Multidimensional replica-exchange method for free-energy calculations

We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in the original replica-exchange method, pairs of replicas with different temperatures and/or different parameters of the potential energy are exchanged in the new algorithm. This greatly enhances the sampling of the conformational space and allows accurate calculations of free energy in a wide temperature range from a single simulation run, using the weighted histogram analysis method.Comment: 13 pages, (ReVTeX), 9 figures. J. Chem. Phys. 113 (2000), in pres

Picosecond fluctuating protein energy landscape mapped by pressure–temperature molecular dynamics simulation

Microscopic statistical pressure fluctuations can, in principle, lead to corresponding fluctuations in the shape of a protein energy landscape. To examine this, nanosecond molecular dynamics simulations of lysozyme are performed covering a range of temperatures and pressures. The well known dynamical transition with temperature is found to be pressure-independent, indicating that the effective energy barriers separating conformational substates are not significantly influenced by pressure. In contrast, vibrations within substates stiffen with pressure, due to increased curvature of the local harmonic potential in which the atoms vibrate. The application of pressure is also shown to selectively increase the damping of the anharmonic, low-frequency collective modes in the protein, leaving the more local modes relatively unaffected. The critical damping frequency, i.e., the frequency at which energy is most efficiently dissipated, increases linearly with pressure. The results suggest that an invariant description of protein energy landscapes should be subsumed by a fluctuating picture and that this may have repercussions in, for example, mechanisms of energy dissipation accompanying functional, structural, and chemical relaxation

Vibrational energy relaxation in proteins

An overview of theories related to vibrational energy relaxation (VER) in proteins is presented. VER of a selected mode in cytochrome c is studied using two theoretical approaches. One is the equilibrium simulation approach with quantum correction factors, and the other is the reduced model approach which describes the protein as an ensemble of normal modes interacting through nonlinear coupling elements. Both methods result in estimates of the VER time (sub ps) for a CD stretching mode in the protein at room temperature. The theoretical predictions are in accord with the experimental data of Romesberg's group. A perspective on future directions for the detailed study of time scales and mechanisms for VER in proteins is presented.Comment: 12 pages, 4 figures, accepted for publication in PNA

Detection of Diatomic Molecules in the Dust Forming Nova V2676 Oph

Novae are generally considered to be hot astronomical objects and show effective temperatures up to 10,000 K or higher at their visual maximum. But, it is theoretically predicted that the outer envelope of the nova outflow can become cool enough to form molecules that would be dissociated at high temperatures. We detected strong absorption bands of C2 and CN radicals in the optical spectrum of Nova V2676 Oph, a very slow nova with dust formation. This is the first report of the detection of C2 and the second one of CN in novae during outburst. Although such simple molecules are predicted to form in the envelope of the outflow based on previous studies, there are few reports of their detection. In the case of V2676 Oph, the presence of the molecular envelope is considered to be very transient, lasting several days only

Electronic and Magnetic Phase Diagram of a Superconductor, SmFeAsO1-xFx

A crystallographic and magnetic phase diagram of SmFeAsO1-xFx is determined as a function of x in terms of temperature based on electrical transport and magnetization, synchrotron powder x-ray diffraction, 57Fe Mossbauer spectra (MS), and 149Sm nuclear resonant forward scattering (NRFS) measurements. MS revealed that the magnetic moments of Fe were aligned antiferromagnetically at ~144 K (TN(Fe)). The magnetic moment of Fe (MFe) is estimated to be 0.34 myuB/Fe at 4.2 K for undoped SmFeAsO; MFe is quenched in superconducting F-doped SmFeAsO. 149Sm NRFS spectra revealed that the magnetic moments of Sm start to order antiferromagnetically at 5.6 K (undoped) and 4.4 K (TN(Sm)) (x = 0.069). Results clearly indicate that the antiferromagnetic Sm sublattice coexists with the superconducting phase in SmFeAsO1-xFx below TN(Sm), while antiferromagnetic Fe sublattice does not coexist with the superconducting phase.Comment: Accepted in New Journal of Physic

Taxing Capital? Not a Bad Idea After All!

Premi a l'excel·lència investigadora. 2010Publicat també com a : CEPR Discussion Paper - ISSN 0265-8003 Núm. 5929 (2006), p. 1-55We quantitatively characterize the optimal capital and labor income tax in an overlapping generations model with idiosyncratic, uninsurable income shocks and permanent productivity differences of households. The optimal capital income tax rate is significantly positive at 36 percent. The optimal progressive labor income tax is, roughly, a flat tax of 23 percent with a deduction of #7,200 (relative to average household income of #42,000). The high optimal capital income tax is mainly driven by the life-cycle structure of the model, whereas the optimal progressivity of the labor income tax is attributable to the insurance and redistribution role of the tax system. (JEL E13, H21, H24, H25

Supersymmetry Breaking in Chern-Simons-matter Theories

Some of supersymmetric Chern-Simons theories are known to exhibit supersymmetry breaking when the Chern-Simons level is less than a certain number. The mechanism of the supersymmetry breaking is, however, not clear from the field theory viewpoint. In this paper, we discuss vacuum states of ${\cal N}=2$ pure Chern-Simons theory and ${\cal N}=2$ Chern-Simons-matter theories of quiver type using related theories in which Chern-Simons terms are replaced with (anti-)fundamental chiral multiplets. In the latter theories, supersymmetry breaking can be shown to occur by examining that the vacuum energy is non-zero.Comment: 17 pages, 3 figures, v2) references adde

N=1 Supersymmetric Product Group Theories in the Coulomb Phase

We study the low-energy behavior of N=1 supersymmetric gauge theories with product gauge groups SU(N)^M and M chiral superfields transforming in the fundamental representation of two of the SU(N) factors. These theories are in the Coulomb phase with an unbroken U(1)^(N-1) gauge group. For N >= 3, M >= 3 the theories are chiral. The low-energy gauge kinetic functions can be obtained from hyperelliptic curves which we derive by considering various limits of the theories. We present several consistency checks of the curves including confinement through the addition of mass perturbations and other limits.Comment: 22 pages, LaTeX, minor changes. Eqs. (20) and (42) correcte

The Coulomb branch of N=1 supersymmetric SU(N_c) x SU(N_c) gauge theories

We analyze the low energy behavior of N=1 supersymmetric gauge theories with SU(N_c) x SU(N_c) gauge group and a Landau-Ginzburg type superpotential. These theories contain fundamentals transforming under one of the gauge groups as well as bifundamental matter which transforms as a fundamentals under each. We obtain the parametrization of the gauge coupling on the Coulomb branch in terms of a hyperelliptic curve. The derivation of this curve involves making use of Seiberg's duality for SQCD as well as the classical constraints for N_f=N_c+1 and the quantum modified constraints for N_f=N_c.Comment: 16 pages, no figures, revtex; typos correcte