On a quest of reverse translation

Explaining the emergence of life is perhaps central and the most challenging question in modern science. Within this area of research, the emergence and evolution of the genetic code is supposed to be a critical transition in the evolution of modern organisms. The canonical genetic code is one of the most dominant aspects of life on this planet, and thus studying its origin is critical to understanding the evolution of life, including life’s emergence. In this sense it is possible to view the ribosome as a digital-to-analogue information converter. Why the translation apparatus evolved, is one of the enduring mysteries of molecular biology. Assuming the hypothesis that during the emergence of life evolution had to first involve autocatalytic systems, which only subsequently acquired the capacity of genetic heredity, in the present article we discuss some aspects and causes of the possible emergence of digital, discrete information arising from analogue information realized in the intra- and inter-molecular interactions throughout molecular evolution. How such reverse translation was achieved at a molecular level is still unclear. The results of such debates and investigations might shift current biological paradigms and might also have a momentous significance for modern philosophy in understanding our place in the universe.     

A general variable neighborhood search variants for the travelling salesman problem with draft limits

In this paper, we present two general variable neighborhood search (GVNS) based variants for solving the traveling salesman problem with draft limits (TSPDL), a recent extension of the traveling salesman problem. TSPDL arises in the context of maritime transportation. It consists of finding optimal Hamiltonian tour for a given ship which has to visit and deliver products to a set of ports while respecting the draft limit constraints. The proposed methods combine ideas in sequential variable neighborhood descent within GVNS. They are tested on a set of benchmarks from the literature as well as on a new one generated by us. Computational experiments show remarkable efficiency and effectiveness of our new approach. Moreover, new set of benchmarks instances is generated.     

Wax treatment of wood slows photodegradation

Waxes and wax emulsions are one of the most important solutions for non-biocidal wood protection. Wax treated wood is designed for outdoor use, therefore it is of considerable importance to elucidate the influence of weathering on the photodegradation processes. It is presumed, that wax treatment will reduce water uptake and thus reduce or slow down photodegradation processes. In order to test this hypothesis, three types of wax emulsions at two different concentrations were vacuum impregnated into Norway spruce wood specimens: an emulsion of montan wax (LGE), an emulsion of polyethylene (WE1) and an emulsion of oxidized polyethylene (WE6) wax. The samples were exposed to artificial accelerated weathering (AAW) for 500 cycles. Before and after AAW colour, the contact angle of water and moisture content were determined. Chemical and morphological changes at exposed surfaces were also investigated with FTIR spectroscopy and SEM. In parallel, the uptake of wax emulsions and water into the axial surfaces of samples was determined with a tensiometer. The moisture content measurements showed that the best hydrophobic effect was achieved with LGE treated wood, where the lowest colour and FTIR changes were observed as well. These results were supported by tensiometer measurements as well. Presented data clearly showed that high loadings of waxes reduce or at least slow down weathering. Among tested waxes, montan wax was found the most effective.     

Theoretical study on transesterification in a combined process consisting of a reactive distillation column and a pervaporation unit

Steady state analysis of a combined hybrid process consisting of a reactive distillation column, pervaporation unit, and a distillation column is presented. This process configuration was first presented by Steinigeweg and Gmehling (2004) for the transesterification of methyl acetate and butanol to butyl acetate and methanol. This system is characteristic for its low reaction rate and complex phase equilibrium. Steinigeweg and Gmehling (2004) have shown that the combination of reactive distillation and pervaporation is favourable since conversions close to 100 % can be reached with a reasonable size of the reactive section in the reactive distillation column. The aim of this paper is to show that although high conversion can be achieved, very complicated steady state behaviour must be expected. The presented analysis is based on mathematical modelling of a process unit, where the steady-state analysis, including continuation and bifurcation analyses, was used. Multiple steady states were predicted for the studied system; three steady states with conversions higher than 98 %. However, not all predicted steady states met the maximal allowed temperature condition in the reactive section (catalyst maximal operation temperature of 393 K). The presence of multiple steady states reduces the operability and controllability of the reactive distillation column during its start-up and during the occurrence of any variation of operating parameters because the system can be shifted from one steady state to another one (concurrent exceeding the maximal allowed temperature) with unwanted consequences, e.g. production loss. Therefore, design and subsequent operation of such a complicated system is an ambitious task requiring knowledge of any possible system behaviour.     

Proton transfer reactions for improved peptide characterisation

The combination of deprotonation (via ion/molecule and ion/ion reactions) and low-energy collision-induced dissociation (CID) has been explored for the enhanced characterisation of tryptic peptides via access to different precursor charge states. This approach allows instant access to fragmentation properties of singly and doubly protonated precursors (arising from the availability of mobile protons) in a single experiment. Considering both charge states extended our base of structurally informative data (in comparison with considering just a single charge state) due to generation of additional sequence ions and by obtaining supplementary structural information derived from selective cleavages. Roughly 37% of combined data sets (CID spectra of doubly and singly charged precursor) showed a greater database identification confidence than each set alone. Moreover, comparison between a number of sequence ions of the singly charged precursor and the doubly charged precursor provided a mean of distinguishing the two classes of tryptic peptides (arginine or lysine containing).     

Guanidiniocarbonyl-pyrrole-aryl conjugates as nucleic acid sensors: switch of binding mode and spectroscopic responses by introducing additional binding sites into the linker

Two novel guanidiniocarbonyl pyrrole-pyrene conjugates 3 and 4 as spectroscopic probes for ds-polynucleotides were synthesized and their interaction with different ds-DNAs/RNAs studied. Compared to a previously reported first set of conjugates (1 and 2) the significant extension and increased rigidity of the central part of the structure resulted in a switch of DNA binding mode from intercalative (previously studied derivatives 1 and 2 with a nonbinding and flexible linker) to minor groove binding of the two novel guanidiniocarbonyl-pyrrole-pyrene conjugates 3 and 4. These two compounds interact strongly with ds-DNAs, but only weakly with ds-RNA. The newly incorporated heterocyclic moieties within the central part of the structure of 3 and 4 were able to control by steric and hydrogen-bonding effects the alignment of the molecules within various, structurally different forms of DNA minor grooves, whereby even small differences in the position of the attached pyrene within the groove were reflected in different fluorimetric responses. In addition, 3 and 4 revealed intriguing in vitro selectivity among various human tumour cell lines.     

On invariants of discrete series representations of classical p-adic groups

To an irreducible square integrable representation ?? of a classical p-adic group, M?glin has attached invariants Jord(??), ?? _cusp and ${\epsilon_\pi}$ . These triples classify square integrable representations modulo cuspidal data (assuming a natural hypothesis). The definition of these invariants in M?glin (J Eur Math Soc 4(2):143?C200, 2002) is rather simple??in terms of induced representations, except at one case when a coherent normalization of standard intertwining operators is required. In this paper we show how one can define this case also in terms of induced representations.     

Effective partitioning method for computing generalized inverses and their gradients

We extend the algorithm for computing {1}, {1, 3}, {1, 4} inverses and their gradients from [11] to the set of multiple-variable rational and polynomial matrices. An improvement of this extension, appropriate to sparse polynomial matrices with relatively small number of nonzero coefficient matrices as well as in the case when the nonzero coefficient matrices are sparse, is introduced. For that purpose, we exploit two effective structures form [6], which make use of only nonzero addends in polynomial matrices, and define their partial derivatives. Symbolic computational package MATHEMATICA is used in the implementation. Several randomly generated test matrices are tested and the CPU times required by two used effective structures are compared and discussed.     

Dynamical properties of a particle in a wave packet: Scaling invariance and boundary crisis

Some dynamical properties present in a problem concerning the acceleration of particles in a wave packet are studied. The dynamics of the model is described in terms of a two-dimensional area preserving map. We show that the phase space is mixed in the sense that there are regular and chaotic regions coexisting. We use a connection with the standard map in order to find the position of the first invariant spanning curve which borders the chaotic sea. We find that the position of the first invariant spanning curve increases as a power of the control parameter with the exponent 2/3. The standard deviation of the kinetic energy of an ensemble of initial conditions obeys a power law as a function of time, and saturates after some crossover. Scaling formalism is used in order to characterise the chaotic region close to the transition from integrability to nonintegrability and a relationship between the power law exponents is derived. The formalism can be applied in many different systems with mixed phase space. Then, dissipation is introduced into the model and therefore the property of area preservation is broken, and consequently attractors are observed. We show that after a small change of the dissipation, the chaotic attractor as well as its basin of attraction are destroyed, thus leading the system to experience a boundary crisis. The transient after the crisis follows a power law with exponent −2.     

Interatomic Coulombic decay in mixed NeKr clusters

We report the occurrence of interatomic Coulombic decay (ICD) in mixed NeKr clusters. A well-defined feature ranging from 9 to 12 eV in kinetic energy is observed in coincidence with the Ne 2s photoelectrons. It derives from an ICD process, in which an initial Ne 2s vacancy is filled by a Ne 2p electron and an electron is emitted from a 4p level on a neighboring Kr atom. We have studied the dependence of the effect on photon energy, cluster composition, and cluster size. Interestingly, the ICD electron energy increases slightly and grows a shoulder on going from 2% to 5% Kr in the coexpansion process, which we interpret in terms of surface versus bulk effects.