arXiv subjects

Marco Baiesi

Publications and source records attributed to Marco Baiesi.

At least 37 records · Page 2Linked to original sources

arXiv2020

A thermodynamic uncertainty relation for a system with memory

We introduce an example of thermodynamic uncertainty relation (TUR) for systems modeled by a one-dimensional generalised Langevin dynamics with memory, determining the motion of a micro-bead driven in a complex fluid. Contrary to TURs typically discussed in the previous years, our observables and the entropy production rate are one-time variables. The bound to the signal-to-noise ratio of such state-dependent observables only in some cases can be mapped to the entropy production rate. For example, this is true in Markovian systems. Hence, the presence of memory in the system complicates the thermodynamic interpretation of the uncertainty relation.

cond-mat.stat-mech↗

arXiv2019

Folding Rate Optimization Promotes Frustrated Interactions in Entangled Protein Structures

Many native structures of proteins accomodate complex topological motifs such as knots, lassos, and other geometrical entanglements. How proteins can fold quickly even in the presence of such topological obstacles is a debated question in structural biology. Recently, the hypothesis that energetic frustration might be a mechanism to avoid topological frustration has been put forward based on the empirical observation that loops involved in entanglements are stabilized by weak interactions between amino-acids at their extrema. To verify this idea, we use a toy lattice model for the folding of proteins into two almost identical structures, one entangled and one not. As expected, the folding time is longer when random sequences folds into the entangled structure. This holds also under an evolutionary pressure simulated by optimizing the folding time. It turns out that optmized protein sequences in the entangled structure are in fact characterized by frustrated interactions at the closures of entangled loops. This phenomenon is much less enhanced in the control case where the entanglement is not present. Our findings, which are in agreement with experimental observations, corroborate the idea that an evolutionary pressure shapes the folding funnel to avoid topological and kinetic traps.

cond-mat.soft↗

arXiv2019

Power Gradient Descent

The development of machine learning is promoting the search for fast and stable minimization algorithms. To this end, we suggest a change in the current gradient descent methods that should speed up the motion in flat regions and slow it down in steep directions of the function to minimize. It is based on a "power gradient", in which each component of the gradient is replaced by its versus-preserving $H$-th power, with $0<H<1$. We test three modern gradient descent methods fed by such variant and by standard gradients, finding the new version to achieve significantly better performances for the Nesterov accelerated gradient and AMSGrad. We also propose an effective new take on the ADAM algorithm, which includes power gradients with varying $H$.

cs.LG↗

arXiv2019

Sequence and structural patterns detected in entangled proteins reveal the importance of co-translational folding

Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence of specific patterns adopted by protein sequences and structures to deal with backbone self-entanglement. A large scale analysis of the Protein Data Bank shows that loops significantly intertwined with another chain portion are typically closed by weakly bound amino acids. Why is this energetic frustration maintained? A possible picture is that entangled loops are formed only toward the end of the folding process to avoid kinetic traps. Consistently, these loops are more frequently found to be wrapped around a portion of the chain on their N-terminal side, the one translated earlier at the ribosome. Finally, these motifs are less abundant in natural native states than in simulated protein-like structures, yet they appear in 32% of proteins, which in some cases display an amazingly complex intertwining.

q-bio.BM↗

arXiv2019

Rate dependence of current and fluctuations in jump models with negative differential mobility

Negative differential mobility is the phenomenon in which the velocity of a particle decreases when the force driving it increases. We study this phenomenon in Markov jump models where a particle moves in the presence of walls that act as traps. We consider transition rates that obey local detailed balance but differ in normalisation, the inclusion of a rate to cross a wall and a load factor. We illustrate the full counting statistics for different choices of the jumping rates. We also show examples of thermodynamic uncertainty relations. The variety of behaviours we encounter highlights that negative differential mobility depends crucially on the chosen rates and points out the necessity that such choices should be based on proper coarse-graining studies of a more microscopic description.

cond-mat.stat-mech↗

arXiv2019

Kinetic uncertainty relation

Relative fluctuations of observables in discrete stochastic systems are bounded at all times by the mean dynamical activity in the system, quantified by the mean number of jumps. This constitutes a kinetic uncertainty relation that is fundamentally different from the thermodynamic uncertainty relation recently discussed in the literature. The thermodynamic constraint is more relevant close to equilibrium while the kinetic constraint is the limiting factor of the precision of a observables in regimes far from equilibrium. This is visualized for paradigmatic simple systems and with an example of molecular motor dynamics. Our approach is based on the recent fluctuation response inequality by Dechant and Sasa [arXiv:1804.08250] and can be applied to generic Markov jump systems, which describe a wide class of phenomena and observables, including the irreversible predator-prey dynamics that we use as an illustration.

cond-mat.stat-mech↗

arXiv2018

Topological Sieving of Rings According to their Rigidity

We present a novel mechanism for resolving the mechanical rigidity of nanoscopic circular polymers that flow in a complex environment. The emergence of a regime of negative differential mobility induced by topological interactions between the rings and the substrate is the key mechanism for selective sieving of circular polymers with distinct flexibilities. A simple model accurately describes the sieving process observed in molecular dynamics simulations and yields experimentally verifiable analytical predictions, which can be used as a reference guide for improving filtration procedures of circular filaments. The topological sieving mechanism we propose ought to be relevant also in probing the microscopic details of complex substrates.

cond-mat.soft↗

arXiv2017

Exploring the correlation between the folding rates of proteins and the entanglement of their native states

The folding of a protein towards its native state is a rather complicated process. However there are empirical evidences that the folding time correlates with the contact order, a simple measure of the spatial organisation of the native state of the protein. Contact order is related to the average length of the main chain loops formed by amino acids which are in contact. Here we argue that folding kinetics can be influenced also by the entanglement that loops may undergo within the overall three dimensional protein structure. In order to explore such possibility, we introduce a novel descriptor, which we call "maximum intrachain contact entanglement". Specifically, we measure the maximum Gaussian entanglement between any looped portion of a protein and any other non-overlapping subchain of the same protein, which is easily computed by discretized line integrals on the coordinates of the $C_α$ atoms. By analyzing experimental data sets of two-state and multistate folders, we show that also the new index is a good predictor of the folding rate. Moreover, being only partially correlated with previous methods, it can be integrated with them to yield more accurate predictions.

cond-mat.soft↗

arXiv2017

Life efficiency does not always increase with the dissipation rate

There does not exist a general positive correlation between important life-supporting properties and the entropy production rate. The simple reason is that nondissipative and time-symmetric kinetic aspects are also relevant for establishing optimal functioning. In fact those aspects are even crucial in the nonlinear regimes around equilibrium where we find biological processing on mesoscopic scales. We make these claims specific via examples of molecular motors, of circadian cycles and of sensory adaptation, whose performance in some regimes is indeed spoiled by increasing the dissipated power. We use the relation between dissipation and the amount of time-reversal breaking to keep the discussion quantitative also in effective models where the physical entropy production is not clearly identifiable.

cond-mat.stat-mech↗

arXiv2017

Thermal response of a Fermi-Pasta-Ulam chain with Andersen thermostats

The linear response to temperature variations is well characterised for equilibrium systems but a similar theory is not available, for example, for inertial heat conducting systems, whose paradigm is the Fermi-Pasta-Ulam (FPU) model driven by two different boundary temperatures. For models of inertial systems out of equilibrium, including relaxing systems, we show that Andersen thermostats are a natural tool for studying the thermal response. We derive a fluctuation-response relation that allows to predict thermal expansion coefficients or the heat capacitance in nonequilibrium regimes. Simulations of the FPU chain of oscillators suggest that estimates of susceptibilities obtained with our relation are better than those obtained via a small perturbation.

cond-mat.stat-mech↗

arXiv2016

A general fluctuation-response relation for noise variations and its application to driven hydrodynamic experiments

The effect of a change of noise amplitudes in overdamped diffusive systems is linked to their unperturbed behavior by means of a nonequilibrium fluctuation-response relation. This formula holds also for systems with state-independent nontrivial diffusivity matrices, as we show with an application to an experiment of two trapped and hydrodynamically coupled colloids, one of which is subject to an external random forcing that mimics an effective temperature. The nonequilibrium susceptibility of the energy to a variation of this driving is an example of our formulation, which improves an earlier version, as it does not depend on the time-discretization of the stochastic dynamics. This scheme holds for generic systems with additive noise and can be easily implemented numerically, thanks to matrix operations.

cond-mat.stat-mech↗

arXiv2016

Linking in domain-swapped protein dimers

The presence of knots has been observed in a small fraction of single-domain proteins and related to their thermodynamic and kinetic properties. The exchanging of identical structural elements, typical of domain-swapped proteins, make such dimers suitable candidates to validate the possibility that mutual entanglement between chains may play a similar role for protein complexes. We suggest that such entanglement is captured by the linking number. This represents, for two closed curves, the number of times that each curve winds around the other. We show that closing the curves is not necessary, as a novel parameter $G'$, termed Gaussian entanglement, is strongly correlated with the linking number. Based on $110$ non redundant domain-swapped dimers, our analysis evidences a high fraction of chains with a significant intertwining, that is with $|G'| > 1$. We report that Nature promotes configurations with negative mutual entanglement and surprisingly, it seems to suppress intertwining in long protein dimers. Supported by numerical simulations of dimer dissociation, our results provide a novel topology-based classification of protein-swapped dimers together with some preliminary evidence of its impact on their physical and biological properties.

cond-mat.soft↗

arXiv2016

Thermal response of nonequilibrium RC-circuits

We analyze experimental data obtained from an electrical circuit having components at different temperatures, showing how to predict its response to temperature variations. This illustrates in detail how to utilize a recent linear response theory for nonequilibrium overdamped stochastic systems. To validate these results, we introduce a reweighting procedure that mimics the actual realization of the perturbation and allows extracting the susceptibility of the system from steady state data. This procedure is closely related to other fluctuation-response relations based on the knowledge of the steady state probability distribution. As an example, we show that the nonequilibrium heat capacity in general does not correspond to the correlation between the energy of the system and the heat flowing into it. Rather, also non-dissipative aspects are relevant in the nonequilbrium fluctuation response relations.

cond-mat.stat-mech↗

arXiv2016

Self-similar aftershock rates

In many important systems exhibiting crackling noise --- intermittent avalanche-like relaxation response with power-law and, thus, self-similar distributed event sizes --- the "laws" for the rate of activity after large events are not consistent with the overall self-similar behavior expected on theoretical grounds. This is in particular true for the case of seismicity and a satisfying solution to this paradox has remained outstanding. Here, we propose a generalized description of the aftershock rates which is both self-similar and consistent with all other known self-similar features. Comparing our theoretical predictions with high resolution earthquake data from Southern California we find excellent agreement, providing in particular clear evidence for a unified description of aftershocks and foreshocks. This may offer an improved way of time-dependent seismic hazard assessment and earthquake forecasting.

cond-mat.stat-mech↗

arXiv2016

Mesoscopic virial equation for nonequilibrium statistical mechanics

We derive a class of mesoscopic virial equations governing energy partition between conjugate position and momentum variables of individual degrees of freedom. They are shown to apply to a wide range of nonequilibrium steady states with stochastic (Langevin) and deterministic (Nosé--Hoover) dynamics, and to extend to collective modes for models of heat-conducting lattices. A generalised macroscopic virial theorem ensues upon summation over all degrees of freedom. This theorem allows for the derivation of nonequilibrium state equations that involve dissipative heat flows on the same footing with state variables, as exemplified for inertial Brownian motion with solid friction and overdamped active Brownian particles subject to inhomogeneous pressure.

cond-mat.stat-mech↗

arXiv2016

Linear response of hydrodynamically-coupled particles under a nonequilibrium reservoir

A recent experiment driving colloids electromagnetically, by Bérut et al. [2014 Europhys. Lett. 107, 60004], is an ideal paradigm for illustrating a linear response theory for nonequilibrium overdamped systems including hydrodynamic interactions and, unusually, a reservoir itself out of equilibrium. Indeed, in this setup one finds a nonequilibrium environment in which the mobility and diffusivity of free particles are not simply proportional to each other. We derive both the response to a mechanical forcing and to temperature variations in terms of correlations between an observable and a path-weight action. The time-antisymmetric component of the latter turns out not to be simply proportional to the heat flowing into the environment. These results are visualized with simulations resembling conditions and protocols easily realizable in the experiment, thereby tracing a path for experimental verifications of the theory.

cond-mat.stat-mech↗

arXiv2016

Torque-Induced Rotational Dynamics in Polymers: Torsional Blobs and Thinning

By using the blob theory and computer simulations, we investigate the properties of a linear polymer performing a stationary rotational motion around a long impenetrable rod. In particular, in the simulations the rotation is induced by a torque applied to the end of the polymer that is tethered to the rod. Three different regimes are found, in close analogy with the case of polymers pulled by a constant force at one end. For low torques the polymer rotates maintaining its equilibrium conformation. At intermediate torques the polymer assumes a trumpet shape, being composed by blobs of increasing size. At even larger torques the polymer is partially wrapped around the rod. We derive several scaling relations between various quantities as angular velocity, elongation and torque. The analytical predictions match the simulation data well. Interestingly, we find a "thinning" regime where the torque has a very weak (logarithmic) dependence on the angular velocity. We discuss the origin of this behavior, which has no counterpart in polymers pulled by an applied force.

cond-mat.soft↗

arXiv2016

Nonequilibrium temperature response for stochastic overdamped systems

The thermal response of nonequilibrium systems requires the knowledge of concepts that go beyond entropy production. This is showed for systems obeying overdamped Langevin dynamics, either in steady states or going through a relaxation process. Namely, we derive the linear response to perturbations of the noise intensity, mapping it onto the quadratic response to a constant small force. The latter, displaying divergent terms, is explicitly regularized with a novel path-integral method. The nonequilibrium equivalents of heat capacity and thermal expansion coefficient are two applications of this approach, as we show with numerical examples.

cond-mat.stat-mech↗