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Mariel Vazquez

Publications and source records attributed to Mariel Vazquez.

10 recordsLinked to original sources

Twist dominates bending in the liquid crystal organization of bacteriophage DNA

DNA frequently adopts liquid-crystalline conformations in both cells and viruses. The Oseen--Frank framework provides a powerful continuum description of these phases through three elastic moduli: splay ($K_1$), twist or cholesteric ($K_2$), and bending ($K_3$). While $K_1$ is typically assumed to dominate, the relative magnitude of $K_2$ and $K_3$ in confined DNA remains poorly understood. Here, we combine cryo-electron microscopy, liquid-crystal modeling, and knot theory to quantify this relationship in bacteriophage P4, whose genome is partially organized in a spool-like liquid-crystalline phase. We first show experimentally that the ordered DNA occupies three concentric layers within the capsid. We then formulate an Oseen--Frank model for this geometry and use it, together with the measured layer radii, to estimate the elastic ratio $α= K_3/K_2$. We find $α\approx 0.0064$, indicating that twist elasticity overwhelmingly dominates bending. To validate this result, we perform Langevin dynamics simulations of DNA trajectories and classify the resulting knots. The predicted knot distribution agrees with experimental data from P4, demonstrating consistency between elasticity, topology, and observed genome organization.

cond-mat.soft

Knotted DNA Configurations in Bacteriophage Capsids: A Liquid Crystal Theory Approach

Bacteriophages, viruses that infect bacteria, store their micron long DNA inside an icosahedral capsid with a typical diameter of 40 nm to 100 nm. Consistent with experimental observations, such confinement conditions induce an arrangement of DNA that corresponds to a hexagonal chromonic liquid-crystalline phase, and increase the topological complexity of the genome in the form of knots. A mathematical model that implements a chromonic liquid-crystalline phase and that captures the changes in topology has been lacking. We adopt a mathematical model that represents the viral DNA as a pair of a vector field and a line. The vector field is a minimizer of the total Oseen-Frank energy for nematic liquid crystals under chromonic constraints, while the line is identified with the tangent to the field at selected locations, representing the central axis of the DNA molecule. The fact that the Oseen-Frank functional assigns infinite energy to topological defects (point defects in two dimensions and line defects in three dimensions) precludes the presence of singularities and, in particular, of knot structures. To address this issue, we begin with the optimal vector field and helical line, and propose a new algorithm to introduce knots through stochastic perturbations associated with splay and twist deformations, modeled by means of a Langevin system. We conclude by comparing knot distributions generated by the model and by interpreting them in the context of previously published experimental results. Altogether, this work relies on the synergy of modeling, analysis and computation in the study of viral DNA organization in capsids.

cond-mat.soft

Entanglement statistics of polymers in a lattice tube and unknotting of 4-plats

The Knot Entropy Conjecture states that the exponential growth rate of the number of $n$-edge lattice polygons with knot-type $K$ is the same as that for unknot polygons. Moreover, the next order growth follows a power law in $n$ with an exponent that increases by one for each prime knot in the knot decomposition of $K$. We provide the first proof of this conjecture by considering knots and non-split links in tube $\mathbb{T}^*$, an $\infty \times 2\times 1$ sublattice of the simple cubic lattice. We establish upper and lower bounds relating the asymptotics of the number of $n$-edge polygons with fixed link-type in $\mathbb{T}^*$ to that of the number of $n$-edge unknots. For the upper bound, we prove that polygons can be unknotted by braid insertions. For the lower bound, we prove a pattern theorem for unknots using information from exact transfer-matrices. This work provides new knot theory results for 4-plats and new combinatorics results for lattice polygons. Connections to modelling polymers such as DNA in nanochannels are highlighted.

math.GT

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.

cond-mat.soft

A note on band surgery and the signature of a knot

Band surgery is an operation relating pairs of knots or links in the three-sphere. We prove that if two quasi-alternating knots $K$ and $K'$ of the same square-free determinant are related by a band surgery, then the absolute value of the difference in their signatures is either 0 or 8. This obstruction follows from a more general theorem about the difference in the Heegaard Floer $d$-invariants for pairs of L-spaces that are related by distance one Dehn fillings and satisfy a certain condition in first homology. These results imply that $T(2, 5)$ is the only torus knot $T(2, m)$ with $m$ square-free that admits a chirally cosmetic banding, i.e. a band surgery operation to its mirror image. We conclude with a discussion on the scarcity of chirally cosmetic bandings.

math.GT

Distance one lens space fillings and band surgery on the trefoil knot

We prove that if the lens space $L(n, 1)$ is obtained by a surgery along a knot in the lens space $L(3,1)$ that is distance one from the meridional slope, then $n$ is in $\{-6, \pm 1, \pm 2, 3, 4, 7\}$. This result yields a classification of the coherent and non-coherent band surgeries from the trefoil to $T(2, n)$ torus knots and links. The main result is proved by studying the behavior of the Heegaard Floer $d$-invariants under integral surgery along knots in $L(3,1)$. The classification of band surgeries between the trefoil and torus knots and links is motivated by local reconnection processes in nature, which are modeled as band surgeries. Of particular interest is the study of recombination on circular DNA molecules.

math.GT

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.

cond-mat.soft

Recent advances on the non-coherent band surgery model for site-specific recombination

Site-specific recombination is an enzymatic process where two sites of precise sequence and orientation along a circle come together, are cleaved, and the ends are recombined. Site-specific recombination on a knotted substrate produces another knot or a two-component link depending on the relative orientation of the sites prior to recombination. Mathematically, site-specific recombination is modeled as coherent (knot to link) or non-coherent (knot to knot) banding. We here survey recent developments in the study of non-coherent bandings on knots and discuss biological implications.

math.GT

A Liquid Crystal Model of Viral DNA Encapsidation

A liquid crystal continuum modeling framework for icosahedra bacteriophage viruses is developed and tested. The main assumptions of the model are the chromonic columnar hexagonal structure of confined DNA, the high resistance to bending and the phase transition from solid to fluid-like states as the concentration of DNA in the capsid decreases during infection. The model predicts osmotic pressure inside the capsid and the ejection force of the DNA as well as the size of the isotropic volume at the center of the capsid. Extensions of the model are discussed.

cond-mat.soft

Tangle analysis of difference topology experiments: applications to a Mu protein-DNA complex

We develop topological methods for analyzing difference topology experiments involving 3-string tangles. Difference topology is a novel technique used to unveil the structure of stable protein-DNA complexes involving two or more DNA segments. We analyze such experiments for the Mu protein-DNA complex. We characterize the solutions to the corresponding tangle equations by certain knotted graphs. By investigating planarity conditions on these graphs we show that there is a unique biologically relevant solution. That is, we show there is a unique rational tangle solution, which is also the unique solution with small crossing number.

math.GT