Controlling Nonlinear Dynamics of Milling Bodies in Mechanochemical Devices Driven by Pendular Forcing.

Understanding the dynamics of milling bodies is key to optimize the mixing and the transfer of mechanical energy in mechanochemical processing. In this work, we present a comparative study of mechanochemical reactors driven by harmonic pendular forcing and characterized by different geometries of the lateral borders. We show that the shape of the reactor bases, either flat or curved, along with the size of the milling body and the elasticity of the collisions, represents relevant parameters that govern the dynamical regimes within the system and can control the transition from periodic to chaotic behaviors. We single out possible criteria to preserve target dynamical scenarios when the size of the milling body is changed, by adapting the relative extent of the spatial domain. This allows us to modulate the average energy of the collisions while maintaining the same dynamics and paves the way for a unifying framework to control the dynamical response in different experimental conditions. We finally explore the dynamical and energetic impact of an increasingly asymmetric mechanical force.

Multifractal properties of ball milling dynamics.

This work focuses on the dynamics of a ball inside the reactor of a ball mill. We show that the distribution of collisions at the reactor walls exhibits multifractal properties in a wide region of the parameter space defining the geometrical characteristics of the reactor and the collision elasticity. This feature points to the presence of restricted self-organized zones of the reactor walls where the ball preferentially collides and the mechanical energy is mainly dissipated.

Chemical Control of Hydrodynamic Instabilities in Partially Miscible Two-Layer Systems.

Hydrodynamic instabilities at the interface between two partially miscible liquids impact numerous applications, including CO2 sequestration in saline aquifers. We introduce here a new laboratory-scale model system on which buoyancy- and Marangoni-driven convective instabilities of such partially miscible two-layer systems can easily be studied. This system consists of the stratification of a pure alkyl formate on top of a denser aqueous solution in the gravitational field. A rich spectrum of convective dynamics is obtained upon partial dissolution of the ester into the water followed by its hydrolysis. The properties of the convective patterns are controlled by the miscibility of the ester in water, the feedback of the dissolved species on its own miscibility, as well as the reactivity of given chemicals in the aqueous solution with the solubilized ester.

Understanding oscillatory phenomena in molecular hydrogen generation via sodium borohydride hydrolysis.

The hydrolysis of borohydride salts represents one of the most promising processes for the generation of high purity molecular hydrogen under mild conditions. In this work we show that the sodium borohydride hydrolysis exhibits a fingerprinting periodic oscillatory transient in the hydrogen flow over a wide range of experimental conditions. We disproved the possibility that flow oscillations are driven by supersaturation phenomena of gaseous bubbles in the reactive mixture or by a nonlinear thermal feedback according to a thermokinetic model. Our experimental results indicate that the NaBH4 hydrolysis is a spontaneous inorganic oscillator, in which the hydrogen flow oscillations are coupled to an "oscillophor" in the reactive solution. The discovery of this original oscillator paves the way for a new class of chemical oscillators, with fundamental implications not only for testing the general theory on oscillations, but also with a view to chemical control of borohydride systems used as a source of hydrogen based green fuel.

Emergy accounting of the Province of Siena: towards a thermodynamic geography for regional studies.

This research is part of the SPIn-Eco project for the Province of Siena, Italy, and applies an environmental accounting method to a region with reference to its population, human activities, natural cycles, infrastructures and other settings. This study asserts that the consumption of resources due to the human economy is a source of great concern because of the load it places on the biosphere. Environmental resources locally used, whether directly or indirectly, from both renewable energy fluxes and storage of materials and energies, are investigated. In this paper emergy analysis is presented and applied to the Province of Siena and to each of its municipalities, in order to evaluate the main flows of energy and materials that supply the territorial system, including human subsystems, with reference to their actual environmental cost. Therefore, the behaviour of the whole system and the interactions between natural and human agents were studied; in other words, the attitudes of the territorial systems toward resource use as revealed by their patterns of emergy consumption were observed. Once expressed in units of the same form of energy through the emergy evaluation, categories of resource consumption and systems of varying scales and organization are compared. Furthermore, indexes of environmental performance based on emergy are calculated. Flows of energy and materials are assessed, and their intensities, which vary throughout the area of the Province, are then visualized on maps.

An environmental analysis for comparing waste management options and strategies.

The debate on different waste management practices has become an issue of utmost importance as human activities have overloaded the assimilative capacity of the biosphere. Recent Italian law on solid waste management recommends an increase in material recycling and energy recovery, and only foresees landfill disposal for inert materials and residues from recovery and recycling. A correct waste management policy should be based on the principles of sustainable development, according to which our refuse is not simply regarded as something to eliminate but rather as a potential resource. This requires the creation of an integrated waste management plan that makes full use of all available technologies. In this context, eMergy analysis is applied to evaluate three different forms of waste treatment and construct an approach capable of assessing the whole strategy of waste management. The evaluation included how much investment is needed for each type of waste management and how much "utility" is extracted from wastes, through the use of two indicators: Environmental yield ratio (EYR) and Net eMergy. Our results show that landfill is the worst system in terms of eMergy costs and eMergy benefits. Composting is the most efficient system in recovering eMergy (highest EYR) from municipal solid waste (MSW) while incineration is capable of saving the greatest quantity of eMergy per gram of MSW (highest net eMergy). This analysis has made it possible to assess the sustainability and the efficiency of individual options but could also be used to assess a greater environmental strategy for waste management, considering a system that might include landfills, incineration, composting, etc.

Onset of chaotic dynamics in a ball mill: Attractors merging and crisis induced intermittency.

In mechanical treatment carried out by ball milling, powder particles are subjected to repeated high-energy mechanical loads which induce heavy plastic deformations together with fracturing and cold-welding events. Owing to the continuous defect accumulation and interface renewal, both structural and chemical transformations occur. The nature and the rate of such transformations have been shown to depend on variables, such as impact velocity and collision frequency that depend, in turn, on the whole dynamics of the system. The characterization of the ball dynamics under different impact conditions is then to be considered a necessary step in order to gain a satisfactory control of the experimental set up. In this paper we investigate the motion of a ball in a milling device. Since the ball motion is governed by impulsive forces acting during each collision, no analytical expression for the complete ball trajectory can be obtained. In addition, mechanical systems exhibiting impacts are strongly nonlinear due to sudden changes of velocities at the instant of impact. Many different types of periodic and chaotic impact motions exist indeed even for simple systems with external periodic excitation forces. We present results of the analysis on the ball trajectory, obtained from a suitable numerical model, under growing degree of impact elasticity. A route to high dimensional chaos is obtained. Crisis and attractors merging are also found. (c) 2002 American Institute of Physics.

Effects of non-ionic micelles on transient chaos in an unstirred Belousov-Zhabotinsky reaction.

The behaviour of the Ce(IV)-catalyzed Belousov-Zhabotinsky (BZ) system has been monitored at 20.0 degrees C in unstirred batch conditions in the absence and presence of different amounts of the non-ionic micelle-forming surfactants hexaethylene glycol monodecyl ether (C10E6) and hexaethylene glycol monotetradecyl ether (C14E6). The influence of the non-ionic surfactants on both the kinetics of the oxidation of malonic acid (MA) by Ce(IV) species and the behaviour of the BZ reaction in stirred batch conditions has also been studied over a wide surfactant concentration range. The experimental results have shown that, in unstirred batch conditions, at surfactant concentrations below the critical micelle concentration (c.m.c.) no significant change in the dynamics of the Belousov-Zhabotinsky system occurs. Beyond this critical concentration the presence of micelles forces the BZ system to undergo a chaos-->quasi-periodicity-->period-1 transition. Thus, the surfactant concentration has been considered as a bifurcation parameter for a Ruelle-Takens-Newhouse (RTN) scenario. Addition of increasing amounts of non-ionic surfactants has no significant effect on the kinetics of the reaction between MA and Ce(IV), but it influences the oscillatory parameters of the stirred BZ system. At surfactant concentrations below the c.m.c. all the oscillatory parameters are practically unaffected by the presence of surfactant, while beyond this critical value the induction period is the same as in aqueous solution but both the oscillation period and the duration of the rising portion of the oscillatory cycle decrease. In all cases, the experimental trends have been ascribed to the enhancement in the medium viscosity due to the presence of micelles.

Alternating oscillations and chaos in a model of two coupled biochemical oscillators driving successive phases of the cell cycle.

The animal cell cycle is controlled by the periodic variation of two cyclin-dependent protein kinases, cdk1 and cdk2, which govern the entry into the M (mitosis) and S (DNA replication) phases, respectively. The ordered progression between these phases is achieved thanks to the existence of checkpoint mechanisms based on mutual inhibition of these processes. Here we study a simple theoretical model for oscillations in cdk1 and cdk2 activity, involving mutual inhibition of the two oscillators. Each minimal oscillator is described by a three-variable cascade involving a cdk, together with the associated cyclin and cyclin-degrading enzyme. The dynamics of this skeleton model of coupled oscillators is determined as a function of the strength of their mutual inhibition. The most common mode of dynamic behavior, obtained under conditions of strong mutual inhibition, is that of alternating oscillations in cdk1 and cdk2, which correspond to the physiological situation of the ordered recurrence of the M and S phases. In addition, for weaker inhibition we obtain evidence for a variety of dynamic phenomena such as complex periodic oscillations, chaos, and the coexistence between multiple periodic or chaotic attractors. We discuss the conditions of occurrence of these various modes of oscillatory behavior, as well as their possible physiological significance.

Hyperchaotic qualities of the ball motion in a ball milling device.

Ball collisions in milling devices are governed by complex dynamics ruled by impredictable impulsive forces. In this paper, nonlinear dynamics techniques are employed to analyze the time series describing the trajectory of a milling ball in an empty container obtained from a numerical model. The attractor underlying the system dynamics was reconstructed by the time delay method. In order to characterize the system dynamics the calculation of the spectrum of Lyapunov exponents was performed. Six Lyapunov exponents, divided into two terns with opposite sign, were obtained. The detection of the positive tern demonstrates the occurrence of the hyperchaotic qualities of the ball motion. A fractal Lyapunov dimension, equal to 5.62, was also obtained confirming the strange features of the attractor. (c) 1999 American Institute of Physics.

Conformations of the third hypervariable region in the VH domain of immunoglobulins.

Antigen-combining sites of antibodies are constructed from six loops from VL and VH domains. The third hypervariable region of the heavy chain is far more variable than the others in length, sequence and structure, and was not included in the canonical-structure description of the conformational repertoire of the three hypervariable regions of V kappa chains and the first two of VH chains. Here we present an analysis of the conformations of the third hypervariable region of VH domains (the H3 regions) in antibodies of known structure. We define the H3 region as comprising the residues between 92Cys and 104Gly. We divide it into a torso comprising residues proximal to the framework, four residues from the N terminus and six residues from the C terminus, and a head. There are two major classes of H3 structures that have more than ten residues between 92Cys and 104Gly: (1) the conformation of the torso has a beta-bulge at residue 101, and (2) the torso does not contain a bulge, but continues the regular hydrogen-bonding pattern of the beta-sheet hairpin. The choice of bulged versus non-bulged torso conformation is dictated primarily by the sequence, through the formation of a salt bridge between the side-chains of an Arg or Lys at position 94 and an Asp at position 101. Thus the torso region appears to have a limited repertoire of conformations, as in the canonical structure model of other antigen-binding loops. The heads or apices of the loops have a very wide variety of conformations. In shorter H3 regions, and in those containing the non-bulged torso conformation, the heads follow the rules relating sequence to structure in short hairpins. We surveyed the heads of longer H3 regions, finding that those with bulged torsos present many very different conformations of the head. We recognize that H3, unlike the other five antigen-binding loops, has a conformation that depends strongly on the environment, and we have analysed the interactions of H3 with residues elsewhere in the VH domain, in the VL domain, and with ligands, and their effects on the conformation of H3. We tested these results by attempts to predict the conformations of H3 regions in antibody structures solved after the results were derived. The general conclusion of this work is that the conformation of H3 shows some regularities, from which rules relating sequence to conformation can be stated, but to a less complete degree than for the other five antigen-binding loops. Accurate prediction of the torso conformation is possible in most cases; predictions of the conformation of the head is possible in some cases. However, our understanding of the sequence-structure relationships has reduced the uncertainty to no more than a few residues at the apex of the H3 region.

Antibody structure, prediction and redesign.

So far the difficulty to predict the structure of the third hypervariable loop of the heavy chain of antibodies has represented the main limitation in modelling the complete antigen binding site. We carefully analysed all available structures of immunoglobulins searching for rules relating the loop conformation to its amino acid sequence. Here, we analyse the conformation of this loop and show that we are able to predict the conformation of the ten residues proximal to the framework. The conformation of the remaining residues of loops longer than 10 residues can also be predicted in many cases. This, combined with the previously defined canonical structures for the other five hypervariable loops, is an important step toward the prediction of the complete immunoglobulin antigen-binding site. We exemplify our prediction protocol using three known immunoglobulin structures as test cases.

Three-dimensional searching for recurrent structural motifs in data bases of protein structures.

The problem of searching a data base of coordinates of proteins for substructures similar to a probe structure or motif is an important problem in computational molecular biology. It is the three-dimensional analog of the one-dimensional case of pattern matching in strings, procedures for which are widely used in molecular biology to search data bases of gene sequences. Typical applications of substructure searching are: (i) Determining whether structural features observed in one protein structure are unique or recurrent, and (ii) in predictions of protein structures, to bridge gaps in an incomplete structural model, by searching the data base for peptides that link the given starting and ending points. We describe our analysis of the problem and our experience in developing software.

A model of the rabies virus glycoprotein active site.

The glycoprotein from the neurotropic rabies virus shows a significant homology with the alpha neurotoxin that binds to the nicotinic acetylcholine receptor. The crystal structure of the alpha neurotoxins suggests that the Arg 37 guanidinium group and the Asp 31 side-chain carboxylate of the erabutoxin have stereochemical features resembling those of acetylcholine. Conformational studies on the Asn194-Ser195-Arg196-Gly197 tetrapeptide, an essential part of the binding site of the rabies virus glycoprotein, indicate that the side chains of Asn and Arg could also mimic the acetylcholine structure. This observation is consistent with the recently proposed mechanism of the viral infection.

Binding of HIV-1 gp120 to the nicotinic receptor.

We previously described a significant sequence homology between HIV-1 gp120 and the functional sites responsible for the specific binding of snake curare-mimetic neurotoxins and rabies virus glycoprotein to the nicotinic acetylcholine receptor. Here we report findings about the existence of a mechanism of functional molecular mimicry which could enable the binding of HIV-1 gp120 to nicotinic acetylcholine receptors in muscle cells and neurons.

An antigenic determinant common to human chorionic somatomammotropin and human growth hormone revealed by limited proteolysis of immune complexes.

An epitope of human chorionic somatomammotropin for one of the monoclonal antibodies raised against the whole antigen has been identified. We compared the release of peptides from limited proteolysis of the antigen in the presence and absence of the related antibody. Using enzymes of different specificity, we could determine the amino acid sequence that can be considered at least inclusive of the epitope. The monoclonal antibody selected is 100% cross-reactive with human growth hormone, so the antigenic determinant identified is shared by the two protein hormones.

1H- and natural abundance 15N-NMR studies of a derivative of a rabies glycoprotein fragment.

Using a combination of one- and two-dimensional methods, 1H- and 15N-nmr spectroscopy has been employed to perform the complete assignment and the structural determination of the immunogenic undecapeptide CTTTNSRGTTT in DMSO solution. Nuclear Overhauser enhancement spectroscopy experiments indicated the presence of secondary structures, mainly turn-like structures, which only represent a family, albeit a dominant one, of an ensemble of conformations available to the peptide. Since reverse turns may play an important role as intermediates in protein folding, the experimental observations described here may link the immunological and theoretical approaches to protein folding.

Solvent spin-labelling for investigating the interaction of biological ligands with macromolecules. A 1H paramagnetic relaxation study.

The paramagnetic contributions to the spin-lattice relaxation rates of khellin protons, induced by the presence in an aqueous solution of TEMPO nitroxide, have been analyzed in the interaction of the furochromone with DNA. The relaxation data obtained at different temperatures, nitroxide and DNA concentrations indicate that the average solvent exposure of the furanic moiety of khellin is lower than that of the pyranic group. This feature suggests that the former is the main site of approach of khellin to DNA.

HPLC immunoaffinity purification of rabies virus glycoprotein using immobilized antipeptide antibodies.

It has been reported that the acetylcholine receptor may be used by the rabies virus to concentrate at sites in proximal to peripheral nerves. It has also been reported that the binding site for the receptor is located within the 190-203 region of the virus glycoprotein on the basis of its structural homology with the toxic center of snake neurotoxins, which are well known cholinergic ligands. We prepared monoclonal antibodies against the synthetic tetradecapeptide having the same sequence as the putative binding site of the rabies virus. One of three antibodies (clone 2PV 36-74) was able to recognize both the whole virus and its peplomeric glycoprotein and could bind acetylcholine. It was also able to inhibit the binding both of alpha-bungarotoxin and rabies virus glycoprotein to the acetylcholine receptor. We have covalently bound 2PV 36-74 to an HPLC affinity column and utilized it for specific purification of rabies virus glycoprotein. The immunoaffinity chromatographic method we describe is very sensitive and highly specific. Moreover this procedure does not denature the sample and is vary rapid and efficient.