Pressure Anisotropy in Polymer Brushes and Its Effects on Wetting.

Polymer brushes, coatings consisting of densely grafted macromolecules, experience an intrinsic lateral compressive pressure, originating from chain elasticity and excluded volume interactions. This lateral pressure complicates a proper definition of the interface and, thereby, the determination and interpretation of the interfacial tension and its relation to the wetting behavior of brushes. Here, we study the link among grafting-induced compressive lateral pressure in polymer brushes, interfacial tension, and brush wettability using coarse-grained molecular dynamics simulations.

Charging and discharging a supercapacitor in molecular simulations.

As the world moves more toward unpredictable renewable energy sources, better energy storage devices are required. Supercapacitors are a promising technology to meet the demand for short-term, high-power energy storage. Clearly, understanding their charging and discharging behaviors is essential to improving the technology.

A simple efficient algorithm for molecular simulations of constant potential electrodes.

Increasingly, society requires high power, high energy storage devices for applications ranging from electric vehicles to buffers on the electric grid. Supercapacitors are a promising contribution to meeting these demands, though there still remain unsolved practical problems. Molecular dynamics simulations can shed light on the relevant molecular level processes in electric double layer capacitors, but these simulations are computationally very demanding.

Stress-dependent macromolecular crowding in the mitochondrial matrix.

Macromolecules of various sizes induce crowding of the cellular environment. This crowding impacts on biochemical reactions by increasing solvent viscosity, decreasing the water-accessible volume and altering protein shape, function, and interactions. Although mitochondria represent highly protein-rich organelles, most of these proteins are somehow immobilized.

The permeability of pillar arrays in microfluidic devices: an application of Brinkman's theory towards wall friction.

Darcy's law describes the flow of Newtonian fluids through bulk porous media as the product of the applied pressure difference, the fluid's viscosity and the medium's permeability. Brinkman extended Darcy's law with a viscous stress term, thereby enabling boundary conditions to the flow field at the surface of the medium. The validity of Brinkman's term, and the value of its effective viscosity, have been heavily debated since their introduction nearly 75 years ago.

Cancer immune therapy using engineered ‛tail-flipping' nanoliposomes targeting alternatively activated macrophages.

Alternatively-activated, M2-like tumor-associated macrophages (TAM) strongly contribute to tumor growth, invasiveness and metastasis. Technologies to disable the pro-tumorigenic function of these TAMs are of high interest to immunotherapy research. Here we show that by designing engineered nanoliposomes bio-mimicking peroxidated phospholipids that are recognised and internalised by scavenger receptors, TAMs can be targeted.

Capillary Imbibition of Binary Fluid Mixtures in Nanochannels.

Many-body Dissipative Particle Dynamics (MDPD) simulations of binary fluid mixtures imbibing cylindrical nanochannels reveal a strong segregation of fluids differing in their affinities to the pore walls. Surprisingly, the imbibition front furthest into the channel is highly enriched in the fluid with the lower affinity for the walls, i.e.

Systematic approach for wettability prediction using molecular dynamics simulations.

We present a fast and efficient approach to predict the wettability and spreading of liquids on polymeric substrates. First, a molecular dynamics parameterization is proposed for the calculation of the solubility parameter for 74 compounds including surfactants typically used in inkjet printing. Then, we introduce a molecular geometrical factor to relate the solubility parameter to the surface tension, obtaining estimates in remarkable agreement with experiments.

Fluctuating Brownian stresslets and the intrinsic viscosity of colloidal suspensions.

The interplay between Brownian colloidal particles and their suspending fluid is well understood since Einstein's seminal work of 1905: the fluid consists of atoms whose thermal motion gives rise to the Brownian motion of the colloids, while the colloids increase the viscosity of the suspension under shear. An alternative route to the viscosity, by exploring the thermal stress fluctuations in a quiescent fluid in the Green-Kubo formalism, however, reveals a marked inconsistency with the viscosity under shear. We show that an additional stress term, accounting for Brownian fluctuating stresslets and coupled to the Brownian forces by a generalized fluctuation-dissipation theorem, is required for the description of the stress and viscosity of a colloidal suspension.

Intrinsic viscosities of non-spherical colloids by Brownian dynamics simulations.

A numerical study is presented on the intrinsic viscosities of sheared dilute suspensions of nonspherical Brownian colloidal particles. The simulations confirm theoretical predictions on the intrinsic viscosities of highly oblate and highly prolate spheroids in the limits of weak and strong Brownian noise (i.e.

Coarse-Grained Simulations of Three-Armed Star Polymer Melts and Comparison with Linear Chains.

Melts of three-armed star polymers have been simulated using a coarse-grained model parameterized by atomistic simulations of polyethylene. The bonds between the highly coarse-grained, and hence soft, polymer beads are explicitly prevented from crossing by the TWENTANGLEMENT algorithm. The three melts of symmetric stars, differing in the lengths of the arms, are compared against five melts of linear polymers with comparable dimensions to study the impact of branched architecture on self-diffusion and bulk rheological properties.

Efficient Brownian Dynamics of rigid colloids in linear flow fields based on the grand mobility matrix.

We present an efficient general method to simulate in the Stokesian limit the coupled translational and rotational dynamics of arbitrarily shaped colloids subject to external potential forces and torques, linear flow fields, and Brownian motion. The colloid's surface is represented by a collection of spherical primary particles. The hydrodynamic interactions between these particles, here approximated at the Rotne-Prager-Yamakawa level, are evaluated only once to generate the body's (11 × 11) grand mobility matrix.

Intrinsic Conformational Preferences and Interactions in α-Synuclein Fibrils: Insights from Molecular Dynamics Simulations.

Amyloid formation by the intrinsically disordered α-synuclein protein is the hallmark of Parkinson's disease. We present atomistic Molecular Dynamics simulations of the core of α-synuclein using enhanced sampling techniques to describe the conformational and binding free energy landscapes of fragments implicated in fibril stabilization. The theoretical framework is derived to combine the free energy profiles of the fragments into the reaction free energy of a protein binding to a fibril.

The attachment of α-synuclein to a fiber: A coarse-grain approach.

We present simulations of the amyloidogenic core of α-synuclein, the protein causing Parkinson's disease, as a short chain of coarse-grain patchy particles. Each particle represents a sequence of about a dozen amino acids. The fluctuating secondary structure of this intrinsically disordered protein is modelled by dynamic variations of the shape and interaction characteristics of the patchy particles, ranging from spherical with weak isotropic attractions for the disordered state to spherocylindrical with strong directional interactions for a β-sheet.

Clathrin Assembly Regulated by Adaptor Proteins in Coarse-Grained Models.

The assembly of clathrin triskelia into polyhedral cages during endocytosis is regulated by adaptor proteins (APs). We explore how APs achieve this by developing coarse-grained models for clathrin and AP2, employing a Monte Carlo click interaction, to simulate their collective aggregation behavior. The phase diagrams indicate that a crucial role is played by the mechanical properties of the disordered linker segment of AP.

A coarse grained protein model with internal degrees of freedom. Application to α-synuclein aggregation.

Particles in simulations are traditionally endowed with fixed interactions. While this is appropriate for particles representing atoms or molecules, objects with significant internal dynamics--like sequences of amino acids or even an entire protein--are poorly modelled by invariable particles. We develop a highly coarse grained polymorph patchy particle with the ultimate aim of simulating proteins as chains of particles at the secondary structure level.

An elementary singularity-free Rotational Brownian Dynamics algorithm for anisotropic particles.

Brownian Dynamics is the designated technique to simulate the collective dynamics of colloidal particles suspended in a solution, e.g., the self-assembly of patchy particles.

Rotational Brownian dynamics simulations of clathrin cage formation.

The self-assembly of nearly rigid proteins into ordered aggregates is well suited for modeling by the patchy particle approach. Patchy particles are traditionally simulated using Monte Carlo methods, to study the phase diagram, while Brownian Dynamics simulations would reveal insights into the assembly dynamics. However, Brownian Dynamics of rotating anisotropic particles gives rise to a number of complications not encountered in translational Brownian Dynamics.

Revisiting the Exact Relation between Potential of Mean Force and Free-Energy Profile.

Constraints are convenient in the calculation of free energy profiles via molecular dynamics simulations, but they subtly alter the phase space distribution. In a recent letter of a related title in this journal, Wong and York [J. Chem.

The generation of curved clathrin coats from flat plaques.

Flat clathrin lattices or 'plaques' are commonly believed to be the precursors to clathrin-coated buds and vesicles. The sequence of steps carrying the flat hexagonal lattice into a highly curved polyhedral cage with exactly 12 pentagons remains elusive, however, and the large numbers of disrupted interclathrin connections in previously proposed conversion pathways make these scenarios rather unlikely. The recent notion that clathrin can make controlled small conformational transitions opens new avenues.

Self-assembly of three-legged patchy particles into polyhedral cages.

The self-assembly of rigid three-legged building blocks into polyhedral cages is investigated by patchy particle simulations. A four-site anisotropic interaction potential is introduced to make pairs of overlapping legs bind in an anti-parallel fashion, thereby forming the edges of a polyhedron of pentagons and hexagons. A torsional potential, reflecting an asymmetry or polarity in the legs' binding potential, proves crucial for the successful formation of closed fullerene-like cages.

Asymmetry as the key to clathrin cage assembly.

The self-assembly of clathrin proteins into polyhedral cages is simulated for the first time (to our knowledge) by introducing a coarse-grain triskelion particle modeled after clathrin's characteristic shape. The simulations indicate that neither this shape, nor the antiparallel binding of four legs along the lattice edges, is sufficient to induce cage formation from a random solution. Asymmetric intersegmental interactions, which probably result from a patchy distribution of interactions along the legs' surfaces, prove to be crucial for the efficient self-assembly of cages.

Free energies of stable and metastable pores in lipid membranes under tension.

The free energy profile of pore formation in a lipid membrane, covering the entire range from a density fluctuation in an intact bilayer to a large tension-stabilized pore, has been calculated by molecular dynamics simulations with a coarse-grained lipid model. Several fixed elongations are used to obtain the Helmholtz free energy as a function of pore size for thermodynamically stable, metastable, and unstable pores, and the system-size dependence of these elongations is discussed. A link to the Gibbs free energy at constant tension, commonly known as the Litster model, is established by a Legendre transformation.

Simulations of skin barrier function: free energies of hydrophobic and hydrophilic transmembrane pores in ceramide bilayers.

Transmembrane pore formation is central to many biological processes such as ion transport, cell fusion, and viral infection. Furthermore, pore formation in the ceramide bilayers of the stratum corneum may be an important mechanism by which penetration enhancers such as dimethylsulfoxide (DMSO) weaken the barrier function of the skin. We have used the potential of mean constraint force (PMCF) method to calculate the free energy of pore formation in ceramide bilayers in both the innate gel phase and in the DMSO-induced fluidized state.

The permeability enhancing mechanism of DMSO in ceramide bilayers simulated by molecular dynamics.

The lipids of the topmost layer of the skin, the stratum corneum, represent the primary barrier to molecules penetrating the skin. One approach to overcoming this barrier for the purpose of delivery of active molecules into or via the skin is to employ chemical permeability enhancers, such as dimethylsulfoxide (DMSO). How these molecules exert their effect at the molecular level is not understood.