10,907 research outputs found

    Chirality and Protein Folding

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    There are several simple criteria of folding to a native state in model proteins. One of them involves crossing of a threshold value of the RMSD distance away from the native state. Another checks whether all native contacts are established, i.e. whether the interacting amino acids come closer than some characteristic distance. We use Go-like models of proteins and show that such simple criteria may prompt one to declare folding even though fragments of the resulting conformations have a wrong sense of chirality. We propose that a better condition of folding should augment the simple criteria with the requirement that most of the local values of the chirality should be nearly native. The kinetic discrepancy between the simple and compound criteria can be substantially reduced in the Go-like models by providing the Hamiltonian with a term which favors native values of the local chirality. We study the effects of this term as a function of its amplitude and compare it to other models such as with the side groups and with the angle-dependent potentials.Comment: To be published in a special issue of J. Phys.: Cond. Mat. (Bedlewo Workshop

    Applications of BGP-reflection functors: isomorphisms of cluster algebras

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    Given a symmetrizable generalized Cartan matrix AA, for any index kk, one can define an automorphism associated with A,A, of the field Q(u1,>...,un)\mathbf{Q}(u_1, >..., u_n) of rational functions of nn independent indeterminates u1,...,un.u_1,..., u_n. It is an isomorphism between two cluster algebras associated to the matrix AA (see section 4 for precise meaning). When AA is of finite type, these isomorphisms behave nicely, they are compatible with the BGP-reflection functors of cluster categories defined in [Z1, Z2] if we identify the indecomposable objects in the categories with cluster variables of the corresponding cluster algebras, and they are also compatible with the "truncated simple reflections" defined in [FZ2, FZ3]. Using the construction of preprojective or preinjective modules of hereditary algebras by Dlab-Ringel [DR] and the Coxeter automorphisms (i.e., a product of these isomorphisms), we construct infinitely many cluster variables for cluster algebras of infinite type and all cluster variables for finite types.Comment: revised versio

    Spherically symmetric space-time with the regular de Sitter center

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    The requirements are formulated which lead to the existence of the class of globally regular solutions to the minimally coupled GR equations which are asymptotically de Sitter at the center. The brief review of the resulting geometry is presented. The source term, invariant under radial boots, is classified as spherically symmetric vacuum with variable density and pressure, associated with an r-dependent cosmological term, whose asymptotic in the origin, dictated by the weak energy condition, is the Einstein cosmological term. For this class of metrics the ADM mass is related to both de Sitter vacuum trapped in the origin and to breaking of space-time symmetry. In the case of the flat asymptotic, space-time symmetry changes smoothly from the de Sitter group at the center to the Lorentz group at infinity. Dependently on mass, de Sitter-Schwarzschild geometry describes a vacuum nonsingular black hole, or G-lump - a vacuum selfgravitating particlelike structure without horizons. In the case of de Sitter asymptotic at infinity, geometry is asymptotically de Sitter at both origin and infinity and describes, dependently on parameters and choice of coordinates, a vacuum nonsingular cosmological black hole, selfgravitating particlelike structure at the de Sitter background and regular cosmological models with smoothly evolving vacuum energy density.Comment: Latex, 10 figures, extended version of the plenary talk at V Friedmann Intern. Conf. on Gravitation and Cosmology, Brazil 2002, to appear in Int.J.Mod.Phys.

    Efficient noninteractive certification of RSA moduli and beyond

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    In many applications, it is important to verify that an RSA public key (N; e) speci es a permutation over the entire space ZN, in order to prevent attacks due to adversarially-generated public keys. We design and implement a simple and e cient noninteractive zero-knowledge protocol (in the random oracle model) for this task. Applications concerned about adversarial key generation can just append our proof to the RSA public key without any other modi cations to existing code or cryptographic libraries. Users need only perform a one-time veri cation of the proof to ensure that raising to the power e is a permutation of the integers modulo N. For typical parameter settings, the proof consists of nine integers modulo N; generating the proof and verifying it both require about nine modular exponentiations. We extend our results beyond RSA keys and also provide e cient noninteractive zero- knowledge proofs for other properties of N, which can be used to certify that N is suitable for the Paillier cryptosystem, is a product of two primes, or is a Blum integer. As compared to the recent work of Auerbach and Poettering (PKC 2018), who provide two-message protocols for similar languages, our protocols are more e cient and do not require interaction, which enables a broader class of applications.https://eprint.iacr.org/2018/057First author draf

    Globalising assessment: an ethnography of literacy assessment, camels and fast food in the Mongolian Gobi

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    What happens when standardised literacy assessments travel globally? The paper presents an ethnographic account of adult literacy assessment events in rural Mongolia. It examines the dynamics of literacy assessment in terms of the movement and re-contextualisation of test items as they travel globally and are received locally by Mongolian respondents. The analysis of literacy assessment events is informed by Goodwin’s ‘participation framework’ on language as embodied and situated interactive phenomena and by Actor Network Theory. Actor Network Theory (ANT) is applied to examine literacy assessment events as processes of translation shaped by an ‘assemblage’ of human and non-human actors (including the assessment texts)

    Statistical mechanics in the context of special relativity II

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    The special relativity laws emerge as one-parameter (light speed) generalizations of the corresponding laws of classical physics. These generalizations, imposed by the Lorentz transformations, affect both the definition of the various physical observables (e.g. momentum, energy, etc), as well as the mathematical apparatus of the theory. Here, following the general lines of [Phys. Rev. E {\bf 66}, 056125 (2002)], we show that the Lorentz transformations impose also a proper one-parameter generalization of the classical Boltzmann-Gibbs-Shannon entropy. The obtained relativistic entropy permits to construct a coherent and selfconsistent relativistic statistical theory, preserving the main features of the ordinary statistical theory, which recovers in the classical limit. The predicted distribution function is a one-parameter continuous deformation of the classical Maxwell-Boltzmann distribution and has a simple analytic form, showing power law tails in accordance with the experimental evidence. Furthermore the new statistical mechanics can be obtained as stationary case of a generalized kinetic theory governed by an evolution equation obeying the H-theorem and reproducing the Boltzmann equation of the ordinary kinetics in the classical limit.Comment: 14 pages, no figures, proof correction
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