Multiscale Modeling of Hepatitis B Virus Capsid Assembly and Its Dimorphism.

Hepatitis B virus (HBV) is an endemic, chronic virus that leads to 800000 deaths per year. Central to the HBV lifecycle, the viral core has a protein capsid assembled from many copies of a single protein. The capsid protein adopts different (quasi-equivalent) conformations to form icosahedral capsids containing 180 or 240 proteins: = 3 or = 4, respectively, in Caspar-Klug nomenclature.

Polymorphic self-assembly of helical tubules is kinetically controlled.

In contrast to most self-assembling synthetic materials, which undergo unbounded growth, many biological self-assembly processes are self-limited. That is, the assembled structures have one or more finite dimensions that are much larger than the size scale of the individual monomers. In many such cases, the finite dimension is selected by a preferred curvature of the monomers, which leads to self-closure of the assembly.

Thermodynamic Size Control in Curvature-Frustrated Tubules: Self-Limitation with Open Boundaries.

We use computational modeling to investigate the assembly thermodynamics of a particle-based model for geometrically frustrated assembly, in which the local packing geometry of subunits is incompatible with uniform, strain-free large-scale assembly. The model considers discrete triangular subunits that drive assembly toward a closed, hexagonal-ordered tubule, but have geometries that locally favor negative Gaussian curvature. We use dynamical Monte Carlo simulations and enhanced sampling methods to compute the free energy landscape and corresponding self-assembly behavior as a function of experimentally accessible parameters that control assembly driving forces and the magnitude of frustration.

Tiling a tubule: how increasing complexity improves the yield of self-limited assembly.

The ability to design and synthesize ever more complicated colloidal particles opens the possibility of self-assembling a zoo of complex structures, including those with one or more self-limited length scales. An undesirable feature of systems with self-limited length scales is that thermal fluctuations can lead to the assembly of nearby, off-target states. We investigate strategies for limiting off-target assembly by using multiple types of subunits.

Yielding in an Integer Automaton Model for Amorphous Solids under Cyclic Shear.

We present results on an automaton model of an amorphous solid under cyclic shear. After a transient, the steady state falls into one of three cases in order of increasing strain amplitude: (i) pure elastic behavior with no plastic activity, (ii) limit cycles where the state recurs after an integer period of strain cycles, and (iii) irreversible plasticity with longtime diffusion. The number of cycles N required for the system to reach a periodic orbit diverges as the amplitude approaches the yielding transition between regimes (ii) and (iii) from below, while the effective diffusivity D of the plastic strain field vanishes on approach from above.

Cell Surface Protein mRNAs Show Differential Transcription in Pyramidal and Fast-Spiking Cells as Revealed by Single-Cell Sequencing.

The prefrontal cortex (PFC) plays a key role in higher order cognitive functions and psychiatric disorders such as autism, schizophrenia, and depression. In the PFC, the two major classes of neurons are the glutamatergic pyramidal (Pyr) cells and the GABAergic interneurons such as fast-spiking (FS) cells. Despite extensive electrophysiological, morphological, and pharmacological studies of the PFC, the therapeutically utilized drug targets are restricted to dopaminergic, glutamatergic, and GABAergic receptors.

Avalanches, thresholds, and diffusion in mesoscale amorphous plasticity.

We present results on a mesoscale model for amorphous matter in athermal, quasistatic (a-AQS), steady-state shear flow. In particular, we perform a careful analysis of the scaling with the lateral system size L of (i) statistics of individual relaxation events in terms of stress relaxation S, and individual event mean-squared displacement M, and the subsequent load increments Δγ, required to initiate the next event; (ii) static properties of the system encoded by x=σ_{y}-σ, the distance of local stress values from threshold; and (iii) long-time correlations and the emergence of diffusive behavior. For the event statistics, we find that the distribution of S is similar to, but distinct from, the distribution of M.

Diffusion in Mesoscopic Lattice Models of Amorphous Plasticity.

We present results on tagged particle diffusion in a mesoscale lattice model for sheared amorphous material in athermal quasistatic conditions. We find a short time diffusive regime and a long time diffusive regime whose diffusion coefficients depend on system size in dramatically different ways. At short time, we find that the diffusion coefficient, D, scales roughly linearly with system length, D∼L^{1.

Anisotropic Superattenuation of Capillary Waves on Driven Glass Interfaces.

Metrological atomic force microscopy measurements are performed on the silica glass interfaces of photonic band-gap fibers and hollow capillaries. The freezing of attenuated out-of-equilibrium capillary waves during the drawing process is shown to result in a reduced surface roughness. The roughness attenuation with respect to the expected thermodynamical limit is determined to vary with the drawing stress following a power law.

From depinning transition to plastic yielding of amorphous media: A soft-modes perspective.

A mesoscopic model of amorphous plasticity is discussed in the context of depinning models. After embedding in a d+1-dimensional space, where the accumulated plastic strain lives along the additional dimension, the gradual plastic deformation of amorphous media can be regarded as the motion of an elastic manifold in a disordered landscape. While the associated depinning transition leads to scaling properties, the quadrupolar Eshelby interactions at play in amorphous plasticity induce specific additional features like shear-banding and weak ergodicity breakdown.

Finite-size effects in a model for plasticity of amorphous composites.

We discuss the plastic behavior of an amorphous matrix reinforced by hard particles. A mesoscopic depinning-like model accounting for Eshelby elastic interactions is implemented. Only the effect of a plastic disorder is considered.