Search

The aggregation of proteins into fibrillar, amyloid-like aggregates generally results in an improved, positive effect on various techno-functional properties within food products, such as gelation, emulsification, and foam stabilization. These highly stable structures, characterized by their repetitive, β-sheet rich motifs, may develop as the result of the thermal treatment of protein-rich food products. Heavy metal ions can influence amyloid-like aggregation of food proteins. Lead(II) and cadmium(II) represent some of the most abundant and common environmental water and food pollutants. In this work, the influence of heavy metal ions, lead and cadmium on amyloid-like aggregation of ovalbumin at high temperatures (90 °C) and under acidic conditions (pH 2.0) was investigated. Ovalbumin is used as a general model for how heavy metals can affect amyloid-like aggregation of a food protein. Structural changes were monitored via Thioflavin T and 8-Anilino-1-naphthalenesulfonic acid fluorescence, Fourier-Transform infrared spectroscopy, atomic force microscopy, dynamic light scattering, as well as computational analyses. The obtained results indicate that the added heavy metal ions bind to different sites within ovalbumin prior to thermal treatment. Lead binding sites are closer to the hydrophobic regions of an protein, while cadmium ion binding sites are more exposed. This specific binding of metal ions affects the morphologies of amyloid-like aggregates, resulting in lead-induced branching of amyloid-like fibrils, or cadmium-induced tangling of fibrils into dense amyloid clusters. This additive effect of heavy metal ions is most evident in ovalbumin samples which contain a mixture of both heavy metal ions.

In this manuscript, we develop a two-dimensional coarse-grained model to study equilibrium properties of fibril-like structures made of amyloid proteins. The phase space of the model is sampled using Monte Carlo computer simulations. At low densities and high temperatures proteins are mostly present as monomers while at low temperatures and high densities particles self-assemble into fibril-like structures. The phase space of the model is explored and divided into different regions based on the structures present. We also estimate free-energies to dissociate proteins from fibrils based on the residual concentration of dissolved proteins. Consistent with experiments, the concentration of proteins in solution does not affects their equilibrium state. Also, we study the temperature dependence of the equilibrium state to estimate thermodynamic quantities, e.g., heat capacity and entropy, of amyloid fibrils.

In this paper we propose a model for the two dimensional fluid with one site-site associating point. We studied its structural and thermodynamic properties by the Monte Carlo computer simulations, the site-site integral equation theory (RISM), the Wertheim's thermodynamic perturbation theory (TPT) and the Wertheim's integral equation theory (WIET) for associative liquids. The model can have arbitrary position of the associating point from the center of particles. All particles have Lennard-Jones core while interactions between associating points are modeled as Gaussian like potential where the interaction depends only on the distance between sites. The methods were used to study the thermodynamic and structural properties as a function of the position of associating point, temperature and density. The accuracy of the analytic theories were checked by comparing the theoretical results with the corresponding Monte Carlo ones. The theories are quite accurate for cases when the associating point is on the surface and only dimers can be formed. In this case, the theories correctly predict the pair correlation functions of the model, internal energy, ratios of free and bonded particles and chemical potential. This is no longer true when associating point is away from the surface of particles and the higher clusters are formed.

Two-dimensional ionic liquids with single site anion and cation-neutral dimer are studied by computer simulations and integral equation techniques, with the aim of characterizing differences with single site anion-cation mixtures, and also with three dimensional equivalents of both models, in order to see the competition between the Coulomb interactions and the clustering restrictions due to reduced dimension. We find that the addition of the neutral site to the cation suppresses the liquid-gas transition which occurs in the case of the monomeric Coulomb system. Instead, bilayer membrane type ordering is found at low temperatures. The agreement between the structural correlations predicted by theory and the simulation is excellent until very close to the no-solution region predicted by the theory. These findings suggest various relations between the nature of the clustering at low temperatures, and the inability of the theory to enter this region, Comment: 27 pages, 13 figures

Monte Carlo simulations, molecular dynamics and integral equation theory were used to study the thermodynamics and structure of particles interacting through the core softened interaction. Core-softened disks have two length scales of interaction, a hard core with one diameter and a soft corona with a larger diameter. We checked the possibility that a fluid with a core-softened potential reproduces anomalies of liquid water and attempted to determine the critical points which we did not observe nor with computer simulations nor with integral equations. We showed that some versions of the integral equation theory completely fail to predict structure and thermodynamics of such system, while others predict it quite well depending on the position in phase space.

We have studied the effect of rotational and translational degrees of freedom on solvation of nonpolar solutes. In this study a simple two-dimensional Mercedes-Benz (MB) water model was used. By separating temperature on rotational and translational part, the effect of different degrees of freedom on solvation was investigated. Increasing rotational temperature reduces tendency of water to form hydrogen bonds, therefore the effect of rotational degrees of freedom on solvation can be used to assess how hydrogen bonds affect solvation and what kind of liquid is more favourable for solvation of different solute. Considering the size there are three different regimes of solvation of nonpolar solutes and the effect of hydrogen bonds. The rotational temperature and thus hydrogen bonds have almost zero effect on solvation and aggregation of small solutes which are equally soluble in liquids that do and liquids that do not form hydrogen bonds. When size of solute is larger than HB length increasing rotational temperature improves solvation and diminishes association of solute molecules, thus large solutes are more soluble in liquids without hydrogen bonds. On the other hand when solute size is similar to HB length, increasing rotational temperature diminishes solvation and improves association of solute molecules, thus solutes of similar size are more soluble in liquid with hydrogen bonds, that means hydrogen bonds have favourable effect on solvation of such solutes. Hydrophobic effect appears only when solute is larger than HB length, on the other hand when solute size is similar to HB length inverse hydrophobic effect appears.

In this manuscript we use a two-dimensional coarse-grained model to study how amyloid fibrils grow towards an equilibrium state where they coexist with proteins dissolved in a solution. Free-energies to dissociate proteins from fibrils are estimated from the residual concentration of dissolved proteins. Consistent with experiments, the concentration of proteins in solution affects the growth rate of fibrils but not their equilibrium state. Also, studies of the temperature dependence of the equilibrium state can be used to estimate thermodynamic quantities, e.g., heat capacity and entropy., Graphical abstract

In this paper we applied an analytical theory for the two dimensional dimerising fluid. We applied Wertheims thermodynamic perturbation theory (TPT) and integral equation theory (IET) for associative liquids to the dimerising model with arbitrary position of dimerising points from center of the particles. The theory was used to study thermodynamical and structural properties. To check the accuracy of the theories we compared theoretical results with corresponding results obtained by Monte Carlo computer simulations. The theories are accurate for the different positions of patches of the model at all values of the temperature and density studied. IET correctly predicts the pair correlation function of the model. Both TPT and IET are in good agreement with the Monte Carlo values of the energy, pressure, chemical potential, compressibility and ratios of free and bonded particles.

In this paper we propose extension of the second-order thermodynamic perturbation theory (TPT2) for the inverse patchy colloids (IPC) with arbitrary number of patches. The theory is used to study thermodynamical properties and liquid-gas phase behavior of the IPC model with one, two and three patches. To validate the accuracy of the TPT2 we compare theoretical predictions against corresponding results obtained by computer simulations. The theory is accurate for the one-patch version of the model at all values of the temperature and density studied and less accurate for two- and three-patch versions at lower temperature and higher density. Theoretical predictions for the critical temperature and density of the two- and three-patch IPC models are relatively accurate, however the overall shape of the theoretical phase diagram appears to be too narrow. No liquid-gas phase coexistence for the one-patch IPC model was found.

The lattice Boltzmann method (LBM) is a computational method for a wide variety of fluid flow and multi-physics phenomena. These include systems governed by reaction-diffusion and reaction-diffusion-advection equations which are of major interest in many scientific and engineering fields. Typically, reactions are incorporated into LBM by means of a reactive source term identical to the macroscopic reaction kinetics equations which is dependent on the local concentration of the chemical species. Alternatively we can formulate the source term at the level of the particle distribution function, which is the main variable in LBM simulations. This way we can mimic the velocity-dependent reactive collisions of particles. This was done in our work and we implemented it to a bimolecular reaction for several geometries and initial conditions. Comparison was made with the macroscopic reaction source term.

We developed a fast theory for studying how the rotational temperature (and rotational degrees of freedom) affects the properties of a simple model of liquid water. Wertheim's Thermodynamic perturbation theory (TPT) for associative liquids was applied to the Mercedes-Benz (MB) model. 2D MB model is one of the simplest models of water. The MB particles are modelled as Lennard-Jones disks with three hydrogen bonding arms arranged symmetrically as in the MB logo. We previously applied TPT to this model. We found that the physical properties were well reproduced by the theory. Here, we propose an modified version of the thermodynamic perturbation theory in which it is possible to treat rotational degrees of freedom by using different averaging then used before. By holding translational or rotational temperature constant and varying the other one, we investigate their effect on the properties of the simple water model and how well TPT reproduces computer simulation results. The new results are in good agreement with the Monte Carlo values of the pressure and energy. We also investigated how rotational temperature affects thermodynamic properties of the critical point. A major advantage of these theories is that they require orders of magnitude less computer time than the Monte Carlo simulations.

We developed an analytical theory for studying of rotational degrees of freedom of a simple model of liquid water. Wertheim's integral equation theory (IET) for associative liquids was applied to the Mercedes-Benz (MB) model, which is among the simplest models of water. The MB water molecules are modeled as 2-dimensional Lennard-Jones disks with three hydrogen bonding arms arranged symmetrically, resembling the MB logo. IET is based on the orientationally averaged version of the Ornstein-Zernike equation. In varying of rotational degrees of freedom we use different averaging then used before. By holding one of the temperatures constant and varying the other one, we investigate the effect of faster motion in the corresponding degrees of freedom on the properties of the simple water model and how well IET reproduce computer simulation results. The pair correlation function of the model water at high rotational or translation temperatures is correctly predicted. IET results are in good agreement with the Monte Carlo values of the pressure, energy, heat capacity. A major advantage of these theories is that they require orders of magnitude less computer time than the Monte Carlo simulations.

Knowledge of water-water potential is important for an accurate description of water. Potential between two molecules depends upon the distance, relative orientation of each molecule and local environment. In simulation, water-water hydrogen bonds are handled by point-charge water potentials and by polarizable models. These models produce good results for bulk water being parameterized for such environment. Water around surfaces and in channels, however is different from bulk water. Using quantum-mechanical methods, hydrogen bond strength was calculated in the vicinity of different monoions. A simple empirical relationship was discovered between the maximum hydrogen bond and the electric field produced by ion.

What are the properties of water in the presence of a 'sea' of inert obstacles? This question arises because biological cells are highly crowded media, and it is of interest to know the properties of water inside them. It also arises for understanding water in confined molecular environments and for mixtures of water with non-polar solutes. We study two-dimensional Mercedes-Benz (MB) water that is freely mobile in a disordered, but fixed, matrix of Lennard-Jones disks. We use the associative replica Ornstein-Zernike equations supplemented by the corresponding hypernetted chain approximation, and we tested the theory using Monte Carlo simulations. We find that the structure of model water is perturbed by the presence of the obstacles. When the density of obstacles is small, the obstacles induce an increased ordering and 'hydrogen bonding' of the MB model molecules and increased compressibility, relative to pure fluid, in agreement with previous theoretical and experimental studies. However, interestingly, high obstacle densities reduce MB water structuring, 'hydrogen bonding', and compressibility, because the obstacles interfere so extensively with all the possible ways that the fluid can form good 'hydrogen bonding' networks. 2003 Elsevier B.V. All rights reserved.