arXiv subjects

Yu. A. Kuznetsov

Publications and source records attributed to Yu. A. Kuznetsov.

29 records · Page 2Linked to original sources

arXiv2001

A Study of Sequence Distribution of a Painted Globule as a Model for Proteins with Good Folding Properties

In this paper we present a method to study the folding structure of a simple model consisting of two kinds of monomers, hydrophobic and hydrophilic. This method has three main steps: an efficient simulation method to bring an open sequence of homopolymer to a folded state, the application of a painting method called (regular hull) to the folded globule and the refolding process of the obtained copolymer sequence. This study allows us to suggest a theoretical function of disorder distribution for copolymer sequences that give rise to a compacted and well micro-phase separated globule.

cond-mat.soft↗

arXiv2001

Equilibrium and kinetics at the coil-to-globule transition of star and comb heteropolymers in infinitely dilute solutions

By means of continuous space Monte Carlo simulation we study conformational structures formed by star and comb heteropolymers during kinetics of folding from the coil to the globule, as well as the corresponding equilibrium states on going from the good to the poor solution. Particular examples of combs with hydrophobic backbone and hydrophilic side-groups (and vice versa), as well as stars with flexible and semi-stiff arms are studied. It is interesting to note that star-like conformations naturally appear for a comb polymer with a strongly hydrophobic backbone. We emphasise the crucial difference in the spatial distribution of hydrophobic and hydrophilic monomers within the globular states for the above mentioned two types of combs. In case of stars, the non-equilibrium states during kinetics of the coil-to-globule transition correspond to formation of localised pearls within flexible arms, whereas semi-stiff arms prefer to join with each other remaining essentially extended. These studies present natural extension of our previous works on the equilibrium and kinetic properties of linear and ring heteropolymers based on the Gaussian self-consistent method and lattice Monte Carlo technique. However, in studying polymers with more nontrivial topology continuous space simulation has some essential advantages.

cond-mat.soft↗

arXiv2001

Micellisation vs aggregation in dilute solutions of amphiphilic heteropolymers

In recent experiments involving PNIPAM copolymers it has been observed that stable spherical nanoparticles are being formed by association of several chains in poor aqueous solution instead of aggregation. This type of mesoscopic structures called mesoglobules has an extremely monodispersed size distribution. Previously we have studied theoretically formation of clusters consisting of several chains in dilute solutions of amphiphilic heteropolymers. We have seen that the mesoglobules often possess an essentially micellar structure. In the current work we argue that formation of mesoglobules is strongly sequence and concentration dependent. In particular, by means of lattice Monte Carlo simulation we consider structures formed by a number of tri-block sequences and their certain mutations. For sequences consisting of two hydrophilic ends with a hydrophobic middle the size distribution of the resulting particles is rather narrow, i.e. mesoglobules are being formed. However, in the case of sequences with two hydrophobic ends and a hydrophilic middle a new type of structures seems to be prevalent. These consist of small mesoglobules interconnected by hydrophilic bridges. Clearly, on increasing the concentration these networked structures would play an important role resulting in a rapid onset of a gel-like behaviour.

cond-mat.soft↗

arXiv2000

Conformations of amphiphilic diblock star copolymers

We study conformations assumed by single diblock star copolymers in a poor solvent by means of the Gaussian variational theory and Monte Carlo simulation in continuous space. Cases of stars with internal and external hydrophobic blocks are analysed. While in the former case the collapsed state has an obvious micellar shape, the latter case exhibits two nontrivial conformational structures. Apart from the equilibrium state of a globular hydrophobic core with hydrophilic daisy loops, one also finds here a metastable state of outstretched hydrophilic blocks with hydrophobic subglobules at their ends. Such a state appears to be rather long-lived during the kinetics of collapse of a swollen star. The plots of monomer densities and other observables computed by both techniques are found to be in good agreement with each other.

cond-mat.soft↗

arXiv2000

Aggregation number distributions and mesoglobules in dilute solutions of diblock and triblock copolymers

We investigate the aggregation number and size distributions for inter-molecular clusters of amphiphilic diblock and triblock copolymers in poor solvent at very low concentrations. Diblocks and triblocks with hydrophilic ends are shown to possess narrow distributions corresponding to formation of monodispersed mesoglobules. Diblocks with hydrophobic ends are found to produce inter-cluster multimers due to bridging by the hydrophilic middle blocks, resulting in polydisperse distributions. Implications of these observations for preparation of monodispersed nanoparticles and, potentially, understanding of the quaternary structure of proteins are discussed.

cond-mat.soft↗

arXiv2000

Influence of reptations on conformations of the homopolymer in Monte Carlo simulation

We study the role of topological restrictions for the conformational structure of a nonphantom homopolymer chain in a lattice Monte Carlo model. In the athermal regime we find that the standard Metropolis algorithm violates the detailed balance condition if both local monomer and global reptational moves are included. However, if about 1 reptation is performed per N local moves the balance is recovered and we obtain the Flory exponent value close to nu=0.588, where N is the degree of polymerisation. We also find that the structure of the collapsed globule is different at equilibrium from that after the late stage of folding kinetics. Namely, due to reptations the end, and even more so, the penultimate monomer groups tend to be buried inside the globule core with other monomers thus being more exposed to the surface.

cond-mat.soft↗

arXiv2000

Analysis of stability of macromolecular clusters in dilute heteropolymer solutions

We study the formation of clusters consisting of several chains in dilute solutions of amphiphilic heteropolymers. By means of the Gaussian variational theory we show that in a region of the phase diagram within the conventional two-phase coexistence region mesoglobules of equal size possess the lowest free energy. Monte Carlo simulation confirms that the mesoglobules are stabilised due to micro-phase separation, which introduces a preferred length scale. The very existence of such mesoscopic structures is related to a delicate balance of the energetic and entropic terms under the connectivity constraints. The issue of size monodispersity and fluctuations for mesoglobules is investigated.

cond-mat.soft↗

arXiv1999

On the conformational structure of a stiff homopolymer

In this paper we complete the study of the phase diagram and conformational states of a stiff homopolymer. It is known that folding of a sufficiently stiff chain results in formation of a torus. We find that the phase diagram obtained from the Gaussian variational treatment actually contains not one, but several distinct toroidal states distinguished by the winding number. Such states are separated by first order transition curves terminating in critical points at low values of the stiffness. These findings are further supported by off-lattice Monte Carlo simulation. Moreover, the simulation shows that the kinetics of folding of a stiff chain passes through various metastable states corresponding to hairpin conformations with abrupt U-turns.

cond-mat.soft↗

arXiv1998

Hydration of a B-DNA Fragment in the Method of Atom-atom Correlation Functions with the Reference Interaction Site Model Approximation

We propose an efficient numerical algorithm for solving integral equations of the theory of liquids in the Reference Interaction Site Model (RISM) approximation for infinitely dilute solution of macromolecules with a large number of atoms. The algorithm is based on applying the nonstationary iterative methods for solving systems of linear algebraic equations. We calculate the solvent-solute atom-atom correlation functions for a fragment of the B-DNA duplex d(GGGGG).d(CCCCC) in infinitely dilute aqueous solution. The obtained results are compared with available experimental data and results from computer simulations.

cond-mat.soft↗

arXiv1998

Conformational transitions of heteropolymers in dilute solutions

In this paper we extend the Gaussian self-consistent method to permit study of the equilibrium and kinetics of conformational transitions for heteropolymers with any given primary sequence. The kinetic equations earlier derived by us are transformed to a form containing only the mean squared distances between pairs of monomers. These equations are further expressed in terms of instantaneous gradients of the variational free energy. The method allowed us to study exhaustively the stability and conformational structure of some periodic and random aperiodic sequences. A typical phase diagram of a fairly long amphiphilic heteropolymer chain is found to contain phases of the extended coil, the homogeneous globule, the micro-phase separated globule, and a large number of frustrated states, which result in conformational phases of the random coil and the frozen globule. We have also found that for a certain class of sequences the frustrated phases are suppressed. The kinetics of folding from the extended coil to the globule proceeds through non-equilibrium states possessing locally compacted, but partially misfolded and frustrated, structure. This results in a rather complicated multistep kinetic process typical of glassy systems.

cond-mat.soft↗

arXiv1997

Random copolymer: Gaussian variational approach

We study the phase transitions of a random copolymer chain with quenched disorder. We apply a replica variational approach based on a Gaussian trial Hamiltonian in terms of the correlation functions of monomer Fourier coordinates. This allows us to study collapse, phase separation and freezing transitions within the same mean field theory. The effective free energy of the system is derived analytically and analysed numerically. Such quantities as the radius of gyration or the average value of the overlap between different replicas are treated as observables and evaluated by introducing appropriate external fields to the Hamiltonian. We obtain the phase diagram and show that this system exhibits a scale dependent freezing transition. The correlations between replicas appear at different length scales as the temperature decreases. This indicates the existence of the topological frustration.

cond-mat.dis-nn↗