@article{luque2024,
  title = {In silico study of heterogeneous tumour-derived organoid response to {CAR} T-cell therapy},
  volume = {14},
  issn = {2045-2322},
  url = {https://www.nature.com/articles/s41598-024-63125-5},
  doi = {10.1038/s41598-024-63125-5},
  pages = {12307},
  number = {1},
  journaltitle = {Scientific Reports},
  shortjournal = {Sci Rep},
  author = {Luque, Luciana Melina and Carlevaro, Carlos Manuel and Rodriguez-Lomba, Enrique and Lomba, Enrique},
  urldate = {2024-05-30},
  date = {2024-05-29},
  year = {2024},
  month = may,
  langid = {english}
}

Abstract
            Chimeric antigen receptor (CAR) T-cell therapy is a promising immunotherapy for treating cancers. This method consists in modifying the patients’ T-cells to directly target antigen-presenting cancer cells. One of the barriers to the development of this type of therapies, is target antigen heterogeneity. It is thought that intratumour heterogeneity is one of the leading determinants of therapeutic resistance and treatment failure. While understanding antigen heterogeneity is important for effective therapeutics, a good therapy strategy could enhance the therapy efficiency. In this work we introduce an agent-based model (ABM), built upon a previous ABM, to rationalise the outcomes of different CAR T-cells therapies strategies over heterogeneous tumour-derived organoids. We found that one dose of CAR T-cell therapy should be expected to reduce the tumour size as well as its growth rate, however it may not be enough to completely eliminate it. Moreover, the amount of free CAR T-cells (i.e. CAR T-cells that did not kill any cancer cell) increases as we increase the dosage, and so does the risk of side effects. We tested different strategies to enhance smaller dosages, such as enhancing the CAR T-cells long-term persistence and multiple dosing. For both approaches an appropriate dosimetry strategy is necessary to produce “effective yet safe” therapeutic results. Moreover, an interesting emergent phenomenon results from the simulations, namely the formation of a shield-like structure of cells with low antigen expression. This shield turns out to protect cells with high antigen expression. Finally we tested a multi-antigen recognition therapy to overcome antigen escape and heterogeneity. Our studies suggest that larger dosages can completely eliminate the organoid, however the multi-antigen recognition increases the risk of side effects. Therefore, an appropriate small dosages dosimetry strategy is necessary to improve the outcomes. Based on our results, it is clear that a proper therapeutic strategy could enhance the therapies outcomes. In that direction, our computational approach provides a framework to model treatment combinations in different scenarios and to explore the characteristics of successful and unsuccessful treatments.

@article{carlevaro2024,
  author = {Carlevaro, C. Manuel and Kozlowski, Ryan and Pugnaloni, Luis A.},
  title = {Flow rate in 2D silo discharge of binary granular mixtures: the role of ordering in monosized systems},
  journal = {Frontiers in Soft Matter},
  volume = {4},
  year = {2024},
  url = {https://www.frontiersin.org/articles/10.3389/frsfm.2024.1340744},
  doi = {10.3389/frsfm.2024.1340744},
  issn = {2813-0499}
}

A long-standing debate regarding the dynamics of silo discharge revolves around the use of mono-dispersed circular or spherical grains in simplified two-dimensional models. It is well-known that granular systems composed of particles of the same size can generate crystal or quasi-crystal domains with specific structural and dynamic behaviors. Can this ordering affect the flow rate to an extent that monosized systems cannot be good models for realistic materials? In this work, we present simulations of the discharge of two-dimensional silos filled with binary mixtures of circular grains that conserve the same mean particle size. We address the question of how ordering affects the mass flow rate, in particular considering the limit of mono-sized systems. We find that the typical hexagonal order observed does not affect the flow rate significantly. However, the flow rate does exhibit a weak, nonmonotonic dependence on packing bidispersity that correlates with changes in the outpouring speed of grains in the vicinity of the orifice.

@article{vega2024,
  author = {Vega, Federico G. and Carlevaro, C. Manuel and Baldini, Mauro and Madrid, Marcos A. and Pugnaloni, Luis A.},
  title = {Simulation of proppant conductivity test: effect of particle size dispersion},
  journal = {Petroleum Science and Technology},
  volume = {0},
  number = {0},
  pages = {1-19},
  year = {2024},
  publisher = {Taylor & Francis},
  doi = {10.1080/10916466.2024.2326653},
  url = {https://doi.org/10.1080/10916466.2024.2326653},
  eprint = {https://doi.org/10.1080/10916466.2024.2326653}
}

 A conductivity test of proppant material consists in confining a sample of the granulate at high pressure and then set a flow through the pack. The proppant particle size is the main variable controlling conductivity, but also particle size dispersion is considered important. Even though several studies consider mixtures of proppants of different meshes, there are not clear evidences as to whether the changes in conductivity with respect to a monosized proppant are caused by the mix itself or by the overall change in mean particle size. Hence, we use numerical simulations to answer the question: Does particle size dispersion significantly affects the proppant conductivity if mean particle size is kept the same? We measure conductivity and permeability by simulating (via a coupled Computational Fluid Dynamics–Discrete Element Method) the flow of water through binary granular packs. We find that size dispersion does not affect conductivity (in the dispersion range explored) if the mean particle size is conserved. However, we observe that in a binary mixture the large particles are subjected to larger stresses than in a monosized system, which makes them prone to crushing. 

@article{basak2023,
  title = {Evolution of force networks during stick-slip motion of an intruder in a granular material: Topological measures extracted from experimental data},
  author = {Basak, Rituparna and Kozlowski, Ryan and Pugnaloni, Luis A. and Kramar, M. and Socolar, Joshua E. S. and Carlevaro, C. Manuel and Kondic, Lou},
  journal = {Phys. Rev. E},
  volume = {108},
  issue = {5},
  pages = {054903},
  numpages = {12},
  year = {2023},
  month = nov,
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.108.054903},
  url = {https://link.aps.org/doi/10.1103/PhysRevE.108.054903}
}

@article{barbosa2023,
  doi = {10.1088/1361-648X/acdebd},
  url = {https://dx.doi.org/10.1088/1361-648X/acdebd},
  year = {2023},
  month = jul,
  publisher = {IOP Publishing},
  volume = {35},
  number = {41},
  pages = {410301},
  author = {Barbosa, Marcia C. and Benavides, Ana Laura and Carlevaro, Manuel and Kahl, Gerhard and Lomba, Enrique},
  title = {Special issue on soft matter research in Latin America},
  journal = {Journal of Physics: Condensed Matter}
}

@article{luque2023,
  doi = {10.1371/journal.pcbi.1010920},
  author = {Luque, Luciana Melina and Carlevaro, Carlos Manuel and Llamoza Torres, Camilo Julio and Lomba, Enrique},
  journal = {PLOS Computational Biology},
  publisher = {Public Library of Science},
  title = {Physics-based tissue simulator to model multicellular systems: A study of liver regeneration and hepatocellular carcinoma recurrence},
  year = {2023},
  month = mar,
  volume = {19},
  url = {https://doi.org/10.1371/journal.pcbi.1010920},
  pages = {1-28},
  number = {3}
}

We present a multiagent-based model that captures the interactions between different types of cells with their microenvironment, and enables the analysis of the emergent global behavior during tissue regeneration and tumor development. Using this model, we are able to reproduce the temporal dynamics of regular healthy cells and cancer cells, as well as the evolution of their three-dimensional spatial distributions. By tuning the system with the characteristics of the individual patients, our model reproduces a variety of spatial patterns of tissue regeneration and tumor growth, resembling those found in clinical imaging or biopsies. In order to calibrate and validate our model we study the process of liver regeneration after surgical hepatectomy in different degrees. In the clinical context, our model is able to predict the recurrence of a hepatocellular carcinoma after a 70% partial hepatectomy. The outcomes of our simulations are in agreement with experimental and clinical observations. By fitting the model parameters to specific patient factors, it might well become a useful platform for hypotheses testing in treatments protocols.

@article{alvarez2023,
  author = {Alvarez, H. Ariel and Cousido-Siah, Alexandra and Espinosa, Yanis R. and Podjarny, Alberto and Carlevaro, C. Manuel and Howard, Eduardo},
  title = {Lipid exchange in crystal-confined fatty acid binding proteins: X-ray evidence and molecular dynamics explanation},
  journal = {Proteins: Structure, Function, and Bioinformatics},
  volume = {91},
  number = {11},
  pages = {1525-1534},
  keywords = {crystal simulations, fatty acid binding protein, fatty acids, lipid trafficking, molecular dynamics, X-ray diffraction},
  doi = {https://doi.org/10.1002/prot.26546},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.26546},
  eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.26546},
  year = {2023}
}

Abstract Fatty acid binding proteins (FABPs) are responsible for the long-chain fatty acids (FAs) transport inside the cell. However, despite the years, since their structure is known and the many studies published, there is no definitive answer about the stages of the lipid entry-exit mechanism. Their structure forms a β-barrel of 10 anti-parallel strands with a cap in a helix-turn-helix motif, and there is some consensus on the role of the so-called portal region, involving the second α-helix from the cap (α2), βC–βD, and βE–βF turns in FAs exchange. To test the idea of a lid that opens, we performed a soaking experiment on an h-FABP crystal in which the cap is part of the packing contacts, and its movement is strongly restricted. Even in these conditions, we observed the replacement of palmitic acid by 2-Bromohexadecanoic acid (Br-palmitic acid). Our MD simulations reveal a two-step lipid entry process: (i) The travel of the lipid head through the cavity in the order of tens of nanoseconds, and (ii) The accommodation of its hydrophobic tail in hundreds to thousands of nanoseconds. We observed this even in the cases in which the FAs enter the cavity by their tail. During this process, the FAs do not follow a single trajectory, but multiple ones through which they get into the protein cavity. Thanks to the complementary views between experiment and simulation, we can give an approach to a mechanistic view of the exchange process.

@article{cervantes2023,
  author = {Cervantes, María José and Basiuk, Lucas O. and González-Suárez, Ana and Carlevaro, C. Manuel and Irastorza, Ramiro M.},
  title = {Low-Frequency Electrical Conductivity of Trabecular Bone: Insights from In Silico Modeling},
  journal = {Mathematics},
  volume = {11},
  year = {2023},
  number = {19},
  article-number = {4038},
  url = {https://www.mdpi.com/2227-7390/11/19/4038},
  issn = {2227-7390},
  doi = {10.3390/math11194038}
}

Background: The electrical conductivity of trabecular bone at 100 kHz has recently been reported as a good predictor of bone volume fraction. However, quantifying its relationship with free water (or physiological solution) content and the conductivities of its constituents is still difficult. Methods: In this contribution, in silico models inspired by microCT images of trabecular bovine samples were used to build realistic geometries. The finite element method was applied to solve the electrical problem and to robustly fit the conductivity of the constituents to the literature data. The obtained effective electrical conductivity was compared with the Bruggeman three-medium mixture model using a physiological solution, bone marrow and a bone matrix. Results: The values for the physiological solution plus bone marrow (together as one material) and the bone matrix that best captured the bone volume fraction in the two-medium finite element model were σps+bm = 298.4 mS/m and σb = 21.0 mS/m, respectively. Additionally, relatively good results were obtained with the three-medium Bruggeman mixture model, with σbm= 103 mS/m, σb= 21.0 mS/m and σps= 1200 mS/m. Simple linear relationships between the proportions of constituents depending on bone volume fraction were tested. Degree of anisotropy and fractal dimension do not show detectable changes in effective conductivity. Conclusions: These results provided some useful findings for simulation purposes. First, a higher value for the electrical conductivity of bone marrow has to be used in order to obtain similar values to those of experimental published data. Second, anisotropy is not detectable with conductivity measurements for small trabecular samples (5 mm cube). Finally, the simulations presented here showed relatively good fitting of the Bruggeman mixture model, which would potentially account for the free water content and could rescale the model for whole-bone electrical simulations.

@article{espinosa2022,
  title = {Molecular basis of the anchoring and stabilization of human islet amyloid polypeptide in lipid hydroperoxidized bilayers},
  journal = {Biochimica et Biophysica Acta (BBA) - General Subjects},
  volume = {1866},
  number = {10},
  pages = {130200},
  year = {2022},
  month = jul,
  issn = {0304-4165},
  doi = {https://doi.org/10.1016/j.bbagen.2022.130200},
  url = {https://www.sciencedirect.com/science/article/pii/S0304416522001180},
  author = {Espinosa, Yanis R. and {Barrera Valderrama}, Daniel I. and Carlevaro, C. Manuel and Llanos, Eugenio J.},
  keywords = {Hydroperoxidized lipid, hIAPP, Peptide-membrane interaction, Helicity, Free energy landscape}
}

The molecular structure of membrane lipids is formed by mono- or polyunsaturations on their aliphatic tails that make them susceptible to oxidation, facilitating the incorporation of hydroperoxide (R-OOH) functional groups. Such groups promote changes in both composition and complexity of the membrane significantly modifying its physicochemical properties. Human Langerhans islets amyloid polypeptide (hIAPP) is the main component of amyloid deposits found in the pancreas of patients with type-2 diabetes (T2D). hIAPP in the presence of membranes with oxidized lipid species accelerates the formation of amyloid fibrils or the formation of intermediate oligomeric structures. However, the molecular bases at the initial stage of the anchoring and stabilization of the hIAPP in a hydroperoxidized membrane are not yet well understood. To shed some light on this matter, in this contribution, three bilayer models were modeled: neutral (POPC), anionic (POPS), and oxidized (POPCOOH), and full atom Molecular Dynamics (MD) simulations were performed. Our results show that the POPCOOH bilayer increases the helicity in hIAPP when compared to POPC or POPS bilayer. The modification in the secondary structure covers the residues of the so-called amyloidogenic core of the hIAPP. Overall, the hydroperoxidation of the neutral lipids modifies both the anchoring and the stabilization of the peptide hIAPP by reducing the random conformations of the peptide and increasing of hydrogen bond population with the hydroperoxidized lipids.

@article{pugnaloni2022,
  title = {Universal features of the stick-slip dynamics of an intruder moving through a confined granular medium},
  author = {Pugnaloni, Luis A. and Carlevaro, C. Manuel and Kozlowski, Ryan and Zheng, Hu and Kondic, Lou and Socolar, Joshua E. S.},
  journal = {Physical Review E},
  volume = {105},
  issue = {4},
  pages = {L042902},
  numpages = {5},
  year = {2022},
  month = apr,
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.105.L042902},
  url = {https://link.aps.org/doi/10.1103/PhysRevE.105.L042902}
}

@article{carlevaro2022,
  author = {Carlevaro, C. Manuel and Kuperman, Marcelo N. and Bouzat, Sebasti{\'a}n and Pugnaloni, Luis A. and Madrid, Marcos A.},
  title = {On the use of magnetic particles to enhance the flow of vibrated grains through narrow apertures},
  journal = {Granular Matter},
  year = {2022},
  volume = {24},
  number = {2},
  pages = {51},
  issn = {1434-7636},
  doi = {10.1007/s10035-022-01209-7},
  url = {https://doi.org/10.1007/s10035-022-01209-7}
}

The flow of grains through narrow apertures possess an extraordinary challenge: clogging. Strategies to alleviate the effect of clogging, such as the use of external vibration or addition of smaller grains, are always part of the design of machinery for the handling of bulk materials. In this work, we study with numerical simulations the effect of adding self-repelling magnetic particles to a sample of grains. We consider a vibrated two-dimensional hopper with a small orifice through which disks flow and clog intermittently. We find that the magnetic repulsion has a second order effect in comparison with the effect of the size of the added grains. Small added grains ease the flow of the original species. However, when the magnetic repulsion is switched on for the added small grains their “lubricating” effect is usually lessened. Only for a narrow range of sizes of the added particles we observe a subtle improvement of flow rate of the original particles with magnetic repulsion.

@article{espinosa2021,
  author = {Espinosa, Yanis R. and Alvarez, H. Ariel and Howard, Eduardo I. and Carlevaro, C. Manuel},
  title = {Molecular dynamics simulation of the heart type fatty acid binding protein in a crystal environment},
  journal = {Journal of Biomolecular Structure and Dynamics},
  volume = {39},
  number = {10},
  pages = {3459-3468},
  year = {2021},
  month = jun,
  publisher = {Taylor & Francis},
  doi = {10.1080/07391102.2020.1773315},
  url = {https://doi.org/10.1080/07391102.2020.1773315},
  eprint = {https://doi.org/10.1080/07391102.2020.1773315}
}

Crystallographic data comes from a space-time average over all the unit cells within the crystal, so dynamic phenomena do not contribute significantly to the diffraction data. Many efforts have been made to reconstitute the movement of the macromolecules and explore the microstates that the confined proteins can adopt in the crystalline network. We explored different strategies to simulate a heart fatty acid binding protein (H-FABP) crystal by means of Molecular Dynamics (MD) simulations. We evaluate the effect of introducing restraints according to experimental isotropic B-factors and we analyzed the H-FABP motions in the crystal using Principal Component Analysis (PCA), isotropic and anisotropic B-factors. We compared the behavior of the protein simulated in the crystal confinement versus in solution, and we observed the effect of that confinement in the mobility of the protein residues. Restraining one-third of Cα atoms based on experimental B-factors produce lower B-factors than simulations without restraints, showing that the position restraint of the atoms with the lowest experimental B-factor is a good strategy to maintain the geometry of the crystal with an obvious decrease in the degrees of motion of the protein. PCA shows that, as position restraint reduces the conformational space explored by the system, the motion of the crystal is better recovered, for an essential subspace of the same size, in the simulations without restraints. Restraining only one Cα seems to be a good balance between giving flexibility to the system and preserving its structure. Communicated by Ramaswamy H. Sarma.

@article{madrid2021,
  title = {Enhancement of the flow of vibrated grains through narrow apertures by addition of small particles},
  author = {Madrid, Marcos A. and Carlevaro, C. Manuel and Pugnaloni, Luis A. and Kuperman, Marcelo and Bouzat, Sebasti\'an},
  journal = {Physical Review E},
  volume = {103},
  issue = {3},
  pages = {L030901},
  numpages = {5},
  year = {2021},
  month = mar,
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.103.L030901},
  url = {https://link.aps.org/doi/10.1103/PhysRevE.103.L030901}
}

@article{vega2021,
  title = {Stability and conductivity of proppant packs during flowback in unconventional reservoirs: A CFD–DEM simulation study},
  journal = {Journal of Petroleum Science and Engineering},
  volume = {201},
  pages = {108381},
  year = {2021},
  issn = {0920-4105},
  doi = {https://doi.org/10.1016/j.petrol.2021.108381},
  url = {https://www.sciencedirect.com/science/article/pii/S0920410521000401},
  author = {Vega, Federico G. and Carlevaro, C. Manuel and Sánchez, Martín and Pugnaloni, Luis A.},
  keywords = {Flowback, CFD-DEM, Multiphase flow, Hydraulic fracture}
}

We present simulations using a coupled Computational Fluid Dynamics–Discrete Element Method (CFD–DEM) approach for a slurry of millimeter-sized particles in water which is squeezed between two walls and then made flow out though a narrow aperture. The process is akin to the flowback stage in the near wellbore zone of a hydraulic-stimulated well for hydrocarbon recovery. We consider different wall roughness and investigate its effect on particle production, final distance between walls, spatial particle distribution between the walls, and fluid production rate. We have found that the final distribution of particles changes significantly with small variations in the roughnesses of the walls. This in turn leads to production flow rates that may vary up to 50%. Although the main driver of the production for unconventional wells is the propped fracture network, these results suggest that the roughness of the fracture walls seems to play an important role in the final conductivity and therefore in the ultimate recovery.

@article{basak2021,
  author = {Basak, Rituparna and Carlevaro, C. Manuel and Kozlowski, Ryan and Cheng, Chao and Pugnaloni, Luis A. and Kramár, Miroslav and Zheng, Hu and Socolar, Joshua E. S. and Kondic, Lou},
  title = {Two Approaches to Quantification of Force Networks in Particulate Systems},
  journal = {Journal of Engineering Mechanics},
  volume = {147},
  number = {11},
  pages = {04021100},
  year = {2021},
  doi = {10.1061/(ASCE)EM.1943-7889.0002003},
  url = {https://ascelibrary.org/doi/abs/10.1061/%28ASCE%29EM.1943-7889.0002003},
  eprint = {https://ascelibrary.org/doi/pdf/10.1061/%28ASCE%29EM.1943-7889.0002003}
}

 The interactions between particles in dense particulate systems are organized in force networks, mesoscale features that influence the macroscopic response to applied stresses. The detailed structure of these networks is, however, difficult to extract from experiments that cannot resolve individual contact forces. In this study, we showed that certain persistent homology (PH) measures extracted from data accessible to experiment are strongly correlated with the same features extracted from the full contact force network. We performed simulations known to accurately model experiments on an intruder being pushed through a two-dimensional (2D) granular layer and compared PH properties of full contact force networks and networks constructed using only the sum of the normal forces on each grain. We found that the main features were highly correlated, suggesting that data commonly available in experiments are sufficient for quantifying the structure of force networks in evolving granular systems. 

@article{fajardo2020,
  doi = {10.1007/s11517-019-02090-y},
  url = {https://doi.org/10.1007/s11517-019-02090-y},
  year = {2020},
  month = feb,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {58},
  number = {2},
  pages = {433--442},
  author = {Fajardo, J. E. and Lotto, F. P. and Vericat, F. and Carlevaro, C. M. and Irastorza, R. M.},
  title = {Microwave tomography with phaseless data on the calcaneus by means of artificial neural networks},
  journal = {Medical {\&} Biological Engineering {\&} Computing}
}

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 ≈ 15%. The location and size of the calcaneus are always properly estimated with absolute error standard deviations up to ≈ 3 mm.

@article{carlevaro2020,
  title = {Intruder in a two-dimensional granular system: Effects of dynamic and static basal friction on stick-slip and clogging dynamics},
  author = {Carlevaro, C. Manuel and Kozlowski, Ryan and Pugnaloni, Luis A. and Zheng, Hu and Socolar, Joshua E. S. and Kondic, Lou},
  journal = {Physical Review E},
  volume = {101},
  issue = {1},
  pages = {012909},
  numpages = {9},
  year = {2020},
  month = jan,
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.101.012909},
  url = {https://link.aps.org/doi/10.1103/PhysRevE.101.012909}
}

We present simulation results for an intruder pulled through a two-dimensional granular system by a spring using a model designed to mimic the experiments 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. We then use simulations to explore a broader range of parameter space, focusing on the friction between the particles and the base. We consider 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 behavior when the coefficient is decreased below 0.1, while static friction plays only a marginal role.

@article{kozlowski2019,
  title = {Dynamics of a grain-scale intruder in a two-dimensional granular medium with and without basal friction},
  author = {Kozlowski, Ryan and Carlevaro, C. Manuel and Daniels, Karen E. and Kondic, Lou and Pugnaloni, Luis A. and Socolar, Joshua E. S. and Zheng, Hu and Behringer, Robert P.},
  journal = {Physical Review E},
  volume = {100},
  issue = {3},
  pages = {032905},
  numpages = {10},
  year = {2019},
  month = sep,
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.100.032905},
  url = {https://link.aps.org/doi/10.1103/PhysRevE.100.032905}
}

We report on a series of experiments in which a grain-sized intruder is pushed by a spring through a two-dimensional granular material composed of photoelastic disks in a Couette geometry. We study the intruder dynamics as a function of packing fraction for two types of supporting substrates: A frictional glass plate and a layer of water for which basal friction forces are negligible. We observe two dynamical regimes: Intermittent flow, in which the intruder moves freely most of the time but occasionally gets stuck, and stick-slip dynamics, in which the intruder advances via a sequence of distinct, rapid events. When basal friction is present, we observe a smooth crossover between the two regimes as a function of packing fraction, and we find that reducing the interparticle friction coefficient causes the stick-slip regime to shift to higher packing fractions. When basal friction is eliminated, we observe intermittent flow at all accessible packing fractions. For all cases, we present results for the statistics of stick events, the intruder velocity, and the force exerted on the intruder by the grains. Our results indicate the qualitative importance of basal friction at high packing fractions and suggest a possible connection between intruder dynamics in a static material and clogging dynamics in granular flows.

@article{fajardo2019,
  doi = {10.1088/2057-1976/ab3330},
  url = {https://doi.org/10.1088%2F2057-1976%2Fab3330},
  year = {2019},
  month = jul,
  publisher = {{IOP} Publishing},
  volume = {5},
  number = {4},
  pages = {045039},
  author = {Fajardo, J. E. and Vericat, F. and Irastorza, G. and Carlevaro, C. M. and Irastorza, R. M.},
  title = {Sensitivity analysis on imaging the calcaneus using microwaves},
  journal = {Biomedical Physics {\&} Engineering Express}
}

The bone quality is associated with changes in its dielectric properties (permittivity and conductivity). The feasibility of detecting changes in these properties was evaluated by using a tomographic array of 16 monopole antennas with z-polarized microwaves at 1.3 GHz. The direct electromagnetic problem was solved computationally with the finite–difference–time–domain (FDTD) method. Local and global sensitivity analyses were implemented for identifying the parameters that most affect the detection. Magnitude and phase of the transmission coefficient of the antennas were evaluated separately. It was observed that the direct problem is highly sensitive to the dielectric properties of the tissues surrounding the calcaneus and to those of the calcaneus itself. Global and local sensitivity methods have shown evidence for feasible detection of variations in dielectric properties of the bone supporting the simplification of considering only two homogeneous media (calcaneus and surrounding tissue).

@article{sanchez2019,
  title = {Uncertainties and temperature correction in molecular dynamic simulations of dielectric properties of condensed polar systems},
  journal = {Journal of Molecular Liquids},
  volume = {278},
  pages = {546 - 552},
  year = {2019},
  month = mar,
  issn = {0167-7322},
  doi = {https://doi.org/10.1016/j.molliq.2019.01.077},
  url = {http://www.sciencedirect.com/science/article/pii/S0167732218357064},
  author = {Sánchez, Hernán R. and Irastorza, Ramiro M. and Carlevaro, C. Manuel}
}

A robust, simple and fast procedure for the calculation of uncertainties in static relative permittivity (εs) computed via molecular dynamics (MD) is proposed. It arises as a direct application of well founded statistical methods for auto-correlated variables. Also, in order to deal with the lack of experimental data on εs and relaxation times at different temperatures, a method for their prediction is suggested. This method requires one experimental value and at least two MD simulations. In the case of relaxation times, a theoretical justification is provided.

@article{fajardo2019b,
  author = {Fajardo, Jes{\'u}s E and Galv{\'a}n, Juli{\'a}n and Vericat, Fernando and Carlevaro, Carlos M and Irastorza, Ramiro M},
  title = {Phaseless Microwave Imaging Of Dielectric Cylinders: An Artificial Neural Networks-Based Approach},
  journal = {Progress In Electromagnetics Research},
  year = {2019},
  volume = {166},
  pages = {95-105},
  doi = {10.2528/PIER19080610}
}

An inverse method for parameters estimation of dielectric cylinders (dielectric properties, location, and radius) from amplitude-only microwave information is presented. To this end two different Artificial Neural Networks (ANN) topologies were compared; a Multilayer Perceptron (MLP) and a Convolutional Neural Network (CNN). Several two-dimensional (2D) simulations, with different sizes and locations of homogeneous dielectric cylinders employing the Finite Differences Time Domain (FDTD) method, were performed to generate training, validation, and test sets for both ANN models. The prediction errors were lower for the CNN in high Signal-to-Noise Ratio (SNR) scenarios, although the MLP was more robust in low SNR situations. The CNN model performance was also tested for 2D simulations of dielectrically homogeneous and heterogeneous cylinders placed in acrylic holders showing potential experimental applications. Moreover, the CNN was also tested for a three-dimensional model simulated as realistic as possible, showing good results in predicting all parameters directly from the S-parameters.

@article{baldini2018,
  title = {Numerical simulation of proppant transport in a planar fracture. A study of perforation placement and injection strategy},
  journal = {International Journal of Multiphase Flow},
  volume = {109},
  pages = {207 - 218},
  year = {2018},
  month = dec,
  issn = {0301-9322},
  doi = {https://doi.org/10.1016/j.ijmultiphaseflow.2018.08.005},
  url = {http://www.sciencedirect.com/science/article/pii/S030193221830051X},
  author = {Baldini, Mauro and Carlevaro, C. Manuel and Pugnaloni, Luis A. and Sánchez, Martín},
  keywords = {Proppant transport, CFD–DEM, Multiphase flow, Hydraulic fracture}
}

We present numerical simulations, based on a CFD–DEM approach, of the transport and settlement of proppant in a planar vertical cell that mimics a hydraulic fracture. These simulations, with resolution at the particle level, allow for a clean measurement of the dune placement and proppant degree of mixing. The effect of the position of the injection points is considered by three different injection heights in the vertical cell. Different proppant injection strategies were also considered by using two different proppant types that can be injected in different orders or simultaneously as a mixture. We evaluate the position and shape of the settled dune. We measure the degree of mixing of the two proppant types by using the concept of mixing entropy. We have found that an injection point placed close to the bottom of the cell leads to a dune close to the injection points, and that an injection point at the middle or at the top of the cell leads to a rather flat dune. Injecting different proppant types in different orders yields distinctive proppant distributions. This helps in evaluating the benefits of positioning perforation clusters close to geological boundaries that favor fracture growth in the upward or downward direction as well as selecting the order of proppant mesh injection. All the simulations correspond to the early stage, before the “traction carpet” effect comes into play.

@article{vericat2018,
  title = {Clustering and percolation theory for continuum systems: Clusters with nonspecific bonds and a residence time in their definition},
  journal = {Journal of Molecular Liquids},
  volume = {270},
  pages = {128 - 137},
  year = {2018},
  month = nov,
  note = {Modern trends in theory of electrolyte solutions. In memory of Lesser Blum},
  issn = {0167-7322},
  doi = {https://doi.org/10.1016/j.molliq.2017.11.046},
  url = {http://www.sciencedirect.com/science/article/pii/S0167732217339740},
  author = {Vericat, Fernando and Carlevaro, C. Manuel and Stoico, César O. and Renzi, Danilo G.},
  keywords = {Time-dependent clusters, Physical clusters, Weak criterion, Strong criterion, Time-dependent pair distribution function, Path-integral}
}

In this article, dedicated to the memory of Lesser Blum, we develop a theory for the physical clusters which were introduced some time ago in our group (J. Chem Phys. 116, 1097–1108, 2002). The physical cluster definition establishes that a system particle belongs to the cluster if it is (nonspecifically) bonded to other particles of the cluster along a finite time period τ (the residence time). Our theory has as main ingredients the Stillinger criterion of instantaneous connectivity, that involves a connectivity distance d, the generalized time-dependent pair distribution function of Oppenheim and Bloom that acts as a classical propagator and also the cluster pair correlation function for a weaker version of the physical clusters that requires connectivity just at the extremes of the time period no matter what happens in between. With these tools we express the time dependent pair connectedness function for the physical clusters in the strong sense as a path integral. The path integral is solved by means of a perturbation expansion where the nonperturbed connectedness function coincides with the generalized pair distribution function of Oppenheim and Bloom. We apply the theory to Lennard-Jones fluids at low densities and perform molecular dynamics simulations to check the goodness of diverse functions that appear in the theory.

@article{goldberg2018,
  author = {Goldberg, Ezequiel and Carlevaro, C Manuel and Pugnaloni, Luis A},
  title = {Clogging in two-dimensions: effect of particle shape},
  journal = {Journal of Statistical Mechanics: Theory and Experiment},
  volume = {2018},
  number = {11},
  pages = {113201},
  url = {http://stacks.iop.org/1742-5468/2018/i=11/a=113201},
  doi = {https://doi.org/10.1088/1742-5468/aae84b},
  year = {2018},
  month = nov
}

We study the discharge of a two-dimensional silo through small openings via discrete element simulations. We consider the effect of the shape of the grains on the clogging of the flow, focusing on regular polygons and disks. We show that the clogging probability presents a non-linear response as a function of the number of vertexes of the polygons. Also, the clogging probability is strongly dependent on the protocol used to trigger the flow after each clog. We found that the size and shape of the blocking arches display a much larger variability for some polygons, particularly for squares, than for disks.

@article{fajardo2018b,
  title = {Effect of the trabecular bone microstructure on measuring its thermal conductivity: A computer modeling-based study},
  journal = {Journal of Thermal Biology},
  volume = {77},
  pages = {131 - 136},
  year = {2018},
  month = oct,
  issn = {0306-4565},
  doi = {https://doi.org/10.1016/j.jtherbio.2018.08.009},
  url = {http://www.sciencedirect.com/science/article/pii/S0306456518302213},
  author = {Fajardo, Jesús E. and Carlevaro, C. Manuel and Vericat, Fernando and Berjano, Enrique and Irastorza, Ramiro M.},
  keywords = {Computer model, Thermal conductivity, Trabecular bone}
}

The objective of this work is to quantify the relation between the value of the effective thermal conductivity of trabecular bone and its microstructure and marrow content. The thermal conductivity of twenty bovine trabecular bone samples was measured prior to and after defatting at 37, 47, and 57 °C. Computer models were built including the microstructure geometry and the gap between the tissue and measurement probe. The thermal conductivity (k) measured was 0.39 ± 0.06 W m−1 K−1 at 37 °C, with a temperature dependence of + 0.2%°C−1. Replacing marrow by phosphate-buffered saline (defatting) increased both the computer simulations and measurement results by 0.04 W m−1 K−1. The computer simulations showed that k increases by 0.02–0.04 W m−1 K−1 when the model includes a gap filled by phosphate-buffered saline between the tissue and measurement probe. In the presence of microstructure and fatty red marrow, k varies by ± 0.01 W m−1 K−1 compared with the case considering matrix only, which suggests that there are no significant differences between cortical and trabecular bone in terms of k. The computer results showed that the presence of a gap filled by phosphate-buffered saline around the energy applicator changes maximum temperature by < 0.7 °C, while including the bone microstructure involved a variation of < 0.2 mm in the isotherm location. Future experimental studies on measuring the value of k involving the insertion of a probe into the bone through a drill hole should consider the bias found in the simulations. Thermal models based on a homogeneous geometry (i.e. ignoring the microstructure) could provide sufficient accuracy.

@article{fajardo2018,
  title = {Effects of Cancellous Bone Dielectric Variability on Microwaves Detection Feasibility. A Simulation Study},
  author = {Fajardo, Jesús E. and Vericat, Fernando and Carlevaro, C. Manuel and Irastorza, Ramiro M.},
  journal = {Revista Argentina de Bioingeniería},
  volume = {22},
  number = {2},
  issn = {2591-376X},
  url = {http://revistasabi.fi.mdp.edu.ar/index.php/revista/article/view/225/179},
  year = {2018}
}

The  biological  variability  and  quality  of  trabecular  bone  yield  variability  of  its  dielectric  properties
(permittivity  and  conductivity).  The  feasibility  of  detecting  such  differences  was  studied  in  a  tomographic  array  of
16  monopole  antennas  using  z-polarized  electromagnetic  waves  (OEM)  at  a  frequency  of  1.3  GHz.  Finite-Difference
Time-Domain  (FDTD)  simulations  were  performed  accounting  for  the  documented  dielectric  variability  of  cancellous
bone.  A  sensitivity  analysis  method  was  proposed  in  order  to  identify  the  parameters  that  most  affect  the  detection

@article{carlevaro2016b,
  title = {Chirality in a quaternionic representation of the genetic code},
  journal = {BioSystems},
  volume = {150},
  number = {},
  pages = {99 - 109},
  year = {2016},
  month = dec,
  issn = {0303-2647},
  doi = {http://dx.doi.org/10.1016/j.biosystems.2016.06.003},
  url = {http://www.sciencedirect.com/science/article/pii/S0303264716301022},
  author = {Carlevaro, C. Manuel and Irastorza, Ramiro M. and Vericat, Fernando},
  keywords = {"Genetic code representation", "Homochirality", "Homochiral protein folding"}
}

A quaternionic representation of the genetic code, previously reported by the authors (BioSystems 141 (10–19), 2016), is updated in order to incorporate chirality of nucleotide bases and amino acids. The original representation associates with each nucleotide base a prime integer quaternion of norm 7 and involves a function that assigns to each codon, represented by three of these quaternions, another integer quaternion (amino acid type quaternion). The assignation is such that the essentials of the standard genetic code (particularly its degeneration) are preserved. To show the advantages of such a quaternionic representation we have designed an algorithm to go from the primary to the tertiary structure of the protein. The algorithm uses, besides of the type quaternions, a second kind of quaternions with real components that we additionally associate with the amino acids according to their order along the proteins (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 conjugate and by putting them into correspondence one to one with the two sets of enantiomers (D and L) of the four nucleotide bases adenine, cytosine, guanine and uracil, respectively. We then propose two diagrams in order to describe the hypothetical evolution of the genetic codes corresponding to both of the chiral systems of affinities: D-nucleotide bases/L-amino acids and L-nucleotide bases/D-amino acids at reading frames 5′ → 3′ and 3′ → 5′, respectively. Guided by these diagrams we define functions that in each case assign to the triplets of D- (L-) bases a L- (D-) amino acid type integer quaternion. Specifically, the integer quaternion associated with a given D-amino acid 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.

@article{pugnaloni2016,
  title = {Structure of force networks in tapped particulate systems of disks and pentagons. I. Clusters and loops},
  author = {Pugnaloni, Luis A. and Carlevaro, C. Manuel and Kram\'ar, M. and Mischaikow, K. and Kondic, L.},
  journal = {Physical Review E},
  volume = {93},
  issue = {6},
  pages = {062902},
  numpages = {9},
  year = {2016},
  month = jun,
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.93.062902},
  url = {http://link.aps.org/doi/10.1103/PhysRevE.93.062902}
}

The force network of a granular assembly, defined by the contact network and the corresponding contact forces, carries valuable information about the state of the packing. Simple analysis of these networks based on the distribution of force strengths is rather insensitive to the changes in preparation protocols or to the types of particles. In this and the companion paper [Kondic et al., Phys. Rev. E 93, 062903 (2016)], we consider two-dimensional simulations of tapped systems built from frictional disks and pentagons, and study the structure of the force networks of granular packings by considering network’s topology as force thresholds are varied. We show that the number of clusters and loops observed in the force networks as a function of the force threshold are markedly different for disks and pentagons if the tangential contact forces are considered, whereas they are surprisingly similar for the network defined by the normal forces. In particular, the results indicate that, overall, the force network is more heterogeneous for disks than for pentagons. Such differences in network properties are expected to lead to different macroscale response of the considered systems, despite the fact that averaged measures (such as force probability density function) do not show any obvious differences. Additionally, we show that the states obtained by tapping with different intensities that display similar packing fraction are difficult to distinguish based on simple topological invariants.

@article{kondic2016,
  title = {Structure of force networks in tapped particulate systems of disks and pentagons. II. Persistence analysis},
  author = {Kondic, L. and Kram\'ar, M. and Pugnaloni, Luis A. and Carlevaro, C. Manuel and Mischaikow, K.},
  journal = {Physical Review E},
  volume = {93},
  issue = {6},
  pages = {062903},
  numpages = {11},
  year = {2016},
  month = jun,
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.93.062903},
  url = {http://link.aps.org/doi/10.1103/PhysRevE.93.062903}
}

In the companion paper [Pugnaloni et al., Phys. Rev. E 93, 062902 (2016)], we use classical measures based on force probability density functions (PDFs), as well as Betti numbers (quantifying the number of components, related to force chains, and loops), to describe the force networks in tapped systems of disks and pentagons. In the present work, we focus on the use of persistence analysis, which allows us to describe these networks in much more detail. This approach allows us not only to describe but also to quantify the differences between the force networks in different realizations of a system, in different parts of the considered domain, or in different systems. We show that persistence analysis clearly distinguishes the systems that are very difficult or impossible to differentiate using other means. One important finding is that the differences in force networks between disks and pentagons are most apparent when loops are considered: the quantities describing properties of the loops may differ significantly even if other measures (properties of components, Betti numbers, force PDFs, or the stress tensor) do not distinguish clearly or at all the investigated systems.

@article{carlevaro2016,
  author = {Carlevaro, C. Manuel and Irastorza, Ramiro M. and Vericat, Fernando},
  doi = {10.1016/j.biosystems.2015.12.009},
  issn = {0303-2647},
  journal = {BioSystems},
  keywords = {Genetic code evolution; Broken symmetry; Hamilton quaternions; Protein folding},
  number = {},
  pages = {10--19},
  title = {{Quaternionic representation of the genetic code}},
  url = {http://www.sciencedirect.com/science/article/pii/S0303264715002087},
  volume = {141},
  year = {2016},
  month = mar
}

Abstract 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 appearance 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.

@article{goldberg2015,
  author = {Goldberg, Ezequiel and Carlevaro, C. Manuel and Pugnaloni, Luis A.},
  doi = {10.4279/PIP.070016},
  journal = {Papers In Physics},
  localfile = {/home/manuel/f-papers/mc/Goldberg-PiP-2015.pdf},
  number = {070016},
  pages = {1--10},
  title = {{Flow rate of polygonal grains through a bottleneck: Interplay between shape and size}},
  url = {http://dx.doi.org/10.4279/PIP.070016},
  volume = {7},
  year = {2015},
  month = nov
}

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\red, 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.

@article{irastorza2014,
  author = {Irastorza, Ramiro M. and Blangino, Eugenia and Carlevaro, Carlos M. and Vericat, Fernando},
  doi = {10.1007/s11517-014-1145-y},
  issn = {0140-0118},
  journal = {Medical \& Biological Engineering \& Computing},
  keywords = {Bone dielectric properties; Microwave tomography; Finite difference time domain},
  language = {English},
  month = may,
  number = {5},
  pages = {439--447},
  publisher = {Springer Berlin Heidelberg},
  title = {{Modeling of the dielectric properties of trabecular bone samples at microwave frequency}},
  url = {http://dx.doi.org/10.1007/s11517-014-1145-y},
  volume = {52},
  year = {2014}
}

In this paper, the dielectric properties of human trabecular bone are evaluated under physiological condition in the microwave range. Assuming a two components medium, simulation and experimental data are presented and discussed. A special experimental setup is developed in order to deal with inhomogeneous samples. Simulation data are obtained using finite difference time domain from a realistic sample. The bone mineral density of the samples are also measured. The simulation and experimental results of the present study suggest that there is a negative relation between bone volume fraction (BV/TV) and permittivity/conductivity: the higher the BV/TV, the lower the permittivity/conductivity. This is in agreement with the recently published in vivo data.

@article{irastorza2013b,
  author = {Irastorza, Ramiro M. and Carlevaro, C. Manuel and Pugnaloni, Luis A.},
  doi = {10.1088/1742-5468/2013/12/P12012},
  journal = {Journal of Statistical Mechanics: Theory and Experiment},
  localfile = {/home/manuel/f-papers/granular/Irastorza-JSTAT-2013.pdf},
  number = {12},
  pages = {P12012},
  title = {{Exact predictions from the Edwards ensemble versus realistic simulations of tapped narrow two-dimensional granular columns}},
  url = {http://stacks.iop.org/1742-5468/2013/i=12/a=P12012},
  volume = {2013},
  year = {2013},
  month = dec
}

We simulate, via a discrete element method, the tapping of a narrow column of disks under gravity. For frictionless disks, this system has a simple analytical 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 which are difficult to predict from simple arguments are captured by the theory.

@article{irastorza2013,
  author = {Irastorza, R.M. and Carlevaro, C.M. and Vericat, F.},
  doi = {10.1016/j.medengphy.2012.12.014},
  issn = {1350-4533},
  journal = {Medical Engineering \& Physics},
  keywords = {\{FDTD\} simulation; Bone dielectric properties; Microwave tomography; Effective permittivity},
  localfile = {/home/manuel/f-papers/mc/Irastorza-MedEngPhys-2013.pdf},
  number = {8},
  pages = {1173--80},
  title = {{Is there any information on micro-structure in microwave tomography of bone tissue?}},
  url = {http://www.sciencedirect.com/science/article/pii/S1350453313000088},
  volume = {35},
  year = {2013},
  month = aug
}

In this work, two-dimensional simulations of the microwave dielectric properties of models with ellipses and realistic models of trabecular bone tissue are performed. In these simulations, finite difference time domain methodology has been applied to simulate two-phase structures containing inclusions. The results presented here show that the micro-structure is an important factor in the effective dielectric properties of trabecular bone. We consider the feasibility of using the dielectric behaviour of bone tissue to be an indicator of bone health. The frequency used was 950 MHz. It was found that the dielectric properties can be used as an estimate of the degree of anisotropy of the micro-structure of the trabecular tissue. Conductivity appears to be the most sensitive parameter in this respect. Models with ellipse shaped-inclusions are also tested to study their application to modelling bone tissue. Models with ellipses that had an aspect ratio of a/b = 1.5 showed relatively good agreement when compared with realistic models of bone tissue. According to the results presented here, the anisotropy of trabecular bone must be accounted for when measuring its dielectric properties using microwave imaging.

@article{sanchez2013b,
  author = {S{\'a}nchez, Mart{\'i}n and Carlevaro, C. Manuel},
  doi = {10.1016/j.jsv.2012.09.042},
  issn = {0022-460X},
  journal = {Journal of Sound and Vibration},
  localfile = {/home/manuel/f-papers/granular/Sanchez-JSoundVibrationOK-2013.pdf},
  number = {8},
  pages = {2070--2080},
  title = {{Nonlinear dynamic analysis of an optimal particle damper}},
  url = {http://www.sciencedirect.com/science/article/pii/S0022460X12008425},
  volume = {332},
  year = {2013},
  month = apr
}

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 or chaotic motion of the granular bed is found and the influence on the damping is analyzed.

@article{sanchez2013,
  author = {S{\'a}nchez, Mart{\'i}n and Carlevaro, C. Manuel and Pugnaloni, Luis A.},
  doi = {10.1177/1077546313480544},
  eprint = {http://jvc.sagepub.com/content/20/12/1846.full.pdf+html},
  journal = {Journal of Vibration and Control},
  number = {12},
  pages = {1846--1854},
  title = {{Effect of particle shape and fragmentation on the response of particle dampers}},
  url = {http://jvc.sagepub.com/content/20/12/1846.abstract},
  volume = {20},
  year = {2013},
  month = mar
}

A particle damper (PD) is a device that can attenuate mechanical vibrations thanks to the dissipative collisions between grains contained in a cavity attached to the vibrating structure. It has been recently suggested that, under working conditions in which the damping is optimal, the PD has a universal response in the sense that the specific dissipative properties of the grains cease to be important for the design of the device. We present evidence from simulations of PDs containing grains of different sizes, shapes and restitution coefficients, that the universal response is also valid when fragmentation of the grains occurs (generally due to intensive operation of the PD). In contrast, the welding of grains (caused by operation under high temperatures) can take the PD out of the universal response and deteriorate the attenuation. Interestingly, we observed that even at working conditions off the optimal damping, the shape of the grains remains unimportant for the response of the PD.

@article{carlevaro2012b,
  author = {Carlevaro, C. Manuel and Martins-Da-Silva, Jo{\~a}o Herm{\'i}nio and Savino, Wilson and Caffarena, Ernesto Ra{\'u}l},
  doi = {10.1142/S0219633612501088},
  eprint = {http://www.worldscientific.com/doi/pdf/10.1142/S0219633612501088},
  journal = {Journal of Theoretical and Computational Chemistry},
  localfile = {/home/manuel/f-papers/proteinas/Carlevaro-JTheoCompChem-2013.pdf},
  number = {02},
  pages = {1250108},
  title = {{Plausible binding Mode of the Active $\alpha 4 \beta 1$ antagonist, MK-0617, determined by Docking and Free Energy Calculations}},
  url = {http://www.worldscientific.com/doi/abs/10.1142/S0219633612501088},
  volume = {12},
  year = {2012},
  month = dec
}

In the last years, the development of small molecule antagonists of VLA-4 for the treatment of diseases, where cell trafficking and activation are important, has increased considerably. Among them, the MK-0617 ligand has proven to be a highly potent and orally active α4β1 antagonist. However, the binding mode of this ligand in the integrin binding site remains unknown. Herein we report a thermodynamic analysis of the interaction between MK-0617 (and one of its isomers) and the VLA-4 protein using molecular docking and the free energy perturbation calculations, based on a comparative model of the α4β1 receptor. Initial complex coordinates were taken from molecular docking assays and submitted to alchemical transformations. Free energy of binding ΔΔG values, derived from experimental IC50 values, were taken as a parameter for determining the most likely binding mode. In addition, molecular dynamics simulations of these ligands within the α4β1 binding site were carried out to elucidate the binding energy profile and identify the most significant residues. Our results indicate that MK-0617 fits within the binding site in a stretched conformation, pointing the carboxylate group towards the MIDAS ion. We observe that, despite the fact that the main contribution to the energetic binding process is due to the electrostatic ion contribution, the nonpolar contribution is not negligible. Additionally, a network of hydrogen bonds participate in stabilizing the ligand-receptor interaction.

@article{carlevaro2012,
  author = {Carlevaro, C. M. and Pugnaloni, L. A.},
  doi = {10.1140/epje/i2012-12044-7},
  encoding = {tex},
  issn = {1292-895X},
  journal = {European Physical Journal E},
  localfile = {/home/manuel/f-papers/mc/Carlevaro-EPJE-2012.pdf},
  month = jun,
  number = {6},
  publisher = {Springer Science + Business Media},
  title = {{Arches and contact forces in a granular pile}},
  url = {http://dx.doi.org/10.1140/epje/i2012-12044-7},
  volume = {35},
  year = {2012}
}

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.

@article{vericat2011,
  author = {Vericat, Fernando and Stoico, C{\'e}sar and Carlevaro, C. and Renzi, Danilo},
  doi = {10.1007/s12539-011-0108-3},
  issn = {1913-2751},
  journal = {Interdisciplinary Sciences: Computational Life Sciences},
  number = {4},
  pages = {283--289},
  publisher = {International Association of Scientists in the Interdisciplinary Areas, co-published with Springer-Verlag GmbH},
  title = {{Genetic algorithm for the pair distribution function of the electron gas}},
  url = {http://dx.doi.org/10.1007/s12539-011-0108-3},
  volume = {3},
  year = {2011},
  month = dec
}

The pair distribution function of the electron gas is calculated using a parameterized generalization of 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.

@article{carlevaro2011,
  doi = {10.1088/1742-5468/2011/01/p01007},
  url = {https://doi.org/10.1088%2F1742-5468%2F2011%2F01%2Fp01007},
  year = {2011},
  month = jan,
  publisher = {{IOP} Publishing},
  volume = {2011},
  number = {01},
  pages = {P01007},
  author = {Carlevaro, Carlos M and Pugnaloni, Luis A},
  title = {Steady state of tapped granular polygons},
  journal = {Journal of Statistical Mechanics: Theory and Experiment}
}

The steady state packing fraction of a tapped granular bed is studied for different grain
shapes via a discrete element method. Grains are monosized regular polygons, from
triangles to icosagons. Comparisons with disc packings show that the steady state packing
fraction as a function of the tapping intensity presents the same general trends in
polygon packings. However, better packing fractions are obtained, as expected, for
shapes that can tessellate the plane (triangles, squares and hexagons). In addition,
we find a sharp transition for packings of polygons with more than 13 vertices
signaled by a discontinuity in the packing fraction at a particular tapping intensity.
Density fluctuations for most shapes are consistent with recent experimental
findings in disc packing; however, a peculiar behavior is found for triangles and
squares.

@article{stoico2010,
  title = {Quantum hypernetted chain approximation for one-dimensional fermionic systems},
  journal = {Physica E: Low-dimensional Systems and Nanostructures},
  volume = {42},
  number = {5},
  pages = {1691 - 1705},
  year = {2010},
  month = mar,
  issn = {1386-9477},
  doi = {https://doi.org/10.1016/j.physe.2010.01.027},
  url = {http://www.sciencedirect.com/science/article/pii/S1386947710000561},
  author = {Stoico, César O. and Carlevaro, C. Manuel and Renzi, Danilo G. and Vericat, Fernando},
  keywords = {Fermi hypernetted chain approximation, Quantum wires, Wigner crystallization, Coupled quantum wires}
}

In this comprehensible article we develop, following Fantoni and Rosati formalism, a hypernetted chain approximation for one-dimensional systems of fermions. Our scheme differs from previous treatments in the form that the whole set of diagrams is grouped: we do it in terms of non-nodal, non-composite and elementary graphs. This choice makes the deduction of equations more transparent. Equations for the pair distribution functions of one component systems as well as binary mixtures are obtained. We apply they to experimentally realizable quasi-one-dimensional systems, the so-called quantum wires which we model, within Sommerfeld–Pauli spirit, as a one-dimensional electron gas or as an electron–hole mixture. In order to use our one-dimensional equations we consider pair potentials that depend on the wires width.

@article{pugnaloni2008b,
  author = {Pugnaloni, Luis A. and Mizrahi, Martin and Carlevaro, Carlos M. and Vericat, Fernando},
  collaboration = {},
  doi = {10.1103/PhysRevE.78.051305},
  eid = {051305},
  journal = {Physical Review E},
  keywords = {granular materials; vibrations},
  localfile = {/home/manuel/f-papers/mc/MC-PRE-2008.pdf},
  number = {5},
  numpages = {7},
  pages = {051305},
  publisher = {APS},
  title = {{Nonmonotonic reversible branch in four model granular beds subjected to vertical vibration}},
  url = {http://link.aps.org/abstract/PRE/v78/e051305},
  volume = {78},
  year = {2008},
  month = nov
}

We present results from four independent models of a granular assembly subjected to tapping. We find that the steady-state packing fraction as a function of the tapping intensity is nonmonotonic. In particular, for high tapping intensities, we observe an increase of the packing fraction with tapping strength. This finding challenges the current understanding of compaction of granular media since the steady-state packing fraction is believed to decrease monotonically with increasing tapping intensity. We propose an explanation of our results based on the properties of the arches formed by the particles.

@article{pugnaloni2008,
  author = {Pugnaloni, Luis A. and Carlevaro, Carlos M. and Valluzzi, Marcos G. and Vericat, Fernando},
  collaboration = {},
  doi = {10.1063/1.2965879},
  eid = {064510},
  journal = {Journal of Chemical Physics},
  keywords = {bonds (chemical); Lennard-Jones potential; molecular clusters; molecular dynamics method; percolation},
  localfile = {/home/manuel/f-papers/mc/MC-JChemPhys-2008.pdf},
  number = {6},
  numpages = {6},
  pages = {064510},
  publisher = {AIP},
  title = {{Continuum percolation of long lifespan clusters in a simple fluid}},
  url = {http://link.aip.org/link/?JCP/129/064510/1},
  volume = {129},
  year = {2008},
  month = aug
}

We present results on the percolation loci for chemical clusters and physical clusters of long lifespan. Chemical clusters are defined as sets of particles connected through particle-particle bonds that last for a given time τ. Physical clusters are sets of particles that remain close together at every instant for a given period of time τ. By using molecular dynamics simulations of a Lennard-Jones system we obtain the percolation loci at different values of τas the lines in the temperature-density plane at which the system presents a spanning cluster in 50% of the configurations. We find that the percolation loci for chemical clusters shifts rapidly toward high densities as τis increased. For moderate values of tau this line converges to the low-density branch of the liquid-solid coexistence curve. This implies that no stable chemical clusters can be found in the fluid phase. In contrast, the percolation loci for physical clusters tend to a limiting line, as τtends to infinity, which is far from the liquid-solid transition line.

@article{carlevaro2008,
  author = {Carlevaro, C. M. and Wilkinson, M. V. and Barrios, L. A.},
  doi = {10.1088/1748-0221},
  issn = {1748-0221},
  journal = {Journal of Instrumentation},
  localfile = {/home/manuel/f-papers/mc/MC-JINST-2008.pdf},
  number = {1},
  pages = {P01001},
  title = {{A genetic algorithm approach to routine gamma spectra analysis}},
  url = {http://iopscience.iop.org/1748-0221/3/01/P01001/?ejredirect=.iopscience},
  volume = {3},
  year = {2008},
  month = jan
}

In this work we present an alternative method for performing routine gamma spectra analysis based on genetic algorithm techniques. The main idea is to search for patterns of single nuclide spectra obtained by simulation in a sample spectrum targeted for analysis. We show how this approach is applied to the analysis of simulated and real target spectra, and also to the study of interference resolution.

@article{carlevaro2004,
  author = {Carlevaro, M. and Quagliano, J. and Fernandez, S. and Cetrangolo, H.},
  journal = {New Medit Journal of Economics, Agriculture and Environment},
  number = {1},
  pages = {47--54},
  title = {{Honey agri-food chain in Argentina: model and simulation}},
  volume = {3},
  year = {2004},
  month = mar
}

This work will show the dynamics involved in the study of the honey agri-food chain in Argentina. The method explained would show how to model and simulate complex feedback mechanisms allowing the behaviour analysis of a determined system over a period of time. We chose the honey agri-food chain as our study objective since it’s a simple product. It does not require industrial processing and is an export-oriented activity. The system model is elaborated from a causal loop diagram, and after comparing some variables of interest with historical series; simulations are made in order to determine the impact of diverse future scenarios, like the effect of the devaluation, China behaviour in markets, and climatic and technological scenarios. The relation of system dynamics and supply chain management is reviewed, and the usefulness of system dynamics as a tool for predicting different scenarios and for supply chain redesign is highlighted.

@article{carlevaro2003,
  author = {Carlevaro, Carlos Manuel and Blum, Lesser and Vericat, Fernando},
  collaboration = {},
  doi = {10.1063/1.1597475},
  journal = {Journal of Chemical Physics},
  keywords = {ab initio calculations; hydrogen bonds; Monte Carlo methods; potential energy functions},
  localfile = {/home/manuel/f-papers/mc/MC-JChemPhys-2003.pdf},
  number = {10},
  pages = {5198--5215},
  publisher = {AIP},
  title = {{Generalized mean spherical approximation for a model of water with dipole, quadrupole, and short-range potential of tetrahedral symmetry}},
  url = {http://link.aip.org/link/?JCP/119/5198/1},
  volume = {119},
  year = {2003},
  month = aug
}

A simplified version of the so-called Yukagua model of water, proposed and studied via Monte Carlo simulations elsewhere by two of the authors [Physica A 265, 396 (1999)], is considered. The model includes dipolar, quadrupolar, and octupolar short-range interactions of tetrahedral symmetry that mimic hydrogen bonds, but it differs from the original Yukagua model in that dipolar and quadrupolar terms are not coupled. For this model we solve, using Baxter-Wertheim factorization technique, the Ornstein-Zernike relation for the molecular pair correlation functions closed by generalized mean spherical closures. From the molecular correlations we derive the atom-atom (oxygen-oxygen, oxygen-hydrogen, and hydrogen-hydrogen) pair correlations. We compare our results with those obtained from diffraction experiments and also from other theoretical treatments available in the recent literature including a modified version of the hypernetted chain integral equation for the SPC/E water model and also ab initio simulations of Car-Parrinello type.

@article{cetrangolo2002,
  author = {Cetr{\'a}ngolo, H. and Carlevaro, M. and Fern{\'a}ndez, S.},
  journal = {New Medit Journal of Economics, Agriculture and Environment},
  number = {2},
  pages = {34--40},
  title = {{Limitations for competitiveness in Argentinian sunflower agrifood chain}},
  volume = {1},
  year = {2002},
  month = jun
}

Argentina is today the first sunflower oil producer and exporter. Its competitiveness relies on being highly efficient in the primary production and industrialization stages. However, this sector is threatened by several implemented mechanisms that distorted the international market. This paper presents an updated overview of Argentinean sunflower agrifood chain situation, describing primary production, industry, commercialization and main mechanisms that limit its competitiveness.

@article{renzi2001,
  author = {Renzi, D. and Carlevaro, C. M. and Stoico, C. and Vericat, F.},
  doi = {10.1080/00268970010027675},
  issn = {0026-8976},
  journal = {Molecular Physics},
  localfile = {/home/manuel/f-papers/mc/MC-MolPhys-2001.pdf},
  month = jun,
  number = {11},
  pages = {913--922},
  title = {{Solvation properties of non-polar amino acids in water and methanol: a molecular dynamics study}},
  volume = {99},
  year = {2001}
}

Solvation properties of the amino acids alanine, valine, leucine and phenylalanine in water and in methanol at infinite dilution have been studied by using molecular dynamics simulations. The free energy transfer of the solutes from water to methanol has been calculated by means of a slow-growth technique and the results compared with diverse hydrophobicity scales available in the literature. Chothia’s linear relation between the accessible surface area and the hydrophobicity is shown. The line obtained has a slope equivalent to 49 cal mol^(-1) A^(-2). The radial distribution of solvent molecules around the amino acids residues is considered, and a comparison is made of the number of hydrogen bonds formed between water molecules in the presence and in the absence, respectively, of the amino acids. The calculations show clearly that the solvation structure near the non-polar amino acids is richer for methanol than for water.

@article{carlevaro1998,
  author = {Carlevaro, Manuel and Caffarena, Ernesto R. and Grigera, J. Raul},
  doi = {10.1016/S0141-8130(98)00038-5},
  journal = {International Journal of Biological Macromolecules},
  key = {Carbohydrate hydration; Molecular dynamics simulation; Xylitol conformation},
  localfile = {/home/manuel/f-papers/mc/MC-IntJofBiolMacromol-1998.pdf},
  number = {2},
  pages = {149--155},
  title = {{Hydration properties of xylitol: computer simulation}},
  url = {http://www.sciencedirect.com/science/article/B6T7J-3TW90PJ-7/1/53db87986da76df1624e98c1ab357fda},
  volume = {23},
  year = {1998},
  month = aug
}

We present a molecular dynamics simulation of xylitol in SPC/E water using classical Gibbs ensemble molecular dynamics simulation. The simulation is done both with and without periodic charge update, and no qualitative difference in the results obtained by both methods is found. The analysis of the radial and angular distribution functions, the water-water hydrogen bond distributions, and water residence times allow the conclusion that there is a relatively strong hydration of xylitol. This polyol adopts a single linear conformation and, from the point of view of the hydration dynamics, it should be classified as positively hydrated.

@article{carlevaro1996,
  author = {Carlevaro, C. Manuel and Stoico, C{\'e}sar and Vericat, Fernando},
  doi = {10.1088/0953-8984},
  issn = {0953-8984},
  journal = {Journal of Physics: Condensed Matter},
  localfile = {/home/manuel/f-papers/mc/MC-JPhysCondensMatt-1996.pdf},
  number = {12},
  pages = {1857--1867},
  title = {{An exponential approximation for continuum percolation in dipolar hard-sphere fluids}},
  url = {http://iopscience.iop.org/0953-8984/8/12/002/?ejredirect=.iopscience},
  volume = {8},
  year = {1996},
  month = mar
}

We consider a generalized mean spherical approximation for the pair-connectedness function of a dipolar hard-sphere fluid. Based on its analytical solution, we propose an exponential approach to the continuum percolation of dipolar fluids. The mean cluster size and the critical percolation density so obtained agree well with previously reported Monte Carlo simulations. The Kirkwood gK factor calculated among connected dipoles, a magnitude that can be taken as a measure of the dipolar ordering inside the cluster, also compares well with the simulation results.

@inproceedings{cetrangolo2002b,
  author = {Cetr{\'a}ngolo, H. and Carlevaro, M. and Fern{\'a}ndez, S.},
  booktitle = {{Paradoxes in food chains and networks: proceedings of the fifth International Conference on Chain and Network Management in Agribusiness and the Food Industry}},
  editor = {Trienekens, J.H. and Omta, S.W.F.},
  location = {Noordwijk, The Netherlands},
  pages = {829--839},
  isbn = {978-90-76998-09-1},
  doi = {10.3920/978-90-8686-507-9},
  publisher = {Wageningen Academic Publishers},
  title = {{Limitations for Efficiency within the Beef Agrifood Chain in Argentina}},
  year = {2002},
  month = jun
}

In this contribution we present a competitiveness study of the beef agrifood chain in Argentina. This sector is one of the most important within the national economy. However, its participation in the international market has been decreasing due to its own efficiency limitations and to external factors as well. We have performed a netchain analysis by identifying the main chain actors and mechanisms of interaction among them. From this
analysis, a strengths, weaknesses, opportunities and threats (SWOT) analysis was made for evaluating chain performance. Finally, a quantitative measure of competitiveness level was obtained in comparison with main competitors through the evaluation of the competitive profile matrix.

@techreport{ytec2022,
  title = {ST5183: Simulación numérica de cinética de reacción de precipitación de sales minerales a partir de suspensiones acuosas en presencia de CO$_2$ a altas presiones y temperaturas. Descomposición térmica de la urea.},
  author = {Carlevaro, M. and Irastorza, R. and Meyra, A. and Sánchez, H.},
  year = {2023},
  type = {Informe técnico},
  institution = {IFLySiB},
  month = dec
}

@techreport{ytec2021,
  title = {ST5183: Simulación numérica de cinética de reacción de precipitación de sales minerales a partir de suspensiones acuosas en presencia de CO$_2$ a altas presiones y temperaturas.},
  author = {Carlevaro, M. and Irastorza, R. and Meyra, A. and Sánchez, H.},
  year = {2021},
  type = {Informe técnico},
  institution = {IFLySiB},
  month = apr
}

@techreport{ytec2018,
  title = {Proyecto 497: Transporte y estabilidad del agente de sostén en fracturas no convencionales},
  author = {Pugnaloni, L.A. and Baldini, M. and Fernández, M. and Roschzttardtz, I. and Vega, F.G. and Carlevaro, C.M.},
  year = {2018},
  type = {Informe técnico},
  institution = {IFLySiB - CONICET y Departamento de Ingeniería Mecánica, Universidad Tecnológica Nacional, Facultad Regional La Plata},
  month = oct
}

@techreport{ytec2016,
  title = {Resumen anual de las actividades desarrolladas durante el primer año de ejecución del proyecto Transporte y estabilidad del agente de sostén en fracturas no convencionales},
  author = {Pugnaloni, L.A. and Baldini, M. and Fernández, M. and Carlevaro, C.M.},
  year = {2016},
  type = {Informe técnico},
  institution = {IFLySiB - CONICET y Departamento de Ingeniería Mecánica, Universidad Tecnológica Nacional, Facultad Regional La Plata},
  month = sep
}

@techreport{ytec2015,
  title = {Especificación de requerimientos y funcionalidades del software a desarrollar en el marco del proyecto Transporte y estabilidad del agente de sostén en fracturas no convencionales},
  author = {Carlevaro, C.M. and Baldini, M. and Pugnaloni, L.A.},
  year = {2015},
  type = {Informe técnico},
  institution = {IFLySiB - CONICET y Departamento de Ingeniería Mecánica, Universidad Tecnológica Nacional, Facultad Regional La Plata},
  month = sep
}