Searcharxiv⌕ Search

arXiv subjects

Simona Cocco

Publications and source records attributed to Simona Cocco.

50 records · Page 3Linked to original sources

Dynamical modelling of molecular constructions and setups for DNA unzipping

We present a dynamical model of DNA mechanical unzipping under the action of a force. The model includes the motion of the fork in the sequence-dependent landscape, the trap(s) acting on the bead(s), and the polymeric components of the molecular construction (unzipped single strands of DNA, and linkers). Different setups are considered to test the model, and the outcome of the simulations is compared to simpler dynamical models existing in the literature where polymers are assumed to be at equilibrium.

q-bio.BM↗

Inferring DNA sequences from mechanical unzipping data: the large-bandwidth case

The complementary strands of DNA molecules can be separated when stretched apart by a force; the unzipping signal is correlated to the base content of the sequence but is affected by thermal and instrumental noise. We consider here the ideal case where opening events are known to a very good time resolution (very large bandwidth), and study how the sequence can be reconstructed from the unzipping data. Our approach relies on the use of statistical Bayesian inference and of Viterbi decoding algorithm. Performances are studied numerically on Monte Carlo generated data, and analytically. We show how multiple unzippings of the same molecule may be exploited to improve the quality of the prediction, and calculate analytically the number of required unzippings as a function of the bandwidth, the sequence content, the elasticity parameters of the unzipped strands.

q-bio.BM↗

Reconstructing a Random Potential from its Random Walks

The problem of how many trajectories of a random walker in a potential are needed to reconstruct the values of this potential is studied. We show that this problem can be solved by calculating the probability of survival of an abstract random walker in a partially absorbing potential. The approach is illustrated on the discrete Sinai (random force) model with a drift. We determine the parameter (temperature, duration of each trajectory, ...) values making reconstruction as fast as possible.

cond-mat.stat-mech↗

Protein-Mediated DNA Loops: Effects of Protein Bridge Size and Kinks

This paper focuses on the probability that a portion of DNA closes on itself through thermal fluctuations. We investigate the dependence of this probability upon the size r of a protein bridge and/or the presence of a kink at half DNA length. The DNA is modeled by the Worm-Like Chain model, and the probability of loop formation is calculated in two ways: exact numerical evaluation of the constrained path integral and the extension of the Shimada and Yamakawa saddle point approximation. For example, we find that the looping free energy of a 100 base pairs DNA decreases from 24 kT to 13 kT when the loop is closed by a protein of r = 10 nm length. It further decreases to 5 kT when the loop has a kink of 120 degrees at half-length.

cond-mat.soft↗

Role of calcium and noise in the persistent activity of an isolated neuron

The activity of an isolated and auto-connected neuron is studied using Hodgkin--Huxley and Integrate-and-Fire frameworks. Main ingredients of the modeling are the auto-stimulating autaptic current observed in experiments, with a spontaneous synaptic liberation noise and a calcium--dependent negative feedback mechanism. The distributions of inter-spikes intervals and burst durations are analytically calculated, and show a good agreement with experimental data.

q-bio.NC↗

Heuristic average-case analysis of the backtrack resolution of random 3-Satisfiability instances

An analysis of the average-case complexity of solving random 3-Satisfiability (SAT) instances with backtrack algorithms is presented. We first interpret previous rigorous works in a unifying framework based on the statistical physics notions of dynamical trajectories, phase diagram and growth process. It is argued that, under the action of the Davis--Putnam--Loveland--Logemann (DPLL) algorithm, 3-SAT instances are turned into 2+p-SAT instances whose characteristic parameters (ratio alpha of clauses per variable, fraction p of 3-clauses) can be followed during the operation, and define resolution trajectories. Depending on the location of trajectories in the phase diagram of the 2+p-SAT model, easy (polynomial) or hard (exponential) resolutions are generated. Three regimes are identified, depending on the ratio alpha of the 3-SAT instance to be solved. Lower sat phase: for small ratios, DPLL almost surely finds a solution in a time growing linearly with the number N of variables. Upper sat phase: for intermediate ratios, instances are almost surely satisfiable but finding a solution requires exponential time (2 ^ (N omega) with omega>0) with high probability. Unsat phase: for large ratios, there is almost always no solution and proofs of refutation are exponential. An analysis of the growth of the search tree in both upper sat and unsat regimes is presented, and allows us to estimate omega as a function of alpha. This analysis is based on an exact relationship between the average size of the search tree and the powers of the evolution operator encoding the elementary steps of the search heuristic.

cs.DS↗

Approximate analysis of search algorithms with "physical" methods

An overview of some methods of statistical physics applied to the analysis of algorithms for optimization problems (satisfiability of Boolean constraints, vertex cover of graphs, decoding, ...) with distributions of random inputs is proposed. Two types of algorithms are analyzed: complete procedures with backtracking (Davis-Putnam-Loveland-Logeman algorithm) and incomplete, local search procedures (gradient descent, random walksat, ...). The study of complete algorithms makes use of physical concepts such as phase transitions, dynamical renormalization flow, growth processes, ... As for local search procedures, the connection between computational complexity and the structure of the cost function landscape is questioned, with emphasis on the notion of metastability.

cs.CC↗

Analysis of the computational complexity of solving random satisfiability problems using branch and bound search algorithms

The computational complexity of solving random 3-Satisfiability (3-SAT) problems is investigated. 3-SAT is a representative example of hard computational tasks; it consists in knowing whether a set of alpha N randomly drawn logical constraints involving N Boolean variables can be satisfied altogether or not. Widely used solving procedures, as the Davis-Putnam-Loveland-Logeman (DPLL) algorithm, perform a systematic search for a solution, through a sequence of trials and errors represented by a search tree. In the present study, we identify, using theory and numerical experiments, easy (size of the search tree scaling polynomially with N) and hard (exponential scaling) regimes as a function of the ratio alpha of constraints per variable. The typical complexity is explicitly calculated in the different regimes, in very good agreement with numerical simulations. Our theoretical approach is based on the analysis of the growth of the branches in the search tree under the operation of DPLL. On each branch, the initial 3-SAT problem is dynamically turned into a more generic 2+p-SAT problem, where p and 1-p are the fractions of constraints involving three and two variables respectively. The growth of each branch is monitored by the dynamical evolution of alpha and p and is represented by a trajectory in the static phase diagram of the random 2+p-SAT problem. Depending on whether or not the trajectories cross the boundary between phases, single branches or full trees are generated by DPLL, resulting in easy or hard resolutions.

cond-mat.stat-mech↗

Trajectories in phase diagrams, growth processes and computational complexity: how search algorithms solve the 3-Satisfiability problem

Most decision and optimization problems encountered in practice fall into one of two categories with respect to any particular solving method or algorithm: either the problem is solved quickly (easy) or else demands an impractically long computational effort (hard). Recent investigations on model classes of problems have shown that some global parameters, such as the ratio between the constraints to be satisfied and the adjustable variables, are good predictors of problem hardness and, moreover, have an effect analogous to thermodynamical parameters, e.g. temperature, in predicting phases in condensed matter physics [Monasson et al., Nature 400 (1999) 133-137]. Here we show that changes in the values of such parameters can be tracked during a run of the algorithm defining a trajectory through the parameter space. Focusing on 3-Satisfiability, a recognized representative of hard problems, we analyze trajectories generated by search algorithms using growth processes statistical physics. These trajectories can cross well defined phases, corresponding to domains of easy or hard instances, and allow to successfully predict the times of resolution.

cond-mat.dis-nn↗

Theoretical study of collective modes in DNA at ambient temperature

The instantaneous normal modes corresponding to base pair vibrations (radial modes) and twist angle fluctuations (angular modes) of a DNA molecule model at ambient temperature are theoretically investigated. Due to thermal disorder, normal modes are not plane waves with a single wave number q but have a finite and frequency dependent damping width. The density of modes rho(nu), the average dispersion relation nu(q) as well as the coherence length xi(nu) are analytically calculated. The Gibbs averaged resolvent is computed using a replicated transfer matrix formalism and variational wave functions for the ground and first excited state. Our results for the density of modes are compared to Raman spectroscopy measurements of the collective modes for DNA in solution and show a good agreement with experimental data in the low frequency regime nu < 150 cm^{-1}. Radial modes extend over frequencies ranging from 50 cm^{-1} to 110 cm^{-1}. Angular modes, related to helical axis vibrations are limited to nu < 25 cm^{-1}. Normal modes are highly disordered and coherent over a few base pairs only (xi < 2 nm) in good agreement with neutron scattering experiments.

cond-mat.stat-mech↗

Statistical Mechanics of Torque Induced Denaturation of DNA

A unifying theory of the denaturation transition of DNA, driven by temperature T or induced by an external mechanical torque Gamma is presented. Our model couples the hydrogen-bond opening and the untwisting of the helicoidal molecular structure. We show that denaturation corresponds to a first-order phase transition from B-DNA to d-DNA phases and that the coexistence region is naturally parametrized by the degree of supercoiling sigma. The denaturation free energy, the temperature dependence of the twist angle, the phase diagram in the T,Gamma plane and isotherms in the sigma, Gamma plane are calculated and show a good agreement with experimental data.

cond-mat.stat-mech↗

Vector Nonlinear Klein-Gordon Lattices: General Derivation of Small Amplitude Envelope Soliton Solutions

Group velocity and group velocity dispersion for a wave packet in vectorial discrete Klein-Gordon models are obtained by an expansion, based on perturbation theory, of the linear system giving the dispersion relation and the normal modes. We show how to map this expansion on the Multiple Scale Expansion in the real space and how to find Non Linear Schrödinger small amplitude solutions when a nonlinear one site potential balances the group velocity dispersion effect.

chao-dyn↗

Helicoidal model for DNA opening

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.

chao-dyn↗