Biomedical subjects

Joseph Rudnick

Publications and source records attributed to Joseph Rudnick.

11 recordsLinked to original sources

PubMed2005

Icosahedral packing of RNA viral genomes.

Many spherelike RNA viruses package a portion of their genome in a manner that mirrors the icosahedral symmetry of the protein container, or capsid. Graph-theoretical constraints forbid exact realization of icosahedral symmetry. This paper explores the consequences of graph-theoretical constraints on quasi-icosahedral genome structures. A key result is the prediction that the genome organization is a Hamiltonian path or cycle and that the associated assembly scenario of such single-stranded spherelike RNA viruses resembles that of cylindrical RNA viruses, such as tobacco mosaic viruses.

Capsid↗

PubMed2004

Origin of icosahedral symmetry in viruses.

With few exceptions, the shells (capsids) of sphere-like viruses have the symmetry of an icosahedron and are composed of coat proteins (subunits) assembled in special motifs, the T-number structures. Although the synthesis of artificial protein cages is a rapidly developing area of materials science, the design criteria for self-assembled shells that can reproduce the remarkable properties of viral capsids are only beginning to be understood. We present here a minimal model for equilibrium capsid structure, introducing an explicit interaction between protein multimers (capsomers). Using Monte Carlo simulation we show that the model reproduces the main structures of viruses in vivo (T-number icosahedra) and important nonicosahedral structures (with octahedral and cubic symmetry) observed in vitro. Our model can also predict capsid strength and shed light on genome release mechanisms.

Biophysical Phenomena↗

PubMed2004

Casimir forces, surface fluctuations, and thinning of superfluid film.

Recent experiments on the wetting of 4He have shown that the film becomes thinner at the lambda transition and in the superfluid phase. The difference in thickness above and below the transition has been attributed to a Casimir interaction which is a consequence of a broken continuous symmetry in the bulk superfluid. However, the observed thinning of the film is larger than can be accounted by this Casimir force. We show that surface fluctuations give rise to an additional force, similar in form but larger in magnitude, which may explain the observations.

Journal Article↗

PubMed2003

Cohesive energy, stability, and structural transitions in polyelectrolyte bundles.

A lattice of uniformly charged, infinitesimally thin rods decorated with an ordered array of counterions exhibits anomalous behavior as the spacing between the rods is varied. In particular, the counterion lattice undergoes a sequence of structural shearing or "tilting," phase transformations as the spacing between the rods decreases. The potential implications of this behavior with respect to the packaging of biologically relevant polyelectrolytic molecules are commented upon.

Biophysical Phenomena↗

PubMed2003

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 that is in general quite different from that of a Brownian ratchet. Furthermore, nonequilibrium effects contribute significantly to the dynamics; 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.

Binding Sites↗

PubMed2003

Anomalous bending of a polyelectrolyte.

We report on a study of the shape of a stiff, charged rod that is subjected to equal and opposite force couples at its two ends. Unlike a neutral elastic rod, which forms a constant curvature configuration under such influences, the charged rod tends to flatten in the interior and accumulate the curvature in the end points, to maximally reduce the electrostatic self-repulsion. The effect of this nonuniform bending on the effective elasticity and on the statistical conformations of a fluctuating charged rod is discussed. An alternative definition for the electrostatic persistence length is suggested. This definition is found to be consistent with a corresponding length that can be deduced from the end-to-end distribution function of a fluctuating polyelectrolyte.

Journal Article↗

PubMed2003

Viral self-assembly as a thermodynamic process.

The protein shells, or capsids, of nearly all spherelike viruses adopt icosahedral symmetry. In the present Letter, 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.

Capsid↗

PubMed2003

Probing polyelectrolyte elasticity using radial distribution function.

We study the effect of electrostatic interactions on the distribution function of the end-to-end distance of a single polyelectrolyte chain in the rodlike limit. The extent to which the radial distribution function of a polyelectrolyte is reproduced by that of a wormlike chain with an adjusted persistence length is investigated. Strong evidence is found for a universal scaling formula connecting the effective persistence length of a polyelectrolyte with its linear charge density and the Debye screening of its self-interaction. An alternative definition of the electrostatic persistence length is proposed based on matching of the maximum of the distribution with that of an effective wormlike chain, as opposed to the traditional matching of the first or the second moments of the distributions. It is shown that this definition provides a more accurate probe of the affinity of the distribution to that of the wormlike chains, as compared to the traditional definition. It is also found that the length of a polyelectrolyte segment can act as a crucial parameter in determining its elastic properties.

Journal Article↗

PubMed2002

Two-level system with a thermally fluctuating transfer matrix element: application to the problem of DNA charge transfer.

Charge transfer along the base-pair stack in DNA is modeled in terms of thermally assisted tunneling between adjacent base pairs. The key element of the approach in this paper is the notion that this tunneling between base pairs that fluctuate significantly from their nominal orientation is rate limited by the requirement of optimal alignment. We focus on this aspect of the process by modeling two adjacent base pairs in terms of a classical damped oscillator subject to thermal fluctuations as described by a Fokker-Planck equation. We find that the process is characterized by two time scales, a result that is in accord with the experimental findings.

Journal Article↗

PubMed2002

Effects of torsional strain on thermal denaturation of DNA.

A class of simple statistical mechanical models for DNA melting, first proposed by Poland and Scheraga, has been demonstrated to exhibit a first or second order thermodynamic singularity, notwithstanding the intrinsic one-dimensional nature of the problem. In the present paper we consider the case of circular DNA and show that the inclusion of twist elastic energy in the Poland-Scheraga models leads either to suppression of the thermodynamic singularity or to a weak, third order singularity. Such behavior may also be present in linear DNA under mechanical influences that preclude the release of torsional strain.

Journal Article↗

PubMed2002

Analysis of a continuous field theory in two dimensions with use of the density matrix renormalization group.

A formulation of the Ginzburg-Landau-Wilson version of the partition function of a system with a continuously varying order parameter as a transfer matrix calculation allows for the application of methods based on the density matrix renormalization group (DMRG) to the calculation of the free energy of the O(1) model. The essence of both the mapping and the DMRG calculation is laid out, along with results that validate this strategy.

Journal Article↗