arXiv subjects

Fabio Cecconi

Publications and source records attributed to Fabio Cecconi.

At least 37 records · Page 2Linked to original sources

arXiv2015

Modulation of current through a nanopore induced by a charged globule: implications for DNA-docking

The passage of DNA through a nanopore can be effectively decomposed into two distinct phases, docking and actual translocation. In experiments each phase is characterized by a distinct current signature which allows the discrimination of the two events. However, at low voltages a clear distinction of the two phases is lost. By using numerical simulations we clarify how the current signature associated to the docking events depends on the applied voltage. The simulations show that at small voltage the DNA globule enhances the pore conductance due to an enrichment of charge carriers. At high voltage, the globule drains substantial charge carriers from the pore region, thereby reducing the overall conductance. The results provide a new interpretation to the experimental data on conductance and show how docking interferes with the translocation signal, of potential interest for sequencing applications.

physics.bio-ph↗

arXiv2014

Transport and fluctuation-dissipation relations in asymptotic and pre-asymptotic diffusion across channels with variable section

We study the asymptotic and pre-asymptotic diffusive properties of Brownian particles in channels whose section varies periodically in space. The effective diffusion coefficient $D_{\mathrm{eff}}$ is numerically determined by the asymptotic behavior of the root mean square displacement in different geometries, considering even cases of steep variations of the channel boundaries. Moreover, we compared the numerical results to the predictions from the various corrections proposed in the literature to the well known Fick-Jacobs approximation. Building an effective one dimensional equation for the longitudinal diffusion, we obtain an approximation for the effective diffusion coefficient. Such a result goes beyond a perturbation approach, and it is in good agreement with the actual values obtained by the numerical simulations. We discuss also the pre-asymptotic diffusion which is observed up to a crossover time whose value, in the presence of strong spatial variation of the channel cross section, can be very large. In addition, we show how the Einstein's relation between the mean drift induced by a small external field and the mean square displacement of the unperturbed system is valid in both asymptotic and pre-asymptotic regimes.

cond-mat.stat-mech↗

arXiv2014

Non-anomalous diffusion is not always Gaussian

Through the analysis of unbiased random walks on fractal trees and continuous time random walks, we show that even if a process is characterized by a mean square displacement (MSD) growing linearly with time (standard behaviour) its diffusion properties can be not trivial. In particular, we show that the following scenarios are consistent with a linear increase of MSD with time: i) the high-order moments, $\langle [x(t)]^q \rangle$ for $q>2$ and the probability density of the process exhibit multiscaling; ii) the random walk on certain fractal graphs, with non integer spectral dimension, can display a fully standard diffusion; iii) positive order moments satisfying standard scaling do not imply an exact scaling property of the probability density.

cond-mat.stat-mech↗

arXiv2014

Coarse-grained modeling of protein unspecifically bound to DNA

There is now a certain consensus that Transcription Factors (TFs) reach their target sites, where they regulate gene transcription, via a mechanism dubbed facilitated diffusion (FD). In FD, the TF cycles between events of 3D-diffusion in solution (jumps), 1D-diffusion along DNA (sliding), and small jumps (hopping) achieving association rates higher than for 3D-diffusion only. We investigate the FD phenomenology through Molecular Dynamics simulations in the framework of coarse-grained modeling. Despite the crude approximations, we show that the model generates, upon varying equilibrium distance of the DNA-TF interaction, a phenomenology matching a number of experimental and numerical results obtained with more refined models. In particular, by focusing on the kinematics of the process, we characterize the geometrical properties of TF trajectories during sliding. We find that sliding occurs via helical paths around the DNA helix leading to a coupling of translation along the DNA-axis with rotation around it. The 1D-diffusion constant measured in simulations is found to be interwoven with the geometrical properties of sliding and we develop a simple argument able to quantitatively reproduce the measured values.

q-bio.BM↗

arXiv2013

Anomalous diffusion and response in branched systems: a simple analysis

We revisit the diffusion properties and the mean drift induced by an external field of a random walk process in a class of branched structures, as the comb lattice and the linear chains of plaquettes. A simple treatment based on scaling arguments is able to predict the correct anomalous regime for different topologies. In addition, we show that even in the presence of anomalous diffusion, Einstein's relation still holds, implying a proportionality between the mean square displacement of the unperturbed systems and the drift induced by an external forcing.

cond-mat.stat-mech↗

arXiv2012

Thermally induced directed currents in hard rod systems

We study the non equilibrium statistical properties of a one dimensional hard-rod fluid undergoing collisions and subject to a spatially non uniform Gaussian heat-bath and periodic potential. The system is able to sustain finite currents when the spatially inhomogeneous heat-bath and the periodic potential profile display an appropriate relative phase shift, $ϕ$. By comparison with the collisionless limit, we determine the conditions for the most efficient transport among inelastic, elastic and non interacting rods. We show that the situation is complex as, depending on shape of the temperature profile, the current of one system may outperform the others.

cond-mat.stat-mech↗

arXiv2008

Temperature dependence of normal mode reconstructions of protein dynamics

Normal mode analysis is a widely used technique for reconstructing conformational changes of proteins from the knowledge of native structures. In this Letter, we investigate to what extent normal modes capture the salient features of the dynamics over a range of temperatures from close to T = 0 to above unfolding. We show that on the one hand, the use of normal modes at physiological temperatures is justified provided proteins are cooperative. On the other hand, it is imperative to consider several modes in order to eliminate the unpredictable temperature dependence of single- mode contributions to the protein fluctuations.

cond-mat.stat-mech↗

arXiv2008

Clustering and coalescence from multiplicative noise: the Kraichnan ensemble

We study the dynamics of the two-point statistics of the Kraichnan ensemble which describes the transport of a passive pollutant by a stochastic turbulent flow characterized by scale invariant structure functions. The fundamental equation of this problem consists in the Fokker-Planck equation for the two-point correlation function of the density of particles performing spatially correlated Brownian motions with scale invariant correlations. This problem is equivalent to the stochastic motion of an effective particle driven by a generic multiplicative noise. In this paper we propose an alternative and more intuitive approach to the problem than the original one leading to the same conclusions. The general features of this new approach make possible to fit it to other more complex contexts.

cond-mat.stat-mech↗

arXiv2008

Role of chaos for the validity of statistical mechanics laws: diffusion and conduction

Several years after the pioneering work by Fermi Pasta and Ulam, fundamental questions about the link between dynamical and statistical properties remain still open in modern statistical mechanics. Particularly controversial is the role of deterministic chaos for the validity and consistency of statistical approaches. This contribution reexamines such a debated issue taking inspiration from the problem of diffusion and heat conduction in deterministic systems. Is microscopic chaos a necessary ingredient to observe such macroscopic phenomena?

nlin.CD↗

arXiv2007

Diffusion-limited unbinding of small peptides from PDZ domains

PDZ domains are typical examples of binding motifs mediating the formation of protein-protein assemblies in many different cells. A quantitative characterization of the mechanisms intertwining structure, chemistry and dynamics with the PDZ function represent a challenge in molecular biology. Here we investigated the influence of native state topology on the thermodynamics and the dissociation kinetics for a complex PDZ-peptide via Molecular Dynamics simulations based on a coarse-grained description of PDZ domains. Our native-centric approach neglects chemical details but incorporates the basic structural information to reproduce the protein functional dynamics as it couples to the binding. We found that at physiological temperatures the unbinding of a peptide from the PDZ domain becomes increasingly diffusive rather than thermally activated, as a consequence of the significant reduction of the free energy barrier with temperature. In turn, this results in a significant slowing down of the process of two orders of magnitude with respect to the conventional Arrhenius extrapolation from low temperature calculations. Finally, a detailed analysis of a typical unbinding event based on the rupture times of single peptide-PDZ contacts allows to shed further light on the dissociation mechanism and to elaborate a coherent picture of the relation between function and dynamics in PDZ domains.

physics.bio-ph↗

arXiv2007

Computational analysis of folding and mutation properties of C5 domain from Myosin binding protein C

Thermal folding Molecular Dynamics simulations of the domain C5 from Myosin Binding Protein C were performed using a native-centric model to study the role of three mutations related to Familial Hypertrophic Cardiomyopathy. Mutation of Asn755 causes the largest shift of the folding temperature, and the residue is located in the CFGA' beta-sheet featuring the highest Phi-values. The mutation thus appears to reduce the thermodynamic stability in agreement with experimental data. The mutations on Arg654 and Arg668, conversely, cause a little change in the folding temperature and they reside in the low Phi-value BDE beta-sheet, so that their pathologic role cannot be related to impairment of the folding process but possibly to the binding with target molecules. As the typical signature of Domain C5 is the presence of a longer and destabilizing CD-loop with respect to the other Ig-like domains we completed the work with a bioinformatic analysis of this loop showing a high density of negative charge and low hydrophobicity. This indicates the CD-loop as a natively unfolded sequence with a likely coupling between folding and ligand binding.

q-bio.GN↗

arXiv2007

Transport properties in chaotic and non-chaotic many particles systems

Two deterministic models for Brownian motion are investigated by means of numerical simulations and kinetic theory arguments. The first model consists of a heavy hard disk immersed in a rarefied gas of smaller and lighter hard disks acting as a thermal bath. The second is the same except for the shape of the particles, which is now square. The basic difference of these two systems lies in the interaction: hard core elastic collisions make the dynamics of the disks chaotic whereas that of squares is not. Remarkably, this difference is not reflected in the transport properties of the two systems: simulations show that the diffusion coefficients, velocity correlations and response functions of the heavy impurity are in agreement with kinetic theory for both the chaotic and the non-chaotic model. The relaxation to equilibrium, however, is very sensitive to the kind of interaction. These observations are used to reconsider and discuss some issues connected to chaos, statistical mechanics and diffusion.

nlin.CD↗

arXiv2007

Diffusion, super-diffusion and coalescence from single step

From the exact single step evolution equation of the two-point correlation function of a particle distribution subjected to a stochastic displacement field $\bu(\bx)$, we derive different dynamical regimes when $\bu(\bx)$ is iterated to build a velocity field. First we show that spatially uncorrelated fields $\bu(\bx)$ lead to both standard and anomalous diffusion equation. When the field $\bu(\bx)$ is spatially correlated each particle performs a simple free Brownian motion, but the trajectories of different particles result to be mutually correlated. The two-point statistical properties of the field $\bu(\bx)$ induce two-point spatial correlations in the particle distribution satisfying a simple but non-trivial diffusion-like equation. These displacement-displacement correlations lead the system to three possible regimes: coalescence, simple clustering and a combination of the two. The existence of these different regimes, in the one-dimensional system, is shown through computer simulations and a simple theoretical argument.

cond-mat.stat-mech↗

arXiv2007

Theory of thermostatted inhomogeneous granular fluids: a self-consistent density functional description

The authors present a study of the non equilibrium statistical properties of a one dimensional hard-rod fluid dissipating energy via inelastic collisions and subject to the action of a Gaussian heat bath, simulating an external driving mechanism. They show that the description of the fluid based on the one-particle phase-space reduced distribution function, in principle necessary because of the presence of velocity dependent collisional dissipation, can be contracted to a simpler description in configurational space. Indeed, by means of a multiple-time scale method the authors derive a self-consistent governing equation for the particle density distribution function. This equation is similar to the dynamic density functional equation employed in the study of colloids, but contains additional terms taking into account the inelastic nature of the fluid. Such terms cannot be derived from a Liapunov generating functional and contribute not only to the relaxational properties, but also to the non equilibrium steady state properties. A validation of the theory against molecular dynamics simulations is presented in a series of cases, and good agreement is found.

cond-mat.mtrl-sci↗

arXiv2007

Kinetics of self-induced aggregation in Brownian particles

We study a model of interacting random walkers that proposes a simple mechanism for the emergence of cooperation in group of individuals. Each individual, represented by a Brownian particle, experiences an interaction produced by the local unbalance in the spatial distribution of the other individuals. This interaction results in a nonlinear velocity driving the particle trajectories in the direction of the nearest more crowded regions; the competition among different aggregating centers generates nontrivial dynamical regimes. Our simulations show that for sufficiently low randomness, the system evolves through a coalescence behavior characterized by clusters of particles growing with a power law in time. In addition, the typical scaling properties of the general theory of stochastic aggregation processes are verified.

cond-mat.stat-mech↗

arXiv2006

Transport of a heated granular gas in a washboard potential

We study numerically the motion of a one dimensional array of Brownian particles in a washboard potential, driven by an external stochastic force and interacting via short range repulsive forces. In particular, we investigate the role of instantaneous elastic and inelastic collisions on the system dynamics and transport. The system displays a locked regime, where particles may move only via activated processes and a running regime where particles drift along the direction of the applied field. By tuning the value of the friction parameter controlling the Brownian motion we explore both the overdamped dynamics and the underdamped dynamics. In the two regimes we considered the mobility and the diffusivity of the system as functions of the tilt and other relevant control parameters such as, coefficient of restitution, particle size and total number of particles. We find that, while in the overdamped regime, the results for the interacting systems present similarities with the known non-interacting case, in the underdamped regime, the inelastic collisions determine a rich variety of behaviors among which is an unexpected enhancement of the inelastic diffusion.

cond-mat.stat-mech↗

arXiv2006

Testing simplified protein models of the hPin1 WW domain

The WW domain of the human Pin1 protein for its simple topology and the large amount of experimental data is an ideal candidate to assess theoretical approaches to protein folding. The purpose of the present work is to compare the reliability of the chemically-based Sorenson/Head-Gordon (SHG) model and a standard native centric model in reproducing through molecular dynamics simulations some of the well known features of the folding transition of this small domain. Our results show that the Gō model correctly reproduces the cooperative, two-state, folding mechanism of the WW-domain, while the SHG model predicts a transition occurring in two stages: a collapse followed by a structural rearrangement. The lack of a cooperative folding in the SHG simulations appears to be related to the non-funnel shape of the energy landscape featuring a partitioning of the native valley in sub-basins corresponding to different chain chiralities. However the SHG approach remains more reliable in estimating the $Φ$-values with respect to Gō-like description. This may suggest that the WW-domain folding process is stirred by energetic and topological factors as well, and it highlights the better suitability of chemically-based models in simulating mutations.

cond-mat.stat-mech↗

arXiv2005

The inelastic Takahashi hard-rod gas

We study a one-dimensional fluid of hard-rods interacting each other via binary inelastic collisions and a short ranged square-well potential. Upon tuning the depth and the sign of the well, we investigate the interplay between dissipation and cohesive or repulsive forces. Molecular dynamics simulations of the cooling regime indicate that the presence of this simple interparticle interaction is sufficient to significantly modify the energy dissipation rates expected by the Haff's law for the free cooling. The simplicity of the model makes it amenable to an analytical approach based on the Boltzmann-Enskog transport equation which allows deriving the behaviour of the granular temperature. Furthermore, in the elastic limit, the model can be solved exactly to provide a full thermodynamic description. A meaningful theoretical approximation explaining the properties of the inelastic system in interaction with a thermal bath can be directly extrapolated from the properties of the corresponding elastic system, upon a proper re-definition of the relevant observables. Simulation results both in the cooling and driven regime can be fairly interpreted according to our theoretical approach and compare rather well to our predictions.

cond-mat.stat-mech↗