but also in the treatment of MS

Sex differences in food choices, adherence to dietary recommendations and plasma lipid profile in type 2 diabetes - The TOSCA.IT study

Diabetic women have a more adverse plasma lipid profile than men. Sex differences in dietary habits may play a role, but are little investigated. The study evaluates the quality of diet, adherence to the nutritional recommendations of the Diabetes and Nutrition Study Group and their relation with plasma lipid in men and women with diabetes. METHODS AND RESULTS: We studied 2573 people, aged 50-75, enrolled in the TOSCA.IT study (clinicaltrials.gov; NCT00700856). Plasma lipids were measured centrally. Diet was assessed with a semi-quantitative food frequency questionnaire. Women had a more adverse plasma lipid profile than men. Women consumed significantly more legumes, vegetables, fruits, eggs, milk, vegetable oils, and added sugar, whereas men consumed more starchy foods, soft drinks and alcoholic beverages. This stands for a higher proportion (%) of energy intake from saturated fat and added sugar (12.0 \ub1 2.4 vs 11.5 \ub1 2.5 and 3.4 \ub1 3.2 vs 2.3 \ub1 3.2, P < 0.04), and a higher intake of fiber (11.2 \ub1 2.8 vs 10.4 \ub1 2.6 g/1000 Kcal/day) in women. Adherence to the recommendations for saturated fat and fiber consumption was associated with significantly lower LDL-cholesterol regardless of sex. Adherence to the recommendations for added sugars was associated with significantly lower triglycerides and higher HDL-cholesterol in men and women. CONCLUSIONS: Men and women with diabetes show significant differences in adherence to nutritional recommendations, but sex differences in plasma lipid profile are unlikely to be explained by nutritional factors. Adherence to the nutritional recommendations is associated with a better plasma lipid profile regardless of sex, thus reinforcing the importance of substituting saturated for unsaturated fat sources, increasing fiber and reducing added sugar intake