Relative Entropy: Free Energy Associated with Equilibrium Fluctuations and Nonequilibrium Deviations

Using a one-dimensional macromolecule in aqueous solution as an illustration, we demonstrate that the relative entropy from information theory, $\sum_k p_k\ln(p_k/p_k^*)$, has a natural role in the energetics of equilibrium and nonequilibrium conformational fluctuations of the single molecule. It is identified as the free energy difference associated with a fluctuating density in equilibrium, and is associated with the distribution deviate from the equilibrium in nonequilibrium relaxation. This result can be generalized to any other isothermal macromolecular systems using the mathematical theories of large deviations and Markov processes, and at the same time provides the well-known mathematical results with an interesting physical interpretations.Comment: 5 page

Structure of Stochastic Dynamics near Fixed Points

We analyze the structure of stochastic dynamics near either a stable or unstable fixed point, where force can be approximated by linearization. We find that a cost function that determines a Boltzmann-like stationary distribution can always be defined near it. Such a stationary distribution does not need to satisfy the usual detailed balance condition, but might have instead a divergence-free probability current. In the linear case the force can be split into two parts, one of which gives detailed balance with the diffusive motion, while the other induces cyclic motion on surfaces of constant cost function. Using the Jordan transformation for the force matrix, we find an explicit construction of the cost function. We discuss singularities of the transformation and their consequences for the stationary distribution. This Boltzmann-like distribution may be not unique, and nonlinear effects and boundary conditions may change the distribution and induce additional currents even in the neighborhood of a fixed point.Comment: 7 page

Mass Hierarchy Resolution in Reactor Anti-neutrino Experiments: Parameter Degeneracies and Detector Energy Response

Determination of the neutrino mass hierarchy using a reactor neutrino experiment at $\sim$60 km is analyzed. Such a measurement is challenging due to the finite detector resolution, the absolute energy scale calibration, as well as the degeneracies caused by current experimental uncertainty of $|\Delta m^2_{32}|$. The standard $\chi^2$ method is compared with a proposed Fourier transformation method. In addition, we show that for such a measurement to succeed, one must understand the non-linearity of the detector energy scale at the level of a few tenths of percent.Comment: 7 pages, 6 figures, accepted by PR

Experimental and Numerical Investigation on Progressive Collapse Resistance of Post-tensioned Precast Concrete Beam-Column Sub-assemblages

In this paper, four 1/2 scaled precast concrete (PC) beam-column sub-assemblages with high performance connection were tested under push-down loading procedure to study the load resisting mechanism of PC frames subjected to different column removal scenarios. The parameters investigated include the location of column removal and effective prestress in tendons. The test results indicated that the failure modes of unbonded post-tensioned precast concrete (PTPC) frames were different from that of reinforced concrete (RC) frames: no cracks formed in the beams and wide opening formed near the beam to column interfaces. For specimens without overhanging beams, the failure of side column was eccentric compression failure. Moreover, the load resisting mechanisms in PC frames were significantly different from that of RC frames: the compressive arch action (CAA) developed in concrete during column removal was mainly due to actively applied pre-compressive stress in the concrete; CAA will not vanish when severe crush in concrete occurred. Thus, it may provide negative contribution for load resistance when the displacement exceeds one-beam depth; the tensile force developed in the tendons could provide catenary action from the beginning of the test. Moreover, to deeper understand the behavior of tested specimens, numerical analyses were carried out. The effects of concrete strength, axial compression ratio at side columns, and loading approaches on the behavior of the sub-assemblages were also investigated based on validated numerical analysis

The Spin Mass of an Electron Liquid

We show that in order to calculate correctly the {\it spin current} carried by a quasiparticle in an electron liquid one must use an effective "spin mass" $m_s$, that is larger than both the band mass, $m_b$, which determines the charge current, and the quasiparticle effective mass $m^*$, which determines the heat capacity. We present microscopic calculations of $m_s$ in a paramagnetic electron liquid in three and two dimensions, showing that the mass enhancement $m_s/m_b$ can be a very significant effect.Comment: 10 pages, 1 figur

The Dynamics of Zeroth-Order Ultrasensitivity: A Critical Phenomenon in Cell Biology

It is well known since the pioneering work of Goldbeter and Koshland [Proc. Natl. Acad. Sci. USA, vol. 78, pp. 6840-6844 (1981)] that cellular phosphorylation- dephosphorylation cycle (PdPC), catalyzed by kinase and phosphatase under saturated condition with zeroth order enzyme kinetics, exhibits ultrasensitivity, sharp transition. We analyse the dynamics aspects of the zeroth order PdPC kinetics and show a critical slowdown akin to the phase transition in condensed matter physics. We demonstrate that an extremely simple, though somewhat mathematically "singular" model is a faithful representation of the ultrasentivity phenomenon. The simplified mathematical model will be valuable, as a component, in developing complex cellular signaling network theory as well as having a pedagogic value.Comment: 8 pages, 3 figure