Thermodynamic origin of cooperativity in actomyosin interactions: The coupling of short-range interactions with actin bending stiffness in an Ising-like model

We present Monte Carlo simulations for a molecular motor system found in virtually all eukaryotic cells, the acto-myosin motor system, composed of a group of organic macromolecules. Cell motors were mapped to an Ising-like model, where the interaction field is transmitted through a tropomyosin polymer chain. The presence of Ca(2+) induces tropomyosin to block or unblock binding sites of the myosin motor leading to its activation or deactivation. We used the Metropolis algorithm to find the transient and the equilibrium states of the acto-myosin system composed of solvent, actin, tropomyosin, troponin, Ca(2+), and myosin-S1 at a given temperature, including the spatial configuration of tropomyosin on the actin filament surface. Our model describes the short- and long-range cooperativity during actin-myosin binding which emerges from the bending stiffness of the tropomyosin complex. We found all transition rates between the states only using the interaction energy of the constituents. The agreement between our model and experimental data also supports the recent theory of flexible tropomyosin.

Higher-derivative supersymmetric gauge theory

We study the one-loop low-energy effective action for the higher-derivative superfield gauge theory coupled to chiral matter.

Noncommutativity due to spin

Using the Berezin-Marinov pseudoclassical formulation of the spin particle we propose a classical model of spin noncommutativity. In the nonrelativistic case, the Poisson brackets between the coordinates are proportional to the spin angular momentum. The quantization of the model leads to the noncommutativity with mixed spatial and spin degrees of freedom. A modified Pauli equation, describing a spin half particle in an external electromagnetic field is obtained. We show that nonlocality caused by the spin noncommutativity depends on the spin of the particle; for spin zero, nonlocality does not appear, for spin half, Delta x Delta y >= theta(2)/2, etc. In the relativistic case the noncommutative Dirac equation was derived. For that we introduce a new star product. The advantage of our model is that in spite of the presence of noncommutativity and nonlocality, it is Lorentz invariant. Also, in the quasiclassical approximation it gives noncommutativity with a nilpotent parameter.

Nonsingular bounce in modified gravity

We investigate bouncing solutions in the framework of the nonsingular gravity model of Brandenberger, Mukhanov and Sornborger. We show that a spatially flat universe filled with ordinary matter undergoing a phase of contraction reaches a stage of minimal expansion factor before bouncing in a regular way to reach the expanding phase. The expansion can be connected to the usual radiation-and matter-dominated epochs before reaching a final expanding de Sitter phase. In general relativity (GR), a bounce can only take place provided that the spatial sections are positively curved, a fact that has been shown to translate into a constraint on the characteristic duration of the bounce. In our model, on the other hand, a bounce can occur also in the absence of spatial curvature, which means that the time scale for the bounce can be made arbitrarily short or long. The implication is that constraints on the bounce characteristic time obtained in GR rely heavily on the assumed theory of gravity. Although the model we investigate is fourth order in the derivatives of the metric (and therefore unstable vis-a-vis the perturbations), this generic bounce dynamics should extend to string-motivated nonsingular models which can accommodate a spatially flat bounce.

Field theory model for dark matter and dark energy in interaction

We propose a field theory model for dark energy and dark matter in interaction. Comparing the classical solutions of the field equations with the observations of the CMB shift parameter, baryonic acoustic oscillations, lookback time, and the Gold supernovae sample, we observe a possible interaction between dark sectors with energy decay from dark energy into dark matter. The observed interaction provides an alleviation to the coincidence problem.

The gross theory model for neutrino-nucleus cross-section

The nuclear gross theory, originally formulated by Takahashi and Yamada (1969 Prog. Theor. Phys. 41 1470) for the beta-decay, is applied to the electronic-neutrino nucleus reactions, employing a more realistic description of the energetics of the Gamow-Teller resonances. The model parameters are gauged from the most recent experimental data, both for beta(-)-decay and electron capture, separately for even-even, even-odd, odd-odd and odd-even nuclei. The numerical estimates for neutrino-nucleus cross-sections agree fairly well with previous evaluations done within the framework of microscopic models. The formalism presented here can be extended to the heavy nuclei mass region, where weak processes are quite relevant, which is of astrophysical interest because of its applications in supernova explosive nucleosynthesis.

Finiteness of the noncommutative supersymmetric Maxwell-Chern-Simons theory

Within the superfield approach, we prove the absence of UV/IR mixing in the three-dimensional noncommutative supersymmetric Maxwell-Chern-Simons theory at any loop order and demonstrate its finiteness in one, three, and higher loop orders.

A Goldstone theorem in thermal relativistic quantum field theory

We prove a Goldstone theorem in thermal relativistic quantum field theory, which relates spontaneous symmetry breaking to the rate of spacelike decay of the two-point function. The critical rate of fall-off coincides with that of the massless free scalar field theory. Related results and open problems are briefly discussed. (C) 2011 American Institute of Physics. [doi:10.1063/1.3526961]

Theory of near-gap second harmonic generation in centrosymmetric magnetic semiconductors: Europium chalcogenides

Second harmonic generation is strictly forbidden in centrosymmetric materials, within the electric dipole approximation. Recently, it was found that the centrosymmetric magnetic semiconductors EuTe and EuSe can generate near-gap second harmonics, if the system is submitted to an external magnetic field. Here, a theoretical model is presented, which well describes the observed phenomena. The model shows that second harmonic generation becomes efficient when the magnetic dipole oscillations between the band-edge excited states of the system, induced by the excitation light, enter the in-phase regime, which can be achieved by applying a magnetic field to the material.

Edge effects in bilayer graphene nanoribbons: Ab initio total-energy density functional theory calculations

We show that the ground state of zigzag bilayer graphene nanoribbons is nonmagnetic. It also possesses a finite gap, which has a nonmonotonic dependence with the width as a consequence of the competition between bulk and strongly attractive edge interactions. All results were obtained using ab initio total-energy density functional theory calculations with the inclusion of parametrized van der Waals interactions.

Approximation to density functional theory for the calculation of band gaps of semiconductors

The local-density approximation (LDA) together with the half occupation (transitionstate) is notoriously successful in the calculation of atomic ionization potentials. When it comes to extended systems, such as a semiconductor infinite system, it has been very difficult to find a way to half ionize because the hole tends to be infinitely extended (a Bloch wave). The answer to this problem lies in the LDA formalism itself. One proves that the half occupation is equivalent to introducing the hole self-energy (electrostatic and exchange correlation) into the Schrodinger equation. The argument then becomes simple: The eigenvalue minus the self-energy has to be minimized because the atom has a minimal energy. Then one simply proves that the hole is localized, not infinitely extended, because it must have maximal self-energy. Then one also arrives at an equation similar to the self- interaction correction equation, but corrected for the removal of just 1/2 electron. Applied to the calculation of band gaps and effective masses, we use the self- energy calculated in atoms and attain a precision similar to that of GW, but with the great advantage that it requires no more computational effort than standard LDA.

Optical absorption and electronic band structure first-principles calculations of alpha-glycine crystals

Light absorption of alpha-glycine crystals grown by slow evaporation at room temperature was measured, indicating a 5.11 +/- 0.02 eV energy band gap. Structural, electronic, and optical absorption properties of alpha-glycine crystals were obtained by first-principles quantum mechanical calculations using density functional theory within the generalized gradient approximation in order to understand this result. To take into account the contribution of core electrons, ultrasoft and norm-conserving pseudopotentials, as well as an all electron approach were considered to compute the electronic density of states and band structure of alpha-glycine crystals. They exhibit three indirect energy band gaps and one direct Gamma-Gamma energy gap around 4.95 eV. The optical absorption related to transitions between the top of the valence band and the bottom of the conduction band involves O 2p valence states and C, O 2p conduction states, with the carboxyl group contributing significantly to the origin of the energy band gap. The calculated optical absorption is highly dependent on the polarization of the incident radiation due to the spatial arrangement of the dipolar glycine molecules; in the case of a polycrystalline sample, the first-principles calculated optical absorption is in good agreement with the measurement when a rigid energy shift is applied.

Gauge invariance and classical dynamics of noncommutative particle theory

We consider a model of classical noncommutative particle in an external electromagnetic field. For this model, we prove the existence of generalized gauge transformations. Classical dynamics in Hamiltonian and Lagrangian form is discussed; in particular, the motion in the constant magnetic field is studied in detail. (C) 2010 American Institute of Physics. [doi: 10.1063/1.3299296]

Consistency restrictions on maximal electric-field strength in quantum field theory

Quantum field theory with an external background can be considered as a consistent model only if backreaction is relatively small with respect to the background. To find the corresponding consistency restrictions on an external electric field and its duration in QED and QCD, we analyze the mean-energy density of quantized fields for an arbitrary constant electric field E, acting during a large but finite time T. Using the corresponding asymptotics with respect to the dimensionless parameter eET(2), one can see that the leading contributions to the energy are due to the creation of particles by the electric field. Assuming that these contributions are small in comparison with the energy density of the electric background, we establish the above-mentioned restrictions, which determine, in fact, the time scales from above of depletion of an electric field due to the backreaction.

Nonmonotonic thickness dependence of spin wave energy in ultrathin Fe films: Experiment and theory

High wave-vector spin waves in ultrathin Fe/W(110) films up to 20 monolayers (MLs) thick have been studied using spin-polarized electron energy-loss spectroscopy. An unusual nonmonotonous dependence of the spin wave energies on the film thickness is observed, featuring a pronounced maximum at 2 ML coverage. First-principles theoretical study reveals the origin of this behavior to be in the localization of the spin waves at the surface of the film, as well as in the properties of the interlayer exchange coupling influenced by the hybridization of the electron states of the film and substrate and by the strain.