Rastko Sknepnek

Modeling the crystallization of spherical nucleic acid nanoparticle conjugates with molecular dynamics simulations.

We use molecular dynamics simulations to study the crystallization of spherical nucleic-acid (SNA) gold nanoparticle conjugates, guided by sequence-specific DNA hybridization events. Binary mixtures of SNA gold nanoparticle conjugates (inorganic core diameter in the 8-15 nm range) are shown to assemble into BCC, CsCl, AlB(2), and Cr(3)Si crystalline structures, depending upon particle stoichiometry, number of immobilized strands of DNA per particle, DNA sequence length, and hydrodynamic size ratio of the conjugates involved in crystallization. These data have been used to construct phase diagrams that are in excellent agreement with experimental data from wet-laboratory studies.

Mechanical model of blebbing in nuclear lamin meshworks

Much of the structural stability of the nucleus comes from meshworks of intermediate filament proteins known as lamins forming the inner layer of the nuclear envelope called the nuclear lamina. These lamin meshworks additionally play a role in gene expression. Abnormalities in nuclear shape are associated with a variety of pathologies, including some forms of cancer and Hutchinson–Gilford Progeria Syndrome, and often include protruding structures termed nuclear blebs. These nuclear blebs are thought to be related to pathological gene expression; however, little is known about how and why blebs form. We have developed a minimal continuum elastic model of a lamin meshwork that we use to investigate which aspects of the meshwork could be responsible for bleb formation. Mammalian lamin meshworks consist of two types of lamin proteins, A type and B type, and it has been reported that nuclear blebs are enriched in A-type lamins. Our model treats each lamin type separately and thus, can assign them different properties. Nuclear blebs have been reported to be located in regions where the fibers in the lamin meshwork have a greater separation, and we find that this greater separation of fibers is an essential characteristic for generating nuclear blebs. The model produces structures with comparable morphologies and distributions of lamin types as real pathological nuclei. Thus, preventing this opening of the meshwork could be a route to prevent bleb formation, which could be used as a potential therapy for the pathologies associated with nuclear blebs.

Platonic and Archimedean geometries in multicomponent elastic membranes

Large crystalline molecular shells, such as some viruses and fullerenes, buckle spontaneously into icosahedra. Meanwhile multicomponent microscopic shells buckle into various polyhedra, as observed in many organelles. Although elastic theory explains one-component icosahedral faceting, the possibility of buckling into other polyhedra has not been explored. We show here that irregular and regular polyhedra, including some Archimedean and Platonic polyhedra, arise spontaneously in elastic shells formed by more than one component. By formulating a generalized elastic model for inhomogeneous shells, we demonstrate that coassembled shells with two elastic components buckle into polyhedra such as dodecahedra, octahedra, tetrahedra, and hosohedra shells via a mechanism that explains many observations, predicts a new family of polyhedral shells, and provides the principles for designing microcontainers with specific shapes and symmetries for numerous applications in materials and life sciences.

Molecular crystallization controlled by pH regulates mesoscopic membrane morphology.

Coassembled molecular structures are known to exhibit a large variety of geometries and morphologies. A grand challenge of self-assembly design is to find techniques to control the crystal symmetries and overall morphologies of multicomponent systems. By mixing +3 and -1 ionic amphiphiles, we assemble crystalline ionic bilayers in a large variety of geometries that resemble polyhedral cellular crystalline shells and archaea wall envelopes. We combine TEM with SAXS and WAXS to characterize the coassembled structures from the mesoscopic to nanometer scale. The degree of ionization of the amphiphiles and their intermolecular electrostatic interactions are controlled by varying pH. At low and high pH values, we observe closed, faceted vesicles with two-dimensional hexagonal molecular arrangements, and at intermediate pH, we observe ribbons with rectangular-C packing. Furthermore, as pH increases, we observe interdigitation of the bilayer leaflets. Accurate atomistic molecular dynamics simulations explain the pH-dependent bilayer thickness changes and also reveal bilayers of hexagonally packed tails at low pH, where only a small fraction of anionic headgroups is charged. Coarse-grained simulations show that the mesoscale geometries at low pH are faceted vesicles where liquid-like edges separate flat crystalline domains. Our simulations indicate that the curved-to-polyhedral shape transition can be controlled by tuning the tail density in regions where sharp bends can form the polyhedral edges. In particular, the pH acts to control the overall morphology of the ionic bilayers by changing the local crystalline order of the amphiphile tails.

Defect dynamics in active nematics.

Topological defects are distinctive signatures of liquid crystals. They profoundly affect the viscoelastic behaviour of the fluid by constraining the orientational structure in a way that inevitably requires global changes not achievable with any set of local deformations. In active nematic liquid crystals, topological defects not only dictate the global structure of the director, but also act as local sources of motion, behaving as self-propelled particles. In this article, we present a detailed analytical and numerical study of the mechanics of topological defects in active nematic liquid crystals.

Nanoparticle Ordering via Functionalized Block Copolymers in Solution

We consider nanoparticles and functionalized copolymers, block copolymers with attached end groups possessing a specific affinity for nanoparticles, in solution. Using molecular dynamics, we show that nanoparticles are able to direct the self-assembly of the polymer/nanoparticle composite. We perform a detailed study for a wide range of nanoparticle sizes and concentrations. We show that the nanoparticles order in a number of distinct phases: simple cubic, layered hexagonal, hexagonal columnar, gyroid, and a novel square columnar. Our results show that nanoparticles ordered with functionalized block copolymers can provide a simple and efficient tool for assembling novel materials with nanometer scale resolution.

Thermally Active Hybridization Drives the Crystallization of DNA- Functionalized Nanoparticles

The selectivity of DNA recognition inspires an elegant protocol for designing versatile nanoparticle (NP) assemblies. We use molecular dynamics simulations to analyze dynamic aspects of the assembly process and identify ingredients that are key to a successful assembly of NP superlattices through DNA hybridization. A scale-accurate coarse-grained model faithfully captures the relevant contributions to the kinetics of the DNA hybridization process and is able to recover all experimentally reported to date binary superlattices (BCC, CsCl, AlB2, Cr3Si, and Cs6C60). We study the assembly mechanism in systems with up to 10(6) degrees of freedom and find that the crystallization process is accompanied with a slight decrease of enthalpy. Furthermore, we find that the optimal range of the DNA linker interaction strengths for a successful assembly is 12-16kBT, and the optimal mean lifetime of a DNA hybridization event is 10(-4)-10(-3) of the total time it takes to form a crystal. We also obtain the optimal percentage of hybridized DNA pairs for different binary systems. On the basis of these results, we propose suitable linker sequences for future nanomaterials design.

A Graphics Processing Unit Implementation of Coulomb Interaction in Molecular Dynamics

We report a GPU implementation in HOOMD Blue of long-range electrostatic interactions based on the orientation-averaged Ewald sum scheme, introduced by Yakub and Ronchi (J. Chem. Phys. 2003, 119, 11556). The performance of the method is compared to an optimized CPU version of the traditional Ewald sum available in LAMMPS, in the molecular dynamics of electrolytes. Our GPU implementation is significantly faster than the CPU implementation of the Ewald method for small to a sizable number of particles (∼10(5)). Thermodynamic and structural properties of monovalent and divalent hydrated salts in the bulk are calculated for a wide range of ionic concentrations. An excellent agreement between the two methods was found at the level of electrostatic energy, heat capacity, radial distribution functions, and integrated charge of the electrolytes.

Orbital coupling and superconductivity in the iron pnictides

We demonstrate that strong inter-orbital interaction is very efficient to achieve superconductivity due to magnetic fluctuations in the iron pnictides. Fermi surface states that are coupled by the antiferromagnetic wave vector are often of different orbital nature, causing pair-hopping interactions between distinct Fe-3d orbitals to become important. Performing a self-consistent FLEX calculation below

Buckling of multicomponent elastic shells with line tension

T_{c}