Minimising the number of gap-zeros in binary matrices

We study a problem of minimising the total number of zeros in the gaps between blocks of consecutive ones in the columns of a binary matrix by permuting its rows. The problem is referred to as the Consecutive Ones Matrix Augmentation Problem, and is known to be NP-hard. An analysis of the structure of an optimal solution allows us to focus on a restricted solution space, and to use an implicit representation for searching the space. We develop an exact solution algorithm, which is linear-time in the number of rows if the number of columns is constant, and two constructive heuristics to tackle instances with an arbitrary number of columns. The heuristics use a novel solution representation based upon row sequencing. In our computational study, all heuristic solutions are either optimal or close to an optimum. One of the heuristics is particularly effective, especially for problems with a large number of rows.     

Computational chemistry in drug lead discovery and design

The main contributions of our group during the last 15 years developing and using biomolecular simulation tools in drug lead discovery and design, in close collaboration with experimental researchers, are presented. Special emphasis has been given to methodological improvements in the following areas: (1) target homology modeling incorporating knowledge about known ligands to accurately characterize the binding site; (2) designing alternative strategies to account for protein flexibility in high-throughput docking; (3) development of stochastic- and normal-mode-based methods to de novo design structurally diverse protein conformers; (4) development and validation of quantum mechanical semi-empirical linear-scaling calculations to correctly estimate ligand binding free energy. Several successful cases of computer-aided drug discovery are also presented, especially our recent work on viral targets.     

Simultaneous determination of proteins in microstructured optical fibers supported by chemometric tools

Analytical and Bioanalytical Chemistry - A new perspective on the relevant problem—creating simple, rapid, and efficient protein sensors based on microstructured optical fibers using a simple...     

Progress and problems in the application of focused ultrasound for blood-brain barrier disruption

Advances in neuroscience have resulted in the development of new diagnostic and therapeutic agents for potential use in the central nervous system (CNS). However, the ability to deliver the majority of these agents to the brain is limited by the blood-brain barrier (BBB), a specialized structure of the blood vessel wall that hampers transport and diffusion from the blood to the brain. Many CNS disorders could be treated with drugs, enzymes, genes, or large-molecule biotechnological products such as recombinant proteins, if they could cross the BBB. This article reviews the problems of the BBB presence in treating the vast majority of CNS diseases and the efforts to circumvent the BBB through the design of new drugs and the development of more sophisticated delivery methods. Recent advances in the development of noninvasive, targeted drug delivery by MRI-guided ultrasound-induced BBB disruption are also summarized.     

Formation of Molybdenum Blue Nanoparticles in the Organic Reducing Area

Molybdenum blue dispersions were synthesized by reducing an acidic molybdate solution with glucose, hydroquinone and ascorbic acid. The influence of the H/Mo molar ratio on the rate of formation of molybdenum particles was established. For each reducing agent, were determined the rate constant and the order of the particle formation and were established the conditions for the formation of aggregative stable dispersion with the maximum concentration of particles. The dispersed phase is represented by toroidal molybdenum oxide nanoclusters, which was confirmed by the results of UV/Vis, FTIR, XPS spectroscopy and DLS.     

Analysis of curing reaction of liquid-crystalline epoxy compositions by using temperature-modulated DSC TOPEM®

Journal of Thermal Analysis and Calorimetry - The curing behaviour of the composition of a liquid-crystalline diepoxy monomer (LCEM) with the central triaromatic mesogenic group was studied using...     

Fluorescent core-shell polymer particles containing luminophore dyes: synthesis and optical response to acetone

Monodisperse dye-containing crosslinked particles are promising for application in novel optical chemical sensors due to their intrinsic sensitivity. However, preparation of these particles in aqueous media still remains a challenge, since luminophores inhibit radical processes or else cannot embed into polymer chains because of difference in monomer reactivity ratios. In this work, novel dye-containing monodisperse crosslinked particles were prepared and characterized. In order to obtain dye-containing monodisperse crosslinked particles, we studied seed copolymerization of styrene in the presence of divinylbenzene. The influence of nature and concentration of the used comonomers and co-solvents on shape, size distributions and surface characteristics of the particles formed was investigated. Shapes and diameters of the particles were analyzed by DLS, TEM and SEM. The data of SEM and optical spectroscopy studies demonstrated that the synthesized particles were able to self-assemble into thin-film three-dimensional ordered structures. Finally, the structures under study are promising for development of sensor devices with optical response to acetone.     

Distinct effect of xenobiotics on the metal‐binding properties of protein molecules

The X‐ray standing‐wave method was applied to study the elemental composition and molecular organization of ordered protein films of alkaline phosphatase exposed to different xenobiotics (drug compounds, lead). Binding of metal ions from triply distilled water to protein molecules has been experimentally observed. Definite differences in the arrangement of impurity metal ions in the films have been established. The considerable enhancement of protein–metal interactions is attributed to partial rearrangement of the protein native structure, induced by xenobiotics.     

Phase behaviour,structural properties and intermolecular interactions of systems based on substituted thiacalix[4]arene and nonionic surfactants

Supramolecular organised materials were prepared from nonionic surfactants and the following macrocyclic ionic liquids: n-tert-butylthiacalix[4]arenes containing quaternary ammonium fragments with amino acid substituents. Tetraethylene glycol monododecyl ether and decadiethylene glycol monododecyl ether were used as nonionic surfactants. They form lamellar and hexagonal mesophases in aqueous media, respectively. Liquid crystal and structural properties of these systems were studied. Intermolecular interactions of system components leading to formation of lyomesophases were estimated. Molecular structure of thiacalixarene contributes to the formation of a hydrogen bonding with surfactants. This process, in turn, initiates formation of a denser packed hexagonal structure.