Computational Design of Novel Allosteric Inhibitors for Plasmodium falciparum DegP

The serine protease, DegP exhibits proteolytic and chaperone activities, essential for cellular protein quality control and normal cell development in eukaryotes. The P. falciparum DegP is essential for the parasite survival and required to combat the oscillating thermal stress conditions during the infection, protein quality checks and protein homeostasis in the extra-cytoplasmic compartments, thereby establishing it as a potential target for drug development against malaria. Previous studies have shown that diisopropyl fluorophosphate (DFP) and the peptide SPMFKGV inhibit E. coli DegP protease activity. To identify novel potential inhibitors specific to PfDegP allosteric and the catalytic binding sites, we performed a high throughput in silico screening using Malaria Box, Pathogen Box, Maybridge library, ChEMBL library and the library of FDA approved compounds. The screening helped identify five best binders that showed high affinity to PfDegP allosteric (T0873, T2823, T2801, {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, CD00811) and the catalytic binding site (T0078L, T1524, T2328, BTB11534 and 552691). Further, molecular dynamics simulation analysis revealed {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, BTB11534 as the best hits forming a stable complex. WaterMap and electrostatic complementarity were used to evaluate the novel bio-isosteric chemotypes of {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, that led to the identification of 231 chemotypes that exhibited better binding affinity. Further analysis of the top 5 chemotypes, based on better binding affinity, revealed that the addition of electron donors like nitrogen and sulphur to the side chains of butanoate group are more favoured than the backbone of butanoate group. In a nutshell, the present study helps identify novel, potent and Plasmodium specific inhibitors, using high throughput in silico screening and bio-isosteric replacement, which may be experimentally validated.     

Flow physics of normal and abnormal bioprosthetic aortic valves

Flow physics of transvalvular flows in the aorta with bioprosthetic valves are investigated using computational modelling. For the efficient simulations of flow-structure-interaction in transvalvular flows, a simplified, reduced degree of freedom valve model is employed with a sharp interface immersed boundary based incompressible flow solver. Simulations are performed for normal as well as abnormal valves with reduced leaflet motion that models the effect of early leaflet thrombosis. The structure of the aortic jet and the hemodynamic stresses on the aortic wall are analysed to understand the hemodynamic impacts and possible long-term clinical implications of sub-clinical, reduced leaflet motion. The simulation results have shown that the reduced leaflet motion tilts the direction of aortic jet and generates stronger flow separation and re-attachment on the aortic wall downstream from the reduced motion leaflets. The modified flow pattern increases the wall pressure fluctuation and average wall shear stress on the downstream aortic wall, and results in the asymmetric oscillatory shear index distributions, which may have long-term clinical implications such as aortic wall damage and remodelling.     

Minimal Ellipsoid Circumscribing a Polytope Defined by a System of Linear Inequalities

In this paper, we will propose algorithms for calculating a minimal ellipsoid circumscribing a polytope defined by a system of linear inequalities. If we know all vertices of the polytope and its cardinality is not very large, we can solve the problem in an efficient manner by a number of existent algorithms. However, when the polytope is defined by linear inequalities, these algorithms may not work since the cardinality of vertices may be huge. Based on a fact that vertices determining an ellipsoid are only a fraction of these vertices, we propose algorithms which iteratively calculate an ellipsoid which covers a subset of vertices. Numerical experiment shows that these algorithms perform well for polytopes of dimension up to seven.     

A characterization of adding machine maps

Let f :X→X be a continuous map of a compact metric space to itself. We prove that f is topologically conjugate to an adding machine map if and only if X is an infinite minimal set for f and each point of X is regularly recurrent. Moreover, if X is an infinite minimal set for f and one point of X is regularly recurrent, then f is semiconjugate to an adding machine map.     

非线性控制系统的最小实现

对于那些由代数微分方程描述的具有输入输出关系的非线性控制系统，本文采用两种方法讨论了其最小实现问题：一种方法是直接计算系统的特征列；另一种方法则采用了本原元定理．两种方法给出的最小实现所需的状态变量最小数目是相等的．文中的大量代数与微分运算则可利用数学机械化来完成     

The set of toric minimal log discrepancies

We describe the set of minimal log discrepancies of toric log varieties, and study its accumulation points. This work is supported by a 21st Century COE Kyoto Mathematics Fellowship, and a JSPS Grant-in-Aid No 17740011.     

Achievable sets, brambles, and sparse treewidth obstructions

One consequence of the graph minor theorem is that for every k there exists a finite obstruction set Obs(TW?k). However, relatively little is known about these sets, and very few general obstructions are known. The ones that are known are the cliques, and graphs which are formed by removing a few edges from a clique. This paper gives several general constructions of minimal forbidden minors which are sparse in the sense that the ratio of the treewidth to the number of vertices n does not approach 1 as n approaches infinity. We accomplish this by a novel combination of using brambles to provide lower bounds and achievable sets to demonstrate upper bounds. Additionally, we determine the exact treewidth of other basic graph constructions which are not minimal forbidden minors.     

Asymmetry in the Multiprotein Systems of Molecular Biology

Signaling in living systems needs to achieve high specificity, to be reversible, and to achieve high signal to noise. Signaling mediated by multiprotein systems has evolved that avoids the requirement for high-affinity binary complexes that would be difficult to reverse and which, in the overcrowded cell, would lead to excessive noise in the system. Symmetrical structures are only occasionally formed. When they are, it is principally to colocate components, for example, the tyrosyl kinases of growth factors, where dimers form. Symmetry is, however, often broken, presumably to create more sensitivity and specificity in the signaling system by assembling other components, into higher-order multiprotein systems. The binding of a single heparin to two 1:1 FGF:FGFR complexes is an example, as is the binding of a single ligase to the Xrcc4 dimer, perhaps so creating a further DNA-binding site.     

“Optimization of aircraft maintenance/support infrastructure using genetic algorithms—level of repair analysis”

Level of repair analysis (LORA) is an approach used during the design stage of complex equipment for analysis of the cost effectiveness of competing maintenance strategies. LORA is carried as a part of the life cycle cost and cost of ownership analysis and plays a significant role in minimizing the life cycle cost and cost of ownership of the capital equipment. Since many purchasing decisions of complex equipment are based on cost of ownership, it has become essential to carry out LORA to compete in the market. In this paper, we develop a mathematical model for LORA and propose a solution methodology based on genetic algorithms. The concept is illustrated using a hypothetical aircraft engine.     

Photoelastic stress freezing analysis of total shoulder replacement systems

Photoelastic stress freezing analyses in the orthopaedic literature have, in the past, been limited to studies where bone-on-bone, bone-on-metal or ultra-high molecular weight polyethylene (UHMWPE)-on-metal constructs are modeled. In these cases photoelastic plastics are used to simulate either bone or UHMWPE as it interacts with a metal implant. In joints such as the shoulder, a UHMWPE component is often cemented directly into the scapula's glenoid concavity using polymethylmethacrylate (PMMA). While a photoelastic material can be used to simulate bone with proper load scaling, UHMWPE and PMMA have very different mechanical properties at elevated stress freezing temperatures as compared within vivo body temperature. In this study, materials were identified such that proper scaling of elastic properties at elevated temperatures was utilized to simulate the metal-UHMWPE-PMMA-bone construct. Stresses on orthogonal planes throughout the glenoid were compared for two different UHMWPE component anchoring geometries (keeled and pegged). High stresses were found at the neck of the glenoid and also at the component-bone interface beneath simulated PMMA inclusions.