Slow energy relaxation of macromolecules and nano-clusters in solution

Many systems in the realm of nanophysics from both the living and inorganic world display slow relaxation kinetics of energy fluctuations. In this paper we propose a general explanation for such phenomenon, based on the effects of interactions with the solvent. Within a simple harmonic model of the system fluctuations, we demonstrate that the inhomogeneity of coupling to the solvent of the bulk and surface atoms suffices to generate a complex spectrum of decay rates. We show for Myoglobin and for a metal nano-cluster that the result is a complex, non-exponential relaxation dynamics.Comment: 5 pages, 3 figure

Comparison of Brans Promethee multicriteria decision method and Promethee modified by authors for the optimization of an erosion control integral plan in Chaco area in Salta province (Argentine)

Chaco area is situated in the Province of Salta at North West of Argentine. The desertification is a big problem. In order to mitigate the problem it is necessary to take into account not only pedologic criteria but the economical, environmental, cultural and sociological criteria. Six sub zones have been established following previous studies. Eight criteria and six alternatives have been introduced in the model. Following the results of the study carried out by a collaborative project between UPM and UCS financed by AECID (1) were established several initial matrix. Brans Promethee multicriteria decision method (MCDM) was applied and the authors modified that method introducing weights like in Electre metho

Bethe approximation for self-interacting lattice trees

In this paper we develop a Bethe approximation, based on the cluster variation method, which is apt to study lattice models of branched polymers. We show that the method is extremely accurate in cases where exact results are known as, for instance, in the enumeration of spanning trees. Moreover, the expressions we obtain for the asymptotic number of spanning trees and lattice trees on a graph coincide with analogous expressions derived through different approaches. We study the phase diagram of lattice trees with nearest-neighbour attraction and branching energies. We find a collapse transition at a tricritical theta point, which separates an expanded phase from a compact phase. We compare our results for the theta transition in two and three dimensions with available numerical estimates.Comment: 10 pages, 3 figures, to be published in Europhysics Letter

Real-time monitoring of protein conformational changes using a nano-mechanical sensor.

Proteins can switch between different conformations in response to stimuli, such as pH or temperature variations, or to the binding of ligands. Such plasticity and its kinetics can have a crucial functional role, and their characterization has taken center stage in protein research. As an example, Topoisomerases are particularly interesting enzymes capable of managing tangled and supercoiled double-stranded DNA, thus facilitating many physiological processes. In this work, we describe the use of a cantilever-based nanomotion sensor to characterize the dynamics of human topoisomerase II (Topo II) enzymes and their response to different kinds of ligands, such as ATP, which enhance the conformational dynamics. The sensitivity and time resolution of this sensor allow determining quantitatively the correlation between the ATP concentration and the rate of Topo II conformational changes. Furthermore, we show how to rationalize the experimental results in a comprehensive model that takes into account both the physics of the cantilever and the dynamics of the ATPase cycle of the enzyme, shedding light on the kinetics of the process. Finally, we study the effect of aclarubicin, an anticancer drug, demonstrating that it affects directly the Topo II molecule inhibiting its conformational changes. These results pave the way to a new way of studying the intrinsic dynamics of proteins and of protein complexes allowing new applications ranging from fundamental proteomics to drug discovery and development and possibly to clinical practice

Anti-cooperativity in diffusion-controlled reactions with pairs of anisotropic domains: a model for the antigen-antibody encounter

The encounter between anisotropic agents in diffusion-controlled reactions is a topic of very general relevance in chemistry and biology. Here we introduce a simplified model of encounter of an isotropic molecule with a pair of partially reacting agents and apply it to the encounter reaction between an antibody and its antigen. We reduce the problem to the solution of dual series relations, which can be solved iteratively, yielding the exact solution for the encounter rate constant at any desired order of accuracy. We quantify the encounter effectiveness by means of a simple indicator and show that the two binding centers systematically behave in an anti-cooperative fashion. However, we demonstrate that a reduction of the binding active sites allows the composite molecule to recover binding effectiveness, in spite of the overall reduction of the rate constant. In addition, we provide a simple formula that enables one to calculate the anti-cooperativity as a function of the size of the binding site for any values of the separation between the two active lobes and of the antigen size. Finally, some biological implications of our results are discussed

Solvent-induced micelle formation in a hydrophobic interaction model

We investigate the aggregation of amphiphilic molecules by adapting the two-state Muller-Lee-Graziano model for water, in which a solvent-induced hydrophobic interaction is included implicitly. We study the formation of various types of micelle as a function of the distribution of hydrophobic regions at the molecular surface. Successive substitution of non-polar surfaces by polar ones demonstrates the influence of hydrophobicity on the upper and lower critical solution temperatures. Aggregates of lipid molecules, described by a refinement of the model in which a hydrophobic tail of variable length interacts with different numbers of water molecules, are stabilized as the length of the tail increases. We demonstrate that the essential features of micelle formation are primarily solvent-induced, and are explained within a model which focuses only on the alteration of water structure in the vicinity of the hydrophobic surface regions of amphiphiles in solution.Comment: 11 pages, 10 figures; some rearrangement of introduction and discussion sections, streamlining of formalism and general compression; to appear in Phys. Rev.

Universal 1/f Noise from Dissipative SOC Models

We introduce a model able to reproduce the main features of 1/f noise: hyper-universality (the power-law exponents are independent on the dimension of the system; we show here results in d=1,2) and apparent lack of a low-frequency cutoff in the power spectrum. Essential ingredients of this model are an activation-deactivation process and dissipation.Comment: 3 Latex pages, 2 eps Figure

Mathematical Model to Select the Optimal Alternative for an Integral Plan to Desertification and Erosion Control for the Chaco Area in Salta Province (Argentine)

Multi-criteria Decision Analysis (MCDA) is concerned with identifying the values, uncertainties and other issues relevant in a given decision, its rationality, and the resulting optimal decision. These decisions are difficult because the complexity of the system or because of determining the optimal situation or behavior. This work will illustrate how MCDA is applied in practice to a complex problem to resolve such us soil erosion and degradation. Desertification is a global problem and recently it has been studied in several forums as ONU that literally says: "Desertification has a very high incidence in the environmental and food security, socioeconomic stability and world sustained development". Desertification is the soil quality loss and one of FAO's most important preoccupations as hunger in the world is increasing. Multiple factors are involved of diverse nature related to: natural phenomena (water and wind erosion), human activities linked to soil and water management, and others not related to the former. In the whole world this problem exists, but its effects and solutions are different. It is necessary to take into account economical, environmental, cultural and sociological criteria. A multi-criteria model to select among different alternatives to prepare an integral plan to ameliorate or/and solve this problem in each area has been elaborated taking in account eight criteria and six alternatives. Six sub zones have been established following previous studies and in each one the initial matrix and weights have been defined to apply on different criteria. Three Multicriteria Decision Methods have been used for the different sub zones: ELECTRE, PROMETHEE and AHP. The results show a high level of consistency among the three different multicriteria methods despite the complexity of the system studied. The methods are described for La Estrella sub zone, indicating election of weights, Initial Matrixes, the MATHCAD8 algorithms used for PROMETHEE, and the Graph of Expert Choice showing the results of AHP. A brief schema of the actions recommended for each of the six different sub zones is reported in Conclusions, with "We can combine Autochthonous and High Value Forest" for La Estrell

Fractal Dimension and Localization of DNA Knots

The scaling properties of DNA knots of different complexities were studied by atomic force microscope. Following two different protocols DNA knots are adsorbed onto a mica surface in regimes of (i) strong binding, that induces a kinetic trapping of the three-dimensional (3D) configuration, and of (ii) weak binding, that permits (partial) relaxation on the surface. In (i) the gyration radius of the adsorbed DNA knot scales with the 3D Flory exponent $\nu\approx 0.58$ within error. In (ii), we find $\nu\approx 0.66$, a value between the 3D and 2D ($\nu=3/4$) exponents, indicating an incomplete 2D relaxation or a different polymer universality class. Compelling evidence is also presented for the localization of the knot crossings in 2D.Comment: 4 pages, 3 figure

On the origin of the Boson peak in globular proteins

We study the Boson Peak phenomenology experimentally observed in globular proteins by means of elastic network models. These models are suitable for an analytic treatment in the framework of Euclidean Random Matrix theory, whose predictions can be numerically tested on real proteins structures. We find that the emergence of the Boson Peak is strictly related to an intrinsic mechanical instability of the protein, in close similarity to what is thought to happen in glasses. The biological implications of this conclusion are also discussed by focusing on a representative case study.Comment: Proceedings of the X International Workshop on Disordered Systems, Molveno (2006