Formation of supported membranes from vesicles

Using a combination of the quartz crystal microbalance and surface plasmon resonance techniques, we have studied the spontaneous formation of supported lipid bilayers from small (approximately 25 nm) unilamellar vesicles. Together these experimental methods measure the amount of lipid adsorbed on the surface and the amount of water trapped by the lipid. With this approach, we have, for the first time, been able to observe in detail the progression from the adsorption of intact vesicles to rupture and bilayer formation. Monte Carlo simulations reproduce the data.

Monte Carlo simulation of diffusion of adsorbed proteins

We present the results of three-dimensional lattice Monte Carlo simulations of protein diffusion on the liquid-solid interface in a wide temperature range including the most interesting temperatures (from slightly below T(f) and up to T(c), where T(f) and T(c) are the folding and collapse temperatures). For the model under consideration (27 monomers of two types), the temperature dependence of the diffusion coefficient is found to obey the Arrhenius law with the normal value (approximately 10(-2)-10(-3) cm(2)/s) of the preexponential factor. Proteins 2000;39:76-81.

Surface restructuring and kinetic oscillations in heterogeneous catalytic reactions

We extend our earlier Monte Carlo simulations of isothermal kinetic oscillations in the NO-H(2)/Pt(100) system [V. P. Zhdanov, Phys. Rev. E 59, 6292 (1999)]. The analysis, based on a lattice-gas model describing surface restructuring in terms of the statistical theory of first-order phase transitions, is primarily focused on adsorbate-diffusion-mediated synchronization of oscillations. The conventional condition for synchronization, (D tau)(1/2)>L (D is the diffusion coefficient, tau the oscillation period, and L the lattice size), is proved to considerably underestimate the role of surface diffusion. Due to the formation of mesoscopic islands, well developed oscillations are found to be possible in the cases when the left part of this condition is much lower than the right part.

Surface restructuring, kinetic oscillations, and chaos in heterogeneous catalytic reactions

We present comprehensive Monte Carlo simulations of isothermal kinetic oscillations and chaos in catalytic reactions accompanied by adsorbate-induced surface restructuring. Our analysis is based on the lattice-gas model describing surface restructuring in terms of the statistical theory of first-order phase transitions. As an example, we treat the kinetics of the NO-H2 reaction on the Pt(100) surface. A proposed reduced mechanism of this reaction includes NO adsorption, desorption, and decomposition occurring on the restructured patches of the surface (the decomposition products are rapidly removed from the surface via N2 desorption and H2O formation and desorption). Calculations are performed with a qualitatively realistic ratio between the rates of different elementary steps. In particular, NO diffusion is several orders of magnitude faster compared to the other steps. On the nm scale, the model predicts formation of restructured islands with atomically sharp boundaries. The shape of the islands is found to change dramatically with varying reaction conditions. Despite phase separation on the surface, the transition from almost harmonic oscillations (with relatively small separate islands) to chaos (with merging islands) is demonstrated to occur via the standard Feigenbaum scenario. Near the critical point, the dependence of the amplitude of oscillations on the governing parameter is shown to be close to that predicted for the Hopf supercritical bifurcation.

Monte Carlo simulation of denaturation of adsorbed proteins

Denaturation of model proteinlike molecules at the liquid-solid interface is simulated over a wide temperature range by employing the lattice Monte Carlo technique. Initially, the molecule containing 27 monomers of two types (A and B) is assumed to be adsorbed in the native folded state (a 3 x 3 x 3 cube) so that one of its sides is in contact with the surface. The details of the denaturation kinetics are found to be slightly dependent on the choice of the side, but the main qualitative conclusions hold for all the sides. In particular, the kinetics obey approximately the conventional first-order law at T > Tc (Tc is the collapse temperature for solution). With decreasing temperature, below Tc but above Tf (Tf is the folding temperature for solution), deviations appear from the first-order kinetics. For the most interesting temperatures, that is, below Tf, the denaturation kinetics are shown to be qualitatively different from the conventional ones. In particular, the denaturation process occurs via several intermediate steps due to trapping in metastable states. Mathematically, this means that (i) the transition to the denatured state of a given molecule is nonexponential, and (ii) the denaturation process cannot be described by a single rate constant kappar. One should rather introduce a distribution of values of this rate constant (different values of kappar correspond to the transitions to the altered state via different metastable states).

Monte Carlo simulation of the kinetics of protein adsorption

Adsorption of proteins occurs via diffusion toward the interface, actual adsorption, and subsequent irreversible conformational changes resulting in denaturation of the native protein structure. The conventional kinetic models describing these steps are based on the assumption that the denaturation transitions obey the first-order law with a single value of the denaturation rate constant kappar. Meanwhile, recent Monte Carlo simulations indicate that, in general, the denaturation process cannot be described by a single rate constant kappar. One should rather introduce a distribution of this rate constant (physically, different values of kappar correspond to the transitions to the altered state via different metastable states). We have calculated the kinetics of irreversible adsorption of proteins with and without distribution of the denaturation rate constant kappar in the limits when protein diffusion in the solution is, respectively, rapid or slow. In both cases, the adsorption kinetics with distribution of kappar are found to be close to those with a single-valued rate constant kappar provided that the average value of kappar in the former case is equal to kappar for the latter case. This conclusion holds even for wide distributions of kappar. The consequences of this finding for the fitting of global experimental kinetics on the basis of phenomenological equations are briefly discussed.

Monte Carlo simulation of protein folding with orientation-dependent monomer-monomer interactions

We present the results of lattice Monte Carlo simulations of protein folding in the framework of a model taking into account (i) the dependence of the energy of interaction of amino-acid residues on their orientation and (ii) the rigidity of the polypeptide chain with respect to the formation of kinks. If the chain is flexible, the final protein structures are predicted to be compact. Increasing the energy cost of creation of kinks is found to favor the formation of flat structures mimicking an ideal antiparallel beta sheet. For compact structures, the kinetics of folding exhibit the standard two-phase regime (a rapid collapse to one of the metastable stable, followed by slow reconfiguration of the chain to the native structure). For flat structures, the transition to the native state is often gradual.