arXiv subjects

Alberto Imparato

Publications and source records attributed to Alberto Imparato.

49 records · Page 3Linked to original sources

arXiv2010

Influence of rotational force fields on the determination of the work done on a driven Brownian particle

For a Brownian system the evolution of thermodynamic quantities is a stochastic process. In particular, the work performed on a driven colloidal particle held in an optical trap changes for each realization of the experimental manipulation, even though the manipulation protocol remains unchanged. Nevertheless, the work distribution is governed by established laws. Here, we show how the measurement of the work distribution is influenced by the presence of rotational, i.e. nonconservative, radiation forces. Experiments on particles of different materials show that the rotational radiation forces, and therefore their effect on the work distributions, increase with the particle refractive index.

cond-mat.stat-mech↗

arXiv2009

Current fluctuations in systems with diffusive dynamics, in and out of equilibrium

For diffusive systems that can be described by fluctuating hydrodynamics and by the Macroscopic Fluctuation Theory of Bertini et al., the total current fluctuations display universal features when the system is closed and in equilibrium. When the system is taken out of equilibrium by a boundary-drive, current fluctuations, at least for a particular family of diffusive systems, display the same universal features as in equilibrium. To achieve this result, we exploit a mapping between the fluctuations in a boundary-driven nonequilibrium system and those in its equilibrium counterpart. Finally, we prove, for two well-studied processes, namely the Simple Symmetric Exclusion Process and the Kipnis-Marchioro-Presutti model for heat conduction, that the distribution of the current out of equilibrium can be deduced from the distribution in equilibrium. Thus, for these two microscopic models, the mapping between the out-of-equilibrium setting and the equilibrium one is exact.

cond-mat.stat-mech↗

arXiv2009

Unfolding times for proteins in a force clamp

The escape process from the native valley for proteins subjected to a constant stretching force is examined using a model for a Beta-barrel. For a wide range of forces, the unfolding dynamics can be treated as one-dimensional diffusion, parametrized in terms of the end-to-end distance. In particular, the escape times can be evaluated as first passage times for a Brownian particle moving on the protein free-energy landscape, using the Smoluchowski equation. At strong forces, the unfolding process can be viewed as a diffusive drift away from the native state, while at weak forces thermal activation is the relevant mechanism. An escape-time analysis within this approach reveals a crossover from an exponential to an inverse Gaussian escape-time distribution upon passing from weak to strong forces. Moreover, a single expression valid at weak and strong forces can be devised both for the average unfolding time as well as for the corresponding variance. The analysis offers a possible explanation of recent experimental findings for ddFLN4 and ubiquitin.

cond-mat.stat-mech↗

arXiv2009

Heat distribution function for motion in a general potential at low temperature

We consider the 1D motion of an overdamped Brownian particle in a general potential in the low temperature limit. We derive an explicit expression for the probability distribution for the heat transferred to the particle. We find that the local minima in the potential yield divergent side bands in the heat distribution in addition to the divergent central peak. The position of the bands are determined by the potential gaps. We, moreover, determine the tails of the heat distribution.

cond-mat.stat-mech↗

arXiv2009

Equilibrium-like fluctuations in some boundary-driven open diffusive systems

There exist some boundary-driven open systems with diffusive dynamics whose particle current fluctuations exhibit universal features that belong to the Edwards-Wilkinson universality class. We achieve this result by establishing a mapping, for the system's fluctuations, to an equivalent open --yet equilibrium-- diffusive system. We discuss the possibility of observing dynamic phase transitions using the particle current as a control parameter.

cond-mat.stat-mech↗

arXiv2008

Changing the mechanical unfolding pathway of FnIII10 by tuning the pulling strength

We investigate the mechanical unfolding of the tenth type III domain from fibronectin, FnIII10, both at constant force and at constant pulling velocity, by all-atom Monte Carlo simulations. We observe both apparent two-state unfolding and several unfolding pathways involving one of three major, mutually exclusive intermediate states. All the three major intermediates lack two of seven native beta-strands, and share a quite similar extension. The unfolding behavior is found to depend strongly on the pulling conditions. In particular, we observe large variations in the relative frequencies of occurrence for the intermediates. At low constant force or low constant velocity, all the three major intermediates occur with a significant frequency. At high constant force or high constant velocity, one of them, with the N- and C-terminal beta-strands detached, dominates over the other two. Using the extended Jarzynski equality, we also estimate the equilibrium free-energy landscape, calculated as a function of chain extension. The application of a constant pulling force leads to a free-energy profile with three major local minima. Two of these correspond to the native and fully unfolded states, respectively, whereas the third one can be associated with the major unfolding intermediates.

q-bio.BM↗

arXiv2008

Probability density functions of work and heat near the stochastic resonance of a colloidal particle

We study experimentally and theoretically the probability density functions of the injected and dissipated energy in a system of a colloidal particle trapped in a double well potential periodically modulated by an external perturbation. The work done by the external force and the dissipated energy are measured close to the stochastic resonance where the injected power is maximum. We show a good agreement between the probability density functions exactly computed from a Langevin dynamics and the measured ones. The probability density function of the work done on the particle satisfies the fluctuation theorem.

cond-mat.stat-mech↗

arXiv2008

Free energy landscape of mechanically unfolded model proteins: extended Jarzinsky versus inherent structure reconstruction

The equilibrium free energy landscape of off-lattice model heteropolymers as a function of an internal coordinate, namely the end-to-end distance, is reconstructed from out-of-equilibrium steered molecular dynamics data. This task is accomplished via two independent methods: by employing an extended version of the Jarzynski equality (EJE) and the inherent structure (IS) formalism. A comparison of the free energies estimated with these two schemes with equilibrium results obtained via the umbrella sampling technique reveals a good quantitative agreement among all the approaches in a range of temperatures around the ``folding transition'' for the two examined sequences. In particular, for the sequence with good foldability properties, the mechanically induced structural transitions can be related to thermodynamical aspects of folding. Moreover, for the same sequence the knowledge of the landscape profile allows for a good estimation of the life times of the native configuration for temperatures ranging from the folding to the collapse temperature. For the random sequence, mechanical and thermal unfolding appear to follow different paths along the landscape.

cond-mat.stat-mech↗

arXiv2007

Reconstructing the free energy landscape of a mechanically unfolded model protein

The equilibrium free energy landscape of an off-lattice model protein as a function of an internal (reaction) coordinate is reconstructed from out-of-equilibrium mechanical unfolding manipulations. This task is accomplished via two independent methods: by employing an extended version of the Jarzynski equality (EJE) and the protein inherent structures (ISs). In a range of temperatures around the ``folding transition'' we find a good quantitative agreement between the free energies obtained via EJE and IS approaches. This indicates that the two methodologies are consistent and able to reproduce equilibrium properties of the examined system. Moreover, for the studied model the structural transitions induced by pulling can be related to thermodynamical aspects of folding.

cond-mat.stat-mech↗

arXiv2006

Surface tension in bilayer membranes with fixed projected area

We study the elastic response of bilayer membranes with fixed projected area to both stretching and shape deformations. A surface tension is associated to each of these deformations. By using model amphiphilic membranes and computer simulations, we are able to observe both the types of deformation, and thus, both the surface tensions, related to each type of deformation, are measured for the same system. These surface tensions are found to assume different values in the same bilayer membrane: in particular they vanish for different values of the projected area. We introduce a simple theory which relates the two quantities and successfully apply it to the data obtained with computer simulations.

cond-mat.soft↗

arXiv2004

Shape fluctuations and elastic properties of two-component bilayer membranes

The elastic properties of two-component bilayer membranes are studied using a coarse grain model for amphiphilic molecules. The two species of amphiphiles considered here differ only in their length. Molecular Dynamics simulations are performed in order to analyze the shape fluctuations of the two-component bilayer membranes and to determine their bending rigidity. Both the bending rigidity and its inverse are found to be nonmonotonic functions of the mole fraction $x_{\rm B}$ of the shorter B-amphiphiles and, thus, do not satisfy a simple lever rule. The intrinsic area of the bilayer also exhibits a nonmonotonic dependence on $x_{\rm B}$ and a maximum close to $x_{\rm B} \simeq 1/2$.

cond-mat.soft↗

arXiv2004

Work probability distribution in single molecule experiments

We derive and solve a differential equation satisfied by the probability distribution of the work done on a single biomolecule in a mechanical unzipping experiment. The unzipping is described as a thermally activated escape process in an energy landscape. The Jarzynski equality is recovered as an identity, independent of the pulling protocol. This approach allows one to evaluate easily, by numerical integration, the work distribution, once a few parameters of the energy landscape are known.

cond-mat.soft↗

arXiv2004

Kinetic barriers in RNA unzipping

We consider a simple model for the unfolding of RNA tertiary structure under dynamic loading. The opening of such a structure is regarded as a two step process, each corresponding to the overcoming of a single energy barrier. The resulting two-barrier energy landscape accounts for the dependence of the unfolding kinetics on the pulling rate. Furthermore at intermediate force, the two barriers cannot be distinguished by the analysis of the opening kinetic, which turns out to be dominated by a single macro-barrier, whose properties depend non-trivially on the two single barriers. Our results suggest that in pulling experiments on RNA molecule containing tertiary structures, the details of the single kinetic barriers can only be obtained using a low pulling rate value, or in the high force regime.

q-bio.BM↗