Reset and switch protocols at Landauer limit in a graphene buckled ribbon

Heat produced during a reset operation is meant to show a fundamental bound known as Landauer limit, while simple switch operations have an expected minimum amount of produced heat equal to zero. However, in both cases, present-day technology realizations dissipate far beyond these theoretical limits. In this paper we present a study based on molecular dynamics simulations, where reset and switch protocols are applied on a graphene buckled ribbon, employed here as a nano electromechanical switch working at the thermodynamic limit.

Motor proteins traffic regulation by supply-demand balance of resources

In cells and in vitro assays the number of motor proteins involved in biological transport processes is far from being unlimited. The cytoskeletal binding sites are in contact with the same finite reservoir of motors (either the cytosol or the flow chamber) and hence compete for recruiting the available motors, potentially depleting the reservoir and affecting cytoskeletal transport. In this work we provide a theoretical framework to study, analytically and numerically, how motor density profiles and crowding along cytoskeletal filaments depend on the competition of motors for their binding sites. We propose two models in which finite processive motor proteins actively advance along cytoskeletal filaments and are continuously exchanged with the motor pool. We first look at homogeneous reservoirs and then examine the effects of free motor diffusion in the surrounding medium. We consider as a reference situation recent in vitro experimental setups of kinesin-8 motors binding and moving along microtubule filaments in a flow chamber. We investigate how the crowding of linear motor proteins moving on a filament can be regulated by the balance between supply (concentration of motor proteins in the flow chamber) and demand (total number of polymerised tubulin heterodimers). We present analytical results for the density profiles of bound motors, the reservoir depletion, and propose novel phase diagrams that present the formation of jams of motor proteins on the filament as a function of two tuneable experimental parameters: the motor protein concentration and the concentration of tubulins polymerized into cytoskeletal filaments. Extensive numerical simulations corroborate the analytical results for parameters in the experimental range and also address the effects of diffusion of motor proteins in the reservoir.

Exclusion processes on networks as models for cytoskeletal transport

We present a study of exclusion processes on networks as models for complex transport phenomena and in particular for active transport of motor proteins along the cytoskeleton. We argue that active transport processes on networks spontaneously develop density heterogeneities at various scales. These heterogeneities can be regulated through a variety of multi-scale factors, such as the interplay of exclusion interactions, the non-equilibrium nature of the transport process and the network topology. We show how an effective rate approach allows to develop an understanding of the stationary state of transport processes through complex networks from the phase diagram of one single segment. For exclusion processes we rationalize that the stationary state can be classified in three qualitatively different regimes: a homogeneous phase as well as inhomogeneous network and segment phases. In particular, we present here a study of the stationary state on networks of three paradigmatic models from non-equilibrium statistical physics: the totally asymmetric simple exclusion process, the partially asymmetric simple exclusion process and the totally asymmetric simple exclusion process with Langmuir kinetics. With these models we can interpolate between equilibrium (due to bi-directional motion along a network or infinite diffusion) and out-of-equilibrium active directed motion along a network. The study of these models sheds further light on the emergence of density heterogeneities in active phenomena.

Modelling cytoskeletal traffic: an interplay between passive diffusion and active transport

We introduce the totally asymmetric exclusion process with Langmuir kinetics (TASEP-LK) on a network as a microscopic model for active motor protein transport on the cytoskeleton, immersed in the diffusive cytoplasm. We discuss how the interplay between active transport along a network and infinite diffusion in a bulk reservoir leads to a heterogeneous matter distribution on various scales. We find three regimes for steady state transport, corresponding to the scale of the network, of individual segments or local to sites. At low exchange rates strong density heterogeneities develop between different segments in the network. In this regime one has to consider the topological complexity of the whole network to describe transport. In contrast, at moderate exchange rates the transport through the network decouples, and the physics is determined by single segments and the local topology. At last, for very high exchange rates the homogeneous Langmuir process dominates the stationary state. We introduce effective rate diagrams for the network to identify these different regimes. Based on this method we develop an intuitive but generic picture of how the stationary state of excluded volume processes on complex networks can be understood in terms of the single-segment phase diagram.

On the spectra of large sparse graphs with cycles

We present a general method for obtaining the spectra of large graphs with short cycles using ideas from statistical mechanics of disordered systems. This approach leads to an algorithm that determines the spectra of graphs up to a high accuracy. In particular, for (un)directed regular graphs with cycles of arbitrary length we derive exact and simple equations for the resolvent of the associated adjacency matrix. Solving these equations we obtain analytical formulas for the spectra and the boundaries of their support.

Spectra of sparse regular graphs with loops

We derive exact equations that determine the spectra of undirected and directed sparsely connected regular graphs containing loops of arbitrary length. The implications of our results to the structural and dynamical properties of networks are discussed by showing how loops influence the size of the spectral gap and the propensity for synchronization. Analytical formulas for the spectrum are obtained for specific length of the loops.

On the localization transition in symmetric random matrices

We study the behaviour of the inverse participation ratio and the localization transition in infinitely large random matrices through the cavity method. Results are shown for two ensembles of random matrices: Laplacian matrices on sparse random graphs and fully-connected Levy matrices. We derive a critical line separating localized from extended states in the case of Levy matrices. Comparison between theoretical results and diagonalization of finite random matrices is shown.

Gallager error correcting codes for binary asymmetric channels

We derive critical noise levels for Gallager codes on asymmetric channels as a function of the input bias and the temperature. Using a statistical mechanics approach we study the space of codewords and the entropy in the various decoding regimes. We further discuss the relation of the convergence of the message passing algorithm with the endogeny property and complexity, characterizing solutions of recursive equations of distributions for cavity fields.