Related papers: Fine Structure of Viral dsDNA Encapsidation
Although carbon nanotubes are potential candidates for DNA encapsulation and subsequent delivery of biological payloads to living cells, the thermodynamical spontaneity of DNA encapsulation under physiological conditions is still a matter…
The conjunction of insights from structural biology, solution biochemistry, genetics and single molecule biophysics has provided a renewed impetus for the construction of quantitative models of biological processes. One area that has been a…
In this work we study how a viral capsid can change conformation using techniques of Large Deviations Theory for stochastic differential equations. The viral capsid is a model of a complex system in which many units - the proteins forming…
A vital constituent of a virus is its protein shell, called the viral capsid, that encapsulates and hence provides protection for the viral genome. Viral capsids are usually spherical, and for a significant number of viruses exhibit overall…
Hard sphere colloidal particles are a basic model system for general research into phase behavior, ordering and out-equilibrium glass transitions. Experimentally it has been shown that oscillatory shearing of a monodisperse hard sphere…
Several controversial issues concerning the packing of linear DNA in bacteriophages and globules are discussed. Exact relations for the osmotic pressure, capsid pressure and loading force are derived in terms of the hole size inside phages…
Understanding how virus capsids assemble around their nucleic acid (NA) genomes could promote efforts to block viral propagation or to reengineer capsids for gene therapy applications. We develop a coarse-grained model of capsid proteins…
Viruses are biological nanosystems with a capsid of protein-made capsomer units that encloses and protects the genetic material responsible for their replication. Here we show how the geometrical constraints of the capsomer-capsomer…
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…
Using a phase field crystal model we study the structure and dynamics of a drop of colloidal suspension during evaporation of the solvent. We model an experimental system where contact line pinning of the drop on the substrate is…
We study phases and phase transitions that can take place in the newly discovered banana (bow-shaped or bent-core) liquid crystal molecules. We show that to completely characterize phases exhibited by such bent-core molecules a third-rank…
Exploring structural order in disordered systems including liquids and glasses is an intriguing but challenging issue in condensed matter physics. Here we construct a new parameter based on the angular distribution function of particles and…
We investigate the mechanical stability of a segment of DNA wrapped around a histone in the nucleosome configuration. The assumption underlying this investigation is that the proper model for this packaging arrangement is that of an elastic…
DNA inside the cellular environment works under a confined space. An intense research of the transcription and replication of DNA in the confined state is structurally significant to command the self assembly of DNA in a chamber or channel.…
Spontaneous self-assembly of hard convex polyhedra are known to form orientationally disordered crystalline phases, where particle orientations do not follow the same pattern as the positional arrangement of the crystal. A distinct type of…
The underlying structural order that transcends the liquid, glass and crystalline states is identified using an efficient genetic algorithm (GA). GA identifies the most common energetically favorable packing motif in crystalline structures…
The unconstrained genomic DNA of bacteria forms a coil, which volume exceeds 1000 times the volume of the cell. Since prokaryotes lack a membrane-bound nucleus, in sharp contrast with eukaryotes, the DNA may consequently be expected to…
Viruses are nanoscale entities containing a nucleic acid genome encased in a protein shell called a capsid, and in some cases surrounded by a lipid bilayer membrane. This review summarizes the physics that govern the processes by which…
Liquid crystals consisting of biaxial particles can exhibit a much richer phase behavior than their uniaxial counterparts. Usually, one has to rely on simulation results to understand the phase diagram of these systems, since very few…
We study an experimental system of hard granular squares in two dimensions, energized by vibration. The interplay of order in the orientations and positions of anisotropic particles allows for a rich set of phases. We measure the structure…