Early Life Relict Feature in Peptide Mass Distribution

Molecular mass of a biomolecule is characterized in mass spectroscopy by the monoisitopic mass M~mono~ and the average isotopic mass M~av~. We found that peptide masses mapped on a plane made by two parameters derived from M~mono~ and M~av~ form a peculiar global feature in form of a band-gap 5-7 ppm wide stretching across the whole peptide galaxy, with a narrow (FWHM 0.2 ppm) line in the centre. The a priori probability of such a feature to emerge by chance is less than 1:100. Peptides contributing to the central line have elemental compositions following the rules S=0; Z = (2C - N - H)/2 =0, which nine out of 20 amino acid residues satisfy. The relative abundances of amino acids in the peptides contributing to the central line correlate with the consensus order of emergence of these amino acids, with ancient amino acids being overrepresented in on-line peptides. Thus the central line is a relic of ancient life, and likely a signature of its emergence in abiotic synthesis. The linear correlation between M~av~ and M~mono~ reduces the complexity of polypeptide molecules, which may have increased the rate of their abiotic production. This, in turn may have influenced the selection of these amino acid residues for terrestrial life. Assuming the line feature is not spurious, life has emerged from elements with isotopic abundances very close to terrestrial levels, which rules out most of the Galaxy

A Green's function decoupling scheme for the Edwards fermion-boson model

Holes in a Mott insulator are represented by spinless fermions in the fermion-boson model introduced by Edwards. Although the physically interesting regime is for low to moderate fermion density the model has interesting properties over the whole density range. It has previously been studied at half-filling in the one-dimensional (1D) case by numerical methods, in particular exact diagonalization and density matrix renormalization group (DMRG). In the present study the one-particle Green's function is calculated analytically by means of a decoupling scheme for the equations of motion, valid for arbitrary density in 1D, 2D and 3D with fairly large boson energy and zero boson relaxation parameter. The Green's function is used to compute some ground state properties, and the one-fermion spectral function, for fermion densities n=0.1, 0.5 and 0.9 in the 1D case. The results are generally in good agreement with numerical results obtained by DMRG and dynamical DMRG and new light is shed on the nature of the ground state at different fillings. The Green's function approximation is sufficiently successful in 1D to justify future application to the 2D and 3D cases.Comment: 19 pages, 7 figures, final version with updated reference

Hydrodynamic Modes in a Trapped Strongly Interacting Fermi Gases of Atoms

The zero-temperature properties of a dilute two-component Fermi gas in the BCS-BEC crossover are investigated. On the basis of a generalization of the variational Schwinger method, we construct approximate semi-analytical formulae for collective frequencies of the radial and the axial breathing modes of the Fermi gas under harmonic confinement in the framework of the hydrodynamic theory. It is shown that the method gives nearly exact solutions.Comment: 11 page

Nonlinear dynamics of the interface of dielectric liquids in a strong electric field: Reduced equations of motion

The evolution of the interface between two ideal dielectric liquids in a strong vertical electric field is studied. It is found that a particular flow regime, for which the velocity potential and the electric field potential are linearly dependent functions, is possible if the ratio of the permittivities of liquids is inversely proportional to the ratio of their densities. The corresponding reduced equations for interface motion are derived. In the limit of small density ratio, these equations coincide with the well-known equations describing the Laplacian growth.Comment: 10 page

An expression for stationary distribution in nonequilibrium steady state

We study the nonequilibrium steady state realized in a general stochastic system attached to multiple heat baths and/or driven by an external force. Starting from the detailed fluctuation theorem we derive concise and suggestive expressions for the corresponding stationary distribution which are correct up to the second order in thermodynamic forces. The probability of a microstate $\eta$ is proportional to $\exp[{\Phi}(\eta)]$ where ${\Phi}(\eta)=-\sum_k\beta_k\mathcal{E}_k(\eta)$ is the excess entropy change. Here $\mathcal{E}_k(\eta)$ is the difference between two kinds of conditioned path ensemble averages of excess heat transfer from the $k$-th heat bath whose inverse temperature is $\beta_k$. Our expression may be verified experimentally in nonequilibrium states realized, for example, in mesoscopic systems.Comment: 4 pages, 2 figure

Quantum Non-Equilibrium Steady States Induced by Repeated Interactions

We study the steady state of a finite XX chain coupled at its boundaries to quantum reservoirs made of free spins that interact one after the other with the chain. The two-point correlations are calculated exactly and it is shown that the steady state is completely characterized by the magnetization profile and the associated current. Except at the boundary sites, the magnetization is given by the average of the reservoirs' magnetizations. The steady state current, proportional to the difference in the reservoirs' magnetizations, shows a non-monotonous behavior with respect to the system-reservoir coupling strength, with an optimal current state for a finite value of the coupling. Moreover, we show that the steady state can be described by a generalized Gibbs state.Comment: to appear in Phys. Rev. Let

Kinetics of the superconducting charge qubit in the presence of a quasiparticle

We investigate the energy and phase relaxation of a superconducting qubit caused by a single quasiparticle. In our model, the qubit is an isolated system consisting of a small island (Cooper-pair box) and a larger superconductor (reservoir) connected with each other by a tunable Josephson junction. If such system contains an odd number of electrons, then even at lowest temperatures a single quasiparticle is present in the qubit. Tunneling of a quasiparticle between the reservoir and the Cooper-pair box results in the relaxation of the qubit. We derive master equations governing the evolution of the qubit coherences and populations. We find that the kinetics of the qubit can be characterized by two time scales - quasiparticle escape time from reservoir to the box, $\Gamma^{-1}_{in}$, and quasiparticle relaxation time $\tau$. The former is determined by the dimensionless normal-state conductance $g_T$ of the Josephson junction and one-electron level spacing $\delta_r$ in the reservoir ($\Gamma_{in}\sim g_T\delta_r$), and the latter is due to electron-phonon interaction. We find that phase coherence is damped on the time scale of $\Gamma^{-1}_{in}$. The qubit energy relaxation depends on the ratio of the two characteristic times, $\tau$ and $\Gamma^{-1}_{in}$, and also on the ratio of temperature $T$ to the Josephson energy $E_J$.Comment: 12 pages, 4 figures, final version as published in PRB, some changes, reference adde

Local orientational order in the Stockmayer liquid

Phase behaviour of the Stockmayer fluid is studied with a method similar to the Monte-Carlo annealing scheme. We introduce a novel order parameter which is sensitive to the local co-orientation of the dipoles of particles in the fluid. We exhibit a phase diagram based on the behaviour of the order parameter in the density region 0.1 \leq {\rho}\ast \leq 0.32. Specifically, we observe and analyse a second order locally disordered fluid \rightarrow locally oriented fluid phase transition.Comment: 13 pages, 7 figure

Self-consistent theory of turbulence

A new approach to the stochastic theory of turbulence is suggested. The coloured noise that is present in the stochastic Navier-Stokes equation is generated from the delta-correlated noise allowing us to avoid the nonlocal field theory as it is the case in the conventional theory. A feed-back mechanism is introduced in order to control the noise intensity.Comment: submitted to J.Tech. Phys.Letters (St. Petersburg

Activated Ion Electron Capture Dissociation (AI ECD) of proteins: synchronization of infrared and electron irradiation with ion magnetron motion.

Here, we show that to perform activated ion electron capture dissociation (AI-ECD) in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer equipped with a CO(2) laser, it is necessary to synchronize both infrared irradiation and electron capture dissociation with ion magnetron motion. This requirement is essential for instruments in which the infrared laser is angled off-axis, such as the Thermo Finnigan LTQ FT. Generally, the electron irradiation time required for proteins is much shorter (ms) than that required for peptides (tens of ms), and the modulation of ECD, AI ECD, and infrared multiphoton dissociation (IRMPD) with ion magnetron motion is more pronounced. We have optimized AI ECD for ubiquitin, cytochrome c, and myoglobin; however the results can be extended to other proteins. We demonstrate that pre-ECD and post-ECD activation are physically different and display different kinetics. We also demonstrate how, by use of appropriate AI ECD time sequences and normalization, the kinetics of protein gas-phase refolding can be deconvoluted from the diffusion of the ion cloud and measured on the time scale longer than the period of ion magnetron motion