Solitons on H-bonds in proteins

A model for soliton dynamics on a hydrogen-bond network in helical proteins is proposed. It employs in three dimensions the formalism of fully integrable Toda lattices which admits phonons as well as solitons along the hydrogen-bonds of the helices. A simulation of the three dimensional Toda lattice system shows that the solitons are spontaneously created and are stable and moving along the helix axis. A perturbation on one of the three H-bond lines forms solitons on the other H-bonds as well. The robust solitary wave may explain very long-lived modes in the frequency range of 100 cm$^{-1}$ which are found in recent X-ray laser experiments. The dynamics parameters of the Toda lattice are in accordance with the usual Lennard-Jones parameters used for realistic H-bond potentials in proteins.Comment: 6 pages, 7 figure

Premartensitic transition driven by magnetoelastic interaction in bcc ferromagnetic Ni2MnGaNi_{2}MnGa

We show that the magnetoelastic coupling between the magnetization and the amplitude of a short wavelength phonon enables the existence of a first order premartensitic transition from a bcc to a micromodulated phase in $Ni_{2}MnGa$. Such a magnetoelastic coupling has been experimentally evidenced by AC susceptibility and ultrasonic measurements under applied magnetic field. A latent heat around 9 J/mol has been measured using a highly sensitive calorimeter. This value is in very good agreement with the value predicted by a proposed model.Comment: 4 pages RevTex, 3 Postscript figures, to be published in Physical Review Letter

Analytical tools for solitons and periodic waves corresponding to phonons on Lennard-Jones lattices in helical proteins

9 pages, 13 figures.-- PACS nrs.: 05.45.Yv, 87.15.-v.-- PMID: 15783440 [PubMed].We study the propagation of solitons along the hydrogen bonds of an alpha helix. Modeling the hydrogen and peptide bonds with Lennard-Jones potentials, we show that the solitons can appear spontaneously and have long lifetimes. Remarkably, even if no explicit solution is known for the Lennard-Jones potential, the solitons can be characterized analytically with a good quantitative agreement using formulas for a Toda potential with parameters fitted to the Lennard-Jones potential. We also discuss and show the robustness of the family of periodic solutions called cnoidal waves, corresponding to phonons. The soliton phenomena described in the simulations of alpha helices may help to explain recent x-ray experiments on long alpha helices in Rhodopsin where a long lifetime of the vibrational modes has been observed.Peer reviewe

Trapped-Ion Quantum Logic Utilizing Position-Dependent ac Stark Shifts

We present a scheme utilizing position-dependent ac Stark shifts for doing quantum logic with trapped ions. By a proper choice of direction, position and size, as well as power and frequency of a far-off-resonant Gaussian laser beam, specific ac Stark shifts can be assigned to the individual ions, making them distinguishable in frequency-space. In contrast to previous all-optical based quantum gates with trapped ions, the present scheme enables individual addressing of single ions and selective addressing of any pair of ions for two-ion quantum gates, without using tightly focused laser beams. Furthermore, the decoherence rate due to off-resonant excitations can be made negligible as compared with other sources of decoherence.Comment: 5 pages, 4 figures. Submitted to Physical Review Letter

Massive CP1^1 theory from a microscopic model for doped antiferromagnets

A path-integral for the t-J model in two dimensions is constructed based on Dirac quantization, with an action found originally by Wiegmann (Phys. Rev. Lett. {\bf 60}, 821 (1988); Nucl. Phys. B323, 311 (1989)). Concentrating on the low doping limit, we assume short range antiferromagnetic order of the spin degrees of freedom. Going over to a local spin quantization axis of the dopant fermions, that follows the spin degree of freedom, staggered CP$^1$ fields result and the constraint against double occupancy can be resolved. The staggered CP$^1$ fields are split into slow and fast modes, such that after a gradient expansion, and after integrating out the fast modes and the dopant fermions, a CP$^1$ field-theory with a massive gauge field is obtained that describes generically incommensurate coplanar magnetic structures, as discussed previously in the context of frustrated quantum antiferromagnets. Hence, the possibility of deconfined spinons is opened by doping a colinear antiferromagnet.Comment: 24 pages, no figure