Collapse of random copolymers

Dendrimer Dynamics: A Review of Analytical Theories and Molecular Simulation Methods

The theoretical study of dendrimers is reviewed, considering both analytical approaches and molecular simulation methods. We discuss the effect of molecular symmetry on the degeneracy of the relaxation times, and then the calculation of observable quantities, in particular the intrinsic viscosity, and then the viscoelastic complex modulus and the dynamic structure factor, in comparison with the available experimental data. In particular, the maximum intrinsic viscosity with increasing molar mass is analyzed in some detail. The approximations and/or assumptions of the adopted methods are also described in connection with analogous results for polymer of a different topology, in particular linear and star polymers.

Adsorption of charged albumin subdomains on a graphite surface

We report some new molecular dynamics simulation results about the adsorption on a hydrophobic graphite surface of two albumin subdomains, each formed by three different alpha-helices, considering the correctly charged side groups at pH = 7 instead of the neutral ones as done in our previous exploratory paper (Raffaini and Ganazzoli, Langmuir 2003;19:3403-3412). We find that the presence of charges affects somewhat the initial adsorption stage on the electrostatically neutral surface, but not the final one. Thus, we recover the result that a monolayer of aminoacids is eventually formed, with a rough parallelism of distant strands to optimize both the intramolecular and the surface interactions. This feature is consistent with the adsorption on the hydrophobic surface being driven by dispersion forces only, and with the "soft" nature of albumin. Additional optimizations of the final monolayer carried out at pH = 3 and 11 do not modify appreciably this picture, suggesting that adsorption on graphite is basically independent of pH. The enhanced hydration of the final adsorption state due to the (delocalized) charges of the side groups is also discussed in comparison with similar results of the neutralized subdomains.

Multicanonical Monte Carlo simulations on intramolecular micelle formation in copolymers

The formation of intramolecular micelles in copolymers with periodic sequence, where hydrophobic units (stickers) are periodically placed along the chain, is studied by using multicanonical Monte Carlo computer simulations for an off-lattice bead-rod model in three dimensions. With decreasing the temperature, a transition from random-coil conformations to micelles occurs and flower-type micelles are formed via the transition. The number of stickers forming a micelle core is limited by the excluded-volume effect of loop chains around micelle cores. By this effect, two intramolecular micelles are formed for long polymer chains with 60 bonds via the coil-to-micelle transition. By further decreasing the temperature, we find that another transition, i.e., a micelle-to-micelle transition, takes place. At this transition point, the two intramolecular micelles merge into one micelle. Furthermore, we extend the multicanonical MC method to study elastic properties of single polymer chains with strong attractive interactions under external force fields, and study how the intramolecular micellization affects the elastic property of single polymer chains.

Computer simulation of polypeptide adsorption on model biomaterials

When biomaterials are inserted in a biological environment, for instance in a body implant, proteins do quickly adsorb on the exposed surface. Such process is of fundamental importance, since it directs the subsequent cell adhesion. Here we review recent advances in this field obtained with molecular simulations. While coarse-grained models can provide important general results, as it has long been recognized in polymer science, the hierarchical structure of a very complex copolymer such as a protein, together with the nature of the biomaterial surface suggest that atomistic models are better suited to investigate these phenomena. Thus, after briefly mentioning some common features of coarse-grained and atomistic force fields, we first discuss early theoretical and coarse-grained simulation results about protein adsorption, and then we highlight the main results recently obtained by us with atomistic models. In particular, we discuss some conformational and energetic aspects of the adsorption of protein fragments with different secondary structure on surfaces of different wettability, including hydrophobic graphite and hydrophilic poly(vinylalcohol). We also consider other features, such as the simulation of the materials wettability, the hydration of the adsorbed fragments, their kinetics of spreading, and the sequential adsorption of two protein fragments on top of each other, highlighting the results of general interest.

Coil-globule transition for regular, random, and specially designed copolymers: Monte Carlo simulation and self-consistent field theory

The coil-globule transition has been studied for A-B copolymer chains both by means of lattice Monte Carlo (MC) simulations using bond fluctuation algorithm and by a numerical self-consistent-field (SCF) method. Copolymer chains of fixed length with A and B monomeric units with regular, random, and specially designed (proteinlike) primary sequences have been investigated. The dependence of the transition temperature on the AB sequence has been analyzed. A proteinlike copolymer is more stable than a copolymer with statistically random sequence. The transition is more sharp for random copolymers. It is found that there exists a temperature below which the chain appears to be in the lowest energy state (ground state). Both for random and proteinlike sequences and for regular copolymers with a relatively long repeating block, a molten globule regime is found between the ground state temperature and the transition temperature. For regular block copolymers the transition temperature increases with block size. Qualitatively, the results from both methods are in agreement. Differences between the methods result from approximations in the SCF theory and equilibration problems in MC simulations. The two methods are thus complementary.