Osmotic force resisting chain insertion in a colloidal suspension

We consider the problem of inserting a stiff chain into a colloidal suspension of particles that interact with it through excluded volume forces. The free energy of insertion is associated with the work of creating a cavity devoid of colloid and sufficiently large to accomodate the chain. The corresponding work per unit length is the force that resists the entry of the chain into the colloidal suspension. In the case of a hard sphere fluid, this work can be calculated straightforwardly within the scaled particle theory; for solutions of flexible polymers, on the other hand, we employ simple scaling arguments. The forces computed in these ways are shown, for nanometer chain and colloid diameters, to be of the order of tens of pN for solution volume fraction for biophysical processes such as the ejection of DNA from viral capsids into the cell cytoplasm.Comment: 16 pages,3 figures. Accepted for publication in European Physical Journal

Viral self-assembly as a thermodynamic process

The protein shells, or capsids, of all sphere-like viruses adopt icosahedral symmetry. In the present paper we propose a statistical thermodynamic model for viral self-assembly. We find that icosahedral symmetry is not expected for viral capsids constructed from structurally identical protein subunits and that this symmetry requires (at least) two internal "switching" configurations of the protein. Our results indicate that icosahedral symmetry is not a generic consequence of free energy minimization but requires optimization of internal structural parameters of the capsid proteins.Comment: pdf file, 13 pages, three figure

Spontaneous patterning of quantum dots at the air-water interface

Nanoparticles deposited at the air-water interface are observed to form circular domains at low density and stripes at higher density. We interpret these patterns as equilibrium phenomena produced by a competition between an attraction and a longer-ranged repulsion. Computer simulations of a generic pair potential with attractive and repulsive parts of this kind, reproduce both the circular and stripe patterns. Such patterns have a potential use in nanoelectronic applications

The effect of genome length on ejection forces in bacteriophage lambda

A variety of viruses tightly pack their genetic material into protein capsids that are barely large enough to enclose the genome. In particular, in bacteriophages, forces as high as 60 pN are encountered during packaging and ejection, produced by DNA bending elasticity and self-interactions. The high forces are believed to be important for the ejection process, though the extent of their involvement is not yet clear. As a result, there is a need for quantitative models and experiments that reveal the nature of the forces relevant to DNA ejection. Here we report measurements of the ejection forces for two different mutants of bacteriophage lambda, lambda b221cI26 and lambda cI60, which differ in genome length by ~30%. As expected for a force-driven ejection mechanism, the osmotic pressure at which DNA release is completely inhibited varies with the genome length: we find inhibition pressures of 15 atm and 25 atm, respectively, values that are in agreement with our theoretical calculations

Attraction Between Like-Charged Walls: Short-Ranged Simulations Using Local Molecular Field Theory

Effective attraction between like-charged walls mediated by counterions is studied using local molecular field (LMF) theory. Monte Carlo simulations of the "mimic system'' given by LMF theory, with short-ranged "Coulomb core" interactions in an effective single particle potential incorporating a mean-field average of the long-ranged Coulomb interactions, provide a direct test of the theory, and are in excellent agreement with more complex simulations of the full Coulomb system by Moreira and Netz [Eur. Phys. J. E 8, 33 (2002)]. A simple, generally-applicable criterion to determine the consistency parameter sigma_{min} needed for accurate use of the LMF theory is presented

Viral RNAs are unusually compact.

A majority of viruses are composed of long single-stranded genomic RNA molecules encapsulated by protein shells with diameters of just a few tens of nanometers. We examine the extent to which these viral RNAs have evolved to be physically compact molecules to facilitate encapsulation. Measurements of equal-length viral, non-viral, coding and non-coding RNAs show viral RNAs to have among the smallest sizes in solution, i.e., the highest gel-electrophoretic mobilities and the smallest hydrodynamic radii. Using graph-theoretical analyses we demonstrate that their sizes correlate with the compactness of branching patterns in predicted secondary structure ensembles. The density of branching is determined by the number and relative positions of 3-helix junctions, and is highly sensitive to the presence of rare higher-order junctions with 4 or more helices. Compact branching arises from a preponderance of base pairing between nucleotides close to each other in the primary sequence. The density of branching represents a degree of freedom optimized by viral RNA genomes in response to the evolutionary pressure to be packaged reliably. Several families of viruses are analyzed to delineate the effects of capsid geometry, size and charge stabilization on the selective pressure for RNA compactness. Compact branching has important implications for RNA folding and viral assembly

Hybrid bounds for twisted L-functions

The aim of this paper is to derive bounds on the critical line Rs 1/2 for L- functions attached to twists f circle times chi of a primitive cusp form f of level N and a primitive character modulo q that break convexity simultaneously in the s and q aspects. If f has trivial nebentypus, it is shown that L(f circle times chi, s) << (N vertical bar s vertical bar q)(epsilon) N-4/5(vertical bar s vertical bar q)(1/2-1/40), where the implied constant depends only on epsilon > 0 and the archimedean parameter of f. To this end, two independent methods are employed to show L(f circle times chi, s) << (N vertical bar s vertical bar q)(epsilon) N-1/2 vertical bar S vertical bar(1/2)q(3/8) and L(g,s) << D-2/3 vertical bar S vertical bar(5/12) for any primitive cusp form g of level D and arbitrary nebentypus (not necessarily a twist f circle times chi of level D vertical bar Nq(2))

Genome organization and interaction with capsid protein in a multipartite RNA virus.

We report the asymmetric reconstruction of the single-stranded RNA (ssRNA) content in one of the three otherwise identical virions of a multipartite RNA virus, brome mosaic virus (BMV). We exploit a sample consisting exclusively of particles with the same RNA content-specifically, RNAs 3 and 4-assembled in planta by agrobacterium-mediated transient expression. We find that the interior of the particle is nearly empty, with most of the RNA genome situated at the capsid shell. However, this density is disordered in the sense that the RNA is not associated with any particular structure but rather, with an ensemble of secondary/tertiary structures that interact with the capsid protein. Our results illustrate a fundamental difference between the ssRNA organization in the multipartite BMV viral capsid and the monopartite bacteriophages MS2 and Qβ for which a dominant RNA conformation is found inside the assembled viral capsids, with RNA density conserved even at the center of the particle. This can be understood in the context of the differing demands on their respective lifecycles: BMV must package separately each of several different RNA molecules and has been shown to replicate and package them in isolated, membrane-bound, cytoplasmic complexes, whereas the bacteriophages exploit sequence-specific "packaging signals" throughout the viral RNA to package their monopartite genomes

What drives the translocation of stiff chains?

We study the dynamics of the passage of a stiff chain through a pore into a cell containing particles that bind reversibly to it. Using Brownian Molecular Dynamics simulations we investigate the mean-first-passage time as a function of the length of the chain inside, for different concentrations of binding particles. As a consequence of the interactions with these particles, the chain experiences a net force along its length whose calculated value from the simulations accounts for the velocity at which it enters the cell. This force can in turn be obtained from the solution of a generalized diffusion equation incorporating an effective Langmuir adsorption free energy for the chain plus binding particles. These results suggest a role of binding particles in the translocation process which is in general quite different from that of a Brownian ratchet. Furthermore, non-equilibrium effects contribute significantly to the dynamics, \emph{e.g.}, the chain often enters the cell faster than particle binding can be saturated, resulting in a force several times smaller than the equilibrium value.Comment: 7 pages, 4 figure