Repositório RCAAP

On the transferability of the SPC/L water model to biomolecular simulation

We investigated the performance of the recently developed SPC/L model for liquid water, as a pure liquid, in binary mixtures with DMSO, and as a solvent model in a peptide folding simulation. Additionally, in order to test the compatibility with the GROMOS biomolecular force field, free energies of hydration of a set of representative compounds were computed. The results are compared to those for the well established SPC water model, which is generally used as a solvent model in conjunction with the GROMOS force field already for more than two decades. It turns out that as a pure liquid and in binary mixtures with DMSO the SPC/L model outperforms SPC, whereas as solvent in combination with the GROMOS force field both models perform equally well.

Ano

2004

Creators

Glättli,Alice Oostenbrink,Chris Daura,Xavier Geerke,Daan P. Yu,Haibo van Gunsteren,Wilfred F.

On the application of simple explicit water models to the simulations of biomolecules

Computer simulations of biomolecular systems have achieved a significant importance in science as they provide information regarding structure, dynamics, and energetics of biomolecules that are inaccessible to experimental measuring techniques. In this work, some important aspects of the simulation of biomolecular systems are described. An overview of the most popular protein force fields, simple explicit water models for the simulation of liquid water, and different approaches to treat the boundaries of the system is presented. Also, studies conducted in our group illustrating successful simulations of three biomolecules (thrombin, L-type calcium channel and human Cytomegalovirus protease) through the application of simple explicit water models combined with protein force fields are discussed.

Ano

2004

Creators

Guimarães,Cristiano Ruch Werneck Barreiro,Gabriela Oliveira,César Augusto Fernandes de Alencastro,Ricardo Bicca de

The effect of temperature and LiClO4 in the water structure: a Raman spectroscopy study

A method to obtain the components of the broad Raman band assigned to the OH stretching vibrations of liquid water was developed, by considering the subtraction of spectra at several temperatures. From these subtractions a set of six components, that we denominate "basis", was determined corresponding to several water structures. This procedure fixes the number of components in the fitting as well as the values of the frequencies, generating a set of six gaussian bands from which the water spectrum can be calculated at any temperature. With such bands the spectrum of lithium perchlorate was calculated at several concentrations and temperatures. It was verified that the spectrum so obtained was identical to that of pure water at a higher temperature. The presence of an isosbestic point is a proof of the existence of equilibrium between the several structures. The enthalpy and entropy values were determined for the isosbestic point and for pairs of structures corresponding to the gaussian bands.

Ano

2004

Creators

Pereira Neto,Ana Maria Sala,Oswaldo

The proton momentum distribution in water and ice

Deep Inelastic Neutron Scattering (Neutron Compton Scattering), is used to measure the momentum distribution of the protons in water from temperatures slightly below freezing to the supercritical phase. The momentum distribution is determined almost entirely by quantum localization effects, and hence is a sensitive probe of the local environment of the proton. The distribution shows dramatic changes as the hydrogen bond network becomes more disordered. Within a single particle interpretation, the proton moves from an essentially harmonic well in ice to a slightly anharmonic well in room temperature water, to a deeply anharmonic potential in the supercritical phase that is best described by a double well potential with a separation of the wells along the bond axis of about 0.3 Angstrom. Confining the supercritical water in the interstices of a C60 powder enhances this anharmonicity and enhances the localization of the protons. The changes in the distribution are consistent with gas phase formation at the hydrophobic boundaries and inconsistent with the formation of ice there.

Ano

2004

Creators

Reiter,G. Li,J. C. Mayers,J. Abdul-Redah,T. Platzman,P.

Strings in flat space and plane waves from N = 4 super Yang Mills

We explain how the string spectrum in flat space and plane waves arises from the large N limit of U(N)  N = 4 super Yang Mills. We reproduce the spectrum by summing a subset of the planar Feynman diagrams. We also describe some other aspects of string propagation on plane wave backgrounds. This talk based on [1].

Gauge theories on the light-front

The light-front quantization of gauge theories in light-cone gauge provides a frame-independent wavefunction representation of relativistic bound states, simple forms for current matrix elements, explicit unitary, and a trivial vacuum. The light-front Hamiltonian form of QCD provides an alternative to lattice gauge theory for the computation of nonperturbative quantities such as the hadronic spectrum and the corresponding eigenfunctions. In the case of the electroweak theory, spontaneous symmetry breaking is represented by the appearance of zero modes of the Higgs field. Light-front quantization then leads to an elegant ghost-free theory of massive gauge particles, automatically incorporating the Lorentz and 't Hooft conditions, as well as the Goldstone boson equivalence theorem.

Perspectives of the ALICE experiment

The Large Hadron Collider, now under contruction at the European Center for Nuclear Research, represents a unique opportunity for Heavy-Ion Physics. It will provide nuclear collisions at a center-of-mass energy 30 times higher then the present Relativistic Heavy Ion Collider at BNL, currelty the highest energy nuclear accelerator. The LHC will open for this field a new era, in which particle production will be dominated by hard processes, and the energy densities will possibly be high enough to treat the generated quark-gluon plasma as an ideal gas. While RHIC is providing a wealth of interesting data, many physicists are working hard to prepare the experiments which will run at the LHC. ALICE, A Large Ion Collider Experiment, the dedicated detector designed to study nucleus-nucleus collisions at the LHC, is developing rapidly: the R&D is essentially complete, and large parts of the main detectors are in production. The scientific motivations and present status of Heavy Ion Physics, can be found in the review by T. Kodama [1]. In the following, I will summarize the experimental conditions at the LHC with nuclear beams, describe the main detector components of ALICE and briefly discuss the physics program of the experiment.

Elementary particles under the lens of the black holes

After a brief review of the historical development and CLASSICAL properties of the BLACK HOLES, we discuss how our present knowledge of some of their QUANTUM properties shed light on the very concept of ELEMENTARY PARTICLE. As an illustration, we discuss in this context the decay of accelerated protons, which may be also relevant to astrophysics.

Collider tests for neutrino mass generation in a supersymmetric world with R-parity violation

We summarize the low energy features of a supersymmetric class of models with bilinear R-parity violation. We analyze two cases where the supersymmetry breaking is mediated either by supergravity or by anomaly induced contributions to the soft parameters and compare both scenarios in the context of recent neutrino conversion data and collider physics. We show that both classes of models have a large potential to discoveries in collider experiments as well as in neutrino experiments.

Topological mass generation and duality transformations in diverse dimensions

In this seminar we shall discuss the issue of duality transformation in the context of f topological mass generation in diverse dimensions. Particular emphasis will be given to the mass generation mechanism as the result of interference between self and anti self-dual components, as disclosed by the soldering formalism. Since this is a gauge embedding procedure derived from an old algorithm of second-class constraint conversion used by the author to approach anomalous gauge theories, a quick review of the subject will be presented. The problem of classification of the electromagnetic duality groups that is closely related will also be briefly discussed. Particular emphasis will be given to a new approach to duality based on the soldering embedding to tackle to problem of mass generation by topological mechanisms in D=3 and D=4 dimensions including the couplings to dynamical matter and nonlinear cases.

Quark-lepton nonuniversality

There is new experimental evidence which may be interpreted as a small departure from quark-lepton universality. We propose to understand this as the result of a hierarchy of mass scales in analogy to m u, m d << L QCD for strong isospin. We show <img id="_x0000_i1026" src="../../img/revistas/bjp/v34n1a/a08img01.gif" align=absbottom>< <img id="_x0000_i1027" src="../../img/revistas/bjp/v34n1a/a08img02.gif" align=absbottom>< <img id="_x0000_i1028" src="../../img/revistas/bjp/v34n1a/a08img03.gif" align=absbottom>< <img id="_x0000_i1029" src="../../img/revistas/bjp/v34n1a/a08img04.gif" align=absbottom>in principle, but all are still approximately equal. New physics is predicted at the TeV scale.

Alternative dark energy models: an overview

A large number of recent observational data strongly suggest that we live in a flat, accelerating Universe composed of ~ 1/3 of matter (baryonic + dark) and ~ 2/3 of an exotic component with large negative pressure, usually named Dark Energy or Quintessence. The basic set of experiments includes: observations from SNe Ia, CMB anisotropies, large scale structure, X-ray data from galaxy clusters, age estimates of globular clusters and old high redshift galaxies (OHRG's). It is now widely believed that such results provide the remaining piece of information connecting the inflationary flatness prediction (W T = 1) with astronomical observations. From a theoretical viewpoint, they have also stimulated the current interest for more general models containing an extra component describing this unknown dark energy, and simultaneously accounting for the present accelerating stage of the Universe. In this review we present a simplified picture of the main results and discuss briefly some difficulties underlying the emerging dark energy paradigm.

Light quark spectroscopy and charm decays

The connection between light quark spectroscopy and hadronic decays of D mesons is discussed, with emphasis on the physics of the light scalar mesons. Recent results from charm decays are presented.

Hunt for the quark-gluon plasma: 20 years later

We review briefly the recent progress in the search for the quark-gluon plasma (QGP) at CERN SPS and BNL RHIC. Several model analyses and observables, such as hadronic thermal equilibrium, hydrodynamical flow, HBT, jet quenching, etc. which lead to the present conception of the formation of QGP are described.

Experimental status of corrections to Newton's gravitational law inspired by extra dimensional physics

Corrections to Newton's gravitational law inspired by extra dimensional physics and by the exchange of light and massless elementary particles between the atoms of two macrobodies are considered. These corrections can be described by the potentials of Yukawa-type and by the power-type potentials with different powers. The strongest up to date constraints on the corrections to Newton's gravitational law are reviewed following from the Eötvos- and Cavendish-type experiments and also from the measurements of the Casimir and van derWaals force.

Preliminary results from DØ run II data

We present recent physics results from the data collected by the DØ detector in this early stage of Run II of the Tevatron proton-antiproton collider. Emphasis is given to the Forward Proton Detector, a new subsystem that will enable detailed studies of diffractive phenomena at Tevatron.

Summary talk: quantum field theory

We present a summary of the contributions to Quantum Field Theory of the XXIII Brazilian National Meeting on Particles and Fields.

QCD glueball sum rules revisited

We discuss several key problems of conventional QCD glueball sum rules in the spin-0 channels and show how they are overcome by nonperturbative Wilson coefficients. The nonperturbative contributions originate from direct instantons and, in the pseudoscalar channel, additionally from topological charge screening. The treatment of the direct-instanton sector is based on realistic instanton size distributions and renormalization at the operator scale. The resulting predictions for spin-0 glueball properties as well as their implications for experimental glueball searches are discussed.

The flavor asymmetry in the polarized proton sea

We perform a careful study on the effect of the Pauli blocking to the light polarized antiquark structure of the proton sea. We develop the formal expressions for the polarized antiquark distributions, highlighting the role played by quark statistics and the vacuum structure. The ratio involving the polarized antiquarks is calculated. In particular, it is found that D<img id="_x0000_i1026" src="../../../../img/revistas/bjp/v34n1a/a17img01.gif" align=absbottom>(x)/D<img id="_x0000_i1027" src="../../../../img/revistas/bjp/v34n1a/a17img02.gif" align=absbottom>(x) should be negative and x independent.

The J/psiDD* vertex

We employ QCD sum rules to calculate the J/psiDD* form factors and coupling constant by studying the threepoint J/psiD*D correlation function. We find that the momentum dependence of the form factor depends on the off-shell meson. We get a value for the coupling which is in agreement with estimates based on constituent quark model.

Ano

2004

Creators

Rodrigues da Silva,R. Matheus,R.D. Navarra,F.S. Nielsen,M.