arXiv subjects

T. Patsahan

Publications and source records attributed to T. Patsahan.

At least 19 recordsLinked to original sources

arXiv2026

Monte Carlo simulation of selective adsorption in a binary hard-disk mixture on patterned adhesive surfaces

Selective adsorption in a two-dimensional model of a binary hard-disk mixture on patterned adhesive surfaces is studied using grand canonical Monte Carlo simulations. The two species have equal diameters and equal bulk chemical potentials, but different attraction strengths to adhesive domains. Thus, affinity-driven selectivity is separated from particle-size asymmetry and unequal chemical potentials. The surface pattern is defined by domain size, domain surface coverage, and ordered or disordered arrangement of circular domains. The results show that selectivity strongly depends on surface geometry, especially at low and intermediate chemical potentials. Domains comparable to the particle size enhance selectivity by forming adsorption regions with large particle--domain overlap, whereas larger domains can provide high selectivity at low chemical potentials. For small domains, further reduction in size can also increase selectivity as the system approaches a uniform attractive surface with corresponding effective affinity parameters of the species.

cond-mat.soft↗

arXiv2026

Behaviour of the model antibody fluid constrained by rigid spherical obstacles: effects of the obstacle-antibody binding

We study a simplified model of monoclonal antibodies confined in a patchy random porous medium. Antibodies are represented as Y-shaped particles composed of seven tangential hard spheres with attractive patches on the terminal beads, while the matrix consists of randomly distributed hard-sphere obstacles bearing adhesive sites. The model captures antibody behavior in crowded biological environments with strong short-range antibody-matrix attractions. The theoretical approach combines Wertheim's multidensity thermodynamic perturbation theory, the Flory-Stockmayer theory of polymerization, and scaled particle theory for fluids in porous media. We analyze thermodynamic properties, percolation thresholds, and phase behavior, and compare the selected results with new computer simulations. The interplay between antibody-antibody and antibody-matrix interactions produces a complex phase behavior, including re-entrant phase separation with a closed-loop coexistence region at higher temperatures and conventional liquid-gas separation at lower temperatures.

cond-mat.soft↗

arXiv2026

Modelling SARS-CoV-2 epidemics via compartmental and cellular automaton SEIRS model with temporal immunity and vaccination

We consider the SEIRS epidemiology model with such features of the COVID-19 outbreak as: abundance of unidentified infected individuals, limited time of immunity and a possibility of vaccination. The control of the pandemic dynamics is possible by restricting the transmission rate, increasing identification and isolation rate of infected individuals, and via vaccination. For the compartmental version of this model, we found stable disease-free and endemic stationary states. The basic reproductive number is analysed with respect to balancing quarantine and vaccination measures. The positions and heights of the first peak of outbreak are obtained numerically and fitted to simple in usage algebraic forms. Lattice-based realization of this model is studied by means of the asynchronous cellular automaton algorithm. This permitted to study the effect of social distancing by varying the neighbourhood size of the model. The attempt is made to match the quarantine and vaccination effects.

q-bio.PE↗

arXiv2024

Phase behaviour of primitive models of molecular ionic liquids in porous media: effects of cation shape, ion association and disordered confinement

The phase behaviour of room-temperature ionic liquids (ILs) confined in disordered porous media is studied using a theoretical approach that combines an extension of scaled particle theory, Wertheim's thermodynamic perturbation theory, and the associative mean spherical approximation. Two models, differing in the shape of the molecular cation, are considered: one with cations formed as charged flexible chains and the other with cations modelled as charged hard spherocylinders. Each model is described by a mixture of dimerized and free ions, while the porous medium is represented as a disordered matrix of hard spheres. We focus on the effects of the molecular cation shape, partial ion association, and disordered confinement on the liquid-vapour-like phase behaviour of the model ILs. In the approximation considered, we find that both the critical temperature and critical density in the model with spherocylinder cations are lower than those in the model with chain cations, and the phase coexistence region is narrower. This is the first theoretical attempt to describe an IL model with molecular ions shaped as spherocylinders, particularly in a disordered porous medium.

cond-mat.soft↗

arXiv2024

Vapour-liquid phase behaviour of primitive models of ionic liquids confined in disordered porous media

We develop a theory for the description of ionic liquids (ILs) confined in a porous medium formed by a matrix of immobile randomly placed uncharged particles. The IL is modelled as an electroneutral mixture of hardsphere anions and flexible linear chain cations, represented by tangentially bonded hard spheres with the charge located on one of the terminal beads. The theory combines a generalization of the scaled particle theory, Wertheim's thermodynamic perturbation theory, and the associative mean-spherical approximation and allows one to obtain analytical expressions for the pressure and chemical potentials of the matrix-IL system. Using the theory, we calculate the vapour-liquid phase diagrams for two versions of the IL model, i.e., when the cation is modelled as a dimer and as a chain, in a complete association limit. The effects of the matrix confinement and of the non-spherical shape of the cations on the vapour-liquid phase diagrams are studied.

cond-mat.soft↗

arXiv2023

Aspects of the microscopic structure of curcumin solutions with water-dimethylsulfoxide solvent. Molecular dynamics computer simulation study

We explore some aspects of the microscopic structure of curcumin solutions with water-dimethylsulfoxide solvent of variable composition. Molecular dynamics computer simulations at isobaric-isothermal conditions are used for this purpose. The model consists of the OPLS-UA type model for the enol conformer of curcumin (J. Mol. Liq., 223, 707, 2016), the OPLS model for the dimethylsulfoxide (DMSO) and the SPC/E water model. Radial distributions for the centers of mass of curcumin molecules are evaluated and the corresponding running coordination numbers are analyzed. The disaggregation of curcumin clusters upon increasing the DMSO content in water-DMSO solvent is elucidated. Changes of the distribution of water and DMSO species around curcumin molecules are investigated. A qualitative comparison of our findings with the results of other authors is performed. A possibility to relate predictions of the model with the experimental observations in terms of the so-called critical wateraggregation percentage is discussed.

cond-mat.soft↗

arXiv2023

Structural aspects of the clustering of curcumin molecules in water. Molecular dynamics computer simulation study

We explore clustering of curcumin molecules in water by using the OPLS-UA model for the enol conformer of curcumin (J. Mol. Liq., 223, 707, 2016) and the SPC-E water model. With this purpose, solutions of 2, 4, 8, 12, 16 and 20 curcumin molecules in 3000 water molecules are studied by using extensive molecular dynamics computer simulations. Radial distributions for the centers of mass of curcumin molecules are evaluated and the running coordination numbers are analyzed. The formation of clusters on time is elucidated. The internal structure of molecules within the cluster is described by using radial distributions of the elements of the curcumin molecule, the orientation descriptors, the order parameter and the radius of gyration. The self-diffusion coefficient of solute molecules in clusters is evaluated. The distribution of water species around clusters is described in detail. A comparison of our findings with computer simulation results of other authors is performed. A possibility to relate predictions of the model with experimental observations is discussed.

cond-mat.soft↗

arXiv2023

Two-Yukawa fluid at a hard wall: Field theory treatment

We apply a field-theoretical approach to study the structure and thermodynamics of a two-Yukawa fluid confined by a hard wall. We derive mean field equations allowing for numerical evaluation of the density profile which is compared to analytical estimations. Beyond the mean field approximation, analytical expressions for the free energy, the pressure, and the correlation function are derived. Subsequently, contributions to the density profile and the adsorption coefficient due to Gaussian fluctuations are found. Both the mean field and the fluctuation terms of the density profile are shown to satisfy the contact theorem. We further use the contact theorem to improve the Gaussian approximation for the density profile based on a better approximation for the bulk pressure. The results obtained are compared to computer simulation data.

cond-mat.soft↗

arXiv2022

Photo-switchable liquid crystalline brush as an aligning surface for liquid crystals: modelling via mesoscopic computer simulations

We consider the mesoscopic model for the liquid crystalline brush that might serve as a photoswitchable aligning surface for preorientation of low molecular weight liquid crystals in a bulk. The brush is built by grafting the polymer chains of a side-chain molecular architecture, with the side chains terminated by a chromophore unit mimicking the azobenzene unit, to a substrate. When irradiated with ultraviolet light, the chromophores photoisomerize into a non-mesogenic cis state and the whole system turns into an ordinary polymer brush with no orientational order and two states: the collapsed and straightened one, depending on the grafting density. When irradiated with visible light, the chromophores photoisomerize into a mesogenic trans state, resulting in formation of a transient network between chains because of a strong attraction between chromophores. Spontaneous self-assembly of the brush in these conditions results in an orientationally isotropic polydomain structure. The desired uniaxial planar ordering of chromophores within a brush can be achieved at certain temperature and grafting density intervals, as the result of a two-stage preparation protocol. An external stimulus orients chromophores uniaxially at the first stage. The system is equilibrated at the second stage at a given temperature and with the external stimulus switched off. The preoriented chromophores either keep or loose their orientations depending on the strength of the memory effect inherent to a transient network of chains that are formed during the first stage, similarly to the case of the liquid crystalline elastomers, where such effects are caused by the covalent crosslinks.

cond-mat.soft↗

arXiv2022

Fluid-fluid phase behaviour in the explicit solvent ionic model: hard spherocylinder solvent molecules

We study a fluid-fluid phase transition of the explicit solvent model represented as a mixture of the restricted primitive model (RPM) of ionic fluid and neutral hard spherocylinders (HSC). To this end, we combine two theoretical approaches, i.e., the scale particle theory (SPT) and the associative mean spherical approximation (AMSA). Whereas the SPT is sufficient to provide a rather good description of a reference system taking into account hard-core interactions, the AMSA is known to be efficient in treating the Coulomb interactions between the ions. Alternatively, we also use the mean spherical approximation (MSA) for comparison. In general, both approximations lead to similar qualitative results for the phase diagrams: the region of coexisting envelope becomes broader and shifts towards larger densities and higher temperatures when the pressure increases. However, the AMSA and the MSA produce different concentration dependences, i.e., contrary to the MSA, the AMSA phase diagrams show that the high-density phase mostly consists of the ions for all pressures considered. To demonstrate the effect of asphericity of solvent molecules on the fluid-fluid phase transition, we consider an "equivalent" mixture in which the HSC particles are replaced by hard spheres (HS) of the same volume. It is observed that in the case of HSC solvent (RPM-HSC model), the region of phase coexistence is wider than for the case of the solvent molecules being of spherical shape (RPM-HS model). It is also found that the critical temperature is higher in the RPM-HSC model than in the RPM-HS model, though it becomes the same at higher pressures in the MSA, while in the AMSA this difference remains essential.

cond-mat.soft↗

arXiv2021

Experimental and computer simulation studies of the micelles formed by comb-like PEG-containing polymeric surfactants as potential enzyme scaffolds

The industrial implementation of biofuel production from lignocellulosic biomass faces a number of economic obstacles. One of these is the cost of enzymes, typically used for cellulose hydrolysis. Nature provides some hints towards the efficiency of this process, exampled in natural enzyme complexes - cellulosomes, produced by some microorganisms. Therefore, many research groups target synthetic routes to mimic such cellulosomes with synthetic structures when many questions remain to be addressed: the optimal chemical structure and size of such synthetic scaffolds, their adsorption on the cellulosic biomass particles, combinations, and best practices arrangement of enzymes in the complex. In this work, polyethylene glycol (PEG) copolymers that form micelles and accommodate enzymes in the micellar structures are systematically studied using both experimental and computer simulation techniques. Preliminary results indicate that the micelles are efficient polymer - enzymes structures for cellulose hydrolysis. While the direct quantitative comparison between the real and model systems is not always straightforward, both approaches agree on the role of the molecular architecture of the copolymers on micelle formation and their structural characteristics.

cond-mat.soft↗

arXiv2019

The effect of short-range interaction and correlations on the charge and electric field distribution in a model solid electrolyte

A simple lattice model of a solid electrolyte presented as a xy-slab geometry system of mobile cations on a background of energetic landscape of the host system and a compensating field of uniformly distributed anions is studied. The system is confined in the z-direction between two oppositely charged walls, which are in parallel to xy-plane. Besides the long-range Coulomb interactions appearing in the system, the short-range attractive potential between cations is considered in our study. We propose the mean field description of this model and extend it by taking into account correlation effects at short distances. Using the free energy minimization at each of z-coordinates, the corresponding set of non-linear equations for the chemical potential is derived. The set of equations was solved numerically with respect to the charge density distribution in order to calculate the cations distribution profile and the electrostatic potential in the system along z-direction under different conditions. An asymmetry of charge distribution profile with respect to the midplane of the system is observed. The effects of the short-range interactions and pair correlations on the charge and electric field distributions are demonstrated.

cond-mat.stat-mech↗

arXiv2019

Isotropic-Nematic Transition and Demixing Behaviour in Binary Mixtures of Hard Spheres and Hard Spherocylinders Confined in a Disordered Porous Medium: Scaled Particle Theory

We develop the scaled particle theory to describe the thermodynamic properties and orientation ordering of a binary mixture of hard spheres (HS) and hard spherocylinders (HSC) confined in a disordered porous medium. Using this theory the analytical expressions of the free energy, the pressure and the chemical potentials of HS and HSC have been derived. The improvement of obtained results is considered by introducing the Carnahan-Starling-like and Parsons-Lee-like corrections. Phase diagrams for the isotropic-nematic transition are calculated from the bifurcation analysis of the integral equation for the orientation singlet distribution function and from the conditions of thermodynamic equilibrium. Both the approaches correctly predict the isotropic-nematic transition at low concentrations of hard spheres. However, the thermodynamic approach provides more accurate results and is able to describe the demixing phenomena in the isotropic and nematic phases. The effects of porous medium on the isotropic-nematic phase transition and demixing behaviour in a binary HS/HSC mixture are discussed.

cond-mat.soft↗

arXiv2017

Stochastic simulation of destruction processes in self-irradiated materials

Self-irradiation damages resulting from fission processes are common phenomena observed in nuclear fuel containing (NFC) materials. Numerous $α$-decays lead to local structure transformations in NFC materials. The damages appearing due to the impacts of heavy nuclear recoils in the subsurface layer can cause detachments of material particles. Such a behaviour is similar to sputtering processes observed during a bombardment of the material surface by a flux of energetic particles. However, in the NFC material, the impacts are initiated from the bulk. In this work we propose a two-dimensional mesoscopic model to perform a stochastic simulation of the destruction processes occurring in a subsurface region of NFC material. We describe the erosion of the material surface, the evolution of its roughness and predict the detachment of the material particles. Size distributions of the emitted particles are obtained in this study. The simulation results of the model are in a qualitative agreement with the size histogram of particles produced from the material containing lava-like fuel formed during the Chernobyl nuclear power plant disaster.

cond-mat.mtrl-sci↗

arXiv2017

Model charged cylindrical nanopore in a colloidal dispersion: charge reversal, overcharging and double overcharging

Using the hypernetted-chain/mean spherical approximation (HNC/MSA) integral equations we study the electrical double layer inside and outside a model charged cylindrical vesicle (nanopore) immersed into a primitive model macroions solution, so that the macroions are only present outside the nanopore, i.e., the vesicle wall is impermeable only to the external macroions. We calculate the ionic and local linear charge density profiles inside and outside the vesicle, and find that the correlation between the inside and outside ionic distributions causes the phenomena of overcharging (also referred to as surface charge amplification) and/or charge reversal. This is the first time overcharging is predicted in an electrical double layer of cylindrical geometry. We also report the new phenomenon of double overcharging. The present results can be of consequence for relevant systems in physical-chemistry, energy storage and biology, e.g., nanofilters, capacitors and cell membranes.

cond-mat.mes-hall↗

arXiv2017

On the properties of a single OPLS-UA model curcumin molecule in water, methanol and dimethyl sulfoxide. Molecular dynamics computer simulation results

The properties of model solutions consisting of a solute --- single curcumin molecule in water, methanol and dimethyl sulfoxide solvents have been studied using molecular dynamics (MD) computer simulations in the isobaric-isothermal ensemble. The united atom OPLS force field (OPLS-UA) model for curcumin molecule proposed by us recently [J. Mol. Liq., 2016, 223, 707] in combination with the SPC/E water, and the OPLS-UA type models for methanol and dimethyl sulfoxide have been applied. We have described changes of the internal structure of the solute molecule induced by different solvent media in very detail. The pair distribution functions between particular fragments of a solute molecule with solvent particles have been analyzed. Statistical features of the hydrogen bonding between different species were explored. Finally, we have obtained a self-diffusion coefficient of curcumin molecules in three model solvents.

cond-mat.soft↗

arXiv2016

Vapour-liquid phase diagram for an ionic fluid in a random porous medium

We study the vapour-liquid phase behaviour of an ionic fluid confined in a random porous matrix formed by uncharged hard sphere particles. The ionic fluid is modelled as an equimolar binary mixture of oppositely charged equisized hard spheres, the so-called restricted primitive model (RPM). Considering the matrix-fluid system as a partly-quenched model, we develop a theoretical approach which combines the method of collective variables with the extension of the scaled-particle theory (SPT) for a hard-sphere fluid confined in a disordered hard-sphere matrix. The approach allows us to formulate the perturbation theory using the SPT for the description of the thermodynamics of the reference system. The phase diagrams of the RPM in matrices of different porosities and for different size ratios of matrix and fluid particles are calculated in the random-phase approximation and also when the effects of higher-order correlations between ions are taken into account. Both approximations correctly reproduce the basic effects of porous media on the vapour-liquid phase diagram, i.e., with a decrease of porosity the critical point shifts toward lower fluid densities and lower temperatures and the coexistence region is getting narrower. For the fixed matrix porosity, both the critical temperature and the critical density increase with an increase of size of matrix particles and tend to the critical values of the bulk RPM.

cond-mat.soft↗

arXiv2016

Maier-Saupe nematogenic fluid with isotropic Yukawa repulsion at a hard wall: Mean field approximation

The mean field approximation is formulated within the framework of the density field theory to study the properties of a Maier-Saupe nematogenic fluid near a hard wall. The density and the order parameter profiles are obtained using the analytical expressions derived in the linearized mean field approximation. The temperature dependencies of the contact values of the density and order parameter profiles are analyzed in detail. To estimate a validity of the applied approximations, the obtained theoretical results are compared with the original computer simulation data.

cond-mat.soft↗