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Source author record

C. Manuel Carlevaro

C. Manuel Carlevaro appears in the imported research catalog. Authorship, coauthor and topic links are available while profile ownership is still unclaimed.

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cond-mat.softBiological Physicscond-mat.stat-mechOther Quantitative Biologyphysics.app-phphysics.med-ph

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Published work

11 published item(s)

preprint2026arXiv

Confinement-controlled chase-escape dynamics

We investigate a minimal chase-and-escape model on a two-dimensional square lattice with randomly distributed static obstacles, focusing on how geometric disorder controls collective pursuit dynamics. Chasers and escapers move according to short-range sensing rules, while the density of obstacles tunes the connectivity of the accessible space. Using a combination of geometric analysis, dynamical observables, survival statistics, and transport characterization, we establish a direct link between lattice connectivity and pursuit efficiency. A Breadth-First Search analysis reveals that obstacle-induced fragmentation leads to a progressive loss of accessibility before the percolation threshold, defining the effective initial conditions for the dynamics. The trapping time and capture cost exhibit a non-monotonic dependence on obstacle density, reflecting a competition between path elongation in connected environments and geometric confinement near the percolation threshold. Survival analysis shows that the decay of the escaper population follows a Weibull form, with characteristic time and shape parameters displaying clear crossovers as a function of obstacle density, signaling the coexistence of cooperative capture and confinement-dominated trapping. Transport properties, quantified through the mean-squared displacement exponent, further support this picture, revealing sub-diffusive dynamics and a convergence toward a geometry-controlled regime near percolation. Overall, our results demonstrate that chase--and--escape dynamics in disordered environments are governed by a geometry-driven crossover, where percolation and connectivity act as unifying control parameters for spatial, temporal, and collective behavior.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Molecular Mechanisms of Urea Interactions with Bovine Serum Albumin in an Acid-Expanded Conformation (pH 3.7)

Understanding the molecular mechanism by which denaturants modulate protein structure remains a central challenge in protein biophysics. In this work, molecular dynamics simulations were employed to investigate the effects of urea on the structural stability of bovine serum albumin, its F isoform at pH 3.7, over a broad range of urea concentrations (0 M to a fully urea/solvated system). The results reveal that urea induces a concentration/dependent dehydration/rehydration mechanism within the protein hydration shell. At low urea concentrations, a marked reduction in protein/water hydrogen bonds is observed, accompanied by a corresponding increase in protein/urea interactions, consistent with a competitive solvation process. At higher concentrations, urea/urea self-association becomes significant, limiting direct protein/urea interactions and promoting partial rehydration of the protein surface. Despite these solvent rearrangements, the secondary structure of BSA remains largely preserved, whereas local and tertiary structural features, particularly in Domain III, exhibit increased solvent exposure and conformational flexibility. These findings support a dynamic compensation mechanism in which urea partially replaces water in the solvation shell without fully disrupting the hydrogen-bonding network. Overall, this study provides molecular-level insight into the interplay between preferential interactions, solvation dynamics, and protein stability under denaturing conditions.

0 citations0 reviewsNo code linkedOpen access
preprint2019arXiv

Intruder in a two-dimensional granular system: Effects of dynamic and static basal friction on stick-slip and clogging dynamics

We discuss the results of simulations of an intruder pulled through a two-dimensional granular system by a spring, using a model designed to lend insight into the experimental findings described by Kozlowski et al. [Phys. Rev. E, 100, 032905 (2019)]. In that previous study the presence of basal friction between the grains and the base was observed to change the intruder dynamics from clogging to stick-slip. Here we first show that our simulation results are in excellent agreement with the experimental data for a variety of experimentally accessible friction coefficients governing interactions of particles with each other and with boundaries. Then, we use simulations to explore a broader range of parameter space, focusing on the friction between the particles and the base. We consider a range of both static and dynamic basal friction coefficients, which are difficult to vary smoothly in experiments. The simulations show that dynamic friction strongly affects the stick-slip behaviour when the coefficient is decreased below 0.1, while static friction plays only a marginal role in the intruder dynamics.

0 citations0 reviewsNo code linkedOpen access
preprint2019arXiv

Microwave Tomography with phaseless data on the calcaneus by means of artificial neural networks

The aim of this study is to use a Multilayer Perceptron (MLP) Artificial Neural Network (ANN) for phaseless imaging the human heel (modeled as a bilayer dielectric media: bone and surrounding tissue) and the calcaneus cross-section size and location using a two dimensional (2D) microwave tomographic array. Computer simulations were performed over 2D dielectric maps inspired by Computed Tomography (CT) images of human heels for training and testing the MLP. A morphometric analysis was performed to account for the scatterer shape influence on the results. A robustness analysis was also conducted in order to study the MLP performance in noisy conditions. The standard deviations of the relative percentage errors on estimating the dielectric properties of the calcaneus bone were relatively high. Regarding the calcaneus surrounding tissue, the dielectric parameters estimations are better, with relative percentage error standard deviations up to $\approx$ 15 %. The location and size of the calcaneus are always properly estimated with absolute error standard deviations up to $\approx $ 3 mm.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

Chirality in a quaternionic representation of the genetic code

A quaternionic representation of the genetic code, previously reported by the authors, is updated in order to incorporate chirality of nucleotide bases and amino acids. The original representation assigns to each nucleotide base a prime integer quaternion of norm 7 and involves a function that associates with each codon, represented by three of these quaternions, another integer quaternion (amino acid type quaternion) in such a way that the essentials of the standard genetic code (particulaty its degeneration) are preserved. To show the advantages of such a quaternionic representation we have, in turn, associated with each amino acid of a given protein, besides of the type quaternion, another real one according to its order along the protein (order quaternion) and have designed an algorithm to go from the primary to the tertiary structure of the protein by using type and order quaternions. In this context, we incorporate chirality in our representation by observing that the set of eight integer quaternions of norm 7 can be partitioned into a pair of subsets of cardinality four each with their elements mutually conjugates and by putting they in correspondence one to one with the two sets of enantiomers (D and L) of the four nucleotide bases adenine, cytosine, guanine and uracil, respectively. Thus, guided by two diagrams proposed for the codes evolution, we define functions that in each case assign a L- (D-) amino acid type integer quaternion to the triplets of D- (L-) bases. The assignation is such that for a given D-amino acid, the associated integer quaternion is the conjugate of that one corresponding to the enantiomer L. The chiral type quaternions obtained for the amino acids are used, together with a common set of order quaternions, to describe the folding of the two classes, L and D, of homochiral proteins.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

Flow rate of polygonal grains through a bottleneck: Interplay between shape and size

We report two-dimensional simulations of circular and polygonal grains passing through an aperture at the bottom of a silo. The mass flow rate for regular polygons is lower than for disks as observed by other authors. We show that both the exit velocity of the grains and the packing fraction are lower for polygons, which leads to the reduced flow rate. We point out the importance of the criteria used to define when two objects of different shape are considered to be of the same size. Depending on this criteria, the mass flow rate may vary significantly for some polygons. Moreover, the particle flow rate is non-trivially related to a combination of mass flow rate, particle shape and particle size. For some polygons, the particle flow rate may be lower or higher than that of the corresponding disks depending on the size comparison criteria.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

Quaternionic representation of the genetic code

A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick on the origin and evolution of the code as well as with the chronological order of appearence of the amino acids along the evolution as inferred from work that mixtures known experimental results with theoretical speculations. Suggested by the diagram we propose a Hamilton quaternions based mathematical representation of the code as it stands now-a-days. The central object in the description is a codon function that assigns to each amino acid an integer quaternion in such a way that the observed code degeneration is preserved. We emphasize the advantages of a quaternionic representation of amino acids taking as an example the folding of proteins. With this aim we propose an algorithm to go from the quaternions sequence to the protein three dimensional structure which can be compared with the corresponding experimental one stored at the Protein Data Bank. In our criterion the mathematical representation of the genetic code in terms of quaternions merits to be taken into account because it describes not only most of the known properties of the genetic code but also opens new perspectives that are mainly derived from the close relationship between quaternions and rotations.

0 citations0 reviewsNo code linkedOpen access
preprint2013arXiv

Exact predictions from Edwards ensemble vs. realistic simulations of tapped narrow two-dimensional granular columns

We simulate via a Discrete Element Method the tapping of a narrow column of disk under gravity. For frictionless disks, this system has a simple analytic expression for the density of states in the Edwards volume ensemble. We compare the predictions of the ensemble at constant compactivity against the results for the steady states obtained in the simulations. We show that the steady states cannot be properly described since the microstates sampled are not in correspondence with the predicted distributions, suggesting that the postulates of flat measure and ergodicity are, either or both, invalid for this simple realization of a static granular system. However, we show that certain qualitative features of the volume fluctuations difficult to predict from simple arguments are captured by the theory.

0 citations0 reviewsNo code linkedOpen access
preprint2012arXiv

Arches and contact forces in a granular pile

Assemblies of granular particles mechanically stable under their own weight contain arches. These are structural units identified as sets of mutually stable grains. It is generally assumed that these arches shield the weight above them and should bear most of the stress in the system. We test such hypothesis by studying the stress born by in-arch and out-of-arch grains. We show that, indeed, particles in arches withstand larger stresses. In particular, the isotropic stress tends to be larger for in-arch-grains whereas the anisotropic component is marginally distinguishable between the two types of particles. The contact force distributions demonstrate that an exponential tail (compatible with the maximization of entropy under no extra constraints) is followed only by the out-of-arch contacts. In-arch contacts seem to be compatible with a Gaussian distribution consistent with a recently introduced approach that takes into account constraints imposed by the local force balance on grains.

0 citations0 reviewsNo code linkedOpen access
preprint2011arXiv

Genetic algorithm for the pair distribution function of the electron gas

The pair distribution function of the electron gas is calculated using a parameterized generalization of quantum hypernetted chain approximation with the parameters being obtained by optimizing the system energy with a genetic algorithm. The functions so obtained are compared with Monte Carlo simulations performed by other authors in its variational and diffusion versions showing a very good agreement especially with the diffusion Monte Carlo results.

0 citations0 reviewsNo code linkedOpen access
preprint2011arXiv

Nonlinear dynamic analysis of an optimal particle damper

We study the dynamical behavior of a single degree of freedom mechanical system with a particle damper. The particle (granular) damping was optimized for the primary system operating condition by using an appropriate gap size for a prismatic enclosure. The particles absorb the kinetic energy of the vibrating structure and convert it into heat through the inelastic collisions and friction. This results in a highly nonlinear mechanical system. Considering linear signal analysis, state space reconstruction, Poincaré sections and the determination of maximal Lyapunov exponents, the motion of the granular system inside the enclosure is characterized for a wide frequency range. With the excitation frequency as control parameter, either regular and chaotic motion of the granular bed are found and their influence on the damping is analyzed.

0 citations0 reviewsNo code linkedOpen access