Properties of low-dimensional collective variables in the molecular dynamics of biopolymers

The description of the dynamics of a complex, high-dimensional system in terms of a low-dimensional set of collective variables Y can be fruitful if the low dimensional representation satisfies a Langevin equation with drift and diffusion coefficients which depend only on Y. We present a computational scheme to evaluate whether a given collective variable provides a faithful low-dimensional representation of the dynamics of a high-dimensional system. The scheme is based on the framework of finite-difference Langevin-equation, similar to that used for molecular-dynamics simulations. This allows one to calculate the drift and diffusion coefficients in any point of the full-dimensional system. The width of the distribution of drift and diffusion coefficients in an ensemble of microscopic points at the same value of Y indicates to which extent the dynamics of Y is described by a simple Langevin equation. Using a simple protein model we show that collective variables often used to describe biopolymers display a non-negligible width both in the drift and in the diffusion coefficients. We also show that the associated effective force is compatible with the equilibrium free--energy calculated from a microscopic sampling, but results in markedly different dynamical properties

An observable for vacancy characterization and diffusion in crystals

To locate the position and characterize the dynamics of a vacancy in a crystal, we propose to represent it by the ground state density of a quantum probe quasi-particle for the Hamiltonian associated to the potential energy field generated by the atoms in the sample. In this description, the h^2/2mu coefficient of the kinetic energy term is a tunable parameter controlling the density localization in the regions of relevant minima of the potential energy field. Based on this description, we derive a set of collective variables that we use in rare event simulations to identify some of the vacancy diffusion paths in a 2D crystal. Our simulations reveal, in addition to the simple and expected nearest neighbor hopping path, a collective migration mechanism of the vacancy. This mechanism involves several lattice sites and produces a long range migration of the vacancy. Finally, we also observed a vacancy induced crystal reorientation process

A Copula-Based Joint Model of Commute Mode Choice and Number of Non-Work Stops during the Commute

At the time of publication A. Portoghese, E. Spissu, and I. Meloni were at University of Cagliari, and C.R. Bhat and N. Eluru were at the University of Texas at Austin.In this paper, in the spirit of a tour-based frame of analysis, we examine the commute mode choice and the number of non-work stops during the commute. Understanding the mode and activity stop dimensions of weekday commute travel is important since the highest level of weekday traffic congestion in urban areas occurs during the commute periods. The paper employs a copula-based joint multinomial logit – ordered modeling framework in which commute mode choice is modeled using a multinomial logit formulation and the number of commute stops is modeled using an ordered response formulation. The data used in this study are drawn from the “Time use” multipurpose survey conducted between 2002 and 2003 by the Turin Town Council and the Italian National Institute of Statistics (ISTAT) in the Greater Turin metropolitan area of Italy. The results highlight the importance of accommodating the inter-relationship between commute mode choice and commute stops behavior. The results also point to the stronger effect of household responsibilities and demographic characteristics in the Italian context compared to the US context.Civil, Architectural, and Environmental Engineerin

Experimental and Theoretical Investigations of the Structure and the Stability of the BNSi Molecule

Theoretical computations were carried out to determine the structure and molecular parameters of the BNSi molecule. The most stable isomer is found to have a BNSi linear geometry. Thermal functions as derived from the theoretical computed molecular parameters were used in the evaluation of the thermodynamic properties of BNSi from high-temperature Knudsen effusion mass spectrometric equilibrium data. From the reactions analyzed by the second-law and third-law methods, the enthalpy of formation,ΔfHo0, and of atomization, ΔaHo0, in kJ mol−1, for BNSi, were obtained as 398±16 and 1078±17, respectively

Perturbative and non-perturbative renormalization results of the Chromomagnetic Operator on the Lattice

The Chromomagnetic operator (CMO) mixes with a large number of operators under renormalization. We identify which operators can mix with the CMO, at the quantum level. Even in dimensional regularization (DR), which has the simplest mixing pattern, the CMO mixes with a total of 9 other operators, forming a basis of dimension-five, Lorentz scalar operators with the same flavor content as the CMO. Among them, there are also gauge noninvariant operators; these are BRST invariant and vanish by the equations of motion, as required by renormalization theory. On the other hand using a lattice regularization further operators with $d \leq 5$ will mix; choosing the lattice action in a manner as to preserve certain discrete symmetries, a minimul set of 3 additional operators (all with $d<5$) will appear. In order to compute all relevant mixing coefficients, we calculate the quark-antiquark (2-pt) and the quark-antiquark-gluon (3-pt) Green's functions of the CMO at nonzero quark masses. These calculations were performed in the continuum (dimensional regularization) and on the lattice using the maximally twisted mass fermion action and the Symanzik improved gluon action. In parallel, non-perturbative measurements of the $K-\pi$ matrix element are being performed in simulations with 4 dynamical ($N_f = 2+1+1$) twisted mass fermions and the Iwasaki improved gluon action.Comment: 7 pages, 1 figure, 3 tables, LATTICE2014 proceeding

K→πK \to \pi matrix elements of the chromomagnetic operator on the lattice

We present the results of the first lattice QCD calculation of the $K \to \pi$ matrix elements of the chromomagnetic operator $O_{CM} = g\, \bar s\, \sigma_{\mu\nu} G_{\mu\nu} d$, which appears in the effective Hamiltonian describing $\Delta S = 1$ transitions in and beyond the Standard Model. Having dimension 5, the chromomagnetic operator is characterized by a rich pattern of mixing with operators of equal and lower dimensionality. The multiplicative renormalization factor as well as the mixing coefficients with the operators of equal dimension have been computed at one loop in perturbation theory. The power divergent coefficients controlling the mixing with operators of lower dimension have been determined non-perturbatively, by imposing suitable subtraction conditions. The numerical simulations have been carried out using the gauge field configurations produced by the European Twisted Mass Collaboration with $N_f = 2+1+1$ dynamical quarks at three values of the lattice spacing. Our result for the B-parameter of the chromomagnetic operator at the physical pion and kaon point is $B_{CMO}^{K \pi} = 0.273 ~ (70)$, while in the SU(3) chiral limit we obtain $B_{CMO} = 0.072 ~ (22)$. Our findings are significantly smaller than the model-dependent estimate $B_{CMO} \sim 1 - 4$, currently used in phenomenological analyses, and improve the uncertainty on this important phenomenological quantity.Comment: 20 pages, 4 figures, 2 table. Refined SU(3) ChPT analysis with no changes in the final result. Version to appear in PR

The chromomagnetic operator on the lattice

We study matrix elements of the "chromomagnetic" operator on the lattice. This operator is contained in the strangeness-changing effective Hamiltonian which describes electroweak effects in the Standard Model and beyond. Having dimension 5, the chromomagnetic operator is characterized by a rich pattern of mixing with other operators of equal and lower dimensionality, including also non gauge invariant quantities; it is thus quite a challenge to extract from lattice simulations a clear signal for the hadronic matrix elements of this operator. We compute all relevant mixing coefficients to one loop in lattice perturbation theory; this necessitates calculating both 2-point (quark-antiquark) and 3-point (gluon-quark-antiquark) Green's functions at nonzero quark masses. We use the twisted mass lattice formulation, with Symanzik improved gluon action. For a comprehensive presentation of our results, along with detailed explanations and a more complete list of references, we refer to our forthcoming publication [1].Comment: 7 pages, 1 figure. Talk presented at the 31st International Symposium on Lattice Field Theory (Lattice 2013), 29 July - 3 August 2013, Mainz, German

Nonzero θ13\theta_{13} and Neutrino Masses from Modified Neutrino Mixing Matrix

The nonzero and relatively large $\theta_{13}$ have been reported by Daya Bay, T2K, MINOS, and Double Chooz Collaborations. In order to accommodate the nonzero $\theta_{13}$, we modified the tribimaximal (TB), bimaxima (BM), and democratic (DC) neutrino mixing matrices. From three modified neutrino mixing matrices, two of them (the modified BM and DC mixing matrices) can give nonzero $\theta_{13}$ which is compatible with the result of the Daya Bay and T2K experiments. The modified TB neutrino mixing matrix predicts the value of $\theta_{13}$ greater than the upper bound value of the latest experimental results. By using the modified neutrino mixing matrices and impose an additional assumption that neutrino mass matrices have two zeros texture, we then obtain the neutrino mass in normal hierarchy when $(M_{\nu})_{22}=(M_{\nu})_{33}=0$ for the neutrino mass matrix from the modified TB neutrino mixing matrix and $(M_{\nu})_{11}=(M_{\nu})_{13}=0$ for the neutrino mass matrix from the modified DC neutrino mixing matrix. For these two patterns of neutrino mass matrices, either the atmospheric mass squared difference or the solar mass squared difference can be obtained, but not both of them simultaneously. From four patterns of two zeros texture to be considered on the obtained neutrino mass matrix from the modified BM neutrino mixing matrix, none of them can predict correctly neutrino mass spectrum (normal or inverted hierarchy).Comment: 13 pages, no figure, some references added, and slight revision due to reviewer(s) comments, to be published in IJMP

Weak insensitivity to initial conditions at the edge of chaos in the logistic map

We extend existing studies of weakly sensitive points within the framework of Tsallis non-extensive thermodynamics to include weakly insensitive points at the edge of chaos. Analyzing tangent points of the logistic map we have verified that the generalized entropy with suitable entropic index q correctly describes the approach to the attractor.Comment: 6 pages, 3 figure