Biomedical subjects

Pavel G Khalatur

Publications and source records attributed to Pavel G Khalatur.

6 recordsLinked to original sources

PubMed2006

The formation of planar ribbonlike aggregates from stiff polyanions in the presence of anisotropic cations.

A dilute salt-free solution of rodlike polyanions in the presence of anisotropic (chain) cations consisting of neutral tails and charged heads is studied. Using Monte Carlo simulation within the framework of the primitive model, different Coulomb coupling regimes were considered. While aggregation in the strong coupling limit is expected, we report new morphology, namely, the formation of ribbonlike nanostructures. At strong electrostatic interaction, the system is found to undergo the self-organization resulting in the formation of planar aggregates that look like a "ladder" of polyanions sandwiched between cationic chains. We investigate the stability of different morphologies and find that these aggregates are thermodynamically stable. Focus has been made on how the chemical structure of anisotropic cations affects the morphology of the aggregates.

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PubMed2006

Recognition of complex patterned substrates by heteropolymer chains consisting of multiple monomer types.

We propose a statistical mechanical model of surface pattern recognition by heteropolymers with quenched monomer sequence distribution. The chemically heterogeneous pattern consists of different adsorption sites specifically distributed on a surface. The heteropolymer sequence is complementary with respect to the pattern. The concepts of recognition probability and recognition temperature are introduced. The algorithm for calculating the recognition probability is based on efficient recurrence procedures for evaluating the single-chain partition function of a chain macromolecule consisting of multiple monomer types, which interact with multiple types of adsorption sites. The temperature dependencies of the recognition probability are discussed. We address the critical role of the commensurability between the heteropolymer sequence and the distribution of the surface adsorbing sites on the polymer adsorption. Also, we address the question of how many types of monomer units in the heteropolymer are required for unambiguous recognition of compact target patterns. It is shown that perfect pattern recognition can be achieved for the strong-adsorption regime in the case of specifically structured compact patterns with multifunctional adsorption sites and heteropolymers with multiple monomer types when the degeneracy of the ground state is suppressed. The pattern recognition ability increases with the number of different types of monomer units and complementary adsorption sites. For random heteropolymers and patterns, the free energy change associated with the recognition process decreases linearly with increasing this number. Correlated random heteropolymers are capable of recognizing related patterns on a random background.

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PubMed2006

Semiflexible amphiphilic polymers: cylindrical-shaped, collagenlike, and toroidal structures.

A coarse-grained model is used to study the conformational properties of semiflexible polymers with amphiphilic monomer units containing both hydrophilic and hydrophobic interaction sites. The hydrophobically driven conformational transitions are studied using molecular dynamics simulations for the chains of varying stiffness, as characterized by intrinsic Kuhn segment lengths that vary over a decade. It is shown that the energy of hydrophobic attraction required for the realization of the coil-to-globule transition increases with increasing chain stiffness. For rather stiff backbone, the coil-to-globule transition corresponds to a first order phase transition. We find that depending on the chain stiffness, a variety of thermodynamically stable anisometric chain morphologies are possible in a solvent selectively poor for hydrophobic sites of amphiphilic monomer units. For flexible chains, the amphiphilic polymer forms a cylindrical globule having blob structure with nearly spherical blobs. With increasing stiffness, the number of blobs composing the globule decreases and the shape of blobs transforms into elongated cylinder. Further increase in stiffness leads to compaction of macromolecules into a collagenlike structure when the chain folds itself several times and different strands wind round each other. In this state, the collagenlike structures coexist with toroidal globules, both conformations having approximately equal energies.

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PubMed2005

Adsorption of multiblock copolymers onto a chemically heterogeneous surface: a model of pattern recognition.

We present a statistical mechanical model, which is used to investigate the adsorption behavior of two-letter (AB) copolymers on chemically heterogeneous surfaces. The surfaces with regularly distributed stripes of two types (A and B) and periodic multiblock copolymers (Al)B(l))(x) are studied. It is assumed that A(B)-type segments selectively adsorb onto A(B)-type stripes. It is shown that the adsorption strongly depends on the copolymer sequence distribution and the arrangement of selectively adsorbing regions on the surface. The polymer-surface binding proceeds as a two-step process. At the first step, the copolymer having short blocks adsorbs onto the surface as an effective homopolymer, which does not feel chemical pattern. At the second step, when the polymer-surface attraction is sufficiently strong, the adsorbed chain adjusts its equilibrium conformation to reach the perfect bound state, thereby demonstrating ability for pattern recognition. The key element of this mechanism is the redistribution of strongly adsorbed copolymer diblocks A(l)B(l), which behave as surfactants, between multiple AB interfaces separating A and B stripes on the adsorbing surface. Such redistribution is accompanied by a well-pronounced decrease in the system entropy. We have found that marked pattern recognition is possible for copolymers with relatively short blocks at high polymer/surface affinities, beyond the adsorption threshold.

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PubMed2004

Template copolymerization near a patterned surface: computer simulation.

We perform a Monte Carlo simulation of irreversible template copolymerization near a chemically heterogeneous surface with a regular distribution of discrete adsorption sites that selectively adsorb from solution one of the two polymerizing monomers and the corresponding chain segments. In the polymerization model, the chain propagation process is simulated by adding individual monomers to the end of growing macroradical. We focus in this paper on the influence of polymerization rate, adsorption energy, and the distance between adsorption sites on the chain conformation and the primary sequence of the resulting two-letter (AB) copolymers and, specifically, on the coupling between polymerization and adsorption. The conditions for the realization of conformation-dependent copolymerization are formulated. For this regime, we observe the formation of a quasiregular copolymer with two types of alternating sections. One of them contains randomly distributed A and B segments. The second one consists mainly of strongly adsorbed A segments. It is found that the average length of the random sections is proportional to the distance between the nearest neighbor adsorption sites. The average length of the A-rich sections is determined by the "adsorption capacity" of adsorption site. By varying the strength of the effective monomer-substrate interaction and the distribution of adsorption sites on the substrate, the copolymers with different surface-induced primary sequences can be designed and synthesized in a controlled fashion.

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PubMed2003

Conformation-dependent evolution of copolymer sequences.

A "toy model" of molecular evolution of sequences in copolymers is proposed and implemented using a molecular-dynamics-based algorithm. The model involves coupling of conformation-dependent and sequence-dependent properties. It is shown that this model allows the realization of two main possibilities: ascending and descending branches of evolution (in terms of information content of a sequence), depending on the interaction parameters shaping the conformation of a polymer globule. The problem of adequate description of information complexity of copolymer sequences is studied. It is shown that Shannon's entropy or compressibility of a sequence gives preference to random sequences and therefore cannot be applied for this purpose. On the other hand, the Jensen-Shannon divergence measure turns out to give the description of information complexity which corresponds to our intuitive expectations. In particular, this characteristic can adequately describe two branches of evolution mentioned above, exhibiting a singularity on the boundary of these regimes.

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