Direction dependent mechanical unfolding and Green Fluorescent Protein as a force sensor

An Ising--like model of proteins is used to investigate the mechanical unfolding of the Green Fluorescent Protein along different directions. When the protein is pulled from its ends, we recover the major and minor unfolding pathways observed in experiments. Upon varying the pulling direction, we find the correct order of magnitude and ranking of the unfolding forces. Exploiting the direction dependence of the unfolding force at equilibrium, we propose a force sensor whose luminescence depends on the applied force.Comment: to appear in Phys Rev

Topological Friction and Relaxation Dynamics of Spatially Confined Catenated Polymers

We study catenated ring polymers confined inside channels and slits with Langevin dynamics simulations and address how the contour position and size of the interlocked or physically linked region evolve with time. We show that the catenation constraints generate a drag, or topological friction, that couples the contour motion of the interlocked regions. Notably, the coupling strength decreases as the interlocking is made tighter, but also shorter, by confinement. Though the coupling strength differs for channel and slit confinement, the data outline a single universal curve when plotted against the size of the linked region. Finally, we study how the relaxation kinetics changes after one of the rings is cut open and conclude that considering interlocked circular polymers is key for isolating the manifestations of topological friction. The results ought to be relevant for linked biomolecules in experimental or biological confining conditions

Effects of confinement on thermal stability and folding kinetics in a simple Ising-like model

In cellular environment, confinement and macromulecular crowding play an important role on thermal stability and folding kinetics of a protein. We have resorted to a generalized version of the Wako-Saito-Munoz-Eaton model for protein folding to study the behavior of six different protein structures confined between two walls. Changing the distance 2R between the walls, we found, in accordance with previous studies, two confinement regimes: starting from large R and decreasing R, confinement first enhances the stability of the folded state as long as this is compact and until a given value of R; then a further decrease of R leads to a decrease of folding temperature and folding rate. We found that in the low confinement regime both unfolding temperatures and logarithm of folding rates scale as R-{\gamma} where {\gamma} values lie in between 1.42 and 2.35

Response of Pinus sylvestris L. to recent climatic events in the French Mediterranean region

International audienceExceptional climatic events from 2003 to 2005 (scorching heat and drought) affected the whole of the vegetation in the French Mediterranean region and in particular Scott pines (Pinus sylvestris L.), one of the most important forest tree species in this area. To understand its response to these extreme conditions, we investigated its radial growth, branch length growth, architectural development and reproduction for the period 19952005, and linked these variables to climatic parameters. We used four plots situated in southeastern France and presenting different levels of site quality and potential forest productivity. The results show that: (1) the climatic episode 20032005 was highly detrimental to the growth (bole and branches), crown development, and cone production but favoured the production of male flowers; (2)these variables depend on climatic factors of both the current and previous years; (3) the 2003 scorching heat impact was strong but was mainly apparent from 2004; it was part of a 6-year-long unfavourable cycle beginning in 2000, characterized by high minimum and maximum temperatures and very dry springs;(4) in spite of a significant effect of site quality, the Scots pine's response to extreme climatic conditions was homogeneous in the French Mediterranean area; and (5) the stress induced by poor site conditions generally resulted in the same consequences for tree growth, architecture, and reproduction as in unfavourable climatic conditions.Des événements climatiques exceptionnels de 2003 à 2005 (canicule et sécheresse) ont affecté la végétation dans la région de la Méditerranée française et en particulier le pin sylvestre (Pinus sylvestris L.), une des principales essences forestières de cette région. Pour comprendre sa réponse à ces conditions extrêmes, nous avons examiné sa croissance radiale, la croissance en longueur des branches, le développement architectural et la reproduction pendant la période 1995-2005 et avons relié ces variables avec les paramètres climatiques. Nous avons utilisé quatre placettes situées dans le sud-est de la France et présentant des niveaux différents de qualité stationnelle et de productivité forestière potentielle. Les résultats montrent que : (1) l'épisode climatique 2003-2005 était fortement néfaste à la croissance (tronc et branches), au développement du houppier et à la production de cônes, mais a favorisé la production de fleurs mâles; (2) ces variables dépendent des facteurs climatiques des années en cours et précédente; (3) l'impact de canicule 2003 était fort, mais était principalement apparent de 2004; il faisait partie d'un cycle défavorable de 6 ans commençant en 2000, caractérisé par des hautes températures minimales et maximales et des printemps très secs; (4) malgré un effet significatif de la qualité stationnelle, la réponse du pin sylvestre aux conditions climatiques extrêmes était homogène dans la zone méditerranéenne française; Et (5) le stress provoqué par de mauvaises conditions stationnelles avait généralement les mêmes conséquences pour la croissance , l'architecture et la reproduction du pin sylvestre que des conditions climatiques défavorables

Entropy inequalities from reflection positivity

We investigate the question of whether the entropy and the Renyi entropies of the vacuum state reduced to a region of the space can be represented in terms of correlators in quantum field theory. In this case, the positivity relations for the correlators are mapped into inequalities for the entropies. We write them using a real time version of reflection positivity, which can be generalized to general quantum systems. Using this generalization we can prove an infinite sequence of inequalities which are obeyed by the Renyi entropies of integer index. There is one independent inequality involving any number of different subsystems. In quantum field theory the inequalities acquire a simple geometrical form and are consistent with the integer index Renyi entropies being given by vacuum expectation values of twisting operators in the Euclidean formulation. Several possible generalizations and specific examples are analyzed.Comment: Significantly enlarged and corrected version. Counterexamples found for the most general form of the inequalities. V3: minor change

Entanglement of excited states in critical spin chians

Renyi and von Neumann entropies quantifying the amount of entanglement in ground states of critical spin chains are known to satisfy a universal law which is given by the Conformal Field Theory (CFT) describing their scaling regime. This law can be generalized to excitations described by primary fields in CFT, as was done in reference (Alcaraz et. al., Phys. Rev. Lett. 106, 201601 (2011)), of which this work is a completion. An alternative derivation is presented, together with numerical verifications of our results in different models belonging to the c=1,1/2 universality classes. Oscillations of the Renyi entropy in excited states and descendant fields are also discussed.Comment: 23 pages, 13 figure

Remarks on the entanglement entropy for disconnected regions

Few facts are known about the entanglement entropy for disconnected regions in quantum field theory. We study here the property of extensivity of the mutual information, which holds for free massless fermions in two dimensions. We uncover the structure of the entropy function in the extensive case, and find an interesting connection with the renormalization group irreversibility. The solution is a function on space-time regions which complies with all the known requirements a relativistic entropy function has to satisfy. We show that the holographic ansatz of Ryu and Takayanagi, the free scalar and Dirac fields in dimensions greater than two, and the massive free fields in two dimensions all fail to be exactly extensive, disproving recent conjectures.Comment: 14 pages, 4 figures, some addition

Holographic View on Quantum Correlations and Mutual Information between Disjoint Blocks of a Quantum Critical System

In (d+1) dimensional Multiscale Entanglement Renormalization Ansatz (MERA) networks, tensors are connected so as to reproduce the discrete, (d + 2) holographic geometry of Anti de Sitter space (AdSd+2) with the original system lying at the boundary. We analyze the MERA renormalization flow that arises when computing the quantum correlations between two disjoint blocks of a quantum critical system, to show that the structure of the causal cones characteristic of MERA, requires a transition between two different regimes attainable by changing the ratio between the size and the separation of the two disjoint blocks. We argue that this transition in the MERA causal developments of the blocks may be easily accounted by an AdSd+2 black hole geometry when the mutual information is computed using the Ryu-Takayanagi formula. As an explicit example, we use a BTZ AdS3 black hole to compute the MI and the quantum correlations between two disjoint intervals of a one dimensional boundary critical system. Our results for this low dimensional system not only show the existence of a phase transition emerging when the conformal four point ratio reaches a critical value but also provide an intuitive entropic argument accounting for the source of this instability. We discuss the robustness of this transition when finite temperature and finite size effects are taken into account.Comment: 21 pages, 5 figures. Abstract and Figure 1 has been modified. Minor modifications in Section 1 and Section

Entanglement entropy of two disjoint intervals in conformal field theory

We study the entanglement of two disjoint intervals in the conformal field theory of the Luttinger liquid (free compactified boson). Tr\rho_A^n for any integer n is calculated as the four-point function of a particular type of twist fields and the final result is expressed in a compact form in terms of the Riemann-Siegel theta functions. In the decompactification limit we provide the analytic continuation valid for all model parameters and from this we extract the entanglement entropy. These predictions are checked against existing numerical data.Comment: 34 pages, 7 figures. V2: Results for small x behavior added, typos corrected and refs adde