Biomedical subjects

Edoardo Milotti

Publications and source records attributed to Edoardo Milotti.

5 recordsLinked to original sources

PubMed2006

Spectral characterization of hydrogen bond network dynamics in water.

Some computational aspects of the characterization of the complex hydrogen bond network dynamics using power spectral analysis are discussed. In the case of hydrogen-bonded liquids, the tagged molecule potential energy is shown to be a useful quantity for capturing the behavior of the networked liquid on different lengths and time scales. The computation of the tagged potential energy for rigid-body effective pair potentials, such as the TIP5P-E and SPC-E models, is discussed. The more structured nature of the TIP5P-E potential, compared to the SPC/E potential, shows up as differences in the high-frequency librational band of the power spectra of the tagged molecule potential energies. The static distributions of the tagged molecule potential energies are also more structured in the case of TIP5P-E, rather than SPC/E, water. The overall behavior of the key power spectral features remains the same in both the models. The possibility of detailed characterization of the power spectrum, and therefore of the underlying dynamics, using a model-based parametric fitting procedure for the power spectra is also discussed. We show that a parametric fitting can allow one to test alternative models of the dynamics underlying the liquid state dynamics.

Journal Article↗

PubMed2005

Exact numerical simulation of power-law noises.

Many simulations of stochastic processes require colored noises: I describe here an exact numerical method to simulate power-law noises: the method can be extended to more general colored noises, and is exact for all time steps, even when they are unevenly spaced [as may often happen for astronomical data; see, e.g., N. R. Lomb, Astrophys. Space Sci. 39, 447 (1976)]. The algorithm has a well-behaved computational complexity, it produces a nearly perfect Gaussian noise, and its computational efficiency depends on the required degree of noise Gaussianity.

Journal Article↗

PubMed2005

A phenomenological approach to the simulation of metabolism and proliferation dynamics of large tumour cell populations.

A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a simplified model of cell metabolism, growth and proliferation, suitable for inclusion in a multicell simulator, now under development (Chignola R and Milotti E 2004 Physica A 338 261-6). Nutrients regulate the proliferation dynamics of tumour cells which adapt their behaviour to respond to changes in the biochemical composition of the environment. This modelling of nutrient metabolism and cell cycle at a mesoscopic scale level leads to a continuous flow of information between the two disparate spatiotemporal scales of molecular and cellular dynamics that can be simulated with modern computers and tested experimentally.

Adenosine Triphosphate↗

PubMed2003

Simulation of protonic fluctuations in hydrated protein powders.

Protons migrating on the surface of weakly hydrated protein powders provide a percolating mesoscopic system which exhibits charge fluctuations near room temperature. In this paper, we describe a simple numerical model where the statistical redistribution of protons on a space distribution of identical side chains lying on a spherical protein surface is varied by random ionization-recombination process to investigate the noise power spectrum of the fluctuating dipole moment, the ergodicity of this system, and the occurrence of localized or extended proton distributions. The case of lysozyme is considered to this end.

Journal Article↗

PubMed2002

Exactly solved dynamics for an infinite-range spin system. II. Antiferromagnetic interactions.

In a previous paper [E. Milotti, Phys. Rev. E 63, 026116 (2001)]. I have shown how to derive both thermodynamical and dynamical properties of an infinite-range Ising spin system with binary ferromagnetic interactions from the master equation for magnetization obtained from a simple spin dynamics. The same method can be adapted to different spin interactions: here I discuss the case of antiferromagnetic interactions. This model permits a study of the static properties of the antiferromagnetic lattice, and it displays very clearly the differences between the antiferromagnetic and the ferromagnetic case with long-range interactions. The dynamical behavior of the antiferromagnetic system is simpler, and the magnetization always relaxes exponentially.

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