arXiv subjects

Alessandro P. S. de Moura

Publications and source records attributed to Alessandro P. S. de Moura.

18 recordsLinked to original sources

arXiv2017

Gene length as a regulator for ribosome recruitment and protein synthesis: theoretical insights

Protein synthesis rates are determined, at the translational level, by properties of the transcript's sequence. The efficiency of an mRNA can be tuned by varying the ribosome binding sites controlling the recruitment of the ribosomes, or the codon usage establishing the speed of protein elongation. In this work we propose transcript length as a further key determinant of translation efficiency. Based on a physical model that considers the kinetics of ribosomes advancing on the mRNA and diffusing in its surrounding, as well as mRNA circularisation and ribosome drop-off, we explain how the transcript length may play a central role in establishing ribosome recruitment and the overall translation rate of an mRNA. According to our results, the proximity of the 3' end to the ribosomal recruitment site of the mRNA could induce a feedback in the translation process that would favour the recycling of ribosomes. We also demonstrate how this process may be involved in shaping the experimental ribosome density-gene length dependence. Finally, we argue that cells could exploit this mechanism to adjust and balance the usage of its ribosomal resources.

q-bio.SC↗

arXiv2017

Cooperative response and clustering: consequences of membrane-mediated interactions among mechanosensitive channels

Mechanosensitive (MS) channels are ion channels which act as cells' safety valves, opening when the osmotic pressure becomes too high and making cells avoid damage by releasing ions. They are found on the cellular membrane of a large number of organisms. They interact with each other by means of deformations they induce in the membrane. We show that collective dynamics arising from the inter-channel interactions lead to first and second-order phase transitions in the fraction of open channels in equilibrium relating to the formation of channel clusters. We show that this results in a considerable delay of the response of cells to osmotic shocks, and to an extreme cell-to-cell stochastic variations in their response times, despite the large numbers of channels present in each cell. We discuss how our results are relevant for {\it E. coli}.

physics.bio-ph↗

arXiv2017

Frontiers of chaotic advection

This work reviews the present position of and surveys future perspectives in the physics of chaotic advection: the field that emerged three decades ago at the intersection of fluid mechanics and nonlinear dynamics, which encompasses a range of applications with length scales ranging from micrometers to hundreds of kilometers, including systems as diverse as mixing and thermal processing of viscous fluids, microfluidics, biological flows, and oceanographic and atmospheric flows.

nlin.CD↗

arXiv2014

Diffusion in randomly perturbed dissipative dynamics

Dynamical systems having many coexisting attractors present interesting properties from both fundamental theoretical and modelling points of view. When such dynamics is under bounded random perturbations, the basins of attraction are no longer invariant and there is the possibility of transport among them. Here we introduce a basic theoretical setting which enables us to study this hopping process from the perspective of anomalous transport using the concept of a random dynamical system with holes. We apply it to a simple model by investigating the role of hyperbolicity for the transport among basins. We show numerically that our system exhibits non-Gaussian position distributions, power-law escape times, and subdiffusion. Our simulation results are reproduced consistently from stochastic Continuous Time Random Walk theory.

nlin.CD↗

arXiv2012

Optimal Placement of Origins for DNA Replication

DNA replication is an essential process in biology and its timing must be robust so that cells can divide properly. Random fluctuations in the formation of replication starting points, called origins, and the subsequent activation of proteins lead to variations in the replication time. We analyse these stochastic properties of DNA and derive the positions of origins corresponding to the minimum replication time. We show that under some conditions the minimization of replication time leads to the grouping of origins, and relate this to experimental data in a number of species showing origin grouping.

q-bio.QM↗

arXiv2012

Reacting particles in open chaotic flows

We study the collision probability $p$ of particles advected by open flows displaying chaotic advection. We show that $p$ scales with the particle size $δ$ as a power law whose coefficient is determined by the fractal dimensions of the invariant sets defined by the advection dynamics. We also argue that this same scaling also holds for the reaction rate of active particles in the low-density regime. These analytical results are compared to numerical simulations, and we find very good agreement with the theoretical predictions.

nlin.CD↗

arXiv2010

Escape from attracting sets in randomly perturbed systems

The dynamics of escape from an attractive state due to random perturbations is of central interest to many areas in science. Previous studies of escape in chaotic systems have rather focused on the case of unbounded noise, usually assumed to have Gaussian distribution. In this paper, we address the problem of escape induced by bounded noise. We show that the dynamics of escape from an attractor's basin is equivalent to that of a closed system with an appropriately chosen "hole". Using this equivalence, we show that there is a minimum noise amplitude above which escape takes place, and we derive analytical expressions for the scaling of the escape rate with noise amplitude near the escape transition. We verify our analytical predictions through numerical simulations of a two-dimensional map with noise.

nlin.CD↗

arXiv2010

Random fluctuation leads to forbidden escape of particles

A great number of physical processes are described within the context of Hamiltonian scattering. Previous studies have rather been focused on trajectories starting outside invariant structures, since the ones starting inside are expected to stay trapped there forever. This is true though only for the deterministic case. We show however that, under finitely small random fluctuations of the field, trajectories starting inside Arnold-Kolmogorov-Moser (KAM) islands escape within finite time. The non-hyperbolic dynamics gains then hyperbolic characteristics due to the effect of the random perturbed field. As a consequence, trajectories which are started inside KAM curves escape with hyperbolic-like time decay distribution, and the fractal dimension of a set of particles that remain in the scattering region approaches that for hyperbolic systems. We show a universal quadratic power law relating the exponential decay to the amplitude of noise. We present a random walk model to relate this distribution to the amplitude of noise, and investigate this phenomena with a numerical study applying random maps.

nlin.CD↗

arXiv2009

Emerging attractors and the transition from dissipative to conservative dynamics

The topological structure of basin boundaries plays a fundamental role in the sensitivity to the initial conditions in chaotic dynamical systems. Herewith we present a study on the dynamics of dissipative systems close to the Hamiltonian limit, emphasising the increasing number of periodic attractors and on the structural changes in their basin boundaries as the dissipation approaches zero. We show numerically that a power law with nontrivial exponent describes the growth of the total number of periodic attractors as the damping is decreased. We also establish that for small scales the dynamics is governed by \emph{effective} dynamical invariants, whose measure depends not only on the region of the phase space, but also on the scale under consideration. Therefore, our results show that the concept of effective invariants is also relevant for dissipative systems.

nlin.CD↗

arXiv2007

Signatures of fractal clustering of aerosols advected under gravity

Aerosols under chaotic advection often approach a strange attractor. They move chaotically on this fractal set but, in the presence of gravity, they have a net vertical motion downwards. In practical situations, observational data may be available only at a given level, for example at the ground level. We uncover two fractal signatures of chaotic advection of aerosols under the action of gravity. Each one enables the computation of the fractal dimension $D_{0}$ of the strange attractor governing the advection dynamics from data obtained solely at a given level. We illustrate our theoretical findings with a numerical experiment and discuss their possible relevance to meteorology.

nlin.CD↗

arXiv2005

Finite-size effects on open chaotic advection

We study the effects of finite-sizeness on small, neutrally buoyant, spherical particles advected by open chaotic flows. We show that, when projected onto configuration space, the advected finite-size particles disperse about the unstable manifold of the chaotic saddle that governs the passive advection. Using a discrete-time system for the dynamics, we obtain an expression predicting the dispersion of the finite-size particles in terms of their Stokes parameter at the onset of the finite-sizeness induced dispersion. We test our theory in a system derived from a flow and find remarkable agreement between our expression and the numerically measured dispersion.

nlin.CD↗

arXiv2005

Effective dynamics in Hamiltonian systems with mixed phase space

An adequate characterization of the dynamics of Hamiltonian systems at physically relevant scales has been largely lacking. Here we investigate this fundamental problem and we show that the finite-scale Hamiltonian dynamics is governed by effective dynamical invariants, which are significantly different from the dynamical invariants that describe the asymptotic Hamiltonian dynamics. The effective invariants depend both on the scale of resolution and the region of the phase space under consideration, and they are naturally interpreted within a framework in which the nonhyperbolic dynamics of the Hamiltonian system is modeled as a chain of hyperbolic systems.

nlin.CD↗

arXiv2003

Signatures of small-world and scale-free properties in large computer programs

A large computer program is typically divided into many hundreds or even thousands of smaller units, whose logical connections define a network in a natural way. This network reflects the internal structure of the program, and defines the ``information flow'' within the program. We show that, (1) due to its growth in time this network displays a scale-free feature in that the probability of the number of links at a node obeys a power-law distribution, and (2) as a result of performance optimization of the program the network has a small-world structure. We believe that these features are generic for large computer programs. Our work extends the previous studies on growing networks, which have mostly been for physical networks, to the domain of computer software.

cond-mat.dis-nn↗

arXiv2002

Topology of the conceptual network of language

We define two words in a language to be connected if they express similar concepts. The network of connections among the many thousands of words that make up a language is important not only for the study of the structure and evolution of languages, but also for cognitive science. We study this issue quantitatively, by mapping out the conceptual network of the English language, with the connections being defined by the entries in a Thesaurus dictionary. We find that this network presents a small-world structure, with an amazingly small average shortest path, and appears to exhibit an asymptotic scale-free feature with algebraic connectivity distribution.

cond-mat.dis-nn↗

arXiv2001

Output functions and fractal dimensions in dynamical systems

We present a novel method for the calculation of the fractal dimension of boundaries in dynamical systems, which is in many cases many orders of magnitude more efficient than the uncertainty method. We call it the Output Function Evaluation (OFE) method. The OFE method is based on an efficient scheme for computing output functions, such as the escape time, on a one-dimensional portion of the phase space. We show analytically that the OFE method is much more efficient than the uncertainty method for boundaries with $D<0.5$, where $D$ is the dimension of the intersection of the boundary with a one-dimensional manifold. We apply the OFE method to a scattering system, and compare it to the uncertainty method. We use the OFE method to study the behavior of the fractal dimension as the system's dynamics undergoes a topological transition.

nlin.CD↗

arXiv1999

Chaos and Fractals in Geodesic Motions Around a Non-Rotating Black-Hole with an External Halo

We investigate the occurrence chaos in the escape of test particles moving in the field of a Schwarzschild black hole surrounded by an external halo. The motion of both material particles and zero rest mass particles is considered. The chaos is characterized by the fractal dimension of boundary between the basins of the different escapes, which is a topologically invariant characterization. We find chaos in the motion of both material particles and null geodesics.

chao-dyn↗

arXiv1999

Fractal escapes in Newtonian and relativistic multipole gravitational fields

We study the planar motion of test particles in gravitational fields produced by an external material halo, of the type found in many astrophysical systems, such as elliptical galaxies and globular clusters. Both the Newtonian and the general-relativistic dynamics are examined, and in the relativistic case the dynamics of both massive and massless particles are investigated. The halo field is given in general by a multipole expansion; we restrict ourselves to multipole fields of pure order, whose Newtonian potentials are homogeneous polynomials in cartesian coordinates. A pure (n)-pole field has (n) different escapes, one of which is chosen by the particle according to its initial conditions. We find that the escape has a fractal dependency on the initial conditions for (n>2) both in the Newtonian and the relativistic cases for massive test particles, but with important differences between them. The relativistic motion of massless particles, however, was found to be regular for all the fields we could study. The box-counting dimension was used in each case to quantify the sensitivity to initial conditions which arises from the fractality of the escape route.

chao-dyn↗

arXiv1999

Scattering map for two black holes

We study the motion of light in the gravitational field of two Schwarzschild black holes, making the approximation that they are far apart, so that the motion of light rays in the neighborhood of one black hole can be considered to be the result of the action of each black hole separately. Using this approximation, the dynamics is reduced to a 2-dimensional map, which we study both numerically and analytically. The map is found to be chaotic, with a fractal basin boundary separating the possible outcomes of the orbits (escape or falling into one of the black holes). In the limit of large separation distances, the basin boundary becomes a self-similar Cantor set, and we find that the box-counting dimension decays slowly with the separation distance, following a logarithmic decay law.

gr-qc↗