Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · cond-mat/0306021

Thermodynamics of DNA packaging inside a viral capsid: the role of DNA intrinsic thickness

Davide Marenduzzo·Cristian Micheletti
View original source ↗Read source document ↗Export metadata ↓

Abstract

We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent characterization of the loading process of the genome inside the $ϕ$29 bacteriophage capsid. Our emphasis is on the modelling of double-stranded DNA as a flexible thick polymer (tube) instead of a beads-and-springs chain. By using finite-size scaling to extrapolate our results to genome lengths appropriate for $ϕ$29, we find that the thickness-induced force may account for up to half the one measured experimentally at high packing densities. An analogous agreement is found for the total work that has to be spent in the packaging process. Remarkably, such agreement can be obtained in the absence of any tunable parameters and is a mere consequence of the DNA thickness. Furthermore, we provide a quantitative estimate of how the persistence length of a polymer depends on its thickness. The expression accounts for the significant difference in the persistence lengths of single- and double-stranded DNA (again with the sole input of their respective sections and natural nucleotide/base-pair spacing).

Explore related subjects

cond-mat.stat-mechcond-mat.softq-bio.BM

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Davide Marenduzzo, Cristian Micheletti. 2003-06-02. Thermodynamics of DNA packaging inside a viral capsid: the role of DNA intrinsic thickness. https://arxiv.org/abs/cond-mat/0306021

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

The meaning of entropy (demonstration of a much needed theorem)

The association of information with entropy has been argued on plausibility arguments involving the operation of imaginary engines and beings, and it is not a universal theorem. In this paper, a theorem by Charles Bennett on reversible computation that associates entropy with erasure of information is recognized as this much needed theorem. It is proposed a real, non thermal engine, operated by humans. It is proved: (1) The engine obeys two laws, identical {\it mutatis mutandis} to the two laws of thermodynamics; therefore, the entropy that arises in the operation of the engine has the same meaning of the entropy that arises in the operation of thermal engines. (2) The engine operates in stages similar to the stages in Bennett's three tapes reversible computer; therefore the entropy in the engine has the same meaning of the entropy in computation. The conclusion is that also the thermal entropy is a measure of erased or missing information. As a side result, information is measured in physical units, which complies with Landauer's principle. A prototype at work is shown in video.

cond-mat.stat-mech↗
arXiv2026

Information geometry of perturbed gradient flow systems on hypergraphs: A perspective towards nonequilibrium physics

This article serves to concisely review the link between gradient flow systems on hypergraphs and information geometry which has been established within the last five years. Gradient flow systems describe a wealth of physical phenomena and provide powerful analytical technquies which are based on the variational energy-dissipation principle. Modern nonequilbrium physics has complemented this classical principle with thermodynamic uncertaintly relations, speed limits, entropy production rate decompositions, and many more. In this article, we formulate these modern principles within the framework of perturbed gradient flow systems on hypergraphs. In particular, we discuss the geometry induced by the Bregman divergence, the physical implications of dual foliations, as well as the corresponding infinitesimal Riemannian geometry for gradient flow systems. Through the geometrical perspective, we are naturally led to new concepts such as moduli spaces for perturbed gradient flow systems and thermodynamical area which is crucial for understanding speed limits. We hope to encourage the readers working in either of the two fields to further expand on and foster the interaction between the two fields.

cond-mat.stat-mech↗
arXiv2026

Anomalous diffusion and singular transport from hydrodynamic recoupling

In charge neutral fluids, such as the Dirac fluid in graphene at the Dirac point, charge transport remains diffusive despite the presence of ballistically propagating sound waves: sound waves ``hydrodynamically decouple'' from the slower charge fluctuations. For quasi-one-dimensional charge neutral fluids, we show that this convective charge diffusion is not smoothly connected to the normal diffusion that arises when momentum conservation is broken by noise (or static impurities). Instead, the charge diffusion constant is a discontinuous function of noise, which (in the weak-noise limit) depends only on the ratio of momentum and energy relaxation rates. In the special limit of momentum-conserving noise (e.g., spatially uniform fluctuations of the Hamiltonian), the diffusion constant diverges in the presence of noise. We describe the resulting superdiffusion in terms of coupled Burgers equations. We present a general mechanism---hydrodynamic recoupling---by which weak noise can induce singular changes in transport coefficients. Our results highlight the limits of zero-noise extrapolation for predicting dynamical quantities like diffusion constants.

cond-mat.stat-mech↗