Filler reinforcement in cross-linked elastomer nanocomposites: insights from fully atomistic molecular dynamics simulation.

Using a fully atomistic model, we perform large-scale molecular dynamics simulations of sulfur-cured polybutadiene (PB) and nanosilica-filled PB composites. A well-integrated network without sol fraction is built dynamically by cross-linking the coarse-grained precursor chains in the presence of embedded silica nanoparticles. Initial configurations for subsequent atomistic simulations are obtained by reverse mapping of the well-equilibrated coarse-grained systems. Based on the concept of "maximally inflated knot" introduced by Grosberg et al., we show that the networks simulated in this study behave as mechanically isotropic systems. Analysis of the network topology in terms of graph theory reveals that mechanically inactive tree-like structures are the dominant structural components of the weakly cross-linked elastomer, while cycles are mainly responsible for the transmission of mechanical forces through the network. We demonstrate that quantities such as the system density, thermal expansion coefficient, glass transition temperature and initial Young's modulus can be predicted in qualitative and sometimes even in quantitative agreement with experiments. The nano-filled system demonstrates a notable increase in the glass transition temperature and an approximately two-fold increase in the nearly equilibrium value of elastic modulus relative to the unfilled elastomer even at relatively small amounts of filler particles. We also examine the structural rearrangement of the nanocomposite subjected to tensile deformation. Under high strain-rate loading, the formation of structural defects (microcavities) within the polymer bulk is observed. The nucleation and growth of cavities in the post-yielding strain hardening regime mainly take place at the elastomer/nanoparticle interfaces. As a result, the cavities are concentrated just near the embedded nanoparticles. Therefore, while the silica nanofiller increases the elastic modulus of the elastomer, it also creates a more defective structure of higher energy in comparison with the unfilled network.

A new concept for molecular engineering of artificial enzymes: a multiscale simulation.

We propose a new concept for the design of artificial enzymes from synthetic protein-like copolymers and non-natural functional monomers which in terms of their affinity for water can be divided into two categories: hydrophobic and hydrophilic. Hydrophilic monomers comprise catalytically active groups similar to those in the corresponding amino acid residues. A key ingredient of our approach is that the target globular conformation of protein-like, core-shell morphology with multiple catalytic groups appears spontaneously in the course of controlled radical polymerization in a selective solvent. As a proof of concept, we construct a fully synthetic analog of serine hydrolase, e.g.α-chymotrypsin, using the conformation-dependent sequence design approach and multiscale simulation that combines the methods of "mesoscale chemistry" and atomistic molecular dynamics (MD). A 100 ns GPU-accelerated MD simulation of the designed polymer-supported catalyst in the aqueous environment provides valuable information on the structural organization of this system that has been synthesized in our Lab.

Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport.

Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic) and minority (hydrophilic) subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25-50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT)-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping) mechanism as a significant contributor to the proton conductivity.

Peptide nanofibrils boost retroviral gene transfer and provide a rapid means for concentrating viruses.

Inefficient gene transfer and low virion concentrations are common limitations of retroviral transduction. We and others have previously shown that peptides derived from human semen form amyloid fibrils that boost retroviral gene delivery by promoting virion attachment to the target cells. However, application of these natural fibril-forming peptides is limited by moderate efficiencies, the high costs of peptide synthesis, and variability in fibril size and formation kinetics. Here, we report the development of nanofibrils that self-assemble in aqueous solution from a 12-residue peptide, termed enhancing factor C (EF-C). These artificial nanofibrils enhance retroviral gene transfer substantially more efficiently than semen-derived fibrils or other transduction enhancers. Moreover, EF-C nanofibrils allow the concentration of retroviral vectors by conventional low-speed centrifugation, and are safe and effective, as assessed in an ex vivo gene transfer study. Our results show that EF-C fibrils comprise a highly versatile, convenient and broadly applicable nanomaterial that holds the potential to significantly facilitate retroviral gene transfer in basic research and clinical applications.

Self-organizing bioinspired oligothiophene-oligopeptide hybrids.

In this minireview, we survey recent advances in the synthesis, characterization, and modeling of new oligothiophene-oligopeptide hybrids capable of forming nanostructured fibrillar aggregates in solution and on solid substrates. Compounds of this class are promising for applications because their self-assembly and stimuli-responsive properties, provided by the peptide moieties combined with the semiconducting properties of the thiophene blocks, can result in novel opportunities for the design of advanced smart materials. These bio-inspired molecular hybrids are experimentally shown to form stable fibrils as visualized by AFM and TEM. While the experimental evidence alone is not sufficient to reveal the exact molecular organization of the fibrils, theoretical approaches based on quantum chemistry calculations and large-scale atomistic molecular dynamics simulations are attempted in an effort to reveal the structure of the fibrils at the nanoscale. Based on the combined theoretical and experimental analysis, the most likely models of fibril formation and aggregation are suggested.

Self-assembling nanofibers from thiophene-peptide diblock oligomers: a combined experimental and computer simulations study.

We report herein the synthesis of a novel type of hybrid compound that consists of a poly(ethylene oxide) (PEO) functionalized ß-sheet peptide sequence covalently linked to an alkylated quaterthiophene moiety. Compounds of this class are highly promising for technological applications because their self-assembly and stimuli-responsive behavior, which is mainly caused by the peptide moieties, combined with the potential semiconducting properties of oligothiophenes provides unprecedented opportunities for the design of advanced materials at the nanoscale in such areas as, for example, organic electronics and sensor design for chemical and biomedical applications. The compound presented herein is experimentally shown to form stable fibrillar aggregates that are visualized by both transmission electron and atomic force microscopy. We developed a theoretical methodology to study the possible intermolecular arrangements and their characteristic features with the help of all-atom MD simulations, while simultaneously incorporating available experimental data into the model. Large-scale atomistic simulations of several fibrillar aggregates with different molecular arrangements were performed. The results of the simulations are compared with experimental data, which leads to the proposition of a likely model for the arrangement of the individual molecules within the observed aggregates.

Nonmonotonic incommensurability effects in lamellar-in-lamellar self-assembled multiblock copolymers.

Using the self-consistent-field theory numerical procedure we find that the period D of the lamellar-in-lamellar morphology formed in symmetric multiblock copolymer melts A(mN/2)(B(N/2)A(N/2))(n)B(mN/2) at intermediate segregations changes nonmonotonically with an increase in the relative tail length m. Therewith D reveals, as a function of the Flory chi-parameter, a drastic change in the vicinity of the internal structure formation, which can be both a drop and a rise, depending on the value of m. It is argued that the unusual behavior found is a particular case of a rather general effect of the incommensurability between the two length scales that characterize the system under consideration.

Scattering study of the conformational structure and aggregation behavior of a conjugated polymer solution.

The conformational structure and the interchain aggregation behavior of a semirigid conjugated polymer bearing a decyl side chain, poly(2,3-diphenyl-5-decyl-1,4-phenylenevinylene) (DP10-PPV), in solutions with chloroform and toluene have been investigated by means of small-angle neutron scattering (SANS), static light scattering (SLS) and dynamic light scattering (DLS). The radius of gyration, persistence length, and the second virial coefficient of the polymer in dilute solution as determined by SLS were higher in chloroform than in toluene; consequently, the polymer assumed a more extended wormlike chain conformation in the former. The difference in the strength of interaction in the two solvents gave rise to contrasting aggregation behavior of the polymer in the semidilute regime. While only a minor fraction of the polymer underwent segmental association in chloroform, a considerable fraction of it formed clusters (microgels) with several micrometers in size in toluene. These clusters were further found to consist of sheetlike nanodomains. Compared with the DP-PPV bearing a shorter hexyl side chain, DP6-PPV, the aggregates of DP10-PPV in toluene were weaker as they could be easily disrupted by moderate heating. This was attributed to a lack of strong pi-pi interaction between the DP10-PPV segments due to the greater steric hindrance imposed by the longer decyl side chains.

Nonconventional morphologies in two-length scale block copolymer systems beyond the weak segregation theory.

The order-disorder and order-order transitions (ODT and OOT) in the linear multiblock copolymers with two-length scale architecture A(fmN)(B(N2)A(N2))(n)B((1-f)mN) are studied under intermediate cooling below the ODT critical point where a nonconventional sequence of the OOTs was predicted previously [Smirnova et al., J. Chem. Phys. 124, 054907 (2006)] within the weak segregation theory (WST). To describe the ordered morphologies appearing in block copolymers (BCs) under cooling, we use the pseudospectral version of the self-consistent field theory (SCFT) with some modifications providing a good convergence speed and a high precision of the solution due to using the Ng iterations [J. Chem. Phys. 61, 2680 (1974)] and a reasonable choice of the predefined symmetries of the computation cell as well as initial guess for the iterations. The WST predicted sequence of the phase transitions is found to hold if the tails of the BCs under consideration are symmetric enough (mid R:0.5-fmid R:0.05, a large region of the face-centered cubic phase stability is found (up to our knowledge, first within the SCFT framework) inside of the body-centered cubic phase stability region. Occurrence of the two-dimensional and three-dimensional phases with the micelles formed, unlike the conventional diblock copolymers, by the longer (rather than shorter) tails, and its relationship to the BC architecture is first described in detail. The calculated spectra of the ordered phases show that nonmonotonous temperature dependence of the secondary peak scattering intensities accompanied by their vanishing and reappearance is rather a rule than exception.

Computer simulation of the assembly of gold nanoparticles on DNA fragments via electrostatic interaction.

Using Monte Carlo simulation, we study the metallization of DNA fragments via the templating of gold nanoparticles. To represent the interaction between metal entities, a nanoparticle-nanoparticle interaction potential was derived on the basis of the many-body Gupta potential. The aggregation of the nanoparticles on the template surface is due to the additive effect of electrostatic attraction between the positive charges on the Au particles and the negative charges of the phosphate groups of DNA molecule and the short-range attraction between the metallic nanoparticles. As a result, the assembly of a continuous nanowire can be templated. Depending on the nanoparticle size and charge, the metallic covering can be both continuous and discontinuous. The question of how size and charge of Au nanoparticles influence the structure of metallic coat is discussed in detail. Both monodisperse and polydisperse nanoparticles are considered. Dispersion in the nanoparticle size was found to have little effect on the calculated characteristics of the aggregate.

Molecular bottle brushes in a solution of semiflexible polyelectrolytes and block copolymers with an oppositely charged block: a molecular dynamics simulation.

Using a coarse-grained model, we performed molecular dynamics simulations of the electrostatically driven self-assembly of strongly charged polyelectrolytes and diblock copolymers composed of oppositely charged and neutral blocks. Stoichiometric micelle-like complexes formed in a dilute solution represent cylindrical brushes whose conformation is determined by the linear charge density on the polyelectrolyte and by temperature. The core-shell morphology of the cylindrical brushes is proven. The core of these anisotropic micelles consists of an insoluble complex coacervate formed by the ionic chains and a shell made up of the neutral solvophilic blocks. As the concentration of macromolecules increases, the orientational ordering of ionic micelles takes place. The complexation can induce effective steric stiffening of the polyelectrolyte chains.

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.

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.

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.

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.

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.

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.