91 research outputs found
Fine Structure of Viral dsDNA Encapsidation
In vivo configurations of dsDNA of bacteriophage viruses in a capsid are
known to form hexagonal chromonic liquid crystal phases. This article studies
the liquid crystal ordering of viral dsDNA in an icosahedral capsid, combining
the chromonic model with that of liquid crystals with variable degree of
orientation. The scalar order parameter of the latter allows us to distinguish
regions of the capsid with well-ordered DNA from the disordered central core.
We employ a state-of-the-art numerical algorithm based on the finite element
method to find equilibrium states of the encapsidated DNA and calculate the
corresponding pressure. With a data-oriented parameter selection strategy, the
method yields phase spaces of the pressure and the radius of the disordered
core, in terms of relevant dimensionless parameters, rendering the proposed
algorithm into a preliminary bacteriophage designing tool. The presence of the
order parameter also has the unique role of allowing for non-smooth capsid
domains as well as accounting for knot locations of the DNA
Ion-dependent DNA Configuration in Bacteriophage Capsids
Bacteriophages densely pack their long dsDNA genome inside a protein capsid.
The conformation of the viral genome inside the capsid is consistent with a
hexagonal liquid crystalline structure. Experiments have confirmed that the
details of the hexagonal packing depend on the electrochemistry of the capsid
and its environment. In this work, we propose a biophysical model that
quantifies the relationship between DNA configurations inside bacteriophage
capsids and the types and concentrations of ions present in a biological
system. We introduce an expression for the free energy which combines the
electrostatic energy with contributions from bending of individual segments of
DNA and Lennard-Jones-type interactions between these segments. The equilibrium
points of this energy solve a partial differential equation that defines the
distributions of DNA and the ions inside the capsid. We develop a computational
approach that allows us to simulate much larger systems than what is currently
possible using the existing simulations, typically done at a molecular level.
In particular, we are able to estimate bending and repulsion between DNA
segments as well as the full electrochemistry of the solution, both inside and
outside of the capsid. The numerical results show good agreement with existing
experiments and molecular dynamics simulations for small capsids
Stability analysis of flow of active extensile fibers in confined domains
In this article, we study shear flow of active extensile filaments confined in a narrow channel. They behave as nematic liquid crystals that we assumed are governed by the Ericksen-Leslie equations of balance of linear and angular momentum. The addition of an activity source term in the Leslie stress captures the role of the biofuel prompting the dynamics. The dimensionless form of the governing system includes the Ericksen, activity, and Reynolds numbers together with the aspect ratio of the channel as the main driving parameters affecting the stability of the system. The active system that guides our analysis is composed of microtubules concentrated in bundles, hundreds of microns long, placed in a narrow channel domain, of aspect ratios in the range between 10(-2) and 10(-3) dimensionless units, which are able to align due to the combination of adenosine triphosphate-supplied energy and confinement effects. Specifically, this work aims at studying the role of confinement on the behavior of active matter. It is experimentally observed that, at an appropriately low activity and channel width, the active flow is laminar, with the linear velocity profile and the angle of alignment analogous to those in passive shear, developing defects and becoming chaotic, at a large activity and a channel aspect ratio. The present work addresses the laminar regime, where defect formation does not play a role. We perform a normal mode stability analysis of the base shear flow. A comprehensive description of the stability properties is obtained in terms of the driving parameters of the system. Our main finding, in addition to the geometry and magnitude of the flow profiles, and also consistent with the experimental observations, is that the transition to instability of the uniformly aligned shear flow occurs at a threshold value of the activity parameter, with the transition also being affected by the channel aspect ratio. The role of the parameters on the vorticity and angular profiles of the perturbing flow is also analyzed and found to agree with the experimentally observed transition to turbulent regimes. A spectral method based on Chebyshev polynomials is used to solve the generalized eigenvalue problems arising in the stability analysis
Tailored carrier/bacteria technology for rehabilitation of areas with pesticide-containing pollution – AQUAREHAB WP2
Postprint (published version
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