Strategies for Optimize Off-Lattice Aggregate Simulations

We review some computer algorithms for the simulation of off-lattice clusters grown from a seed, with emphasis on the diffusion-limited aggregation, ballistic aggregation and Eden models. Only those methods which can be immediately extended to distinct off-lattice aggregation processes are discussed. The computer efficiencies of the distinct algorithms are compared.Comment: 6 pages, 7 figures and 3 tables; published at Brazilian Journal of Physics 38, march, 2008 (http://www.sbfisica.org.br/bjp/files/v38_81.pdf

Crystallization, data collection and data processing of maltose-binding protein (MalE) from the phytopathogen Xanthomonas axonopodis pv. citri

Maltose-binding protein is the periplasmic component of the ABC transporter responsible for the uptake of maltose/maltodextrins. The Xanthomonas axonopodis pv. citri maltose-binding protein MalE has been crystallized at 293 Kusing the hanging-drop vapour-diffusion method. The crystal belonged to the primitive hexagonal space group P6_122, with unit-cell parameters a = 123.59, b = 123.59, c = 304.20 Å, and contained two molecules in the asymetric unit. It diffracted to 2.24 Å resolution

Aggregation in a mixture of Brownian and ballistic wandering particles

In this paper, we analyze the scaling properties of a model that has as limiting cases the diffusion-limited aggregation (DLA) and the ballistic aggregation (BA) models. This model allows us to control the radial and angular scaling of the patterns, as well as, their gap distributions. The particles added to the cluster can follow either ballistic trajectories, with probability $P_{ba}$, or random ones, with probability $P_{rw}=1-P_{ba}$. The patterns were characterized through several quantities, including those related to the radial and angular scaling. The fractal dimension as a function of $P_{ba}$ continuously increases from $d_f\approx 1.72$ (DLA dimensionality) for $P_{ba}=0$ to $d_f\approx 2$ (BA dimensionality) for $P_{ba}=1$. However, the lacunarity and the active zone width exhibt a distinct behavior: they are convex functions of $P_{ba}$ with a maximum at $P_{ba}\approx1/2$. Through the analysis of the angular correlation function, we found that the difference between the radial and angular exponents decreases continuously with increasing $P_{ba}$ and rapidly vanishes for $P_{ba}>1/2$, in agreement with recent results concerning the asymptotic scaling of DLA clusters.Comment: 7 pages, 6 figures. accepted for publication on PR

Multiscale model for the effects of adaptive immunity suppression on the viral therapy of cancer

Oncolytic virotherapy - the use of viruses that specifically kill tumor cells - is an innovative and highly promising route for treating cancer. However, its therapeutic outcomes are mainly impaired by the host immune response to the viral infection. In the present work, we propose a multiscale mathematical model to study how the immune response interferes with the viral oncolytic activity. The model assumes that cytotoxic T cells can induce apoptosis in infected cancer cells and that free viruses can be inactivated by neutralizing antibodies or cleared at a constant rate by the innate immune response. Our simulations suggest that reprogramming the immune microenvironment in tumors could substantially enhance the oncolytic virotherapy in immune-competent hosts. Viable routes to such reprogramming are either in situ virus-mediated impairing of CD$8^+$ T cells motility or blockade of B and T lymphocytes recruitment. Our theoretical results can shed light on the design of viral vectors or new protocols with neat potential impacts on the clinical practice.Comment: 14 pages, 4 figure

Upper bound for the conductivity of nanotube networks

Films composed of nanotube networks have their conductivities regulated by the junction resistances formed between tubes. Conductivity values are enhanced by lower junction resistances but should reach a maximum that is limited by the network morphology. By considering ideal ballistic-like contacts between nanotubes we use the Kubo formalism to calculate the upper bound for the conductivity of such films and show how it depends on the nanotube concentration as well as on their aspect ratio. Highest measured conductivities reported so far are approaching this limiting value, suggesting that further progress lies with nanowires other than nanotubes.Comment: 3 pages, 1 figure. Minor changes. Accepted for publication in Applied Physics Letter

Integrable theories and loop spaces: fundamentals, applications and new developments

We review our proposal to generalize the standard two-dimensional flatness construction of Lax-Zakharov-Shabat to relativistic field theories in d+1 dimensions. The fundamentals from the theory of connections on loop spaces are presented and clarified. These ideas are exposed using mathematical tools familiar to physicists. We exhibit recent and new results that relate the locality of the loop space curvature to the diffeomorphism invariance of the loop space holonomy. These result are used to show that the holonomy is abelian if the holonomy is diffeomorphism invariant. These results justify in part and set the limitations of the local implementations of the approach which has been worked out in the last decade. We highlight very interesting applications like the construction and the solution of an integrable four dimensional field theory with Hopf solitons, and new integrability conditions which generalize BPS equations to systems such as Skyrme theories. Applications of these ideas leading to new constructions are implemented in theories that admit volume preserving diffeomorphisms of the target space as symmetries. Applications to physically relevant systems like Yang Mills theories are summarized. We also discuss other possibilities that have not yet been explored.Comment: 64 pages, 8 figure

Dynamic Scaling of Non-Euclidean Interfaces

The dynamic scaling of curved interfaces presents features that are strikingly different from those of the planar ones. Spherical surfaces above one dimension are flat because the noise is irrelevant in such cases. Kinetic roughening is thus a one-dimensional phenomenon characterized by a marginal logarithmic amplitude of the fluctuations. Models characterized by a planar dynamical exponent $z>1$, which include the most common stochastic growth equations, suffer a loss of correlation along the interface, and their dynamics reduce to that of the radial random deposition model in the long time limit. The consequences in several applications are discussed, and we conclude that it is necessary to reexamine some experimental results in which standard scaling analysis was applied

A reaction-diffusion model for the growth of avascular tumor

A nutrient-limited model for avascular cancer growth including cell proliferation, motility and death is presented. The model qualitatively reproduces commonly observed morphologies for primary tumors, and the simulated patterns are characterized by its gyration radius, total number of cancer cells, and number of cells on tumor periphery. These very distinct morphological patterns follow Gompertz growth curves, but exhibit different scaling laws for their surfaces. Also, the simulated tumors incorporate a spatial structure composed of a central necrotic core, an inner rim of quiescent cells and a narrow outer shell of proliferating cells in agreement with biological data. Finally, our results indicate that the competition for nutrients among normal and cancer cells may be a determinant factor in generating papillary tumor morphology.Comment: 9 pages, 6 figures, to appear in PR

Exponential behavior of the interlayer exchange coupling across non-magnetic metallic superlattices

It is shown that the coupling between magnetic layers separated by non-magnetic metallic superlattices can decay exponentially as a function of the spacer thickness $N$, as opposed to the usual $N^{-2}$ decay. This effect is due to the lack of constructive contributions to the coupling from extended states across the spacer. The exponential behavior is obtained by properly choosing the distinct metals and the superlattice unit cell composition.Comment: To appear in Phys. Rev.