A series of H-bonded supramolecular architectures were built from monofunctional M-C≡C-R and bifunctional R-C≡C-M-C≡C-R trans-alkynylbis(1,2-bis(diphenylphosphino)ethane)ruthenium(II) complexes and π-conjugated modules containing 2,5-dialkoxy-p-phenylene. Incorporation on each partner of a cyanuric end and of the complementary Hamilton receptor provided the necessary means to keep the constituents together via strong hydrogen bonding. Characterization of all architectures has been performed on the basis of NMR and photophysical methods. In particular, the formation of a Hamilton receptor/cyanuric acid complex has been exemplified by an X-ray single-crystal structure determination. Both self-assembly and accurate modification of the complementary blocks were ensured in such a way that the resulting materials maintain the responsiveness of the electron-rich 2,5-dialkoxy-p-phenylene spacers toward nitroaromatics.

We analyse the collective dynamics of self-propelled particles in the large density regime where passive particles undergo a kinetic arrest to an amorphous glassy state. We capture the competition between self-propulsion and crowding effects using a two-dimensional model of self-propelled hard disks, which we study using Monte-Carlo simulations. Although the activity drives the system far from equilibrium, self-propelled particles undergo a kinetic arrest, which we characterize in detail and compare with its equilibrium counterpart. In particular, the critical density for dynamic arrest continuously shifts to larger density with increasing activity, and the relaxation time is surprisingly well described by an algebraic divergence resulting from the emergence of highly collective dynamics. These results show that dense assemblies of active particles undergo a nonequilibrium glass transition which is profoundly affected by self-propulsion mechanisms.

Gene expression program in eukaryotic cells is strongly dependent on physical state of the genome carrier. Physical state of the chromatin fiber constituting chromosomes is a key element in this program. However, despite the efforts to elucidate the structure and physical principles underlying chromatin organization, they remain not clear. On the one hand, chromosomes are highly hierarchical structures with quite different interactions involved on different scales of organization. On the other hand, the interactions involved at each scale are extremely complex (e.g. at 30 nm scale these are direct electrostatic, solvent mediated structural and polyelectrolyte mediated bridging interactions, DNA tension, etc.). Usual approach consisting in taking into account all the interactions between various molecular elements on the microscopic scale remains in this case out of reach. In the present work we suggest the approach which studies mesoscopic properties of the chromatin components and their interactions. Corresponding phenomenological theory helps to analyze the thermodynamically probable chromatin organization. We focus on liquid-crystalline order in chromatin resulting from the balance of thermal disorder and electrostatic (and mechanical) interactions. Using generally accepted experimental facts we identify robust mesogenic parameters of nucleosomes (DNA-protein nanoassemblies) at the smaller scale and show how the correlations of these parameters control the ordering into a chromatin structure at the bigger scale. The model is based on correlation of polar and chiral characteristics of nucleosomes. Phenomenological theory allows us to describe the condensed phases in aqueous solutions of nucleosomes with digested linker DNA, both in physiological conditions and in a wide range of monovalent salt concentration. Using the hypothesis of similar physical mechanism acting in condensed solutions and in the fiber in the same physiological conditions, we perform detailed symmetry analysis, construct the free energy model and reveal the thermodynamically favorable helical liquid-crystalline states of the fiber. In addition to « solenoid » and « two-start-helix » models abundantly discussed previously, we show the possibility of multi-start helix arrangements of nucleosomes in the chromatin and possible biaxiality of the structures. The effects of homogeneous mechanical force field applied to the chromatin in biochemical experiments are also studied. We show that helical state unwinding is a multi-step process and we give its structural and thermodynamic details.

Gene expression program in eukaryotic cells is strongly dependent on physical state of the genome carrier. Physical state of the chromatin fiber constituting chromosomes is a key element in this program. However, despite the efforts to elucidate the structure and physical principles underlying chromatin organization, they remain not clear. On the one hand, chromosomes are highly hierarchical structures with quite different interactions involved on different scales of organization. On the other hand, the interactions involved at each scale are extremely complex (e.g. at 30 nm scale these are direct electrostatic, solvent mediated structural and polyelectrolyte mediated bridging interactions, DNA tension, etc.). Usual approach consisting in taking into account all the interactions between various molecular elements on the microscopic scale remains in this case out of reach. In the present work we suggest the approach which studies mesoscopic properties of the chromatin components and their interactions. Corresponding phenomenological theory helps to analyze the thermodynamically probable chromatin organization. We focus on liquid-crystalline order in chromatin resulting from the balance of thermal disorder and electrostatic (and mechanical) interactions. Using generally accepted experimental facts we identify robust mesogenic parameters of nucleosomes (DNA-protein nanoassemblies) at the smaller scale and show how the correlations of these parameters control the ordering into a chromatin structure at the bigger scale.

We report on the growth and microstructure analysis of high Cd content ZnCdO/ZnO multiple quantum wells (MQW) within a nanowire. Heterostructures consisting of ten wells with widths from 0.7 to 10nm are demonstrated, and show photoluminescence emissions ranging from 3.03 to 1.97eV. The wells with thicknesses⩽2nm have high radiative efficiencies compared to the thickest ones, consistent with the presence of quantum confinement. However, a nanometric analysis of the Cd profile along the heterostructures shows the presence of Cd diffusion from the ZnCdO well to the ZnO barrier. This phenomenon modifies the band structure and the optical properties of the heterostructure, and is considered in order to correctly identify quantum effects in the ZnCdO/ZnO MQWs.

Despite extensive recent research efforts on material-specific peptides, the fundamental problem to be explored yet is the molecular interactions between peptides and inorganic surfaces. Here we used computer simulations (density functional theory and classical molecular dynamics) to investigate the adsorption mechanism of silicon-binding peptides and the role of individual amino acids in the affinity of peptides for an n-type silicon (n+-Si) semiconductor. Three silicon binding 12-mer peptides previously elaborated using phage display technology have been studied. The peptides' conformations close to the surface have been determined and the best-binding amino acids have been identified. Adsorption energy calculations explain the experimentally observed different degrees of affinity of the peptides for n+-Si. Our residual scanning analysis demonstrates that the binding affinity relies on both the identity of the amino acid and its location in the peptide sequence.