Abstract: Abstract
A self-consistent mean-field computer simulation of ordering in melts of diblock copolymers consisting of flexible and rigid rodlike blocks is performed. A three-dimensional model is considered, and a corresponding algorithm for solving mean-field equations in sequential and parallelized versions is developed. The coexistence of microphase separation and orientational ordering gives rise to the appearance of new types of spatial arrangements. In particular, phases with the cubic symmetry and the morphology of hexagonally arranged chiral cylinders are found. The transition of achiral cylinders to chiral cylinders in the melt of achiral diblock copolymers consisting of rigid and flexible blocks is revealed for the first time. The origination of chirality is due to the presence of rigid blocks in the system and orientational interactions between them. With a decrease in temperature, microphase separation caused by incompatibility of chemically different blocks initially occurs in these systems. As a result, the hexagonally ordered structure in which rigid blocks are concentrated in cylindrical microdomains arises. A further decrease in temperature results in the involution of cylindrical microdomains and the formation of a helical structure. To quantify the degree of chirality, a new pseudoscalar index, depending on the linear-scale parameter for which the chirality is studied, is suggested. PubDate: 2013-09-01

Abstract: Abstract
A molecular-level understanding of cavitation in polymer networks upon imposition of mechanical stress is still lacking. Molecular Dynamics simulations of crosslinked amorphous Polyethylene (PE) were conducted in order to study cavitation as a function of the prevailing stress. We first show that the characteristic relaxation times related to tube confinement and chain connectivity can be obtained by examining the mean square displacement of middle chain monomers. Then, we present a methodology for predicting the cavitation strength and understanding its dependence on cohesive interactions and entropic elasticity. Our simulations show that experimental observations and predictions of continuum mechanics analysis, which relate the critical stress for cavitation to the Young’s modulus of the rubber, are in agreement with the observed tensile triaxial stress below which a pre-existing cavity cannot survive in a cavitated sample. PubDate: 2013-09-01

Abstract: Abstract
A coarse-grained model for studying the phase behavior of rod-coil block copolymer systems on mesoscopic length scales is proposed. The polymers are represented on a particle level (monomers, rods) whereas the interactions between the system’s constituents are formulated in terms of local densities. This conversion to density fields allows an efficient Monte Carlo sampling of the phase space. We demonstrate the applicability of the model and of the simulation approach by illustrating the formation of typical micro-phase separated configurations for exemplary model parameters. PubDate: 2013-09-01

Abstract: Abstract
A self-consistent mean-field computer simulation of ordering in blends of flexible and rigid rodlike diblock copolymers is performed. Each type of rigid block is selective toward one of the types of flexible blocks and is incompatible with the other. Flexible diblocks form a predominant component of the blend with parameters providing formation of a stable hexagonal morphology. As a result, orientational ordering is induced in the blend by a minor admixture of rigid diblocks, while the type of ordering is determined by the composition of the rigid diblocks. Three different types of orientational ordering, which having a clearly pronounced electromagnetic analogy, are established during variation in the composition of the rigid diblocks. Near a cylindrical micelle of the hexagonal morphology, the vector fields of primary directions of the orientational-order-parameter tensors for the three orientation types are highly similar to the magnetic field of the infinitely long rectilinear direct current, the cylindrical solenoid magnetic field with a constant linear current density, and the electrostatic field of a uniformly charged straight line, respectively. PubDate: 2013-09-01

Abstract: Abstract
A new approach to the Monte Carlo simulation of high-molecular weight compounds is given. It is shown within the generalized ensemble concept that the energy of deformation of covalent bonds and angles can be excluded from consideration. The consistency of the chemical structure of the molecule is retained by sorting out the trial configurations, which does not violate the detailed balance. The efficiency of the suggested approach is confirmed via calculations of the structural features of various molecules with the use of Hamiltonian exchange for a two-parameter system of Markov chains. PubDate: 2013-09-01

Abstract: Abstract
Results of entropic sampling of several polymer systems are presented: a neutral chain at a flat surface; a polyelectrolyte at a charged flat surface; a system of two neutral chains or of two polyions; and star polymers. Both lattice and continuous models for chains are used. The method enables the energy distribution to be obtained in a very wide range of values, which in turn allows the thermal and structural properties of the systems to be calculated in a wide temperature range. PubDate: 2013-09-01

Abstract: Abstract
The Wang-Landau (WL) algorithm is a Monte Carlo simulation technique providing a direct computation of the density of states of a many-body system. The temperature independent density of states function encodes all thermodynamic information about a system, and thus, its construction allows for a very efficient determination of phase behavior. Here we describe the application of the WL approach to continuum interaction-site polymer chains and compute single-chain phase diagrams for three specific models (flexible and semiflexible homopolymer chains built from square-well sphere monomers and a flexible AB-heteropolymer comprised of alternating square-well and hard-sphere monomers). We provide details on the implementation of the WL algorithm, the underlying Monte Carlo move set, and the subsequent thermodynamic and structural analysis required to characterize phase behavior. PubDate: 2013-09-01

Abstract: Abstract
The mathematical simulation of second- and fourth-generation lysine dendrimers is performed via the molecular-dynamics method. Temperature dependences of primary structural characteristics are obtained. It is shown that the sizes and atomic distributions of these dendrimers are weakly temperature-dependent. Together with the structural properties, the local mobility of CH2 groups in the dendrimers is investigated via the molecular-dynamics method and NMR spectroscopy. It is shown that the orientational mobility of internal groups of the lysine dendrimers is lower than that of terminal groups, in agreement with the data available for flexible-chain dendrimers. Changes in correlation times with temperature are well described by the Arrhenius dependence. At the same time, the orientational mobility of internal groups in the lysine dendrimers depends on the generation number. This behavior is different from that of flexible-chain dendrimers, in which the mobility of internal groups is the same for dendrimers of different generations. PubDate: 2013-09-01

Abstract: Abstract
We study translocation dynamics of a semi-flexible polymer through a nanoscopic pore in two dimensions (2D) using Langevin dynamics simulation in presence of an external force inside the pore. We observe that for a given chain length N the mean first passage time (MFPT)〈τ〉 increases for a stiffer chain. By repeating the calculation for various chain lengths N and bending rigidity parameter κ
b
we calculate the translocation exponent α (〈τ〉 ∼ N
α). For chain lengths N and bending rigidity κ
b
considered in this paper we find that the translocation exponent satisfies the inequality α < 1 + ν, where is the equilibrium Flory exponent for a given chain stiffness, as previously observed in various simulation studies for fully flexible chains. We observe that the peak position of the residence time W(s) as a function of the monomer index s shifts at a lower s-value with increasing chain stiffness κ
b
. We also monitor segmental gyration 〈R
g
(s)〉 both at the cis and trans side during the translocation process and find that for κ
b
≠ 0 the late time cis conformations are nearly identical to the early time trans conformations, and this overlap continues to increase for stiffer chains. Finally, we try to rationalize dependence of various quantities on chain stiffness κ
b
using Sakaue’s tension propagation (TP) theory [Phys. Rev. E 76, 021803 (2007)] and Brownian Dynamics Tension Propagation (BDTP) theory due to Ikonen et al. [Phys. Rev. E 85 051803 (2012); J. Chem. Phys. 137 085101 (2012)] originally developed for a fully flexible chain to a semi-flexible chain. PubDate: 2013-09-01

Abstract: Abstract
Rapid development of computer power during the last decade has made molecular simulations of lipid bilayers feasible for many research groups, which, together with the growing general interest in investigations of these very important biological systems has lead to tremendous increase of the number of research on the computational modeling of lipid bilayers. In this review, we give account of the recent progress in computer simulations of lipid bilayers covering mainly the period of the last 7 years, and covering only several selected subjects: methodological (development of the force fields for lipid bilayer simulations, use of coarse-grained models) and scientific (studies of the role of lipid unsaturation, and the effect of cholesterol and other inclusions on properties of the bilayer). PubDate: 2013-09-01

Abstract: Abstract
Dendrimers are macromolecules with a regular-treelike, branched architecture of their skeleton. In terms of the branching number and the number of terminal groups they represent an extreme case among branched polymers. Dendrimers can occur in neutral and various charged states. Due to their highly branched architecture excluded volume effects are of great importance and conformational properties and monomer distribution profiles of dendrimers differ considerably from those of linear polymers. We give an overview of the state-of-the-art knowledge of physical properties of dendrimers as seen from coarse-grained computer simulations. Our main focus is on isolated dendrimers with flexible spacers both in the neutral and in the charged state, as well as complexation of dendrimers with oppositely charged linear polyelectrolytes. We briefly address problems of adsorption and concentration effects in dendrimer solutions and outline recent progress and open questions in this field. PubDate: 2013-09-01

Abstract: Abstract
We present results for a recently introduced soft-particle type model for diblock copolymers. Our focus will be the interaction of this model with confining walls and the possibility to direct the microphase morphologies by tailoring the interactions with these walls. We begin by presenting its bulk phase diagram and our method for determination of the different phases. We interpret the phase behavior in comparison to experimental data as well as other model results. By a systematic coarse-graining of chemically realistic simulations, one can obtain the effective potential acting between the walls and the repeat units of our soft quadrumer model. We employ this coarse-grained potential then for simulations of the confined case for several strengths of attraction to the walls and determine when extending the film thickness leads to nucleation of a new lamella in the center of the film and when it leads to reorientation transitions of the lamellar microphase. PubDate: 2013-09-01

Abstract: Abstract
The persistence length of macromolecules is one of their basic characteristics, describing their intrinsic local stiffness. However, it is difficult to extract this length from physical properties of the polymers, different recipes may give answers that disagree with each other. Monte Carlo simulations are used to elucidate this problem, giving a comparative discussion of two lattice models, the self-avoiding walk model extended by a bond bending energy, and bottle-brush polymers described by the bond fluctuation model. The conditions are discussed under which a description of such macromolecules by Kratky-Porod worm-like chains holds, and the question to what extent the persistence length depends on external conditions (such as solvent quality) is considered. The scattering function of semiflexible polymers is discussed in detail, a comparison to various analytic treatments is given, and an outlook to experimental work is presented. PubDate: 2013-09-01

Abstract: Abstract
The density crossover scaling of thermodynamic and conformational properties of solutions and melts of self-avoiding and highly flexible polymer chains without chain intersections confined to strictly two dimensions (d = 2) is investigated by means of molecular dynamics and Monte Carlo simulations of a standard coarse grained bead-spring model. We focus on properties related to the contact exponent set by the intrachain subchain size distribution. With R ∼ N
ν being the size of chains of length N and ρ the monomer density, the interaction energy e
int between monomers from different chains and the corresponding number n
int of interchain contacts per monomer are found to scale as
with ν = 3/4 and θ2 = 19/12 for dilute solutions and ν = 1/d and θ2 = 3/4 for N≫ g(ρ) ≈ 1/ρ2. Irrespective of ρ, long chains thus become compact packings of blobs of contour length
with d
p = d − θ2 = 5/4 being the fractal line dimension. Due to the generalized Porod scattering of the compact chains, the Kratky representation of the intramolecular form factor F(q) reveals a non-monotonous behavior approaching with increasing chain length and density a power-law slope
$F(q)q^d /\rho \approx 1/(qR)^{\theta _2 } $
in the intermediate regime of the wavevector q. The specific intermolecular contact probability is argued to imply an enhanced compatibility for polymer blends confined to ultrathin films. We comment briefly on finite persistence length effects. PubDate: 2013-09-01

Abstract: Abstract
A review of studies on the computer simulation of the phase behavior of various stiff-chain polymer systems is presented. Methods for calculating phase diagrams of a polymer solution in a computer experiment are discussed, including the methods of extended ensembles, entropic simulation, and the Wang-Landau algorithm to obtain the density-of-states function. The authors’ original results on studying the intramolecular orientational and spatial ordering of monomer units in a single stiff-chain macromolecule in the bulk and near a planar adsorbing surface by means of the Wang-Landau algorithm and using the bond-fluctuation lattice model are presented. Corresponding state diagrams are presented for these two cases. For systems of multiple chains, the phenomenon of nematic liquid-crystalline ordering in semi-dilute solutions in the bulk and in a planar layer is considered, and the phase diagrams for these cases are presented. A survey of the published data on some other promising directions of investigation of stiff-chain polymer systems is presented. PubDate: 2013-09-01

Abstract: Abstract
Compaction of DNA by nonbinding macromolecules such as uncharged flexible polymer chains and negatively charged globular proteins is thought to have various applications in biophysics, for example in the formation of a nucleoid structure in bacteria. A simple experimental model that has been very well studied is the classic DNA ψ-condensation induced by polymers and salt. In recent years, compaction of DNA by nonbinding macromolecules has been reconsidered under conditions that are closer to the biophysical applications, in various respect. This work is reviewed here. Topics that are considered are: DNA compaction by nonbinding globular proteins, the influence of DNA binding proteins and DNA topology on ψ-condensation, and finally, the impact of confinement on DNA ψ-condensation. PubDate: 2012-09-01

Abstract: Abstract
During the past decade biomacromolecules attracted tremendous attention as versatile materials for self-assembly, nanoconstruction, and templating. An increasing number of reports highlights creative applications of DNA, proteins, and their assemblies for construction of materials, which synthesis by traditional top-down techniques is not possible. This review summarizes various aspects of the application of biomacromolecules and their self-organized structures for building-up inorganic nanomaterials of different complicity by metallization or mineralization of natural templates. The central focus of the review is given to DNA-templated and DNA-directed synthesis of nanostructures, as the progress in the utilization of DNA for nanoconstruction is most considerable. PubDate: 2012-09-01

Abstract: Abstract
A recent experiment has confirmed the theoretical prediction of the fractal properties of DNA packaged in the cell nucleus of eukaryotes, particularly in interphase chromosomes. In this study, both the main theoretical ideas and the experimental results are presented in a compact form. Other properties of chromosomes, that is, the so-called territories, which allow for a natural explanation through the concepts of polymer physics, are discussed. At the end, some open questions are formulated. PubDate: 2012-09-01

Abstract: Abstract
The theory of DNA compaction in solutions of highly charged proteins carrying charge of the same sign as DNA is developed. It is shown that the introduction of a negatively charged protein may induce the collapse of DNA that occurs as a first-order phase transition. The concentration of protein in the vicinity of DNA practically coincides with the concentration of protein in solution on the whole, and the introduction of protein into a solution is equivalent to the effective worsening of solvent quality. The higher the absolute value of the protein charge, the more pronounced this worsening. The higher the charge of the protein, the smaller its content that causes the compaction of DNA. The properties of the transition depend on the effective charge of DNA and on the concentration of a low-molecular-mass salt. An increase in the concentration of the salt may weaken the action of protein as a compaction agent and cause the reverse transition of a DNA macromolecule to the coiled state. PubDate: 2012-09-01