Peptidyl-Resin Substrates as a Tool in the Analysis of Caspase Activity

Caspases, proteolytic enzymes belonging to the group of cysteine proteases, play a crucial role in apoptosis. Understanding their activity and substrate specificity is extremely important. Fluorescence-based approaches, including fluorogenic substrates, are generally used to confirm cleavage preferences. Here we present a new method of substrate specificity and activity analysis based on the application of fix-charge tagged peptides located on the resin. The proteolysis of peptide bond on the resin, occurring even with low efficiency, results in the formation of N-terminal fragments of model peptide containing ionization enhancers in the form of quaternary ammonium groups, allowing for ultrasensitive and reliable analysis by LC-MS/MS. The possibility of application of the proposed solution was tested through the analysis of substrate specificity and activity of caspase 3 or 7. The obtained results confirm the known substrate specificity of executioner caspases. Our solution also allowed us to observe that caspases can hydrolyze peptides shorter than those presented to date in the scientific literature.     

A subspace limited memory quasi-Newton algorithm for large-scale nonlinear bound constrained optimization

In this paper we propose a subspace limited memory quasi-Newton method for solving large-scale optimization with simple bounds on the variables. The limited memory quasi-Newton method is used to update the variables with indices outside of the active set, while the projected gradient method is used to update the active variables. The search direction consists of three parts: a subspace quasi-Newton direction, and two subspace gradient and modified gradient directions. Our algorithm can be applied to large-scale problems as there is no need to solve any subproblems. The global convergence of the method is proved and some numerical results are also given.

     

矩阵乘积形式的有限存贮拟牛顿法

1 引言 考虑无约束优化问题 minf(x),(1.1) x∈R~n其中f为非线性町微函数。 对于中小规模的无约束优化问题,拟牛顿法(如BFGS方法)是十分有效的。但对于大规模问题,即n相当大时,算法所需存贮相当重要,并且在每次迭代中线代数计算量也影响算法的效率。 有限存贮((1imited memory)拟牛顿法可看成是共轭梯度法的推广。这一类方法最早由Perry和Shanno提出,此后有不少人进行研究,如Gill和Murray,Buckley,Buckley和LeNir及Nocedal。 有限存贮BFGS方法由Nocedal提出,是目前一种十分有效的有限存贮拟牛顿方法,其基本出法点是减少存贮。由于BFGS修正公式可写成     

Updating the Self-Scaling Symmetric Rank One Algorithm with Limited Memory for Large-Scale Unconstrained Optimization

A new limited memory quasi-Newton algorithm is developed, in which the self-scaling symmetric rank one update with Davidon's optimal condition is applied. Preliminary numerical tests show that the new algorithm is very efficient for large-scale problems as well as general nonlinear optimization.     

Some Stratigraphic Control Problems

In this paper, we are interested in lithology diffusion models applied in the field of stratigraphic basin simulations for large-scale depositional transport processes of sediments. Such models describe erosion-sedimentation processes and take into account limited weathering via nonstandard unilateral problems. Various theoretical results, illustrations, and numerical solutions are presented for the monolithologic column case. A new conservation law involved in modeling is formulated, and mathematical tools for solving the problem are described.     

Polynomials and limited sets

We prove that scalar-valued polynomials are weakly continuous on limited sets and that, as in the case of linear mappings, every -valued polynomial maps limited sets into relatively compact ones. We also show that a scalar-valued polynomial whose derivative is limited is weakly sequentially continuous.

     

Global convergence of a modified limited memory BFGS method for non-convex minimization

In this paper, a modified limited memory BFGS method for solving large-scale unconstrained optimization problems is proposed. A remarkable feature of the proposed method is that it possesses global convergence property without convexity assumption on the objective function. Under some suitable conditions, the global convergence of the proposed method is proved. Some numerical results are reported which illustrate that the proposed method is efficient.     

An insight into the viscosity prediction of ternary alloys with limited solubility

Geometrical models have been successfully applied into the calculation of viscosity of alloys. However, traditional geometrical (TG) models are feasible only in systems with a complete solubility area. Otherwise, they will not work. In this paper, a new method has been introduced for the calculation of alloy systems with limited solubility. How the new method overcomes the drawbacks of the TG models is discussed and analysed. The viscosity of two alloy systems with limited solubility is calculated by the present model. Comparisons between the experimental viscosity and the calculated values by different models show that our model gives the best results, especially for the data nearby the limited solubility area. The introduction of this model provides a way to solve the calculation problems of ternary alloys with limited solubility, which will extend geometrical models to more practical systems.     

Accelerated brush growth on nanoparticle surfaces by reversible addition‐fragmentation chain transfer polymerization

It is now well established that controlling the grafted chain lengths and densities on nanoparticle surfaces determines the effective interactions between particles, and their assembly. Here, we present unusual kinetic results for achieving grafted chain lengths longer than the free chains using reversible addition‐fragmentation chain transfer (RAFT) polymerization and discuss the limitations to obtaining polymer grafting density higher than ～0.06 chains/nm². We observe that surface initiated polymerization grows faster than the free chains in solution with high RAFT agent coverage (1.95 agents/nm²) on nanoparticles. The time‐dependence of graft density suggests that activation of the anchored chain transfer agent (CTA) is limited by the diffusion of macro‐radicals within growing grafts. Thus, radical transfer and exchange reactions become inefficient between grafts and free polymer, and convert the surface‐initiated RAFT mechanism to a free radical polymerization. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014 , 52, 1700–1705     

An Infectious Disease Model With Media Coverage and Limited Medical Resources北大核心CSCD

该文建立和分析了一类具有媒体报道效应和有限医疗资源的传染病动力学模型,定义了疾病的基本再生数,分析了平衡点的存在性和稳定性,给出了系统发生前向分支、后向分支和Hopf分支的条件.通过数值模拟发现：提高媒体报道的信息覆盖率或医院对病人的最大容纳量,可以显著降低疾病流行的峰值或稳态时的感染人数;随着参数变化,系统不仅可能会产生后向分支或前向分支,还可能会出现鞍结点分支、Hopf分支以及地方病平衡点稳定性随参数变化而变化等动力学行为.