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

Deconfinement at the Argyres-Douglas point in SU(2) gauge theory with broken N=2 supersymmetry

We consider chiral condensates in SU(2) gauge theory with broken N=2 supersymmetry. The matter sector contains an adjoint multiplet and one fundamental flavor. Matter and gaugino condensates are determined by integrating out the adjoint field. The only nonperturbative input is the Affleck-Dine-Seiberg (ADS) superpotential generated by one instanton plus the Konishi anomaly. These results are consistent with those obtained by the `integrating in' procedure, including a reproduction of the Seiberg-Witten curve from the ADS superpotential. We then calculate monopole, dyon, and charge condensates using the Seiberg-Witten approach. We show that the monopole and charge condensates vanish at the Argyres-Douglas point where the monopole and charge vacua collide. We interpret this phenomenon as a deconfinement of electric and magnetic charges at the Argyres-Douglas point.Comment: LaTeX file, 21 pages, no figures. Dependence of monopole condensate on Yukawa coupling is corrected, references adde

M\"{o}ssbauer study of the '11' iron-based superconductors parent compound Fe(1+x)Te

57Fe Moessbauer spectroscopy was applied to investigate the superconductor parent compound Fe(1+x)Te for x=0.06, 0.10, 0.14, 0.18 within the temperature range 4.2 K - 300 K. A spin density wave (SDW) within the iron atoms occupying regular tetrahedral sites was observed with the square root of the mean square amplitude at 4.2 K varying between 9.7 T and 15.7 T with increasing x. Three additional magnetic spectral components appeared due to the interstitial iron distributed over available sites between the Fe-Te layers. The excess iron showed hyperfine fields at approximately 16 T, 21 T and 49 T for three respective components at 4.2 K. The component with a large field of 49 T indicated the presence of isolated iron atoms with large localized magnetic moment in interstitial positions. Magnetic ordering of the interstitial iron disappeared in accordance with the fallout of the SDW with the increasing temperature

Targeted free energy perturbation

A generalization of the free energy perturbation identity is derived, and a computational strategy based on this result is presented. A simple example illustrates the efficiency gains that can be achieved with this method.Comment: 8 pages + 1 color figur

Renormalization group approach to vibrational energy transfer in protein

Renormalization group method is applied to the study of vibrational energy transfer in protein molecule. An effective Lagrangian and associated equations of motion to describe the resonant energy transfer are analyzed in terms of the first-order perturbative renormalization group theory that has been developed as a unified tool for global asymptotic analysis. After the elimination of singular terms associated with the Fermi resonance, amplitude equations to describe the slow dynamics of vibrational energy transfer are derived, which recover the result obtained by a technique developed in nonlinear optics [S.J. Lade, Y.S. Kivshar, Phys. Lett. A 372 (2008) 1077].Comment: 11 page

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