Origin of the Immirzi Parameter

Using quadratic spinor techniques we demonstrate that the Immirzi parameter can be expressed as ratio between scalar and pseudo-scalar contributions in the theory and can be interpreted as a measure of how Einstein gravity differs from a generally constructed covariant theory for gravity. This interpretation is independent of how gravity is quantized. One of the important advantage of deriving the Immirzi parameter using the quadratic spinor techniques is to allow the introduction of renormalization scale associated with the Immirzi parameter through the expectation value of the spinor field upon quantization

Protein mechanical unfolding: importance of non-native interactions

Mechanical unfolding of the fourth domain of Distyostelium discoideum filamin (DDFLN4) was studied by all-atom molecular dynamics simulations, using the GROMOS96 force field 43a1 and the simple point charge explicit water solvent. Our study reveals an important role of non-native interactions in the unfolding process. Namely, the existence of a peak centered at the end-to-end extension 22 nm in the force-extension curve, is associated with breaking of non-native hydrogen bonds. Such a peak has been observed in experiments but not in Go models, where non-native interactions are neglected. We predict that an additional peak occurs at 2 nm using not only GROMOS96 force field 43a1 but also Amber 94 and OPLS force fields. This result would stimulate further experimental studies on elastic properties of DDFLN4.Comment: 27 pages, 15 figure

Quasi-Local Energy Flux of Spacetime Perturbation

A general expression for quasi-local energy flux for spacetime perturbation is derived from covariant Hamiltonian formulation using functional differentiability and symplectic structure invariance, which is independent of the choice of the canonical variables and the possible boundary terms one initially puts into the Lagrangian in the diffeomorphism invariant theories. The energy flux expression depends on a displacement vector field and the 2-surface under consideration. We apply and test the expression in Vaidya spacetime. At null infinity the expression leads to the Bondi type energy flux obtained by Lindquist, Schwartz and Misner. On dynamical horizons with a particular choice of the displacement vector, it gives the area balance law obtained by Ashtekar and Krishnan.Comment: 8 pages, added appendix, version to appear in Phys. Rev.

An improved system to measure leaf gas exchange on adaxial and abaxial surfaces

Measurement of leaf carbon gain and water loss (gas exchange) in planta is a standard procedure in plant science research for attempting to understand physiological traits related to water use and photosynthesis. Leaves carry out gas exchange through the upper (adaxial) and lower (abaxial) surfaces at different magnitudes, depending on the stomatal density, stomatal aperture, cuticular permeability, etc., of each surface, which we account for in gas exchange parameters such as stomatal conductance. Most commercial devices measure leaf gas exchange by combining the adaxial and abaxial fluxes and calculating bulk gas exchange parameters, missing details of the plant's physiological response on each side. Additionally, the widely used equations to estimate gas exchange parameters neglect the contribution of small fluxes such as cuticular conductance, adding extra uncertainties to measurements performed in water-stress or low-light conditions. Accounting for the gas exchange fluxes from each side of the leaf allows us to better describe plants' physiological traits under different environmental conditions and account for genetic variability. Here, apparatus and materials are presented for adapting two LI-6800 Portable Photosynthesis Systems to work as one gas exchange system to measure adaxial and abaxial gas exchange simultaneously. The modification includes a template script with the equations to account for small fluxes. Instructions are provided for incorporating the add-on script into the device's computational sequence, display, variables, and spreadsheet results. We explain the method to obtain an equation to estimate boundary layer conductance to water for the new setup and how to embed this equation in the devices' calculations using the provided add-on script. The apparatus, methods, and protocols presented here provide a simple adaptation combining two LI-6800s to obtain an improved system to measure leaf gas exchange on adaxial and abaxial surfaces

The Hamiltonian boundary term and quasi-local energy flux

The Hamiltonian for a gravitating region includes a boundary term which determines not only the quasi-local values but also, via the boundary variation principle, the boundary conditions. Using our covariant Hamiltonian formalism, we found four particular quasi-local energy-momentum boundary term expressions; each corresponds to a physically distinct and geometrically clear boundary condition. Here, from a consideration of the asymptotics, we show how a fundamental Hamiltonian identity naturally leads to the associated quasi-local energy flux expressions. For electromagnetism one of the four is distinguished: the only one which is gauge invariant; it gives the familiar energy density and Poynting flux. For Einstein's general relativity two different boundary condition choices correspond to quasi-local expressions which asymptotically give the ADM energy, the Trautman-Bondi energy and, moreover, an associated energy flux (both outgoing and incoming). Again there is a distinguished expression: the one which is covariant.Comment: 12 pages, no figures, revtex

Delineation of the Native Basin in Continuum Models of Proteins

We propose two approaches for determining the native basins in off-lattice models of proteins. The first of them is based on exploring the saddle points on selected trajectories emerging from the native state. In the second approach, the basin size can be determined by monitoring random distortions in the shape of the protein around the native state. Both techniques yield the similar results. As a byproduct, a simple method to determine the folding temperature is obtained.Comment: REVTeX, 6 pages, 5 EPS figure

Finite size effects on thermal denaturation of globular proteins

Finite size effects on the cooperative thermal denaturation of proteins are considered. A dimensionless measure of cooperativity, Omega, scales as N^zeta, where N is the number of amino acids. Surprisingly, we find that zeta is universal with zeta = 1 + gamma, where the exponent gamma characterizes the divergence of the susceptibility for a self-avoiding walk. Our lattice model simulations and experimental data are consistent with the theory. Our finding rationalizes the marginal stability of proteins and substantiates the earlier predictions that the efficient folding of two-state proteins requires the folding transition temperature to be close to the collapse temperature.Comment: 3 figures. Physical Review Letters (in press