Simona Cocco

Neuronal couplings between retinal ganglion cells inferred by efficient inverse statistical physics methods

Complexity of neural systems often makes impracticable explicit measurements of all interactions between their constituents. Inverse statistical physics approaches, which infer effective couplings between neurons from their spiking activity, have been so far hindered by their computational complexity. Here, we present 2 complementary, computationally efficient inverse algorithms based on the Ising and “leaky integrate-and-fire” models. We apply those algorithms to reanalyze multielectrode recordings in the salamander retina in darkness and under random visual stimulus. We find strong positive couplings between nearby ganglion cells common to both stimuli, whereas long-range couplings appear under random stimulus only. The uncertainty on the inferred couplings due to limitations in the recordings (duration, small area covered on the retina) is discussed. Our methods will allow real-time evaluation of couplings for large assemblies of neurons.

Force and kinetic barriers to unzipping of the DNA double helix

A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss) simply determine the sequence dependent =12 pN force threshold for DNA strand separation. Using a semi-microscopic model of the binding between nucleotide strands, we show that the greater rigidity of the strands when formed into dsDNA, relative to that of isolated strands, gives rise to a potential barrier to unzipping. The effects of this barrier are derived analytically. The force to keep the extremities of the molecule at a fixed distance, the kinetic rates for strand unpairing at fixed applied force, and the rupture force as a function of loading rate are calculated. The dependence of the kinetics and of the rupture force on molecule length is also analyzed.A theory of the unzipping of double-stranded DNA is presented and is compared to recent micromanipulation experiments. It is shown that the interactions that stabilize the double helix and the elastic rigidity of single strands simply determine the sequence-dependent ≈12-pN force threshold for DNA strand separation. Using a semimicroscopic model of the binding between nucleotide strands, we show that the greater rigidity of the strands when formed into double-stranded DNA, relative to that of isolated strands, gives rise to a potential barrier to unzipping. The effects of this barrier are derived analytically. The force to keep the extremities of the molecule at a fixed distance, the kinetic rates for strand unpairing at fixed applied force, and the rupture force as a function of loading rate are calculated. The dependence of the kinetics and of the rupture force on molecule length is also analyzed.

Helicoidal model for DNA opening

Abstract We present a new dynamical model of DNA. This model has two degrees of freedom per base-pair: one radial variable related to the opening of the hydrogen bonds and an angular one related to the twisting of each base-pair responsible for the helicoidal structure of the molecule. The small amplitude dynamics of the model is studied analytically: we derive small amplitude envelope solutions made of a breather in the radial variables combined with a kink in the angular variables, showing the role of the topological constraints associated to the helicoidal geometry. We check the stability of the solutions by numerical integration of the motion equations.

Statistical Mechanics of Torque Induced Denaturation of DNA

A unifying theory of the denaturation transition of DNA, driven by temperature

Adaptive Cluster Expansion for Inferring Boltzmann Machines with Noisy Data

T

Rigorous Decimation-Based Construction of Ground Pure States for Spin-Glass Models on Random Lattices

or induced by an external mechanical torque

From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction

\ensuremath{\Gamma}

Slow nucleic acid unzipping kinetics from sequence-defined barriers

is presented. Our model couples the hydrogen-bond opening and the untwisting of the helicoidal molecular structure. We describe denaturation as a first order transition from

Adaptive Cluster Expansion for the Inverse Ising Problem: Convergence, Algorithm and Tests

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A Twist Opening Model for DNA

-DNA to