arXiv subjects

Viktoria Blavatska

Publications and source records attributed to Viktoria Blavatska.

At least 19 recordsLinked to original sources

arXiv2023

The size and shape of snowflake star polymers in dilute solutions: analytical and numerical approaches

We investigate the conformational properties of a multi-branched polymer structure with a dendrimer-like topology, known as a snowflake polymer. This polymer is characterized by two parameters: $f_s$, which represents the functionality of the central star-like core, and $f$, which represents the functionality of the side branching points. To analyze the conformational properties, we have employed various approaches, including analytical methods based on direct polymer renormalization and the Wei's approach as well as numerical molecular dynamics simulations. These methods have allowed us to estimate a size and shape characteristics of the snowflake polymer as functions of $f$ and $f_s$. Our findings consistently demonstrate the effective compactification of the typical polymer conformation as the number of branching points increases. Overall, our study provides valuable insights into the conformational behavior of the snowflake polymer and highlights the impact of branching parameters on its overall compactness.

cond-mat.soft↗

arXiv2023

Molecular conformations of dumbbell-shaped polymers in good solvent

We study conformational properties of diluted dumbbell polymers which consist of two rings that are attached to both ends of a linear spacer segment by using analytical methods of field theory and bead-spring coarse-grained molecular dynamics simulations. We investigate the influence of the relative length of the spacer segment to the length of side rings on the shape and the relative size of dumbbells as compared to linear polymers of equal mass. We find that dumbbells with short spacers are much more compact than linear polymers. Oppositely, we observe that the influence of side rings on the size of dumbbells becomes negligible with increasing length of a spacer. Consequently dumbbell molecules with long spacers become comparable in size with corresponding linear chains. Our analytical theory predicts quantitative cross-over between short- and long-spacer behavior and is confirmed by numerical simulations.

cond-mat.soft↗

arXiv2023

Evolutionary adaptation is facilitated by the presence of lethal genotypes

The adaptation rate in theoretical models of biological evolution increases with the mutation rate but only to a point when mutations into lethal states cause extinction. One would expect that removing such states should be beneficial for evolution. We show here that, counter-intuitively, lethal mutations speed up adaptation on rugged fitness landscapes with many fitness maxima and minima, if strong competition for resources exist. We consider a modified stochastic version of the quasispecies model with two types of genotypes, viable and lethal, and show that increasing the rate of lethal mutations decreases the time to evolve the best-fit genotype. This can be explained by an increased rate of crossing fitness valleys, facilitated by reduced selection against less-fit variants.

q-bio.PE↗

arXiv2022

Swelling of asymmetric pom-pom polymers in dilute solutions

In this paper we continue our recent analysis [K. Haydukivska et al., J. Mol. Liq., 2021, 328, 115456] of complex molecules with two branching points at both ends of the linear backbone with $f_1$ and $f_2$ side arms starting from them, known as the pom-pom polymers. Here, we analyze the asymmetric case, $f_1 \neq f_2$, by applying both the analytical approach, based on the direct polymer renormalization, and computer simulations using both dissipative particle dynamics and Monte Carlo methods. We study the role played by the molecular asymmetry of average polymer conformations, considering the infinite dilution regime and good solvent conditions.The quantitative estimates are reported for the set of universal size and shape characteristics of such molecules and for their individual branches, all the functions of $f_1$ and $f_2$. In particular, we evaluate the size ratio of the gyration radii of symmetric and asymmetric pom-pom topologies with the same molecular weight and quantitatively reveal an increase of the effective size of a molecule caused by its asymmetry. We also introduce and analyse the asymmetry factor and estimate the shift of the center of mass caused by the presence of side stars, which can serve as another characteristic of the asymmetry of pom-pom structure.

cond-mat.soft↗

arXiv2022

Survival in two-species reaction-superdiffusion system: Renormalization group treatment and numerical simulations

We analyze the two-species reaction-diffusion system including trapping reaction $A + B \to A$ as well as coagulation/annihilation reactions $A + A \to (A,0)$ where particles of both species are performing Lévy flights with control parameter $0 < σ< 2$, known to lead to superdiffusive behaviour. The density, as well as the correlation function for target particles $B$ in such systems, are known to scale with nontrivial universal exponents at space dimension $d \leq d_{c}$. Applying the renormalization group formalism we calculate these exponents in a case of superdiffusion below the critical dimension $d_c=σ$. The numerical simulations in one-dimensional case are performed as well. The quantitative estimates for the decay exponent of the density of survived particles $B$ are in good agreement with our analytical results. In particular, it is found that the surviving probability of the target particles in a superdiffusive regime is higher than that in a system with ordinary diffusion.

cond-mat.stat-mech↗

arXiv2020

On the swelling properties of pom-pom polymers in dilute solutions. Part 1: symmetric case

We consider the simplest representative of the class of multiply branched polymer macromolecules, known as a pom-pom structure. The molecule consists of a backbone linear chain terminated by two branching points with functionalities (numbers of side chains) of $f_1$ and $f_2$, respectively. In a symmetrical case, considered in the present study, one has $f_1=f_2=f$ with the total number of chains $F=2f+1$. Whereas rheological behaviour of melts of pom-pom molecules are intensively studied so far, we turn our attention towards conformational properties of such polymers in a regime of dilute solution. The universality concept, originated in the critical phenomena and in scaling properties of polymers, is used in this study. To be able to compare the outcome of the direct polymer renormalization approach with that obtained via dissipative particle dynamics simulations, we concentrated on the universal ratios of the shape characteristics. In this way the differences in the energy and length scales are eliminated and the universal ratios depend only on space dimension, solvent quality and a type of molecular branching. Such universal ratios were evaluated both for a whole molecule and for its individual branches. For some shape properties, theory and simulations are in excellent agreement, for other we found the interval of $F$ where both agree reasonably well. Combination of theoretical and simulation approaches provide thorough quantitative description of the peculiarities of swelling effects and spatial extension of pom-pom molecules and are compared with the known results for simpler molecular topologies.

cond-mat.soft↗

arXiv2019

Universal size and shape ratios for arms in star-branched polymers: theory and mesoscopic simulations

Star polymer undergoes a transformation from a group of loosely coupled chains at low number of arms to a dense hairy colloid at their high number. This change affects solubility, aggregation and rheological behavior and is of much practical interest. We study the range of size and shape properties of the star molecule and of its individual arms upon this transformation. Theoretical calculations are based on a continuous chain model and are performed in the first order in $ε=4-d$. Computer simulations are done by the dissipative particle dynamics and in part by Monte Carlo method and the results demonstrate very good agreement with the selected set of properties known from the previous simulations. Theory and simulations provide qualitatively similar trends upon increase of the number of arms, but higher order of approximation is required in a theory to achieve a good quantitative agreement.

cond-mat.soft↗

arXiv2018

Percolation thresholds and fractal dimensions for square and cubic lattices with long-range correlated defects

We study long-range power-law correlated disorder on square and cubic lattices. In particular, we present high-precision results for the percolation thresholds and the fractal dimension of the largest clusters as function of the correlation strength. The correlations are generated using a discrete version of the Fourier filtering method. We consider two different metrics to set the length scales over which the correlations decay, showing that the percolation thresholds are highly sensitive to such system details. By contrast, we verify that the fractal dimension $d_{\rm f}$ is a universal quantity and unaffected by the choice of metric. We also show that for weak correlations, its value coincides with that for the uncorrelated system. In two dimensions we observe a clear increase of the fractal dimension with increasing correlation strength, approaching $d_{\rm f}\rightarrow 2$. The onset of this change does not seem to be determined by the extended Harris criterion.

cond-mat.stat-mech↗

arXiv2016

Critical behavior of the 2D Ising model with long-range correlated disorder

We study critical behavior of the diluted 2D Ising model in the presence of disorder correlations which decay algebraically with distance as $\sim r^{-a}$. Mapping the problem onto 2D Dirac fermions with correlated disorder we calculate the critical properties using renormalization group up to two-loop order. We show that beside the Gaussian fixed point the flow equations have a non trivial fixed point which is stable for $0.995<a<2$ and is characterized by the correlation length exponent $ν= 2/a + O((2-a)^3)$. Using bosonization, we also calculate the averaged square of the spin-spin correlation function and find the corresponding critical exponent $η_2=1/2-(2-a)/4+O((2-a)^2)$.

cond-mat.dis-nn↗

arXiv2015

Conformational properties of complex polymers: rosette versus star-like structures

Multiple loop formation in polymer macromolecules is an important feature of the chromatin organization and DNA compactification in the nuclei. We analyze the size and shape characteristics of complex polymer structures, containing in general $f_1$ loops (petals) and $f_2$ linear chains (branches). Within the frames of continuous model of Gaussian macromolecule, we apply the path integration method and obtain the estimates for gyration radius $R_g$ and asphericity $\hat{A}$ of typical conformation as functions of parameters $f_1$, $f_2$. In particular, our results qualitatively reveal the extent of anisotropy of star-like topologies as compared to the rosette structures of the same total molecular weight.

cond-mat.soft↗

arXiv2013

Conformational transitions in random heteropolymer models

We study the conformational properties of heteropolymers containing two types of monomers A and B, modeled as self-avoiding random walks on a regular lattice. Such a model can describe in particular the sequences of hydrophobic and hydrophilic residues in proteins (K.F. Lau and K.A. Dill, Macromolecules {\bf 22}, 3986 (1989)) and polyampholytes with oppositely charged groups (Y. Kantor and M. Kardar, Europhys. Lett.{\bf 28}, 169 (1994)). Treating the sequences of the two types of monomers as quenched random variables, we provide a systematic analysis of possible generalizations of this model. To this end we apply the pruned-enriched Rosenbluth chain-growth algorithm (PERM), which allows us to obtain the phase diagrams of extended and compact states coexistence as function of both the temperature and fraction of A and B monomers along the heteropolymer chain.

cond-mat.dis-nn↗

arXiv2012

Polymer adsorption on a fractal substrate: numerical study

We study the adsorption of flexible polymer macromolecules on a percolation cluster, formed by a regular two-dimensional disordered lattice at critical concentration p_c of attractive sites. The percolation cluster is characterized by a fractal dimension d_s^{p_c}=91/49. The conformational properties of polymer chains grafted to such a fractal substrate are studied by means of the pruned-enriched Rosenbluth method (PERM). We find estimates for the surface crossover exponent governing the scaling of the adsorption energy in the vicinity of the transition point, ϕ_s^{p_c}=0.425\pm0.009, and for the adsorption transition temperature, T_A^{p_c}=2.64\pm0.02. As expected, the adsorption is diminished when the fractal dimension of the substrate is smaller than that of a plain Euclidean surface. The universal size and shape characteristics of a typical spatial conformation which attains a polymer chain in the adsorbed state are analyzed as well.

cond-mat.dis-nn↗

arXiv2010

Star copolymers in porous environments: scaling and its manifestations

We consider star polymers, consisting of two different polymer species, in a solvent subject to quenched correlated structural obstacles. We assume that the disorder is correlated with a power-law decay of the pair correlation function g(x)\sim x^{-a}. Applying the field-theoretical renormalization group approach in d dimensions, we analyze different scenarios of scaling behavior working to first order of a double ε=4-d, δ=4-a expansion. We discuss the influence of the correlated disorder on the resulting scaling laws and possible manifestations such as diffusion controlled reactions in the vicinity of absorbing traps placed on polymers as well as the effective short-distance interaction between star copolymers.

cond-mat.soft↗

arXiv2010

Shape anisotropy of polymers in disordered environment

We study the influence of structural obstacles in a disordered environment on the size and shape characteristics of long flexible polymer macromolecules. We use the model of self-avoiding random walks on diluted regular lattices at the percolation threshold in space dimensions d=2, 3. Applying the Pruned-Enriched Rosenbluth Method (PERM), we numerically estimate rotationally invariant universal quantities such as the averaged asphericity A_d and prolateness S of polymer chain configurations. Our results quantitatively reveal the extent of anisotropy of macromolecules due to the presence of structural defects.

cond-mat.soft↗

arXiv2010

Theta-polymers in crowded media under the stretching force

We study the peculiarities of stretching of globular polymer macromolecules in a disordered (crowded) environment, using the model of self-attracting self-avoiding walks on site-diluted percolative lattices in space dimensions d=3. Applying the pruned-enriched Rosenbluth chain-growth method (PERM), we construct the phase diagram of collapsed-extended state coexistence when varying temperature and stretching force. The change in shape characteristics of globular polymers under stretching is analyzed as well.

cond-mat.soft↗

arXiv2010

Universal features of polymer shapes in crowded environment

We study the universal characteristics of the shape of a polymer chain in an environment with correlated structural obstacles, applying the field-theoretical renormalization group approach. Our results qualitatively indicate an increase of the asymmetry of the polymer shape in crowded environment comparing with the pure solution case.

cond-mat.soft↗

arXiv2008

Walking on fractals: diffusion and self-avoiding walks on percolation clusters

We consider random walks (RWs) and self-avoiding walks (SAWs) on disordered lattices directly at the percolation threshold. Applying numerical simulations, we study the scaling behavior of the models on the incipient percolation cluster in space dimensions d=2, 3, 4. Our analysis yields estimates of universal exponents, governing the scaling laws for configurational properties of RWs and SAWs.

cond-mat.dis-nn↗

arXiv2008

Multifractality of self-avoiding walks on percolation clusters

We consider self-avoiding walks (SAWs) on the backbone of percolation clusters in space dimensions d=2, 3, 4. Applying numerical simulations, we show that the whole multifractal spectrum of singularities emerges in exploring the peculiarities of the model. We obtain estimates for the set of critical exponents, that govern scaling laws of higher moments of the distribution of percolation cluster sites visited by SAWs, in a good correspondence with an appropriately summed field-theoretical \varepsilon=6-d-expansion (H.-K. Janssen and O. Stenull, Phys. Rev. E 75, 020801(R) (2007)).

cond-mat.dis-nn↗