89 research outputs found
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
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