The signaling apparatus mediating bacterial chemotaxis can adapt to a wide range of persistent ex... more The signaling apparatus mediating bacterial chemotaxis can adapt to a wide range of persistent external stimuli. In many cases, the bacterial activity returns to its pre-stimulus level exactly and this " perfect adaptability " is robust against variations in various chemotaxis protein concentrations. We model the bacterial chemotaxis signaling pathway, from ligand binding to CheY phosphorylation. By solving the steady-state equations of the model analytically, we derive a full set of conditions for the system to achieve perfect adaptation. The conditions related to the phosphorylation part of the pathway are discovered for the first time, while other conditions are generalization of the ones found in previous works. Sensitivity of the perfect adaptation is evaluated by perturbing these conditions. We find that, even in the absence of some of the perfect adaptation conditions, adaptation can be achieved with near perfect precision as a result of the separation of scales in both chemotaxis protein concentrations and reaction rates, or specific properties of the receptor distribution in different methylation states. Since near perfect adaptation can be found in much larger regions of the parameter space than that defined by the perfect adaptation conditions, their existence is essential to understand robustness in bacterial chemotaxis.
In this paper, we propose a methodology that bears close resemblance to the Fourier analysis of t... more In this paper, we propose a methodology that bears close resemblance to the Fourier analysis of the first harmonic to study networks subjected to pendular behavior. In this context, pendular behavior is characterized by the phenomenon of people's dislocation from their homes to work in the morning and people's dislocation in the opposite direction in the afternoon. Pendular behavior is a relevant phenomenon that takes place in public transport networks because it may reduce the overall efficiency of the system as a result of the asymmetric utilization of the system in different directions. We apply this methodology to the bus transport system of Brasília, which is a city that has commercial and residential activities in distinct boroughs. We show that this methodology can be used to characterize the pendular behavior of this system, identifying the most critical nodes and times of the day when this system is in more severe demanded.
Physica A: Statistical Mechanics and its Applications, 2015
ABSTRACT Stochastic models of surface growth are usually based on randomly choosing a substrate s... more ABSTRACT Stochastic models of surface growth are usually based on randomly choosing a substrate site to perform iterative steps, as in the etching model, Mello et al. (2001) [5]. In this paper I modify the etching model to perform sequential, instead of random, substrate scan. The randomicity is introduced not in the site selection but in the choice of the rule to be followed in each site. The change positively affects the study of dynamic and asymptotic properties, by reducing the finite size effect and the short-time anomaly and by increasing the saturation time. It also has computational benefits: better use of the cache memory and the possibility of parallel implementation.
Journal of Physics A: Mathematical and Theoretical, 2014
ABSTRACT In this work we generalize the etching model (Mello et al 2001 Phys. Rev. E 63 041113) t... more ABSTRACT In this work we generalize the etching model (Mello et al 2001 Phys. Rev. E 63 041113) to d + 1 dimensions. The dynamic exponents of this model are compatible with those of the Kardar–Parisi–Zhang universality class. We investigate the roughness dynamics with surfaces up to d = 6. We show that the data from all substrate lengths and for all dimensions can be collapsed into one common curve. We determine the dynamic exponents as a function of the dimension. Moreover, our results suggest that d = 4 is not an upper critical dimension for the etching model, and that it fulfills the Galilean invariance.
ABSTRACT In this work we extend the etching model to $d+1$ dimensions. This permits us to investi... more ABSTRACT In this work we extend the etching model to $d+1$ dimensions. This permits us to investigate its exponents behaviour on higher dimensions, to try to verify the existence of an upper critical dimension for the KPZ equations, with our results sugesting that $d=4$ is not an upper critical dimension for the etching model.
Logistic processes are a challenge to collective organizations of rural producers. The lack of te... more Logistic processes are a challenge to collective organizations of rural producers. The lack of technological support in those processes is an obstacle for the maintenance of the small producers in the distribution channels. A research theme is the adaptation of some logistic models normally adequate for urban reality to the context of small rural organizations. This adaptation seems pertinent, since some particularities of this kind of organization can be associated to complex problems related to the supply chain. In the case presented in this work, the first stage in the development of the system consisted in defining the main problems related to the inefficiency of the collection and distribution processes. Costs concerning the logistics processes were also measured. In this paper we propose the reasoning elements regarding a routing system and methods for cost estimation adapted to small rural organizations.
The signaling apparatus mediating bacterial chemotaxis can adapt to a wide range of persistent ex... more The signaling apparatus mediating bacterial chemotaxis can adapt to a wide range of persistent external stimuli. In many cases, the bacterial activity returns to its pre-stimulus level exactly and this " perfect adaptability " is robust against variations in various chemotaxis protein concentrations. We model the bacterial chemotaxis signaling pathway, from ligand binding to CheY phosphorylation. By solving the steady-state equations of the model analytically, we derive a full set of conditions for the system to achieve perfect adaptation. The conditions related to the phosphorylation part of the pathway are discovered for the first time, while other conditions are generalization of the ones found in previous works. Sensitivity of the perfect adaptation is evaluated by perturbing these conditions. We find that, even in the absence of some of the perfect adaptation conditions, adaptation can be achieved with near perfect precision as a result of the separation of scales in both chemotaxis protein concentrations and reaction rates, or specific properties of the receptor distribution in different methylation states. Since near perfect adaptation can be found in much larger regions of the parameter space than that defined by the perfect adaptation conditions, their existence is essential to understand robustness in bacterial chemotaxis.
In this paper, we propose a methodology that bears close resemblance to the Fourier analysis of t... more In this paper, we propose a methodology that bears close resemblance to the Fourier analysis of the first harmonic to study networks subjected to pendular behavior. In this context, pendular behavior is characterized by the phenomenon of people's dislocation from their homes to work in the morning and people's dislocation in the opposite direction in the afternoon. Pendular behavior is a relevant phenomenon that takes place in public transport networks because it may reduce the overall efficiency of the system as a result of the asymmetric utilization of the system in different directions. We apply this methodology to the bus transport system of Brasília, which is a city that has commercial and residential activities in distinct boroughs. We show that this methodology can be used to characterize the pendular behavior of this system, identifying the most critical nodes and times of the day when this system is in more severe demanded.
Physica A: Statistical Mechanics and its Applications, 2015
ABSTRACT Stochastic models of surface growth are usually based on randomly choosing a substrate s... more ABSTRACT Stochastic models of surface growth are usually based on randomly choosing a substrate site to perform iterative steps, as in the etching model, Mello et al. (2001) [5]. In this paper I modify the etching model to perform sequential, instead of random, substrate scan. The randomicity is introduced not in the site selection but in the choice of the rule to be followed in each site. The change positively affects the study of dynamic and asymptotic properties, by reducing the finite size effect and the short-time anomaly and by increasing the saturation time. It also has computational benefits: better use of the cache memory and the possibility of parallel implementation.
Journal of Physics A: Mathematical and Theoretical, 2014
ABSTRACT In this work we generalize the etching model (Mello et al 2001 Phys. Rev. E 63 041113) t... more ABSTRACT In this work we generalize the etching model (Mello et al 2001 Phys. Rev. E 63 041113) to d + 1 dimensions. The dynamic exponents of this model are compatible with those of the Kardar–Parisi–Zhang universality class. We investigate the roughness dynamics with surfaces up to d = 6. We show that the data from all substrate lengths and for all dimensions can be collapsed into one common curve. We determine the dynamic exponents as a function of the dimension. Moreover, our results suggest that d = 4 is not an upper critical dimension for the etching model, and that it fulfills the Galilean invariance.
ABSTRACT In this work we extend the etching model to $d+1$ dimensions. This permits us to investi... more ABSTRACT In this work we extend the etching model to $d+1$ dimensions. This permits us to investigate its exponents behaviour on higher dimensions, to try to verify the existence of an upper critical dimension for the KPZ equations, with our results sugesting that $d=4$ is not an upper critical dimension for the etching model.
Logistic processes are a challenge to collective organizations of rural producers. The lack of te... more Logistic processes are a challenge to collective organizations of rural producers. The lack of technological support in those processes is an obstacle for the maintenance of the small producers in the distribution channels. A research theme is the adaptation of some logistic models normally adequate for urban reality to the context of small rural organizations. This adaptation seems pertinent, since some particularities of this kind of organization can be associated to complex problems related to the supply chain. In the case presented in this work, the first stage in the development of the system consisted in defining the main problems related to the inefficiency of the collection and distribution processes. Costs concerning the logistics processes were also measured. In this paper we propose the reasoning elements regarding a routing system and methods for cost estimation adapted to small rural organizations.
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Papers by Bernardo Mello