Artigos
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Item Ab initio molecular dynamics simulation of methanol and acetonitrile: the effect of van der Waals interactions(Chemical Physics Letters, 2019-01-16) Dias, Rafael F.; Costa, Cleidineia C. da; Manhabosco, Taise M.; Oliveira, Alan B. de; Matos, Matheus J. S.; Soares, Jaqueline S.; Batista, Ronaldo J. C.We employed PBE and BLYP semi-local functionals and the van der Waals density functional of Dion et al. (2004) (vdW-DF) to investigate structural properties of liquid acetonitrile and methanol. Among those functionals the vdW-DF is the only one that correctly predicts energy minima in inter-molecular interactions between acetonitrile molecules. We found that van der Waals interactions have a negligible effect on H-bonds in methanol chains. However, it significantly increases chain packing resulting in a more dense liquid in comparison to the other two functionals. The overall trend is that the vdW-DF tends to overestimate density and bulk modulus, meanwhile the semi-local functionals tend to underestimate density. Thus, van der Waals interactions play an important role in the properties of liquids in which much stronger dipole-dipole interactions are present.Item Absorbing state transition in a one-dimensional contact replication process(Physical Review E, 2004-09-29) Ferreira Jr., S. C.In this work, the contact process (CP) is modified in order to model a contact replication process (CRP) for monoclonal reproduction. The occupation rates of an empty site depend on the nearest-neighbor and next- nearest-neighbor sites. The CRP exhibits an absorbing state transition studied through cluster approximations and Monte Carlo simulations. The critical rate obtained from simulations,λc = 2.0263(4), is smaller than that for CP. However, the CRP critical exponents are in agreement with those for CP and, consequently, the model belongs to the directed percolation universality class.Item Activation thresholds in epidemic spreading with motile infectious agents on scale-free networks(Chaos: An Interdisciplinary Journal of Nonlinear Science, 2018) Silva, Diogo H.; Ferreira, Silvio C.We investigate a fermionic susceptible-infected-susceptible model with the mobility of infected individuals on uncorrelated scale-free networks with power-law degree distributions P(k)∼k−γP(k)∼k−γ of exponents 2<γ<32<γ<3. Two diffusive processes with diffusion rate DD of an infected vertex are considered. In the standard diffusion, one of the nearest-neighbors is chosen with equal chance, while in the biased diffusion, this choice happens with probability proportional to the neighbor’s degree. A non-monotonic dependence of the epidemic threshold on DD with an optimum diffusion rate D∗D∗, for which the epidemic spreading is more efficient, is found for standard diffusion while monotonic decays are observed in the biased case. The epidemic thresholds go to zero as the network size is increased and the form that this happens depends on the diffusion rule and the degree exponent. We analytically investigated the dynamics using quenched and heterogeneous mean-field theories. The former presents, in general, a better performance for standard and the latter for biased diffusion models, indicating different activation mechanisms of the epidemic phases that are rationalized in terms of hubs or max kk-core subgraphs. Nowadays, we live in an interwoven world where information, goods, and people move through a complex structure with widely diversified types of interactions such as on-line friendship and airport connections. These and many other systems of completely distinct nature can be equally suited in a theoretical representation called complex networks, in which the elements are represented by vertices and the interactions among them by edges connecting these vertices. The study of epidemic processes on complex networks represents one of the cornerstones in modern network science and can aid the prevention (or even stimulation) of disease or misinformation spreading. The relevance of the interplay between diffusion and epidemic spreading in real systems is self-evident since hosts of infectious agents, such as people and mobile devices, are constantly moving, being the carriers that promote the quick transition from a localized outbreak to a large scale epidemic scenario. In this work, we perform a theoretical analysis and report nontrivial roles played by mobility of infected agents on the efficiency of epidemic spreading running on the top of complex networks. We expect that our results will render impacts for forthcoming research related to the area.Item Alternative uses of a megavolt tandem accelerator for few-keV studies with ion-source SIMS monitoring(Review of Scientific Instruments, 2016-06-20) Mello, S. L. A.; Codeço, C. F. S.; Magnani, B. F.; Sant’Anna, M. M.We increase the versatility of a tandem electrostatic accelerator by implementing simple modifications to the standard operation procedure. While keeping its ability to deliver MeV ion beams, we show that the experimental setup can (i) provide good quality ion beams in the few-keV energy range and (ii) be used to study ion-beam surface modification with simultaneous secondary ion mass spectrometry. This latter task is accomplished without using any chamber connected to the accelerator exit. We perform mass spectrometry of the few-keV anions produced in the ion source by measuring their neutral counterparts at the accelerator exit with energies up to 1.7 MeV. With an additional modification, a high-current few-keV regime is obtained, using the ion source as an irradiation chamber and the accelerator itself only as a mass spectrometer. As an example of application, we prepare a sample for the study of ion-beam assisted dewetting of a thin Au film on a Si substrate.Item Analytical verification of scaling laws for the Ising model with external field in fractal lattices(Physical Review E, 1999-09-01) Redinz, José ArnaldoWe use an exact recursion procedure to verify analytically, without any intermediary numerical calculation, the validity of the hyperscaling (Josephson) law extended to fractals, the Rushbrooke and Griffiths scaling laws for the Ising ferromagnet with external magnetic field in the whole family of Migdal-Kadanoff-like hierarchical lattices.Item Anisotropy in rupture lines of paper sheets(Physical Review E, 2005-06-22) Menezes-Sobrinho, I. L.; Couto, M. S.; Ribeiro, I. R. B.We have experimentally investigated the fracture process in paper samples submitted to a uniaxial force. Five types of paper sheets (newsprint, towel, sulfite, silk, and couche papers) were fractured along two orthogonal orientations. In order to characterize the rupture lines of the paper sheets we utilized the Hurst exponent. Our results indicate a dependence of the Hurst exponent on the orientation of the paper sheets for samples of newsprint and, probably, towel and silk papers. For the other types of paper the Hurst exponent does not depend on the direction of crack propagation.Item Anomalous diffusion and q-Weibull velocity distributions in epithelial cell migration(Plos One, 2017-07-10) Podestá, Tatiane Souza Vilela; Rosembach, Tiago Venzel; Santos, Anésia Aparecida dos; Martins, Marcelo LobatoIn multicellular organisms, cell motility is central in all morphogenetic processes, tissue maintenance, wound healing and immune surveillance. Hence, the control of cell motion is a major demand in the creation of artificial tissues and organs. Here, cell migration assays on plastic 2D surfaces involving normal (MDCK) and tumoral (B16F10) epithelial cell lines were performed varying the initial density of plated cells. Through time-lapse microscopy quantities such as speed distributions, velocity autocorrelations and spatial correlations, as well as the scaling of mean-squared displacements were determined. We find that these cells exhibit anomalous diffusion with q-Weibull speed distributions that evolves non-monotonically to a Maxwellian distribution as the initial density of plated cells increases. Although short-ranged spatial velocity correlations mark the formation of small cell clusters, the emergence of collective motion was not observed. Finally, simulational results from a correlated random walk and the Vicsek model of collective dynamics evidence that fluctuations in cell velocity orientations are sufficient to produce q-Weibull speed distributions seen in our migration assays.Item Antimonide-based membranes synthesis integration and strain engineering(Proceedings of the National Academy of Sciences of the United States of America, 2016-11-15) Ferreira, Sukarno O.; Zamiri, Marziyeh; Anwar, Farhana; Klein, Brianna A.; Rasoulof, Amin; Dawson, Noel M.; Schuler-Sandy, Ted; Deneke, Christoph F.; Cavallo, Francesca; Krishna, SanjayAntimonide compounds are fabricated in membrane form to enable materials combinations that cannot be obtained by direct growth and to support strain fields that are not possible in the bulk. InAs/(InAs,Ga)Sb type II superlattices (T2SLs) with different in-plane geometries are transferred from a GaSb substrate to a variety of hosts, including Si, polydimethylsiloxane, and metal-coated substrates. Electron microscopy shows structural integrity of transferred membranes with thickness of 100 nm to 2.5μm and lateral sizes from 24×24 μm2 to 1×1 cm2. Electron microscopy reveals the excellent quality of the membrane interface with the new host. The crystalline structure of the T2SL is not altered by the fabrication process, and a minimal elastic relaxation occurs during the release step, as demonstrated by X-ray diffraction and mechanical modeling. A method to locally strain-engineer antimonide-based membranes is theoretically illustrated. Continuum elasticity theory shows that up to ∼3.5% compressive strain can be induced in an InSb quantum well through external bending. Photoluminescence spectroscopy and characterization of an IR photodetector based on InAs/GaSb bonded to Si demonstrate the functionality of transferred membranes in the IR range.Item Atomic Force Microscopy of spermidine-induced DNA condensates on silicon surfaces(Materials Science and Engineering: C, 2011-09-21) Carrasco, I.S.S.; Bastos, F.M.; Munford, M.L.; Ramos, E.B.; Rocha, M.S.In the present work, we show that oxidized silicon may be successfully used to image multivalent cation-induced DNA condensates under the Atomic Force Microscope (AFM). The images thus obtained are good enough, allowing us to distinguish between different condensate forms and to perform nanometer-sized measurements. Qualitative results previously obtained using mica as a substrate are recovered here. We additionally show that the interactions between the cation spermidine (the condensing agent) and the DNA molecules are not significantly disturbed by the silicon surface, since the phase behavior of an ensemble of DNA molecules deposited on the silicon substrate as a function of the cation concentration is very similar to that found in solution.Item Avoiding trap states in poly(n-vinylcarbazole) thin films(Organic Electronics, 2012-12) Valadares, M.; Calado, H. D. R.; Araujo, K. A. S.; Guimarães, P. S. S.; Cury, L. A.; Akcelrud, L.; Sanvitto, D.; Giorgi, M. deOptical properties of poly(n-vinylcarbazole) (PVK) thin films are revisited. Steady-state emission spectra put in evidence a strong red band whose intensity increases with decreasing temperature when the solid state PVK film is excited by a continuous 375 nm laser line. This red band is assigned to the emission from PVK aggregate states which act as trap states for the monomeric PVK triplet high energy (blue) excitons. At the same low temperatures, these trap states can be avoided when the excitation of the PVK film is made by a 355 nm pulsed laser line with 10 Hz repetition rate. The red band was also observed to compete with the emission of guest poly(3-octadecylthiophene) (PODT) molecules in a PVK/PODT sequential bilayer structure. Different optical geometries enabled us to show that the exciton energy transfer effect from PVK donor to PODT acceptor states dominates the scenario in the bilayer structure, suppressing almost completely the trap state emissions.Item Behaviour of charged spinning massless particles(Symmetry, 2018) Morales, Ivan; Neves, Bruno; Oporto, Zui; Piguet, OlivierWe revisit the classical theory of a relativistic massless charged point particle with spin and interacting with an external electromagnetic field. In particular, we give a proper definition of its kinetic energy and its total energy, the latter being conserved when the external field is stationary. We also write the conservation laws for the linear and angular momenta. Finally, we find that the particle’s velocity may differ from c as a result of the spin—electromagnetic field interaction, without jeopardizing Lorentz invariance.Item Berry phases and zero-modes in toroidal topological insulator(The European Physical Journal B, 2016-06) Fonseca, Jakson M.; Moura-Melo, Winder A.; Pereira, Afranio R.; Carvalho-Santos, Vagson L.An effective Hamiltonian describing the surface states of a toroidal topological insulator is obtained, and it is shown to support both bound-states and charged zero-modes. Actually, the spin connection induced by the toroidal curvature can be viewed as an position-dependent effective vector potential, which ultimately yields the zero-modes whose wave-functions harmonically oscillate around the toroidal surface. In addition, two distinct Berry phases are predicted to take place by the virtue of the toroidal topology.Item Biophysical characterization of the DNA interaction with the biogenic polyamine putrescine: a single molecule study(International Journal of Biological Macromolecules, 2018-02-26) Publio, B.C.; Moura, T.A.; Lima, C.H.M.; Rocha, M.S.We have performed a biophysical characterization, at single molecule level, of the interaction between the DNA molecule and the biogenic polyamine putrescine. By using force spectroscopy, we were able to monitor the complexes formation as putrescine is added to the sample, determining the mechanical properties of such complexes and the physicochemical (binding) parameters of the interaction for three different ionic strengths. In particular, it was shown that the behavior of the equilibrium binding constant as a function of the counterion concentration deviates from the prediction of the Record-Lohman model. The measured constants were (1.3 ± 0.2) × 10^5 M^- 1 for [Na] = 150 mM, (2.1 ± 0.2) × 10^5 M^- 1 for [Na] = 10 mM, and (2.2 ± 0.3) × 10^5 M^- 1 for [Na] = 1 mM. The cooperativity degree of the binding reaction, on the other hand, increases with the ionic strength. From these analysis, the DNA-putrescine binding mechanisms are inferred, and a comparison with results reported for ordinary bivalent ions like magnesium is performed. Such study provides new insights on the general behavior of the DNA interactions with biogenic polyamines.Item Boolean network model for cancer pathways: predicting carcinogenesis and targeted therapy outcomes(Plos One, 2013-07-26) Fumiã, Herman F.; Martins, Marcelo L.A Boolean dynamical system integrating the main signaling pathways involved in cancer is constructed based on the currently known protein-protein interaction network. This system exhibits stationary protein activation patterns – attractors – dependent on the cell’s microenvironment. These dynamical attractors were determined through simulations and their stabilities against mutations were tested. In a higher hierarchical level, it was possible to group the network attractors into distinct cell phenotypes and determine driver mutations that promote phenotypic transitions. We find that driver nodes are not necessarily central in the network topology, but at least they are direct regulators of central components towards which converge or through which crosstalk distinct cancer signaling pathways. The predicted drivers are in agreement with those pointed out by diverse census of cancer genes recently performed for several human cancers. Furthermore, our results demonstrate that cell phenotypes can evolve towards full malignancy through distinct sequences of accumulated mutations. In particular, the network model supports routes of carcinogenesis known for some tumor types. Finally, the Boolean network model is employed to evaluate the outcome of molecularly targeted cancer therapies. The major find is that monotherapies were additive in their effects and that the association of targeted drugs is necessary for cancer eradication.Item Carboplatin as an alternative to Cisplatin in chemotherapies: New insights at single molecule level(Biophysical Chemistry, 2018-10) Oliveira, L.; Caquito Jr., J. M.; Rocha, M. S.Here we report a new study performed at single molecule level on the interaction of the antineoplastic drug Carboplatin and the DNA molecule - the main target of the drug inside cells in cancer chemotherapies. By using optical tweezers, we measure how the mechanical properties of the DNA-Carboplatin complexes changes as a function of the drug concentration in the sample, for two different ionic strengths ([Na] = 150 mM and [Na] = 1 mM). From these measurements, the binding mechanism and the physicochemical (binding) parameters of the interaction were inferred and directly compared to those obtained for the precursor drug Cisplatin under equivalent conditions. As the main conclusion, we show that Carboplatin binds preferentially forming covalent monoadducts in contrast to Cisplatin, which is hydrolyzed easier and presents a higher efficiency in forming covalent diadducts along the double-helix. In addition, we explicitly show that Carboplatin is much less sensitive to ionic strength changes when compared to Cisplatin. These findings provide new insights on the interactions of platinum-based compounds with the DNA molecule, being important to improve the current treatments and in the development of new antineoplastic agents.Item Cellular automata model for citrus variegated chlorosis(Physical Review E., 2000-06-14) Martins, M. L.; Ceotto, G.; Alves, S. G.; Bufon, C. C. B.; Silva, J. M.; Laranjeira, F. F.A cellular automata model is proposed to analyze the progress of citrus variegated chlorosis epidemics in São Paulo orange plantations. In this model epidemiological and environmental features, such as motility of sharpshooter vectors that perform Lévy flights, level of plant hydric and nutritional stress, and seasonal climatic effects, are included. The observed epidemic data were quantitatively reproduced by the proposed model on varying the parameters controlling vector motility, plant stress, and initial population of diseased plants.Item Chern–Simons gravity in four dimensions(The European Physical Journal C, 2017-02) Morales, Ivan; Neves, Bruno; Oporto, Zui; Piguet, OlivierFive-dimensional Chern–Simons theory with (anti-)de Sitter SO(1,5) or SO(2,4) gauge invariance presents an alternative to general relativity with cosmological constant. We consider the zero modes of its Kaluza–Klein compactification to four dimensions. Solutions with vanishing torsion are obtained in the cases of a spherically symmetric 3-space and of a homogeneous and isotropic 3-space, which reproduce the Schwarzshild–de Sitter and ΛΛ CDM cosmological solutions of general relativity. We also check that vanishing torsion is a stable feature of the solutions.Item Collapse transition in polymer models with multiple monomers per site and multiple bonds per edge(Physical Review E, 2017-12) Rodrigues, Nathann T.; Oliveira, Tiago J.We present results from extensive Monte Carlo simulations of polymer models where each lattice site can be visited by up to K monomers and no restriction is imposed on the number of bonds on each lattice edge. These multiple monomer per site (MMS) models are investigated on the square and cubic lattices, for K=2 and 3, by associating Boltzmann weights ω0=1, ω1=eβ1, and ω2=eβ2 to sites visited by 1, 2, and 3 monomers, respectively. Two versions of the MMS models are considered for which immediate reversals of the walks are allowed (RA) or forbidden (RF). In contrast to previous simulations of these models, we find the same thermodynamic behavior for both RA and RF versions. In three dimensions, the phase diagrams, in space β2×β1, are featured by coil and globule phases separated by a line of Θ points, as thoroughly demonstrated by the metric νt, crossover ϕt, and entropic γt exponents. The existence of the Θ lines is also confirmed by the second virial coefficient. This shows that no discontinuous collapse transition exists in these models, in contrast to previous claims based on a weak bimodality observed in some distributions, which indeed exists in a narrow region very close to the Θ line when β1<0. Interestingly, in two dimensions, only a crossover is found between the coil and globule phases.Item Collective versus hub activation of epidemic phases on networks(Physical Review E., 2016-03-14) Ferreira, Silvio C.; Sander, Renan S.; Pastor-Satorras, RomualdoWe consider a general criterion to discern the nature of the threshold in epidemic models on scale-free (SF) networks. Comparing the epidemic lifespan of the nodes with largest degrees with the infection time between them, we propose a general dual scenario, in which the epidemic transition is either ruled by a hub activation process, leading to a null threshold in the thermodynamic limit, or given by a collective activation process, corresponding to a standard phase transition with a finite threshold. We validate the proposed criterion applying it to different epidemic models, with waning immunity or heterogeneous infection rates in both synthetic and real SF networks. In particular, a waning immunity, irrespective of its strength, leads to collective activation with finite threshold in scale-free networks with large degree exponent, at odds with canonical theoretical approaches.Item Contact process on a Voronoi triangulation(Physical Review E, 2008-09-29) Oliveira, Marcelo M. de; Alves, S. G.; Ferreira, S. C.; Dickman, RonaldWe study the continuous absorbing-state phase transition in the contact process on the Voronoi-Delaunay lattice. The Voronoi construction is a natural way to introduce quenched coordination disorder in lattice models. We simulate the disordered system using the quasistationary simulation method and determine its critical exponents and moment ratios. Our results suggest that the critical behavior of the disordered system is unchanged with respect to that on a regular lattice, i.e., that of directed percolation.