Quantum chemical modeling of enzymatic reactions: The case of histone lysine methyltransferase

Quantum chemical cluster models of enzyme active sites are today an important and powerful tool in the study of various aspects of enzymatic reactivity. This methodology has been applied to a wide spectrum of reactions and many important mechanistic problems have been solved. Herein, we report a systematic study of the reaction mechanism of the histone lysine methyltransferase (HKMT) SET7/9 enzyme, which catalyzes the methylation of the N‐terminal histone tail of the chromatin structure. In this study, HKMT SET7/9 serves as a representative case to examine the modeling approach for the important class of methyl transfer enzymes. Active site models of different sizes are used to evaluate the methodology. In particular, the dependence of the calculated energies on the model size, the influence of the dielectric medium, and the particular choice of the dielectric constant are discussed. In addition, we examine the validity of some technical aspects, such as geometry optimization in solvent or with a large basis set, and the use of different density functional methods. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Convergence estimates of a projection-difference method for an operator-differential equation

This article investigates the projection-difference method for a Cauchy problem for a linear operator-differential equation with a leading self-adjoint operator A(t) and a subordinate linear operator K(t) in Hilbert space. This method leads to the solution of a system of linear algebraic equations on each time level; moreover, the projection subspaces are linear spans of eigenvectors of an operator similar to A(t). The convergence estimates are obtained. The application of the developed method for solving the initial boundary value problem is given.     

Adhesion models: from single to multiple asperity contacts

This review presents a summary of the current adhesion models available to date, between real rough surfaces, starting from single asperity models and expanding to multiple asperity contacts. The focus is made on multi-asperity contact interactions. Both van der Waals and contact mechanics approaches have been considered and relevant adhesion models are reviewed and discussed. The influence of the meniscus forces on adhesion has been considered, along with a summary of the various meniscus models. The effect of surface geometry, its topography and environmental conditions on meniscus action are also discussed along with its integration into multi-asperity adhesion models.     

Varying molecular interactions by coverage in supramolecular surface chemistry

The possibility of modifying the intermolecular interactions of absorbed benzene-carboxylic acids from coordination to hydrogen bonding by changing their surface coverage is demonstrated through a combination of scanning tunnelling microscopy, X-ray photoemission spectroscopy and density functional theory calculations.     

Is graphene on copper doped?

Angle‐resolved photoemission spectroscopy (ARPES) and X‐ray photoemission spectroscopy have been used to characterise epitaxially ordered graphene grown on copper foil by low‐pressure chemical vapour deposition. A short vacuum anneal to 200 °C allows observation of ordered low energy electron diffraction patterns. High quality Dirac cones are measured in ARPES with the Dirac point at the Fermi level (undoped graphene). Annealing above 300 °C produces n‐type doping in the graphene with up to 350 meV shift in Fermi level, and opens a band gap of around 100 meV.

     

Analysis of Wavelength-Routed Optical Burst-Switched Network Performance

This paper studies a novel scalable network architecture combining optical burst switching (OBS) with dynamic wavelength allocation to guarantee quality of service (QoS), forming a wavelength-routed optical burst-switched network. All processing and buffering functions are concentrated at the network edge and bursts are assigned to fast tuneable lasers and routed over a bufferless optical transport core using dynamic wavelength assignment. Different burst aggregation mechanisms are evaluated for a range of traffic statistics in terms of delay and packet loss rate. New network performance parameters in an analytical model quantify the advantages of dynamic wavelength allocation. The results define the operational gain achievable with dynamic wavelength assignment compared to quasi-static wavelength routed optical networks.     

Models for capacity and electricity market design

The paper employs Operations Research methods for analysis of electricity and capacity markets. We provide two algorithms that determine the optimal capacity structure with account of fixed and variable costs. The first one relates to the case where there are several capacity types, and for each type the capacity constraint is not binding. The second algorithm is applicable when electricity is produced by standard small generators with the same capacity and different costs. Then we study two typical architectures of the market and examine their Nash equilibria. We consider a uniform price supply function auction in the electricity market. For pay-as-bid and uniform price versions of the capacity market design, we compare the equilibrium outcomes with the optimal capacity structure. The paper shows that the market equilibrium corresponds to the optimal capacity structure under conditions of pure competition, full rationality, and completely informed agents in the market. However, under more realistic assumptions, selection of the optimal structure is unlikely. Finally we provide the auction design that realizes such selection of capacities and does not require any additional information of each producer besides his own production costs. We establish sufficient conditions for perfect competition in the market.     

On a space of smooth functions on a convex unbounded set in ℝ<Superscript><Emphasis Type="Italic">n</Emphasis></Superscript> admitting holomorphic extension in ℂ<Superscript><Emphasis Type="Italic">n</Emphasis></Superscript>

For some given logarithmically convex sequence M of positive numbers we construct a subspace of the space of rapidly decreasing infinitely differentiable functions on an unbounded closed convex set in ? ⁿ . Due to the conditions on M each function of this space admits a holomorphic extension in ? ⁿ . In the current article, the space of holomorphic extensions is considered and Paley-Wiener type theorems are established. To prove these theorems, some auxiliary results on extensions of holomorphic functions satisfying some weighted L ²-bounds in a domain of holomorphy in ? ⁿ are obtained with the aid of L. Hörmander’s method of L ²-bounds for the \(\bar \partial\) operator. Also, some new facts on the Fourier-Laplace transform of tempered distributions complementing some well-known results of V.S. Vladimirov are employed.     

Hypersensitive transitions of Tm3+, Ho3+ and Dy3+ rare-earth ions in garnet crystals

In this work, spectroscopic characteristics (oscillator strengths, intensity parameters) of intermanifold f–f transitions of Tm^{3 +}, Ho³⁺and Dy³⁺ions in garnet crystals are investigated. It has been found that the intensity change of the hypersensitive intermanifold f–f transitions of rare-earth ions in garnet crystals is determined by the characteristics of their local environment.