We report atomistic computer simulations of some albumin subdomains on a hydrophobic graphite surface. The simulations are carried out in an effective dielectric medium by simple energy minimization and by long molecular dynamics (MD) runs. Further energy minimizations and shorter MD runs in the explicit presence of water are also performed to assess the stability of the geometries found and to describe the change of solvation of the adsorbed subdomains. We find that the initial adsorption is accompanied by significant rearrangements of the strands in contact with the surface, otherwise preserving the secondary structure and the overall globular shape. Much larger rearrangements take place at longer times during the MD runs, eventually yielding a thin layer of amino acids covering the surface as much as possible with complete denaturation. The interaction and strain energies of the adsorbed subdomains are discussed, together with their size and overall shape changes. The proposed adsorption mechanism is fully consistent with recent experimental findings for albumin on hydrophobic surfaces.

Adsorption of human lysozyme on hydrophobic graphite is investigated through atomistic computer simulations with molecular mechanics (MM) and molecular dynamics (MD) techniques. The chosen strategy follows a simulation protocol proposed by the authors to model the initial and the final adsorption stage on a bare surface. Adopting an implicit solvent and considering 10 starting molecular orientations so that all the main sides of the protein can face the surface, we first carry out an energy minimization to investigate the initial adsorption stage, and then long MD runs of selected arrangements to follow the surface spreading of the protein maximizing its adsorption strength. The results are discussed in terms of the kinetics of surface spreading, the interaction energy, and the molecular size, considering both the footprint and the final thickness of the adsorbed protein. The structural implications of the final adsorption geometry for surface aggregation and nanoscale structural organization are also pointed out. Further MD runs are carried out in explicit water for the native structure and the most stable adsorption state to assess the local stability of the geometry obtained in implicit solvent, and to calculate the statistical distribution of the water molecules around the whole lysozyme and its backbone.

Molecular modeling and computer simulations can yield significant new insight at the atomistic level about the performance of biomaterials in a biological environment. In this paper, we review our approach to a consistent theoretical picture of the bulk and surface properties of biomaterials. The predicted properties do encompass in particular the mechanical behavior and the surface hydration of these materials, and the surface physisorption of proteins, or polypeptides in general. The behavior of nanomaterials such as the carbon allotropes, nanotubes and fullerenes, in a biological environment is also briefly considered.

Single-chain simulations of densely branched comb polymers, or "molecular bottle-brushes" with side-chains attached to every (or every second) backbone monomer, were carried out by off-lattice Monte Carlo technique. A coarse-grained model, described by hard spheres connected by harmonic springs, was employed. Backbone lengths of up to 100 units were considered, and compared with the corresponding linear chains. The backbone molecular size was investigated as a function of its length at fixed arm size, and as a function of the arm size at fixed backbone length. The apparent swelling exponents obtained by a power-law fit were found to be larger than those for the corresponding linear polymers, indicative of stiffening of the comb backbone. The probability distribution function for the backbone end-to-end distance was also investigated for different backbone lengths and arm sizes. Analysis of this function yielded the critical exponents, which revealed an increase in the swelling exponent consistent with values found from the molecular size. The apparent persistence length of the backbone was also determined, and was found to increase with increasing branching density. Finally, the static structure factors of the whole bottle-brushes and of their backbones are discussed, which provides another consistent estimate of the swelling exponents.

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.

We report a molecular dynamics (MD) simulation study of protein adsorption on the surface of nanosized carbon allotropes, namely single-walled carbon nanotubes (SWNT) considering both the convex outer surface and the concave inner surface, together with a graphene sheet for comparison. These systems are chosen to investigate the effect of the surface curvature on protein adsorption at the same surface chemistry, given by sp(2) carbon atoms in all cases. The simulations show that proteins do favorably interact with these hydrophobic surfaces, as previously found on graphite which has the same chemical nature. However, the main finding of the present study is that the adsorption strength does depend on the surface topography: in particular, it is slightly weaker on the outer convex surfaces of SWNT and is conversely enhanced on the inner concave SWNT surface, being therefore intermediate for flat graphene. We additionally find that oligopeptides may enter the cavity of common SWNT, provided their size is small enough and the tube diameter is large enough for both entropic and energetic reasons. Therefore, we suggest that proteins can effectively be used to solubilize in water single-walled (and by analogy also multiwalled) carbon nanotubes through adsorption on the outer surface, as indeed experimentally found, and to functionalize them after insertion of oligopeptides within the cavity of nanotubes of appropriate size.

The dilute-solution dynamical properties of dendrimers in a good solvent are derived in the framework of the Rouse−Zimm approach. On the basis of a normal-coordinates treatment with preaveraged hydrodynamic interaction, we obtain the spectrum of relaxation times and some dynamical observables such as the viscoelastic complex modulus and the dynamic structure factor with its first cumulant. Since the latter quantity can also be calculated without preaveraging the hydrodynamic interaction, we can assess the accuracy of this approximation. The effect of both the structural symmetry and of the excluded-volume interactions on the intramolecular dynamics is discussed and the qualitative similarities with the effect of local stiffness are pointed out.

Single-chain Monte Carlo simulations were carried out, in continuous space, of polymers with various topologies (branched and linear) in the good solvent. Using an inherently flexible beadand-spring model, the backbone of linear polymers with either linear or dendritic side-groups attached was found to be elongated, indicative of an induced stiffness. This "topological stiffness" was compared to the "intrinsic stiffness" of semiflexible linear polymers in terms of various observables. Semiflexible comb polymers, which contained both types of stiffness, were also considered.