Origin and Prediction of Highly Specific Bond Cleavage Sites in the Thermal Activation of Intact Protein Ions

Predicting the fragmentation patterns of proteins would be beneficial for the reliable identification of intact proteins by mass spectrometry. However, the ability to accurately make such predictions remains elusive. An approach to predict the specific cleavage sites in whole proteins resulting from collision-induced dissociation by use of an improved electrostatic model for calculating the proton configurations of highly-charged protein ions is reported. Using ubiquitin, cytochrome c, lysozyme and β-lactoglobulin as prototypical proteins, this approach can be used to predict the fragmentation patterns of intact proteins. For sufficiently highly charged proteins, specific cleavages occur near the first low-basicity amino acid residues that are protonated with increasing charge state. Hybrid QM/QM′ (QM=quantum mechanics) and molecular dynamics (MD) simulations and energy-resolved collision-induced dissociation measurements indicated that the barrier to the specific dissociation of the protonated amide backbone bond is significantly lower than competitive charge remote fragmentation. Unlike highly charged peptides, the protons at low-basicity sites in highly charged protein ions can be confined to a limited sequence of low-basicity amino acid residues by electrostatic repulsion, which results in highly specific fragmentation near the site of protonation. This research suggests that the optimal charge states to form specific sequence ions of intact proteins in higher abundances than the use of less specific ion dissociation methods can be predicted a priori.     

Multistrain edge‐based compartmental model on networks

Multistrain diseases, which are infected through individual contacts, pose severe public health threat nowadays. In this paper, we build competitive and mutative two‐strain edge‐based compartmental models using probability generation function (PGF) and pair approximation (PA). Both of them are ordinary differential equations. Their basic reproduction numbers and final size formulas are explicitly derived. We show that the formula gives a unique positive final epidemic size when the reproduction number is larger than unity. We further consider competitive and mutative multistrain diseases spreading models and compute their basic reproduction numbers. We perform numerical simulations that show some dynamical properties of the competitive and mutative two‐strain models.     

Solvability of a nonlinear fifth‐order difference equation

Some formulas for well‐defined solutions to four very special cases of a nonlinear fifth‐order difference equation have been presented recently in this journal, where some of them were proved by the method of induction, some are only quoted, and no any theory behind the formulas was given. Here, we show in an elegant constructive way how the general solution to the difference equation can be obtained, from which the special cases very easily follow, which is also demonstrated here. We also give some comments on the local stability results on the special cases of the nonlinear fifth‐order difference equation previously publish in this journal.     

Existence of strong minimizers for the Griffith static fracture model in dimension two

We consider the Griffith fracture model in two spatial dimensions, and prove existence of strong minimizers, with closed jump set and continuously differentiable deformation fields. One key ingredient, which is the object of the present paper, is a generalization to the vectorial situation of the decay estimate by De Giorgi, Carriero, and Leaci. This is based on replacing the coarea formula by a method to approximate $SB{D}^p$ functions with small jump set by Sobolev functions, and is restricted to two dimensions. The other two ingredients will appear in companion papers and consist respectively in regularity results for vectorial elliptic problems of the elasticity type and in a method to approximate in energy $GSB{D}^p$ functions by $SB{V}^p$ ones.     

NUMERICAL SIMULATION OF FIBROBLAST DUROTAXIS MIGRATION INDUCED BY STIFFNESS GRADIENT OF SUBSTRATE1)

建立了一种细胞趋硬性迁移的理论模型和有限元分析框架,为连续变刚度人工基质的试验设计提供理论依据。考虑了细胞体的黏弹性属性,以及细胞与基质间的配受体动态反应过程,并以配受体合成时间为时间步长,将细胞运动方程化为静力学形式进行求解。对有限元过程提出一种动约束,便于消除其结构矩阵的奇异性。结果表明,模型能够模拟黏着斑内部力的快速波动现象,细胞的运动速度与观测数据一致,可有效模拟20,h以上的长时程问题。     

Thermal decomposition of model compound of algal biomass

This contribution investigates thermal decomposition of leucine, as a representative model compound for amino acids in algal biomass. We map out potential energy surface for a wide array of unimolecular and self-condensation reactions operating in the decomposition of leucine. Decarboxylation and dehydration of leucine ensues by eliminating CO₂ and –OH, respectively, from the –COOH group attached to the α-carbon. The molecular channel for deamination involves cleavage of NH₂ from α-carbon of leucine. The activation energies for direct elimination of CO₂, NH₃, and H₂O from a leucine molecule lie within 20.7 kJ/mol of each other. Activation energies for these decomposition pathways reside below the bond dissociation enthalpy of H–C(α) of 323.1 kJ/mol. The decarboxylation, deamination, and dehydration pathways, via radical-prompted pathways, systematically require lower energy barriers, in reference to closed-shell reaction corridors. Detailed computations at the CBS-QB3 level provide the Arrhenius rate parameters for the unimolecular and bimolecular reactions, and standard enthalpies of formation, standard entropies, and heat capacities for all the products and intermediates. A kinetic analysis of gas-phase reactions, within the context of a plug-flow reactor model, accounts qualitatively for the formation of major products observed experimentally in the thermal degradation of the condensed-phase leucine. Among notable N-containing species, the model predicts the prevailing of NH₃ over HCN and HNCO, in addition to corresponding appreciable concentrations of amines, imines, and nitriles. Our detailed kinetic investigation illustrates a negligible contribution of the self-condensation reactions of leucine in the gas phase.