Microphase separation in thin block copolymer films: a weak segregation mean-field approach

In this paper we consider thin films of AB block copolymer melts confined between two parallel plates. The plates are identical and may have a preference for one of the monomer types over the other. The system is characterized by four parameters: the Flory-Huggins chi-parameter, the fraction f of A-monomers in the block copolymer molecules, the film thickness d, and a parameter h quantifying the preference of the plates for the monomers of type A. In certain regions of parameter space, the film will be microphase separated. Various structures have been observed experimentally, each of them characterized by a certain symmetry, orientation, and periodicity. We study the system theoretically using the weak segregation approximation to mean field theory. We restrict our analysis to the region of the parameter space where the film thickness d is close to a small multiple of the natural periodicity. We will present our results in the form of phase diagrams in which the absolute value of the deviation of the film thickness from a multiple of the bulk periodicity is placed along the horizontal axis, and the chi-parameter is placed along the vertical axis; both axes are rescaled with a factor which depends on the A-monomer fraction f. We present a series of such phase diagrams for increasing values of the surface affinity for the A-monomers. We find that if the film thickness is almost commensurate with the bulk periodicity, parallel orientations of the structures are favoured over perpendicular orientations. We also predict that on increasing the surface affinity, the region of stability of the bcc phase shrinks.Comment: 35 pages, 20 figure

Theoretical Study of Comb-Polymers Adsorption on Solid Surfaces

We propose a theoretical investigation of the physical adsorption of neutral comb-polymers with an adsorbing skeleton and non-adsorbing side-chains on a flat surface. Such polymers are particularly interesting as "dynamic coating" matrices for bio-separations, especially for DNA sequencing, capillary electrophoresis and lab-on-chips. Separation performances are increased by coating the inner surface of the capillaries with neutral polymers. This method allows to screen the surface charges, thus to prevent electro-osmosis flow and adhesion of charged macromolecules (e.g. proteins) on the capillary walls. We identify three adsorption regimes: a "mushroom" regime, in which the coating is formed by strongly adsorbed skeleton loops and the side-chains anchored on the skeleton are in a swollen state, a "brush" regime, characterized by a uniform multi-chains coating with an extended layer of non-adsorbing side-chains and a non-adsorbed regime. By using a combination of mean field and scaling approaches, we explicitly derive asymptotic forms for the monomer concentration profiles, for the adsorption free energy and for the thickness of the adsorbed layer as a function of the skeleton and side-chains sizes and of the adsorption parameters. Moreover, we obtain the scaling laws for the transitions between the different regimes. These predictions can be checked by performing experiments aimed at investigating polymer adsorption, such as Neutron or X-ray Reflectometry, Ellipsometry, Quartz Microbalance, or Surface Force Apparatus.Comment: 30 pages, 7 figures, to be published in Macromolecule

Crunching Biofilament Rings

We discuss a curious example for the collective mechanical behavior of coupled non-linear monomer units entrapped in a circular filament. Within a simple model we elucidate how multistability of monomer units and exponentially large degeneracy of the filament's ground state emerge as a collective feature of the closed filament. Surprisingly, increasing the monomer frustration, i.e., the bending prestrain within the circular filament, leads to a conformational softening of the system. The phenomenon, that we term polymorphic crunching, is discussed and applied to a possible scenario for membrane tube deformation by switchable dynamin or FtsZ filaments. We find an important role of cooperative inter-unit interaction for efficient ring induced membrane fission

Competition between B-Z and B-L transitions in a single DNA molecule: Computational studies

Under negative torsion, DNA adopts left-handed helical forms, such as Z-DNA and L-DNA. Using the random copolymer model developed for a wormlike chain, we represent a single DNA molecule with structural heterogeneity as a helical chain consisting of monomers which can be characterized by different helical senses and pitches. By Monte Carlo simulation, where we take into account bending and twist fluctuations explicitly, we study sequence dependence of B-Z transitions under torsional stress and tension focusing on the interaction with B-L transitions. We consider core sequences, (GC)(n) repeats or (TG)(n) repeats, which can interconvert between the right-handed B form and the left-handed Z form, imbedded in a random sequence, which can convert to left-handed L form with different (tension dependent) helical pitch. We show that Z-DNA formation from the (GC)(n) sequence is always supported by unwinding torsional stress but Z-DNA formation from the (TG)(n) sequence, which are more costly to convert but numerous, can be strongly influenced by the quenched disorder in the surrounding random sequence.National Research Foundation NRF-2012 R1A1A3013044 NRF-2014R1A1A2055681NRF-2012R1A1A2021736IBS-R023-D1NRF-2015R1A2A2A01005916Chemistr

Helices at Interfaces

Helically coiled filaments are a frequent motif in nature. In situations commonly encountered in experiments coiled helices are squeezed flat onto two dimensional surfaces. Under such 2-D confinement helices form "squeelices" - peculiar squeezed conformations often resembling looped waves, spirals or circles. Using theory and Monte-Carlo simulations we illuminate here the mechanics and the unusual statistical mechanics of confined helices and show that their fluctuations can be understood in terms of moving and interacting discrete particle-like entities - the "twist-kinks". We show that confined filaments can thermally switch between discrete topological twist quantized states, with some of the states exhibiting dramatically enhanced circularization probability while others displaying surprising hyperflexibility

Unveiling the pathway to Z-DNA in the protein-induced B–Z transition

Left-handed Z-DNA is an extraordinary conformation of DNA, which can form by special sequences under specific biological, chemical or physical conditions. Human ADAR1, prototypic Z-DNA binding protein (ZBP), binds to Z-DNA with high affinity. Utilizing single-molecule FRET assays for Z-DNA forming sequences embedded in a long inactive DNA, we measure thermodynamic populations of ADAR1-bound DNA conformations in both GC and TG repeat sequences. Based on a statistical physics model, we determined quantitatively the affinities of ADAR1 to both Z-form and B-form of these sequences. We also reported what pathways it takes to induce the B–Z transition in those sequences. Due to the high junction energy, an intermediate B* state has to accumulate prior to the B–Z transition. Our study showing the stable B* state supports the active picture for the protein-induced B–Z transition that occurs under a physiological setting. (c)The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research

The venom composition of the parasitic wasp Chelonus inanitus resolved by combined expressed sequence tags analysis and proteomic approach

<p>Abstract</p> <p>Background</p> <p>Parasitic wasps constitute one of the largest group of venomous animals. Although some physiological effects of their venoms are well documented, relatively little is known at the molecular level on the protein composition of these secretions. To identify the majority of the venom proteins of the endoparasitoid wasp <it>Chelonus inanitus </it>(Hymenoptera: Braconidae), we have randomly sequenced 2111 expressed sequence tags (ESTs) from a cDNA library of venom gland. In parallel, proteins from pure venom were separated by gel electrophoresis and individually submitted to a nano-LC-MS/MS analysis allowing comparison of peptides and ESTs sequences.</p> <p>Results</p> <p>About 60% of sequenced ESTs encoded proteins whose presence in venom was attested by mass spectrometry. Most of the remaining ESTs corresponded to gene products likely involved in the transcriptional and translational machinery of venom gland cells. In addition, a small number of transcripts were found to encode proteins that share sequence similarity with well-known venom constituents of social hymenopteran species, such as hyaluronidase-like proteins and an Allergen-5 protein.</p> <p>An overall number of 29 venom proteins could be identified through the combination of ESTs sequencing and proteomic analyses. The most highly redundant set of ESTs encoded a protein that shared sequence similarity with a venom protein of unknown function potentially specific of the <it>Chelonus </it>lineage. Venom components specific to <it>C. inanitus </it>included a C-type lectin domain containing protein, a chemosensory protein-like protein, a protein related to yellow-e3 and ten new proteins which shared no significant sequence similarity with known sequences. In addition, several venom proteins potentially able to interact with chitin were also identified including a chitinase, an imaginal disc growth factor-like protein and two putative mucin-like peritrophins.</p> <p>Conclusions</p> <p>The use of the combined approaches has allowed to discriminate between cellular and truly venom proteins. The venom of <it>C. inanitus </it>appears as a mixture of conserved venom components and of potentially lineage-specific proteins. These new molecular data enrich our knowledge on parasitoid venoms and more generally, might contribute to a better understanding of the evolution and functional diversity of venom proteins within Hymenoptera.</p