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  1. Article ; Online: Phase behavior of patchy colloids confined in patchy porous media.

    Kalyuzhnyi, Yurij V / Patsahan, Taras / Holovko, Myroslav / Cummings, Peter T

    Nanoscale

    2024  Volume 16, Issue 9, Page(s) 4668–4677

    Abstract: A simple model for functionalized disordered porous media is proposed and the effects of confinement on self-association, percolation and phase behavior of a fluid of patchy particles are studied. The media are formed by randomly distributed hard-sphere ... ...

    Abstract A simple model for functionalized disordered porous media is proposed and the effects of confinement on self-association, percolation and phase behavior of a fluid of patchy particles are studied. The media are formed by randomly distributed hard-sphere obstacles fixed in space and decorated by a certain number of off-center square-well sites. The properties of the fluid of patchy particles, represented by the fluid of hard spheres each bearing a set of the off-center square-well sites, are studied using an appropriate combination of the scaled particle theory for the porous media, Wertheim's thermodynamic perturbation theory, and Flory-Stockmayer theory. To assess the accuracy of the theory a set of computer simulations have been performed. In general, predictions of the theory appeared to be in good agreement with the computer simulation results. Confinement and competition between the formation of bonds connecting the fluid particles, and connecting fluid particles and obstacles of the matrix, gave rise to a re-entrant phase behavior with three critical points and two separate regions of the liquid-gas phase coexistence.
    Language English
    Publishing date 2024-02-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 2515664-0
    ISSN 2040-3372 ; 2040-3364
    ISSN (online) 2040-3372
    ISSN 2040-3364
    DOI 10.1039/d3nr02866f
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Protein Association in Solution: Statistical Mechanical Modeling.

    Vlachy, Vojko / Kalyuzhnyi, Yurij V / Hribar-Lee, Barbara / Dill, Ken A

    Biomolecules

    2023  Volume 13, Issue 12

    Abstract: Protein molecules associate in solution, often in clusters beyond pairwise, leading to liquid phase separations and high viscosities. It is often impractical to study these multi-protein systems by atomistic computer simulations, particularly in multi- ... ...

    Abstract Protein molecules associate in solution, often in clusters beyond pairwise, leading to liquid phase separations and high viscosities. It is often impractical to study these multi-protein systems by atomistic computer simulations, particularly in multi-component solvents. Instead, their forces and states can be studied by liquid state statistical mechanics. However, past such approaches, such as the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, were limited to modeling proteins as spheres, and contained no microscopic structure-property relations. Recently, this limitation has been partly overcome by bringing the powerful Wertheim theory of associating molecules to bear on protein association equilibria. Here, we review these developments.
    MeSH term(s) Proteins ; Solvents ; Computer Simulation
    Chemical Substances Proteins ; Solvents
    Language English
    Publishing date 2023-11-24
    Publishing country Switzerland
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2701262-1
    ISSN 2218-273X ; 2218-273X
    ISSN (online) 2218-273X
    ISSN 2218-273X
    DOI 10.3390/biom13121703
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Behaviour of the model antibody fluid constrained by rigid spherical obstacles: Effects of the obstacle-antibody attraction.

    Hvozd, Taras / Kalyuzhnyi, Yurij V / Vlachy, Vojko

    Soft matter

    2022  Volume 18, Issue 47, Page(s) 9108–9117

    Abstract: This study investigates the behaviour of a fluid of monoclonal antibodies (mAbs) when trapped in a confinement represented by rigid spherical obstacles that attract antibodies. The antibody molecule is depicted as an assembly of seven hard spheres (7- ... ...

    Abstract This study investigates the behaviour of a fluid of monoclonal antibodies (mAbs) when trapped in a confinement represented by rigid spherical obstacles that attract antibodies. The antibody molecule is depicted as an assembly of seven hard spheres (7-bead model), organized to resemble a
    MeSH term(s) Antibodies, Monoclonal
    Chemical Substances Antibodies, Monoclonal
    Language English
    Publishing date 2022-12-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 2191476-X
    ISSN 1744-6848 ; 1744-683X
    ISSN (online) 1744-6848
    ISSN 1744-683X
    DOI 10.1039/d2sm01258h
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Integral equation theory for mixtures of spherical and patchy colloids. 2. Numerical results.

    Kalyuzhnyi, Yurij V / Nezbeda, Ivo / Cummings, Peter T

    Soft matter

    2021  Volume 17, Issue 12, Page(s) 3513–3519

    Abstract: Thermodynamic properties and structure of binary mixtures of patchy and spherical colloids are studied using a recently developed theory [Y. V. Kalyuzhnyi, et al., Soft Matter, 2020, 16, 3456]. The theory is based on a solution of the multidensity ... ...

    Abstract Thermodynamic properties and structure of binary mixtures of patchy and spherical colloids are studied using a recently developed theory [Y. V. Kalyuzhnyi, et al., Soft Matter, 2020, 16, 3456]. The theory is based on a solution of the multidensity Ornstein-Zernike equation and provides completely analytical expressions for the structure factors of these systems and for all their major thermodynamical quantities. The considered mixtures are made up of particles of different size and with a different number of patches. A set of molecular simulation data has been generated to enable a systematic comparison and to access thus accuracy of the theoretical predictions. In general, the predictions of the theory appear to be in good agreement with computer simulation data. For the models with a lower number of patches (n
    Language English
    Publishing date 2021-03-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 2191476-X
    ISSN 1744-6848 ; 1744-683X
    ISSN (online) 1744-6848
    ISSN 1744-683X
    DOI 10.1039/d0sm02284e
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Aggregation, liquid-liquid phase separation, and percolation behaviour of a model antibody fluid constrained by hard-sphere obstacles.

    Hvozd, Taras / Kalyuzhnyi, Yurij V / Vlachy, Vojko

    Soft matter

    2020  Volume 16, Issue 36, Page(s) 8432–8443

    Abstract: This study is concerned with the behaviour of proteins within confinement created by hard-sphere obstacles. An individual antibody molecule is depicted as an assembly of seven hard spheres, organized to resemble a Y-shaped (on average) antibody (7-bead ... ...

    Abstract This study is concerned with the behaviour of proteins within confinement created by hard-sphere obstacles. An individual antibody molecule is depicted as an assembly of seven hard spheres, organized to resemble a Y-shaped (on average) antibody (7-bead model) protein. For comparison with other studies we, in one case, model the protein as a hard sphere decorated by three short-range attractive sites. The antibody has two Fab and one Fc domains located in the corners of the letter Y. In this calculation, only the Fab-Fab and Fab-Fc attractive pair interactions are possible. The confinement is formed by the randomly distributed hard-sphere obstacles fixed in space. Aside from size exclusion, the obstacles do not interact with antibodies, but they affect the protein-protein correlation. We used a combination of the scaled-particle theory, Wertheim's thermodynamic perturbation theory and the Flory-Stockmayer theory to calculate: (i) the second virial coefficient of the protein fluid, (ii) the percolation threshold, (iii) cluster size distributions, and (iv) the liquid-liquid phase separation as a function of the strength of the various pair interactions of the protein and the model parameters, such as protein concentration and the packing fraction of obstacles. The conclusion is that hard-sphere obstacles strongly decrease the critical density and also, but to a much lesser extent, the critical temperature. Also, the confinement enhances clustering, making the percolating region broader. The effect depends on the model parameters, such as the packing fraction of obstacles η0, the inter-site interaction strength εIJ, and the ratio between the size of the obstacle σ0 and the size of one bead of the model antibody σhs; the value of this ratio is varied here from 2 to 5. Interestingly, at low to moderate packing fractions of obstacles, the second virial coefficient first slightly decreases (destabilization), and the slope depends on the observation temperature, but then at higher values of η0 it increases. The calculated values of the second virial coefficient also depend on the size of the obstacles.
    MeSH term(s) Proteins ; Temperature ; Thermodynamics
    Chemical Substances Proteins
    Language English
    Publishing date 2020-08-18
    Publishing country England
    Document type Journal Article
    ZDB-ID 2191476-X
    ISSN 1744-6848 ; 1744-683X
    ISSN (online) 1744-6848
    ISSN 1744-683X
    DOI 10.1039/d0sm01014f
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Integral equation theory for a mixture of spherical and patchy colloids: analytical description.

    Kalyuzhnyi, Yurij V / Nezbeda, Ivo / Cummings, Peter T

    Soft matter

    2020  Volume 16, Issue 14, Page(s) 3456–3465

    Abstract: An analytic theory for the structure and thermodynamics of two-component mixtures of patchy and spherical colloids is developed. The theory is based on an analytical solution of the multidensity Ornstein-Zernike equation supplemented by the associative ... ...

    Abstract An analytic theory for the structure and thermodynamics of two-component mixtures of patchy and spherical colloids is developed. The theory is based on an analytical solution of the multidensity Ornstein-Zernike equation supplemented by the associative Percus-Yevick closure relations. We derive closed-form analytic expressions for the partial structure factors and thermodynamic properties using the energy route for the model with arbitrary number of patches and any hard-sphere size ratio of the particles. To assess the accuracy of the theoretical predictions we compare them against existing and newly generated set of computer simulation data. In our numerical calculations we consider the model with equal hard-sphere sizes and one patch. Very good agreement between results of the theory and simulation for the pair correlation functions, excess internal energy and pressure is observed for almost all values of the system density, temperature and composition studied. Only in the region of low concentrations of spherical colloids the theoretical results become less accurate.
    Language English
    Publishing date 2020-03-23
    Publishing country England
    Document type Journal Article
    ZDB-ID 2191476-X
    ISSN 1744-6848 ; 1744-683X
    ISSN (online) 1744-6848
    ISSN 1744-683X
    DOI 10.1039/c9sm02309g
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Two- and three-phase equilibria of polydisperse Yukawa hard-sphere fluids confined in random porous media: high temperature approximation and scaled particle theory.

    Hvozd, Taras V / Kalyuzhnyi, Yurij V

    Soft matter

    2017  Volume 13, Issue 7, Page(s) 1405–1412

    Abstract: We have studied the phase behavior of polydisperse Yukawa hard-sphere fluid confined in random porous media using extension and combination of high temperature approximation and scaled particle theory. The porous media are represented by the matrix of ... ...

    Abstract We have studied the phase behavior of polydisperse Yukawa hard-sphere fluid confined in random porous media using extension and combination of high temperature approximation and scaled particle theory. The porous media are represented by the matrix of randomly placed hard-sphere obstacles. Due to the confinement, polydispersity effects are substantially enhanced. At an intermediate degree of fluid polydispersity and low density of the matrix, we observe two-phase coexistence with two critical points, and cloud and shadow curves forming closed loops of ellipsoidal shape. With the increase of the matrix density and the constant degree of polydispersity, these two critical points merge and disappear, and at lower temperatures the system fractionates into three coexisting phases. A similar phase behavior was observed in the absence of the porous media caused, however, by the increase of the polydispersity.
    Language English
    Publishing date 2017-02-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 2191476-X
    ISSN 1744-6848 ; 1744-683X
    ISSN (online) 1744-6848
    ISSN 1744-683X
    DOI 10.1039/c6sm02613c
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Phase Equilibria of Polydisperse Square-Well Chain Fluid Confined in Random Porous Media: TPT of Wertheim and Scaled Particle Theory.

    Hvozd, Taras V / Kalyuzhnyi, Yurij V / Cummings, Peter T

    The journal of physical chemistry. B

    2018  Volume 122, Issue 21, Page(s) 5458–5465

    Abstract: Extension of Wertheim's thermodynamic perturbation theory and its combination with scaled particle theory is proposed and applied to study the liquid-gas phase behavior of polydisperse hard-sphere square-well chain fluid confined in the random porous ... ...

    Abstract Extension of Wertheim's thermodynamic perturbation theory and its combination with scaled particle theory is proposed and applied to study the liquid-gas phase behavior of polydisperse hard-sphere square-well chain fluid confined in the random porous media. Thermodynamic properties of the reference system, represented by the hard-sphere square-well fluid in the matrix, are calculated using corresponding extension of the second-order Barker-Henderson perturbation theory. We study effects of polydispersity and confinement on the phase behavior of the system. While polydispersity causes increase of the region of phase coexistence due to the critical temperature increase, confinement decreases the values of both critical temperature and critical density making the region of phase coexistence smaller. This effect is enhanced with the increase of the size ratio of the fluid and matrix particles. The increase of the average chain length at fixed values of polydispersity and matrix density shifts the critical point to a higher temperature and a slightly lower density.
    Language English
    Publishing date 2018-04-18
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.7b11741
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Melting upon cooling and freezing upon heating: fluid-solid phase diagram for Švejk-Hašek model of dimerizing hard spheres.

    Kalyuzhnyi, Yurij V / Jamnik, Andrej / Cummings, Peter T

    Soft matter

    2017  Volume 13, Issue 6, Page(s) 1156–1160

    Abstract: A simple model of dimerizing hard spheres with highly nontrivial fluid-solid phase behavior is proposed and studied using the recently proposed resummed thermodynamic perturbation theory for central force (RTPT-CF) associating potentials. The phase ... ...

    Abstract A simple model of dimerizing hard spheres with highly nontrivial fluid-solid phase behavior is proposed and studied using the recently proposed resummed thermodynamic perturbation theory for central force (RTPT-CF) associating potentials. The phase diagram has the fluid branch of the fluid-solid coexistence curve located at temperatures lower than those of the solid branch. This unusual behavior is related to the strong dependence of the system excluded volume on the temperature, which for the model at hand decreases with increasing temperature. This effect can be also seen for a wide family of fluid models with an effective interaction that combines short range attraction and repulsion at a larger distance. We expect that for sufficiently high repulsive barrier, such systems may show similar phase behavior.
    Language English
    Publishing date 2017-02-08
    Publishing country England
    Document type Journal Article
    ZDB-ID 2191476-X
    ISSN 1744-6848 ; 1744-683X
    ISSN (online) 1744-6848
    ISSN 1744-683X
    DOI 10.1039/c6sm02572b
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Modeling phase transitions in mixtures of β-γ lens crystallins.

    Kastelic, Miha / Kalyuzhnyi, Yurij V / Vlachy, Vojko

    Soft matter

    2016  Volume 12, Issue 35, Page(s) 7289–7298

    Abstract: We analyze the experimentally determined phase diagram of a γD-βB1 crystallin mixture. Proteins are described as dumbbells decorated with attractive sites to allow inter-particle interaction. We use thermodynamic perturbation theory to calculate the free ...

    Abstract We analyze the experimentally determined phase diagram of a γD-βB1 crystallin mixture. Proteins are described as dumbbells decorated with attractive sites to allow inter-particle interaction. We use thermodynamic perturbation theory to calculate the free energy of such mixtures and, by applying equilibrium conditions, also the compositions and concentrations of the co-existing phases. Initially we fit the Tcloudversus packing fraction η measurements for a pure (x2 = 0) γD solution in 0.1 M phosphate buffer at pH = 7.0. Another piece of experimental data, used to fix the model parameters, is the isotherm x2vs. η at T = 268.5 K, at the same pH and salt content. We use the conventional Lorentz-Berthelot mixing rules to describe cross interactions. This enables us to determine: (i) model parameters for pure βB1 crystallin protein and to calculate; (ii) complete equilibrium surface (Tcloud-x2-η) for the crystallin mixtures. (iii) We present the results for several isotherms, including the tie-lines, as also the temperature-packing fraction curves. Good agreement with the available experimental data is obtained. An interesting result of these calculations is evidence of the coexistence of three phases. This domain appears for the region of temperatures just out of the experimental range studied so far. The input parameters, leading good description of experimental data, revealed a large difference between the numbers of the attractive sites for γD and βB1 proteins. This interesting result may be related to the fact that γD has a more than nine times smaller quadrupole moment than its partner in the mixture.
    Language English
    Publishing date 2016-08-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 2191476-X
    ISSN 1744-6848 ; 1744-683X
    ISSN (online) 1744-6848
    ISSN 1744-683X
    DOI 10.1039/c6sm01513a
    Database MEDical Literature Analysis and Retrieval System OnLINE

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