Potential energy landscape equation of state

Depth, number, and shape of the basins of the potential energy landscape are the key ingredients of the inherent structure thermodynamic formalism introduced by Stillinger and Weber [F. H. Stillinger and T. A. Weber, Phys. Rev. A 25, 978 (1982)]. Within this formalism, an equation of state based only on the volume dependence of these landscape properties is derived. Vibrational and configurational contributions to pressure are sorted out in a transparent way. Predictions are successfully compared with data from extensive molecular dynamics simulations of a simple model for the fragile liquid orthoterphenyl.     

Nonconservative earthquake model of self-organized criticality on a random graph

We numerically investigate the Olami-Feder-Christensen model on a quenched random graph. Contrary to the case of annealed random neighbors, we find that the quenched model exhibits self-organized criticality deep within the nonconservative regime. The probability distribution for avalanche size obeys finite size scaling, with universal critical exponents. In addition, a power law relation between the size and the duration of an avalanche exists. We propose that this may represent the correct mean-field limit of the model rather than the annealed random neighbor version.     

Truncation of power law behavior in "scale-free" network models due to information filtering

We formulate a general model for the growth of scale-free networks under filtering information conditions-that is, when the nodes can process information about only a subset of the existing nodes in the network. We find that the distribution of the number of incoming links to a node follows a universal scaling form, i.e., that it decays as a power law with an exponential truncation controlled not only by the system size but also by a feature not previously considered, the subset of the network "accessible" to the node. We test our model with empirical data for the World Wide Web and find agreement.     

Photoinhibition in vivo and in vitro involves weakly coupled chlorophyll-protein complexes

In the present study the analysis of the relation between the excited state population in the photosystem II (PSII) antenna and photoinactivation has been extended from an in vitro system, isolated thylakoids, to an in vivo system, Chlamydomonas reinhardtii cells. The results indicate that the excited state quenching by an added singlet quencher induces maximal protection against photoinhibition of about 30% of that expected on the basis of the observed light intensity-treatment time reciprocity rule. Similar results, obtained previously with thylakoids, have been interpreted in terms of damaged or incorrectly assembled complexes that play an important role in photoinhibition in the thylakoid membranes (Santabarbara, S., K. Neverov, F. M. Garlaschi, G. Zucchelli and R. C. Jennings [2001] Involvement of uncoupled antenna chlorophylls in photoinhibition in thylakoids. FEBS Lett. 491, 109-113.). In an attempt to better define this aspect, the photoinhibition action spectra were determined for mutant barley thylakoids, lacking the chlorophyll (Chl) a-b complexes of the outer antenna, and for its wild type. The results indicate that in both systems the action spectra are significantly blueshifted (2-4 nm) and are broader than the PSII absorption in the membranes. These data are interpreted in terms of a heterogeneous population of outer and inner antenna pigment-protein complexes that contain significant levels of uncoupled Chl.     

New insights into the mechanism of purple acid phosphatase through (1)H NMR spectroscopy of the recombinant human enzyme

Proton NMR spectra of FeIII-FeII recombinant single polypeptide human PAP (recHPAP) have been measured at, above, and below its pH optimum, as have the spectra of inhibited forms containing fluoride and phosphate, analogues of the substrates hydroxide and phosphate esters, respectively. The results demonstrate that binding of inhibitory anions to the dinuclear mixed-valent site of recHPAP is controlled by protonation of a ligand to the dinuclear center. Thus, the group that is responsible for pKa,1 in the enzymatic activity versus pH profile functions as a "gatekeeper", whose protonation state controls anion binding to the mixed-valent dinuclear site. The correlation between the pKa values observed in kinetics studies and for the spectroscopic changes strongly suggests that this group is the nucleophilic hydroxide that attacks the phosphate ester substrate.     

Finite Element Matrix Sequences: the Case of Rectangular Domains

In the present paper, we consider a preconditioning strategy for Finite Element (FE) matrix sequences {A _n (a)} _n discretizing the elliptic problem $$\left\{ \begin{gathered} A_a u \equiv ( - )^k \nabla ^k [a(x,y)\nabla ^k u(x,y)] = f(x,y),{ }(x,y) \in \Omega = (0,1)^2 , \hfill \\ \left. {\left( {\frac{{\partial ^s }}{{\partial v^s }}u(x,y)} \right)} \right|_{\partial \Omega } \equiv 0,{ }s = 0,...,k - 1,{ }^{^{^{^{^{^{(1)} } } } } } \hfill \\ \end{gathered} \right.$$ with a(x,y) being a uniformly positive function and ν denoting the unit outward normal direction. More precisely, in connection with preconditioned conjugate gradient (PCG) like methods, we define the preconditioning sequence: {P _n (a)} _n , P _n (a):= $$\widetilde D$$ _n ^1/2(a)A _n (1) $$\widetilde D$$ _n ^1/2(a), where $$\widetilde D$$ _n (a) is the suitable scaled main diagonal of A _n (a). In fact, under the mild assumption of Lebesgue integrability of a(x), the weak clustering at the unity of the corresponding preconditioned sequence is proved. Moreover, if a(x,y) is regular enough and if a uniform triangulation is considered, then the preconditioned sequence shows a strong clustering at the unity so that the sequence {P _n (a)} _n turns out to be a superlinear preconditioning sequence for {A _n (a)} _n . The computational interest is due to the fact that the computation with A _n (a) is reduced to computations involving diagonals and two-level Toeplitz structures {A _n (1)} _n with banded pattern. Some numerical experimentations confirm the efficiency of the discussed proposal.     

Approximating the Approximant: A Numerical Code for Polynomial Compression of Discrete Integral Operators

The action of various one-dimensional integral operators, discretized by a suitable quadrature method, can be compressed and accelerated by means of Chebyshev series approximation. Our approach has a different conception with respect to other well-known fast methods: its effectiveness rests on the smoothing effect of integration, and it works in linear as well as nonlinear instances, with both smooth and nonsmooth kernels. We describe a Matlab toolbox which implements Chebyshev-like compression of discrete integral operators, and we present several numerical tests, where the basic O(n ²) complexity is shown to be reduced to O(mn), with mn.     

Polymer Chain Size from Geodesic Path and Geometrical Bolyai–Lobachevskij Partition Function. Application to Swelling of Macromolecules in Solution and Micellar Growth

The Bolyai–Lobachevskij (BL) formula, relating parallelism angle and distance in a Non-Euclidean space, is used to introduce a geometrical partition function. Employing a correspondence between Boltzmann factor and BL characteristic length, allows us to get a simple relation for average size and space curvature, which is the analogy to the equation for the mean energy derived from the ordinary partition function. Due to the equivalence, recently proposed, between a chain molecule in a liquid and a geodesic path in a relativistic space, the equation obtained is expected to be suitable for describing geometrical phenomena in polymer-like networks. Simple applications to swelling of polymer solutions and micellar growth are presented and discussed.     

Branched Polyethylenes by Cationic Benzyl Zirconium Heteroscorpionate Complexes: Role of the Borate Anion

Summary: A comparative study of the performances of (bpzmp)ZrBz₃ ( 1 ) and (hppzm)ZrBz₃ ( 2 ) activated with B(C₆F₅)₃ or [Ph₃C][B(C₆F₅)₄] in ethylene polymerisation pointed out that the steric properties of the metal complex and the boron activator affect the productivity of the catalyst and, more remarkably, the microstructure of the polyethylenes produced. A polymerisation mechanism accounting for these results has been proposed.

Structure of two heteroscorpionate zirconium complexes (bpzmp)ZrBz₃ ( 1 ) and (hppzm)ZrBz₃ ( 2 ).     

On the Use of the Nanoindentation Unloading Curve to Measure the Young's Modulus of Polymers on a Nanometer Scale

Summary: The nanoindentation test is a fundamental tool to assess the link between morphology and mechanical properties. The preliminary results of a more exhaustive study about the applicability to polymers of the most used procedure to determine elastic modulus by indentation are reported in this short communication. A departure of the experimental conditions from the theoretical assumptions and results that give rise to the Oliver and Pharr analysis is shown to occur under a wide range of experimental conditions, with applied loads and penetration depths covering several orders of magnitude and using different indenter geometries. Unloading curves with exponents significantly larger than 2 are observed in disagreement with the contact mechanics approach used by Oliver and Pharr.

An AFM image obtained in non contact mode of an indentation induced by a sharp AFM tip with a maximum applied load of ca 1.2 µN on amorphous PET.