124 research outputs found
Fluid of fused spheres as a model for protein solution
In this work we examine thermodynamics of fluid with "molecules" represented
by two fused hard spheres, decorated by the attractive square-well sites.
Interactions between these sites are of short-range and cause association
between the fused-sphere particles. The model can be used to study the
non-spherical (or dimerized) proteins in solution. Thermodynamic quantities of
the system are calculated using a modification of Wertheim's thermodynamic
perturbation theory and the results compared with new Monte Carlo simulations
under isobaric-isothermal conditions. In particular, we are interested in the
liquid-liquid phase separation in such systems. The model fluid serves to
evaluate the effect of the shape of the molecules, changing from spherical to
more elongated (two fused spheres) ones. The results indicate that the effect
of the non-spherical shape is to reduce the critical density and temperature.
This finding is consistent with experimental observations for the antibodies of
non-spherical shape.Comment: 12 pages, 5 figure
Correlation between flexibility of chain-like polyelectrolyte and thermodynamic properties of its solution
Structural and thermodynamic properties of the model solution containing
charged oligomers and the equivalent number of counterions were studied by
means of the canonical Monte Carlo simulation technique. The oligomers are
represented as (flexible) freely jointed chains or as a linear (rigid) array of
charged hard spheres. In accordance with the primitive model of electrolyte
solutions, the counterions are modeled as charged hard spheres and the solvent
as dielectric continuum. Significant differences in the pair distribution
functions, obtained for the rigid (rod-like) and flexible model are found but
the differences in thermodynamic properties, such as, enthalpy of dilution and
excess chemical potential, are less significant. The results are discussed in
light of the experimental data an aqueous polyelectrolyte solutions. The
simulations suggest that deviations from the fully extended (rod-like)
conformation yield slightly stronger binding of counterions. On the other hand,
the flexibility of polyions, even when coupled with the ion-size effects,
cannot be blamed for qualitative differences between the theoretical results
and experimental data for enthalpy of dilution.Comment: 14 pages, 10 figure
Effects of translational and rotational degrees of freedom on the properties of model water
Molecular dynamics simulations with separate thermostats for rotational and
translational motions were used to study the effects of these degrees of
freedom on the structure of water at a fixed density. To describe water
molecules, we used the SPC/E model. The results indicate that an increase of
the rotational temperature, , causes a significant breaking of
the hydrogen bonds. This is not the case, at least not to such an extent, when
the translational temperature, , is raised. The probability of
finding an empty spherical cavity (no water molecule present) of a given size,
strongly decreases with an increase of , but this only marginally
affects the free energy of the hydrophobe insertion. The excess internal energy
increases proportionally with an increase of , while an increase
of yields a much smaller effect at high temperatures. The
diffusion coefficient of water exhibits a non-monotonous behaviour with an
increase of the rotational temperature.Comment: 9 pages, 9 figure
Primitive model electrolytes. A comparison of the HNC approximation for the activity coefficient with Monte Carlo data
Accuracy of the mean activity coefficient expression
(Hansen-Vieillefosse-Belloni equation), valid within the hypernetted chain
(HNC) approximation, was tested in a wide concentration range against new Monte
Carlo (MC) data for +1:-1 and +2:-2 primitive model electrolytes. The
expression has an advantage that the excess chemical potential can be obtained
directly, without invoking the time consuming Gibbs-Duhem calculation. We found
the HNC results for the mean activity coefficient to be in good agreement with
the machine calculations performed for the same model. In addition, the
thermodynamic consistency of the HNC approximation was tested. The mean
activity coefficients, calculated via the Gibbs-Duhem equation, seem to follow
the MC data slightly better than the Hansen-Vieillefosse-Belloni expression.
For completeness of the calculation, the HNC excess internal energies and
osmotic coefficients are also presented. These results are compared with the
calculations based on other theories commonly used to describe electrolyte
solutions, such as the mean spherical approximation, Pitzer's extension of the
Debye-H\"uckel theory, and the Debye-H\"uckel limiting law.Comment: 15 pages, 6 figure
Modelling the ion-exchange equilibrium in nanoporous materials
Distribution of a two component electrolyte mixture between the model
adsorbent and a bulk aqueous electrolyte solution was studied using the replica
Ornstein-Zernike theory and the grand canonical Monte Carlo method. The
electrolyte components were modelled to mimic the HCl/NaCl and HCl/CaCl_2
mixtures, respectively. The matrix, invaded by the primitive model electrolyte
mixture, was formed from monovalent negatively charged spherical obstacles. The
solution was treated as a continuous dielectric with the properties of pure
water. Comparison of the pair distribution functions (obtained by the two
methods) between the various ionic species indicated a good agreement between
the replica Ornstein-Zernike results and machine calculations. Among
thermodynamic properties, the mean activity coefficient of the invaded
electrolyte components was calculated. Simple model for the ion-exchange resin
was proposed. The selectivity calculations yielded qualitative agreement with
the following experimental observations: (i) selectivity increases with the
increasing capacity of the adsorbent (matrix concentration), (ii) the adsorbent
is more selective for the ion having higher charge density if its fraction in
mixture is smaller.Comment: 12 pages, 9 figure
Modelling Bi-specific Antibodies in Aqueous Solution
This study presents theoretical results for physico-chemical properties of
system of molecules modeling bi-specific antibodies, such as,
dual-variable-domain monoclonal antibodies (DVD-Ig) and Fabs-In-Tandem
Immunoglobulin (FIT-Ig). These molecules are representatives of the engineered
proteins that combine the function and specificity of two monoclonal
antibodies. Individual molecules are here depicted as an assembly of nine (or
in case of the Fit-Ig eleven) hard spheres, organized to resemble the Y-shaped
object. The effects of the increased size, asymmetry, and flexibility of
individual molecules on measurable properties of such systems of molecules are
investigated. We examined the liquid-liquid phase separation, the second virial
coefficient , and viscosity under various experimental conditions. The
calculations are compared with the data for regular monoclonal antibodies and
discussed in view of the experimental results for DVD-Ig solutions available in
literature
The Activity Coefficients of Amino Acids and Peptides in Aqueous Solutions Containing Guanidinium Chloride
Six systems of the type amino acid- or peptide-guanidinium
chloride-water have been investigated over wide solute molality
ranges using vapor pressure osmometry. The amino acids used
were glycine and L-leucine, while the peptides were diglycine,
triglycine, glycyl-L-leucine and L-leucyl-L-leucine. Equations for
the ratios of the activity coefficients of these compounds in the
salt solutions and water, respectively, were obtained in terms of
the molalities of the solutes. The activity coefficient ratios for
glycine are not much below one, whereas those for i.-leucine are
considerably smaller reflecting the presence of the leucyl side
chain. The activity coefficient ratios for the peptides are generally
smaller than those for the amino acids which can be attributed to
. the presence of the peptide group
On the nature of long-range contributions to pair interactions between charged colloids in two dimensions
We perform a detailed analysis of solutions of the inverse problem applied to
experimentally measured two-dimensional radial distribution functions for
highly charged latex dispersions. The experiments are carried out at high
colloidal densities and under low-salt conditions. At the highest studied
densities, the extracted effective pair potentials contain long-range
attractive part. At the same time, we find that for the best distribution
functions available the range of stability of the solutions is limited by the
nearest neighbour distance between the colloidal particles. Moreover, the
measured pair distribution functions can be explained by purely repulsive pair
potentials contained in the stable part of the solution.Comment: 6 pages, 5 figure
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