Panagiotis E. Theodorakis

Computer simulation of bottle-brush polymers with flexible backbone: Good solvent versus theta solvent conditions

By molecular dynamics simulation of a coarse-grained bead-spring-type model for a cylindrical molecular brush with a backbone chain of N(b) effective monomers to which with grafting density σ side chains with N effective monomers are tethered, several characteristic length scales are studied for variable solvent quality. Side chain lengths are in the range 5 ≤ N ≤ 40, backbone chain lengths are in the range 50 ≤ N(b) ≤ 200, and we perform a comparison to results for the bond fluctuation model on the simple cubic lattice (for which much longer chains are accessible, N(b) ≤ 1027, and which corresponds to an athermal, very good, solvent). We obtain linear dimensions of the side chains and the backbone chain and discuss their N-dependence in terms of power laws and the associated effective exponents. We show that even at the theta point the side chains are considerably stretched, their linear dimension depending on the solvent quality only weakly. Effective persistence lengths are extracted both from the orientational correlations and from the backbone end-to-end distance; it is shown that different measures of the persistence length (which would all agree for Gaussian chains) are not mutually consistent with each other and depend distinctly both on N(b) and the solvent quality. A brief discussion of pertinent experiments is given.

Microphase separation in bottlebrush polymers under poor-solvent conditions

Molecular-dynamics simulations are used to study the structure of bottlebrush polymers with rigid backbones, for various grafting densities, side chain lengths, and varying solvent quality. While we confirm different states of the bottlebrush proposed by Sheiko et al. (Eur. Phys. J. E, 13 (2004) 125) we find that the transition between stretched and collapsed brushes occurs in a rather gradual manner. The pearl-necklace structure occurring at intermediate grafting densities and rather low temperatures has a pronounced medium-range order along the backbone.

Superspreading: mechanisms and molecular design.

The intriguing ability of certain surfactant molecules to drive the superspreading of liquids to complete wetting on hydrophobic substrates is central to numerous applications that range from coating flow technology to enhanced oil recovery. Despite significant experimental efforts, the precise mechanisms underlying superspreading remain unknown to date. Here, we isolate these mechanisms by analyzing coarse-grained molecular dynamics simulations of surfactant molecules of varying molecular architecture and substrate affinity. We observe that for superspreading to occur, two key conditions must be simultaneously satisfied: the adsorption of surfactants from the liquid-vapor surface onto the three-phase contact line augmented by local bilayer formation. Crucially, this must be coordinated with the rapid replenishment of liquid-vapor and solid-liquid interfaces with surfactants from the interior of the droplet. This article also highlights and explores the differences between superspreading and conventional surfactants, paving the way for the design of molecular architectures tailored specifically for applications that rely on the control of wetting.

Mesophase formation in two-component cylindrical bottlebrush polymers

When two types of side chains (A,B) are densely grafted to a (stiff) backbone and the resulting bottlebrush polymer is in a solution under poor solvent conditions, an incompatibility between A and B leads to microphase separation in the resulting cylindrical brush. The possible types of ordering are reminiscent of the ordering of block copolymers in cylindrical confinement. Starting from this analogy, Leiblers theory of microphase separation in block copolymer melts is generalized to derive a description of the system in the weak segregation limit. Also molecular dynamics simulation results of a corresponding coarse-grained bead-spring model are presented. Using side chain lengths up to N = 50 effective monomers, the ratio of the Lennard-Jones energy parameter between unlike monomers (ε(AB)) and monomers of the same kind (ε(AA) = ε(BB)) is varied. Various correlation functions are analyzed to study the conditions when (local) Janus-cylinder-type ordering and when (local) microphase separation in the direction along the cylinder axis occurs. Both the analytical theory and the simulations give evidence for short-range order due to a tendency toward microphase separation in the axial direction, with a wavelength proportional to the side chain gyration radius, irrespective of temperature and grafting density, for a wide range of these parameters.

A coarse-grained model for DNA-functionalized spherical colloids, revisited: Effective pair potential from parallel replica simulations

We discuss a coarse-grained model recently proposed by Starr and Sciortino [J. Phys.: Condens. Matter 18, L347 (2006)] for spherical particles functionalized with short single DNA strands. The model incorporates two key aspects of DNA hybridization, i.e., the specificity of binding between DNA bases and the strong directionality of hydrogen bonds. Here, we calculate the effective potential between two DNA-functionalized particles of equal size using a parallel replica protocol. We find that the transition from bonded to unbonded configurations takes place at considerably lower temperatures compared to those that were originally predicted using standard simulations in the canonical ensemble. We put particular focus on DNA-decorations of tetrahedral and octahedral symmetry, as they are promising candidates for the self-assembly into a single-component diamond structure. Increasing colloid size hinders hybridization of the DNA strands, in agreement with experimental findings.

Self-assembly of DNA-functionalized colloids

Colloidal particles grafted with single-stranded DNA (ssDNA) chains can self-assemble into a number of different crystalline structures, where hybridization of the ssDNA chains creates links between colloids stabilizing their structure. Depending on the geometry and the size of the particles, the grafting density of the ssDNA chains, and the length and choice of DNA sequences, a number of different crystalline structures can be fabricated. However, understanding how these factors contribute synergistically to the self-assembly process of DNA-functionalized nano- or micro-sized particles remains an intensive field of research. Moreover, the fabrication of long-range structures due to kinetic bottlenecks in the self-assembly are additional challenges. Here, we discuss the most recent advances from theory and experiment with particular focus put on recent simulation studies.

Physical insights into the blood–brain barrier translocation mechanisms

The number of individuals suffering from diseases of the central nervous system (CNS) is growing with an aging population. While candidate drugs for many of these diseases are available, most of these pharmaceutical agents cannot reach the brain rendering most of the drug therapies that target the CNS inefficient. The reason is the blood-brain barrier (BBB), a complex and dynamic interface that controls the influx and efflux of substances through a number of different translocation mechanisms. Here, we present these mechanisms providing, also, the necessary background related to the morphology and various characteristics of the BBB. Moreover, we discuss various numerical and simulation approaches used to study the BBB, and possible future directions based on multi-scale methods. We anticipate that this review will motivate multi-disciplinary research on the BBB aiming at the design of effective drug therapies.

Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins

The application of coarse-grained (CG) models in biology is essential to access large length and time scales required for the description of many biological processes. The ELNEDIN protein model is based on the well-known MARTINI CG force-field and incorporates additionally harmonic bonds of a certain spring constant within a defined cutoff distance between pairs of residues, in order to preserve the native structure of the protein. In this case, the use of unbreakable harmonic bonds hinders the study of unfolding and folding processes. To overcome this barrier we have replaced the harmonic bonds with Lennard-Jones interactions based on the contact map of the native protein structure as is done in Go̅-like models. This model exhibits very good agreement with all-atom simulations and the ELNEDIN. Moreover, it can capture the structural motion linked to particular catalytic activity in the Man5B protein, in agreement with all-atom simulations. In addition, our model is based on the van der Waals radii, instead of a cutoff distance, which results in a smaller contact map. In conclusion, we anticipate that our model will provide further possibilities for studying biological systems based on the MARTINI CG force-field by using advanced-sampling methods, such as parallel tempering and metadynamics.

Modelling the superspreading of surfactant-laden droplets with computer simulation

The surfactant-driven superspreading of droplets on hydrophobic substrates is considered. A key element of the superspreading mechanism is the adsorption of surfactant molecules from the liquid-vapour interface onto the substrate through the contact line, which must be coordinated with the replenishment of interfaces with surfactant from the interior of the droplet. We use molecular dynamics simulations with coarse-grained force fields to provide a detailed structural description of the droplet shape and surfactant dynamics during the superspreading process. We also provide a simple method for accurate estimation of the contact angle subtended by the droplets at the contact line.

Phase behavior of symmetric linear multiblock copolymers

Molecular-dynamics simulations are used to study the phase behavior of a single linear multiblock copolymer with blocks of A- and B-type monomers under poor solvent conditions, varying the block length N, number of blocks n, and the solvent quality (by variation of the temperature T). The fraction f of A-type monomers is kept constant and equal to 0.5, and always the lengths of A and B blocks are equal (NA=NB=N), as well as the number of blocks (nA=nB). We identify the three following regimes where: i) full microphase separation between blocks of different type occurs (all blocks of A-type monomers form a single cluster, while all blocks of B-type monomers form another); ii) full microphase separation is observed with a certain probability; and iii) full microphase separation cannot take place. For a very high number of blocks n and very high N (not accessible to our simulations) further investigation is needed.