Related papers: Nanoindentation of virus capsids in a molecular mo…
Physical properties of capsids of plant and animal viruses are important factors in capsid self-assembly, survival of viruses in the extracellular environment, and their cell infectivity. Virus shells can have applications as nanocontainers…
Recent Atomic Force Microscope (AFM) nanoindentation experiments measuring mechanical response of the protein shells of viruses have provided a quantitative description of their strength and elasticity. To better understand and interpret…
Cowpea chlorotic mottle virus (CCMV) is a widely used model for virus replication studies. A major challenge lies in distinguishing between the roles of the interaction between coat proteins and that between the coat proteins and the viral…
The cowpea chlorotic mottle virus (CCMV) has emerged as an exemplary model system to assess the balance between electrostatic and topological features of ssRNA viruses, specifically in the context of the viral self-assembly process. Yet, in…
We consider self-assembly of proteins into a virus capsid by the methods of molecular dynamics. The capsid corresponds either to SPMV or CCMV and is studied with and without the RNA molecule inside. The proteins are flexible and described…
We simulate the assembly dynamics of icosahedral capsids from subunits that interconvert between different conformations (or quasi-equivalent states). The simulations identify mechanisms by which subunits form empty capsids with only one…
We demonstrate that Multi-Body Dissipative Particle Dynamics (MDPD) can be used as an efficient computational tool for the investigation of nanoscale capillary impregnation of confined geometries. As an essential prerequisite, a novel model…
We develop coarse-grained models that describe the dynamic encapsidation of functionalized nanoparticles by viral capsid proteins. We find that some forms of cooperative interactions between protein subunits and nanoparticles can…
Refractory complex concentrated alloys (RCCA) exhibit exceptional strength and thermal stability, yet their plastic deformation mechanisms under complex contact loading remain insufficiently understood. Here, the nanoindentation response of…
Nanoindentation, a common technique for probing the mechanical properties of crystalline materials, exhibits both surface and bulk-dominated responses that are linked to the parent crystal's elasticity and plasticity. For FCC crystals, the…
Coupling of nano-indentation and crystal plasticity finite element (CPFE) simulations is widely used to quantitatively probe the small-scale mechanical behaviour of materials. Earlier studies showed that CPFE can successfully reproduce the…
We develop equilibrium and kinetic theories that describe the assembly of viral capsid proteins on a charged central core, as seen in recent experiments in which brome mosaic virus (BMV) capsids assemble around nanoparticles functionalized…
In this work we present a computational study of the small strain mechanics of freestanding ultrathin CNT films under in-plane loading. The numerical modeling of the mechanics of representatively large specimens with realistic micro- and…
Microsecond time-resolved cryo-electron microscopy has emerged as a novel approach for directly observing proteins dynamics. By providing microsecond temporal and near-atomic spatial resolution, it has the potential to elucidate a wide…
The dynamics of many macromolecular machines is characterized by chemically-mediated structural changes that achieve large scale functional deployment through local rearrangements of constitutive protein sub-units. Motivated by recent high…
Nanoindentation cycles measured with an atomic force microscope on hydrated collagen fibrils exhibit a rate-independent hysteresis with return point memory. This previously unknown energy dissipation mechanism describes in unified form…
We study the microrheology of nanoparticle shells [Dinsmore et al. Science 298, 1006 (2002)] and viral capsids [Ivanovska et al. PNAS 101, 7600 (2004)] by computing the mechanical response function and thermal fluctuation spectrum of a…
We study the elastic properties and mechanical stability of viral capsids under external force-loading with computer simulations. Our approach allows the implementation of specific geometries corresponding to specific phages such as…
A method is presented for the registration and correlation of intrinsic property maps of materials, including data from nanoindentation hardness, Electron Back-Scattered Diffraction (EBSD), Electron Micro-Probe Analysis (EPMA). This highly…
A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms.…