Transitions of tethered polymer chains: A simulation study with the bond fluctuation lattice model

A polymer chain tethered to a surface may be compact or extended, adsorbed or desorbed, depending on interactions with the surface and the surrounding solvent. This leads to a rich phase diagram with a variety of transitions. To investigate these transitions we have performed Monte Carlo simulations of a bond-fluctuation model with Wang-Landau and umbrella sampling algorithms in a two-dimensional state space. The simulations' density of states results have been evaluated for interaction parameters spanning the range from good to poor solvent conditions and from repulsive to strongly attractive surfaces. In this work, we describe the simulation method and present results for the overall phase behavior and for some of the transitions. For adsorption in good solvent, we compare with Metropolis Monte Carlo data for the same model and find good agreement between the results. For the collapse transition, which occurs when the solvent quality changes from good to poor, we consider two situations corresponding to three-dimensional (hard surface) and two-dimensional (very attractive surface) chain conformations, respectively. For the hard surface, we compare tethered chains with free chains and find very similar behavior for both types of chains. For the very attractive surface, we find the two-dimensional chain collapse to be a two-step transition with the same sequence of transitions that is observed for three-dimensional chains: a coil-globule transition that changes the overall chain size is followed by a local rearrangement of chain segments.Comment: 17 pages, 12 figures, to appear in J. Chem. Phy

Modulating the Fibrillization of Parathyroid-Hormone (PTH) Peptides: Azo-Switches as Reversible and Catalytic Entities

We here report a novel strategy to control the bioavailability of the fibrillizing parathyroid hormone (PTH)-derived peptides, where the concentration of the bioactive form is controlled by an reversible, photoswitchable peptide. PTH1–84, a human hormone secreted by the parathyroid glands, is important for the maintenance of extracellular fluid calcium and phosphorus homeostasis. Controlling fibrillization of PTH1–84 represents an important approach for in vivo applications, in view of the pharmaceutical applications for this protein. We embed the azobenzene derivate 3-{[(4- aminomethyl)phenyl]diazenyl}benzoic acid (3,40-AMPB) into the PTH-derived peptide PTH25–37 to generate the artificial peptide AzoPTH25–37 via solid-phase synthesis. AzoPTH25–37 shows excellent photostability (more than 20 h in the dark) and can be reversibly photoswitched between its cis/trans forms. As investigated by ThT-monitored fibrillization assays, the trans-form of AzoPTH25–37 fibrillizes similar to PTH25–37, while the cis-form of AzoPTH25–37 generates only amorphous aggregates. Additionally, cis-AzoPTH25–37 catalytically inhibits the fibrillization of PTH25–37 in ratios of up to one-fifth. The approach reported here is designed to control the concentration of PTH-peptides, where the bioactive form can be catalytically controlled by an added photoswitchable peptide

Mesophase formation in two-component cylindrical bottle-brush polymers

When two types of side chains (A,B) are densely grafted to a (stiff) backbone and the resulting bottle-brush polymer is in a solution under poor solvent conditions, an incompatibility between A and B leads to microphase separation in the resulting cylindrical brush. The possible types of ordering are reminiscent of the ordering of block copolymers in cylindrical confinement. Starting from this analogy, Leibler's theory of microphase separation in block copolymer melts is generalized to derive a description of the system in the weak segregation limit. Also molecular dynamics simulation results of a corresponding coarse-grained bead-spring model are presented. Using side chain lengths up to N = 50 effective monomers, the ratio of the Lennard-Jones energy parameter between unlike monomers $(\epsilon_{AB})$ and monomers of the same kind $(\epsilon _{AA} = \epsilon_{BB})$ is varied. Various correlation functions are analyzed to study the conditions when (local) Janus cylinder-type ordering and when (local) microphase separation in the direction along the cylinder axis occurs. Both the analytical theory and the simulations give evidence for short range order due to a tendency towards microphase separation in the axial direction, with a wavelength proportional to the side chain gyration radius, irrespective of temperature and grafting density, for a wide range of these parameters.Comment: 26 pages, 19 figure

Structure of bottle-brush polymers in solution: A Monte Carlo test of models for the scattering function

Extensive Monte Carlo results are presented for a lattice model of a bottle-brush polymer under good solvent or Theta solvent conditions. Varying the side chain length, backbone length, and the grafting density for a rigid straight backbone, both radial density profiles of monomers and side chain ends are obtained, as well as structure factors describing the scattering from a single side chain and from the total bottle-brush polymer. To describe the structure in the interior of a very long bottle-brush, a periodic boundary condition in the direction along the backbone is used, and to describe effects due to the finiteness of the backbone length, a second set of simulations with free ends of the backbone is performed. In the latter case, the inhomogeneity of the structure in the direction along the backbone is carefully investigated. We use these results to test various phenomenological models that have been proposed to interpret experimental scattering data for bottle-brush macromolecules. These models aim to extract information on the radial density profile of a bottle-brush from the total scattering via suitable convolution approximations. Possibilities to improve such models, guided by our simulation results, are discussed.Comment: 15 pages, 16 figure

Timescales of self-healing in human bone tissue and polymeric ionic liquids

Strain (stress-free) relaxation in mechanically prestrained bone has a time constant of 75 s. It occurs by a reorganization of the proteoglycan-glycoprotein matrix between collagen fibers, which requires ionic interactions. Dissolving and relinking the ionic bonds is thus an important tool of nature to enable plastic deformation and to develop self-healing tissues. A way to transfer this approach to technical materials is the attachment of ionic end groups to polymeric chains. In these classes of materials, the so-called polymeric ionic liquids, structural recovery of thermally disorganized material is observed. A time constant between minutes and a week could be achieved, also by ionic rearrangement. The same mechanism, rearrangement of ionic bonds, can lead to vastly different relaxation times when the ionic interaction is varied by exchange of the cationic end groups or the anions

Molecular Dynamics Simulations

A tutorial introduction to the technique of Molecular Dynamics (MD) is given, and some characteristic examples of applications are described. The purpose and scope of these simulations and the relation to other simulation methods is discussed, and the basic MD algorithms are described. The sampling of intensive variables (temperature T, pressure p) in runs carried out in the microcanonical (NVE) ensemble (N= particle number, V = volume, E = energy) is discussed, as well as the realization of other ensembles (e.g. the NVT ensemble). For a typical application example, molten SiO2, the estimation of various transport coefficients (self-diffusion constants, viscosity, thermal conductivity) is discussed. As an example of Non-Equilibrium Molecular Dynamics (NEMD), a study of a glass-forming polymer melt under shear is mentioned.Comment: 38 pages, 11 figures, to appear in J. Phys.: Condens. Matte

Hopping Transport in the Presence of Site Energy Disorder: Temperature and Concentration Scaling of Conductivity Spectra

Recent measurements on ion conducting glasses have revealed that conductivity spectra for various temperatures and ionic concentrations can be superimposed onto a common master curve by an appropriate rescaling of the conductivity and frequency. In order to understand the origin of the observed scaling behavior, we investigate by Monte Carlo simulations the diffusion of particles in a lattice with site energy disorder for a wide range of both temperatures and concentrations. While the model can account for the changes in ionic activation energies upon changing the concentration, it in general yields conductivity spectra that exhibit no scaling behavior. However, for typical concentrations and sufficiently low temperatures, a fairly good data collapse is obtained analogous to that found in experiment.Comment: 6 pages, 4 figure

Position dependent mismatch discrimination on DNA microarrays – experiments and model

<p>Abstract</p> <p>Background</p> <p>The propensity of oligonucleotide strands to form stable duplexes with complementary sequences is fundamental to a variety of biological and biotechnological processes as various as microRNA signalling, microarray hybridization and PCR. Yet our understanding of oligonucleotide hybridization, in particular in presence of surfaces, is rather limited. Here we use oligonucleotide microarrays made in-house by optically controlled DNA synthesis to produce probe sets comprising all possible single base mismatches and base bulges for each of 20 sequence motifs under study.</p> <p>Results</p> <p>We observe that mismatch discrimination is mostly determined by the defect position (relative to the duplex ends) as well as by the sequence context. We investigate the thermodynamics of the oligonucleotide duplexes on the basis of double-ended molecular zipper. Theoretical predictions of defect positional influence as well as long range sequence influence agree well with the experimental results.</p> <p>Conclusion</p> <p>Molecular zipping at thermodynamic equilibrium explains the binding affinity of mismatched DNA duplexes on microarrays well. The position dependent nearest neighbor model (PDNN) can be inferred from it. Quantitative understanding of microarray experiments from first principles is in reach.</p

Uniform hopping approach to the FM Kondo Model at finite temperature

We study the ferromagnetic Kondo model with classical corespins via unbiased Monte-Carlo simulations and derive a simplified model for the treatment of the corespins at any temperature. Our simplified model captures the main aspects of the Kondo model and can easily be evaluated both numerically and analytically. It provides a better qualitative understanding of the physical features of the Kondo model and rationalizes the Monte-Carlo results, including the spectral density A_k(omega) of a 1D chain with nearest neighbor Coulomb repulsion. By calculating the specific heat and the susceptibility of systems up to size 16^3, we determine the Curie temperature of the 3D one-orbital double-exchange model, which agrees with experimental values.Comment: 11 pages, 9 figures, RevTex4, additional references cite

Genomewide Association Scan of Suicidal Thoughts and Behaviour in Major Depression

Background Suicidal behaviour can be conceptualised as a continuum from suicidal ideation, to suicidal attempts to completed suicide. In this study we identify genes contributing to suicidal behaviour in the depression study RADIANT. Methodology/Principal Findings A quantitative suicidality score was composed of two items from the SCAN interview. In addition, the 251 depression cases with a history of serious suicide attempts were classified to form a discrete trait. The quantitative trait was correlated with younger onset of depression and number of episodes of depression, but not with gender. A genome-wide association study of 2,023 depression cases was performed to identify genes that may contribute to suicidal behaviour. Two Munich depression studies were used as replication cohorts to test the most strongly associated SNPs. No SNP was associated at genome-wide significance level. For the quantitative trait, evidence of association was detected at GFRA1, a receptor for the neurotrophin GDRA (p = 2e-06). For the discrete trait of suicide attempt, SNPs in KIAA1244 and RGS18 attained p-values of <5e-6. None of these SNPs showed evidence for replication in the additional cohorts tested. Candidate gene analysis provided some support for a polymorphism in NTRK2, which was previously associated with suicidality. Conclusions/Significance This study provides a genome-wide assessment of possible genetic contribution to suicidal behaviour in depression but indicates a genetic architecture of multiple genes with small effects. Large cohorts will be required to dissect this further