The Reality and Measurement of the Wavefunction

Using a simple version of the model for the quantum measurement of a two level system, the contention of Aharonov, Anandan, and Vaidman that one must in certain circumstances give the wavefunction an ontological as well as an epistemological significance is examined. I decide that their argument that the wave function of a system can be measured on a single system fails to establish the key point and that what they demonstrate is the ontological significance of certain operators in the theory, with the wave function playing its usual epistemological role.Comment: 10p

Operational Semantics of Process Monitors

CSPe is a specification language for runtime monitors that can directly express concurrency in a bottom-up manner that composes the system from simpler, interacting components. It includes constructs to explicitly flag failures to the monitor, which unlike deadlocks and livelocks in conventional process algebras, propagate globally and aborts the whole system's execution. Although CSPe has a trace semantics along with an implementation demonstrating acceptable performance, it lacks an operational semantics. An operational semantics is not only more accessible than trace semantics but also indispensable for ensuring the correctness of the implementation. Furthermore, a process algebra like CSPe admits multiple denotational semantics appropriate for different purposes, and an operational semantics is the basis for justifying such semantics' integrity and relevance. In this paper, we develop an SOS-style operational semantics for CSPe, which properly accounts for explicit failures and will serve as a basis for further study of its properties, its optimization, and its use in runtime verification

Nanosecond molecular relaxations in lipid bilayers studied by high energy resolution neutron scattering and in-situ diffraction

We report a high energy-resolution neutron backscattering study to investigate slow motions on nanosecond time scales in highly oriented solid supported phospholipid bilayers of the model system DMPC -d54 (deuterated 1,2-dimyristoyl-sn-glycero-3-phoshatidylcholine), hydrated with heavy water. Wave vector resolved quasi-elastic neutron scattering (QENS) is used to determine relaxation times $\tau$, which can be associated with different molecular components, i.e., the lipid acyl chains and the interstitial water molecules in the different phases of the model membrane system. The inelastic data are complemented both by energy resolved and energy integrated in-situ diffraction. From a combined analysis of the inelastic data in the energy and time domain, the respective character of the relaxation, i.e., the exponent of the exponential decay is also determined. From this analysis we quantify two relaxation processes. We associate the fast relaxation with translational diffusion of lipid and water molecules while the slow process likely stems from collective dynamics

The Discovery of Vibrationally-Excited H_2 in the Molecular Cloud near GRB 080607

GRB 080607 has provided the first strong observational signatures of molecular absorption bands toward any galaxy hosting a gamma-ray burst. Despite the identification of dozens of features as belonging to various atomic and molecular (H_2 and CO) carriers, many more absorption features remained unidentified. Here we report on a search among these features for absorption from vibrationally-excited H_2, a species that was predicted to be produced by the UV flash of a GRB impinging on a molecular cloud. Following a detailed comparison between our spectroscopy and static, as well as dynamic, models of H_2* absorption, we conclude that a column density of 10^{17.5+-0.2} cm^{-2} of H_2* was produced along the line of sight toward GRB 080607. Depending on the assumed amount of dust extinction between the molecular cloud and the GRB, the model distance between the two is found to be in the range 230--940 pc. Such a range is consistent with a conservative lower limit of 100 pc estimated from the presence of Mg I in the same data. These distances show that substantial molecular material is found within hundreds of pc from GRB 080607, part of the distribution of clouds within the GRB host galaxy.Comment: Submitted to ApJL, 6 pages emulate

Mechanical coupling in flashing ratchets

We consider the transport of rigid objects with internal structure in a flashing ratchet potential by investigating the overdamped behavior of a rod-like chain of evenly spaced point particles. In 1D, analytical arguments show that the velocity can reverse direction multiple times in response to changing the size of the chain or the temperature of the heat bath. The physical reason is that the effective potential experienced by the mechanically coupled objects can have a different symmetry than that of individual objects. All analytical predictions are confirmed by Brownian dynamics simulations. These results may provide a route to simple, coarse-grained models of molecular motor transport that incorporate an object's size and rotational degrees of freedom into the mechanism of transport.Comment: 9 pages, 10 figure

Thermal and Electrical Properties of gamma-NaxCoO2 (0.70 < x < 0.78)

We have performed specific heat and electric resistivity measurements of Na$_{x}$CoO$_{2}$ ($x=0.70$-0.78). Two anomalies have been observed in the specific heat data for $x=0.78$, corresponding to magnetic transitions at $T_{c}=22$ K and $T_{k}\simeq 9$ K reported previously. In the electrical resistivity, a steep decrease at $T_{c}$ and a bending-like variation at $T_{b}$(=120K for $x=0.78$) have been observed. Moreover, we have investigated the $x$-dependence of these parameters in detail. The physical properties of this system are very sensitive to $x$, and the inconsistent results of previous reports can be explained by a small difference in $x$. Furthermore, for a higher $x$ value, a phase separation into Na-rich and Na-poor domains occurs as we previously proposed, while for a lower $x$ value, from characteristic behaviors of the specific heat and the electrical resistivity at the low-temperature region, the system is expected to be in the vicinity of the magnetic instability which virtually exists below $x=0.70$.Comment: 4 pages (3 figures included) and an extra figure (gif), to be published in J. Phys. Soc. Jpn. 73 (9) with possible minor revision

Evolution favors protein mutational robustness in sufficiently large populations

BACKGROUND: An important question is whether evolution favors properties such as mutational robustness or evolvability that do not directly benefit any individual, but can influence the course of future evolution. Functionally similar proteins can differ substantially in their robustness to mutations and capacity to evolve new functions, but it has remained unclear whether any of these differences might be due to evolutionary selection for these properties. RESULTS: Here we use laboratory experiments to demonstrate that evolution favors protein mutational robustness if the evolving population is sufficiently large. We neutrally evolve cytochrome P450 proteins under identical selection pressures and mutation rates in populations of different sizes, and show that proteins from the larger and thus more polymorphic population tend towards higher mutational robustness. Proteins from the larger population also evolve greater stability, a biophysical property that is known to enhance both mutational robustness and evolvability. The excess mutational robustness and stability is well described by existing mathematical theories, and can be quantitatively related to the way that the proteins occupy their neutral network. CONCLUSIONS: Our work is the first experimental demonstration of the general tendency of evolution to favor mutational robustness and protein stability in highly polymorphic populations. We suggest that this phenomenon may contribute to the mutational robustness and evolvability of viruses and bacteria that exist in large populations

The Afterglow, Energetics and Host Galaxy of the Short-Hard Gamma-Ray Burst 051221a

We present detailed optical, X-ray and radio observations of the bright afterglow of the short gamma-ray burst 051221a obtained with Gemini, Swift/XRT, and the Very Large Array, as well as optical spectra from which we measure the redshift of the burst, z=0.5464. At this redshift the isotropic-equivalent prompt energy release was about 1.5 x 10^51 erg, and using the standard afterglow synchrotron model we find that the blastwave kinetic energy is similar, E_K,iso ~ 8.4 x 10^51 erg. An observed jet break at t ~ 5 days indicates that the opening angle is ~ 7 degrees and the total beaming-corrected energy is therefore ~ 2.5 x 10^49 erg, comparable to the values inferred for previous short GRBs. We further show that the burst experienced an episode of energy injection by a factor of 3.4 between t=1.4 and 3.4 hours, which was accompanied by reverse shock emission in the radio band. This result provides continued evidence that the central engines of short GRBs may be active significantly longer than the duration of the burst and/or produce a wide range of Lorentz factors. Finally, we show that the host galaxy of GRB051221a is actively forming stars at a rate of about 1.6 M_solar/yr, but at the same time exhibits evidence for an appreciable population of old stars (~ 1 Gyr) and near solar metallicity. The lack of bright supernova emission and the low circumburst density (n ~ 10^-3 cm^-3) continue to support the idea that short bursts are not related to the death of massive stars and are instead consistent with a compact object merger. Given that the total energy release is a factor of ~ 10 larger than the predicted yield for a neutrino annihilation mechanism, this suggests that magnetohydrodynamic processes may be required to power the burst.Comment: Final version (to appear in ApJ on 20 September 2006