Condensed Matter Theory

Abstract:

The resistance of DNA to stretch, twist and bend is broadly well estimated by experiments and is important for gene regulation and chromosome packing. However, their sequence-dependence and how bulk elastic constants emerge from local fluctuations is less understood. Here, we present SerraNA, which is an open software that calculates elastic parameters of double-stranded nucleic acids from dinucleotide length up to the whole molecule using ensembles from numerical simulations. The program reveals that global bendability emerge from local periodic bending angles in phase with the DNA helicoidal shape. We apply SerraNA to the whole set of 136 tetra-bp combinations and we observe a high degree of sequence-dependence with differences over 200% for all elastic parameters. Tetramers with TA and CA base-pair steps are especially flexible, while the ones containing AA and AT tend to be the most rigid. Thus, AT-rich motifs can generate extreme mechanical properties, which are critical for creating strong global bends when phased properly. Our results also indicate base mismatches would make DNA more flexible, while protein binding would make it more rigid. SerraNA is a tool to be applied in the next generation of interdisciplinary investigations to further understand what determines the elasticity of DNA.

Abstract:

In nature, interactions between biopolymers and motor proteins give rise to biologically essential emergent behaviors. Besides cytoskeleton mechanics, active nematics arise from such interactions. Here we present a study on 3D active nematics made of microtubules, kinesin motors, and depleting agent. It shows a rich behavior evolving from a nematically ordered space-filling distribution of microtubule bundles toward a flattened and contracted 2D ribbon that undergoes a wrinkling instability and subsequently transitions into a 3D active turbulent state. The wrinkle wavelength is independent of the ATP concentration and our theoretical model describes its relation with the appearance time. We compare the experimental results with a numerical simulation that confirms the key role of kinesin motors in cross-linking and sliding the microtubules. Our results on the active contraction of the network and the independence of wrinkle wavelength on ATP concentration are important steps forward for the understanding of these 3D systems.

Abstract:

Collective chemotaxis plays a key role in the navigation of cell clusters in e.g. embryogenesis and cancer metastasis. Using the active nematic continuum equations, coupled to a chemical field that regulates activity, we demonstrate and explain a physical mechanism that results in collective chemotaxis. The activity naturally leads to cell polarisation at the cluster interface which induces outwards flows. The chemical gradient then breaks the symmetry of the flow field, leading to a net motion. The velocity is independent of the cluster size in agreement with experiment.

Abstract:

We consider a model of two tunnel-coupled one-dimensional Bose gases with hard-wall boundary conditions. Bosonizing the model and retaining only the most relevant interactions leads to a decoupled theory consisting of a quantum sine-Gordon model and a free boson, describing respectively the antisymmetric and symmetric combinations of the phase fields. We go beyond this description by retaining the perturbation with the next smallest scaling dimension. This perturbation carries conformal spin and couples the two sectors. We carry out a detailed investigation of the effects of this coupling on the non-equilibrium dynamics of the model. We focus in particular on the role played by spatial inhomogeneities in the initial state in a quantum quench setup.

Abstract:

For an interacting spatio-temporal lattice system we introduce a formal way of expressing multi-time correlation functions of local observables located at the same spatial point with a time state, i.e. a statistical distribution of configurations observed along a time lattice. Such a time state is defined with respect to a particular equilibrium state that is invariant under space and time translations. The concept is developed within the rule 54 reversible cellular automaton, for which we explicitly construct a matrix product form of the time state, with matrices that act on the three-dimensional auxiliary space. We use the matrix-product state to express equal-space time-dependent density-density correlation function, which, for special maximum-entropy values of equilibrium parameters, agrees with the previous results. Additionally, we obtain an explicit expression for the probabilities of observing all multi-time configurations, which enables us to study distributions of times between consecutive excitations and prove the absence of decoupling of timescales in the rule 54 model.