Optimal localization patterns in bacterial protein synthesis

In $\textit{Escherichia coli}$ bacterium, the molecular compounds involved in protein synthesis, messenger RNAs (mRNAs) and ribosomes, show marked intracellular localization patterns. Yet a quantitative understanding of the physical principles which would allow one to control protein synthesis by designing, bioengineering, and optimizing these localization patterns is still lacking. In this study, we consider a scenario where a synthetic modification of mRNA reaction-diffusion properties allows for controlling the localization and stoichiometry of mRNAs and polysomes$\mathrm{-}$complexes of multiple ribosomes bound to mRNAs. Our analysis demonstrates that protein synthesis can be controlled, e.g., optimally enhanced or inhibited, by leveraging mRNA spatial localization and stoichiometry only, without resorting to alterations of mRNA expression levels. We identify the physical mechanisms that control the protein-synthesis rate, highlighting the importance of colocalization between mRNAs and freely diffusing ribosomes, and the interplay between polysome stoichiometry and excluded-volume effects due to the DNA nucleoid. The genome-wide, quantitative predictions of our work may allow for a direct verification and implementation in cell-biology experiments, where localization patterns and protein-synthesis rates may be monitored by fluorescence microscopy in single cells and populations

Non-perturbative effects in spin glasses

We present a numerical study of an Ising spin glass with hierarchical interactions - the hierarchical Edwards-Anderson model with an external magnetic field (HEA). We study the model with Monte Carlo (MC) simulations in the mean-field (MF) and non-mean-field (NMF) regions corresponding to $d\geq4$ and $d<4$ for the $d$-dimensional ferromagnetic Ising model respectively. We compare the MC results with those of a renormalization-group (RG) study where the critical fixed point is treated as a perturbation of the MF one, along the same lines as in the $\epsilon$-expansion for the Ising model. The MC and the RG method agree in the MF region, predicting the existence of a transition and compatible values of the critical exponents. Conversely, the two approaches markedly disagree in the NMF case, where the MC data indicates a transition, while the RG analysis predicts that no perturbative critical fixed point exists. Also, the MC estimate of the critical exponent $\nu$ in the NMF region is about twice as large as its classical value, even if the analog of the system dimension is within only $\sim 2\%$ from its upper-critical-dimension value. Taken together, these results indicate that the transition in the NMF region is governed by strong non-perturbative effects

A renormalization group computation of the critical exponents of hierarchical spin glasses

The infrared behaviour of a non-mean field spin-glass system is analysed, and the critical exponent related to the divergence of the correlation length is computed at two loops within the epsilon-expansion technique with two independent methods. Both methods yield the same result confirming that the infrared behaviour of the theory if well-defined and the underlying ideas of the Renormalization Group hold also in such non-mean field disordered model. By pushing such calculation to high orders in epsilon, a consistent and predictive non-mean field theory for such disordered system could be established

Reply to comment on 'Real-space renormalization-group methods for hierarchical spin glasses'

In their comment, Angelini et al. object to the conclusion of [J. Phys. A: Math. Theor., 52:445002, 2019] (1), where we show that in [Phys. Rev. B, 87:134201, 2013] the exponent $\nu$ has been obtained by applying a mathematical relation in a regime where this relation is not valid. We observe that the criticism above on the mathematical validity of such relation has not been addressed in the comment. Our criticism thus remains valid, and disproves the conclusions of the comment. This constitutes the main point of this reply. We also provide a point-by-point response and discussion of Angelini et al.'s claims. First, Angelini et al. claim that the prediction $2^{1/\nu}=1$ of [1] is incorrect, because it results from the relation $\lambda_{\rm max}=2^{1/\nu}$ between the largest eigenvalue of the linearized renormalization-group (RG) transformation and $\nu$, which cannot be applied to the ensemble renormalization group (ERG) method, because for the ERG $\lambda_{\rm max} =1$. However, the feature $\lambda_{\rm max}=1$ is specific to the ERG transformation and it does not give any grounds for questioning the validity of the general relation $\lambda_{\rm max}=2^{1/\nu}$ specifically for the ERG transformation. Second, Angelini et al. claim that $\nu$ should be extracted from an early RG regime (A), as opposed to the asymptotic regime (B) used to estimate $\nu$ in [1] and that (B) is dominated by finite-size effects. Still, (A) is a small-wavelength, non-critical regime, which cannot characterize the critical exponent $\nu$ related to the divergence of the correlation length. Also, the fact that (B) involves finite-size effects is a feature specific to the ERG, and gives no rationale for extracting $\nu$ from (A). Finally, we refute the remaining claims made by Angelini et al., and thus stand by our assertion that the ERG method yields a prediction given by $2^{1/\nu}=1$.Comment: Reply to arXiv:1911.0232

Free-energy bounds for hierarchical spin models

In this paper we study two non-mean-field spin models built on a hierarchical lattice: The hierarchical Edward-Anderson model (HEA) of a spin glass, and Dyson's hierarchical model (DHM) of a ferromagnet. For the HEA, we prove the existence of the thermodynamic limit of the free energy and the replica-symmetry-breaking (RSB) free-energy bounds previously derived for the Sherrington-Kirkpatrick model of a spin glass. These RSB mean-field bounds are exact only if the order-parameter fluctuations (OPF) vanish: Given that such fluctuations are not negligible in non-mean-field models, we develop a novel strategy to tackle part of OPF in hierarchical models. The method is based on absorbing part of OPF of a block of spins into an effective Hamiltonian of the underlying spin blocks. We illustrate this method for DHM and show that, compared to the mean-field bound for the free energy, it provides a tighter non-mean-field bound, with a critical temperature closer to the exact one. To extend this method to the HEA model, a suitable generalization of Griffith's correlation inequalities for Ising ferromagnets is needed: Since correlation inequalities for spin glasses are still an open topic, we leave the extension of this method to hierarchical spin glasses as a future perspective