Structural chemistry at Lomonosov Moscow State University: a special issue

Structural Chemistry -     

Sydney Brenner (1927–2019)—One of the greats of our science on new frontiers

Structural Chemistry - Sydney Brenner was among those who created the modern science of molecular genetics. He was primarily an experimentalist yet his philosophical views on science will also have...     

Nadrian C. Seeman (1945–2021): pioneer of DNA nanotechnology

Structural Chemistry - Nadrian (Ned) Seeman (1945-2021) was a crystallographer turned nanoscientist who pioneered a new direction of research at the borderline of the two fields. He constructed new...     

Forty years of quasicrystals: a bumpy road to triumph

Structural Chemistry - On April 8, 1982, Dan Shechtman conducted an electron diffraction experiment on an aluminum/manganese alloy. The diffraction pattern showed tenfold symmetry although the...     

Block-structured compressible Navier–Stokes solution using the OPS high-level abstraction

abstract

In this paper, we report the development and validation of a compressible solver with shock capturing, using a domain-specific high-level abstraction framework, OPS, that is being developed at the University of Oxford. OPS uses an active library approach for block-structured meshes, capable of generating codes for a variety of parallel implementations with different parallelisation strategies. Performance results on various architectures are reported for the 1D Shu–Osher test case.     

Single drop microextraction of homoserine lactones based quorum sensing signal molecules, and the separation of their enantiomers using gas chromatography mass spectrometry in the presence of biological matrices

N-acylated homoserine lactones (AHLs) are produced by Gram-negative bacteria as communication signals and are frequently studied as mediators of the “quorum sensing” response of bacterial communities. AHLs are optically active components and the L-form is known to have activity in the quorum sensing. However, the knowledge regarding the stereospecific production of the AHLs in bacterial cultures is limited; therefore, there is a need for a fast and easy method for their chiral analysis. A method was developed for the preconcentration of the AHLs using single drop microextraction or liquid-liquid microphase extraction in toluene for their analysis using GC-MS. The performance of the method were determined and discussed for the chiral separation of these autoinducers using a capillary column coated with heptakis-(2,3-di-O-acetyl-6-O-t-butyldimethyl-silyl)-β-cyclodextrin. The salient feature of this study is the demonstration, that Burkholderia cepacia LA3 produced D-decanoyl-homoserine lactone beside L-decanoyl- and L-octaonyl- enantiomers.     

On the law of the iterated logarithm for the discrepancy of 〈n k x〉

By a well known result of Philipp (1975), the discrepancy D _N (ω) of the sequence (n _k ω) _k≥1 mod 1 satisfies the law of the iterated logarithm under the Hadamard gap condition n _{k + 1}/n _k ≥ q > 1 (k = 1, 2, …). Recently Berkes, Philipp and Tichy (2006) showed that this result remains valid, under Diophantine conditions on (n _k ), for subexpenentially growing (n _k ), but in general the behavior of (n _k ω) becomes very complicated in the subexponential case. Using a different norming factor depending on the density properties of the sequence (n _k ), in this paper we prove a law of the iterated logarithm for the discrepancy D _N (ω) for subexponentially growing (n _k ) without number theoretic assumptions. C. Aistleitner, Research supported by FWF grant S9603-N13. I. Berkes, Research supported by FWF grant S9603-N13 and OTKA grants K 61052 and K 67961. Authors’ addresses: C. Aistleitner, Institute of Mathematics A, Graz University of Technology, Steyrergasse 30, 8010 Graz, Austria; I. Berkes, Institute of Statistics, Graz University of Technology, Steyrergasse 17/IV, 8010 Graz, Austria     

Characterization of Turbulent Structures in a Transonic Backward-Facing Step Flow

A transonic backward-facing step flow, at a free stream Mach number of 0.8 and a Reynolds number of 1.86 × 10⁵ with respect to the step height, was investigated experimentally by means of planar and stereo Particle Image Velocimetry (PIV) measurements for multiple fields of view. The primary aim of this analysis is to examine whether the large temporal variations of the reattachment location is associated with the presence of large scale coherent flow structures. The mean flow reattaches ≈6.1±0.2 times the step height downstream of the step. This value fluctuates temporally as much as ±3 step heights. Measurements of the wake flow in horizontal planes show that the strong variations of the reattachment length are associated with spanwise variations of the streamwise velocity. Two-point correlations revealed large–scale coherent regions with a length of up to 7 step heights and a dominant spanwise wave-length of 1.5…2.5 step heights. Furthermore, close to the step large structures are found, which span more than 5 step heights in spanwise direction. The Reynolds stress distribution of the separated region strongly suggests that the initial streamwise momentum is transferred to the vertical component as well as to the spanwise component in comparable portions by the deformation of the initial Kelvin-Helmholtz vortices and the generation of secondary ones. As a result, the separated shear layer is characterized by eddies of various sizes and orientations. The mean flow field only shows the primary separation bubble and a secondary recirculation region. No stationary streamwise vortices could be found for the tested Reynolds number.     

Metabolic network dynamics in open chaotic flow

We have analyzed the dynamics of metabolically coupled replicators in open chaotic flows. Replicators contribute to a common metabolism producing energy-rich monomers necessary for replication. The flow and the biological processes take place on a rectangular grid. There can be at most one molecule on each grid cell, and replication can occur only at localities where all the necessary replicators (metabolic enzymes) are present within a certain neighborhood distance. Due to this finite metabolic neighborhood size and imperfect mixing along the fractal filaments produced by the flow, replicators can coexist in this fluid system, even though coexistence is impossible in the mean-field approximation of the model. We have shown numerically that coexistence mainly depends on the metabolic neighborhood size, the kinetic parameters, and the number of replicators coupled through metabolism. Selfish parasite replicators cannot destroy the system of coexisting metabolic replicators, but they frequently remain persistent in the system. (c) 2002 American Institute of Physics.