Bacteriorhodopsin folds through a poorly organized transition state.

The folding mechanisms of helical membrane proteins remain largely uncharted. Here we characterize the kinetics of bacteriorhodopsin folding and employ φ-value analysis to explore the folding transition state. First, we developed and confirmed a kinetic model that allowed us to assess the rate of folding from SDS-denatured bacteriorhodopsin (bRU) and provides accurate thermodynamic information even under influence of retinal hydrolysis. Next, we obtained reliable φ-values for 16 mutants of bacteriorhodopsin with good coverage across the protein. Every φ-value was less than 0.4, indicating the transition state is not uniquely structured. We suggest that the transition state is a loosely organized ensemble of conformations

Crystallization of the Wahnstr\"om Binary Lennard-Jones Liquid

We report observation of crystallization of the glass-forming binary Lennard-Jones liquid first used by Wahnstr\"om [G. Wahnstr\"om, Phys. Rev. A 44, 3752 (1991)]. Molecular dynamics simulations of the metastable liquid on a timescale of microseconds were performed. The liquid crystallized spontaneously. The crystal structure was identified as MgZn_2. Formation of transient crystallites is observed in the liquid. The crystallization is investigate at different temperatures and compositions. At high temperature the rate of crystallite formation is the limiting factor, while at low temperature the limiting factor is growth rate. The melting temperature of the crystal is estimated to be T_m=0.93 at rho=0.82. The maximum crystallization rate of the A_2B composition is T=0.60+/-0.02.Comment: 4 pages, 4 figures; corrected typo

Exponential distributions of collective flow-event properties in viscous liquid dynamics

We study the statistics of flow events in the inherent dynamics in supercooled two- and three-dimensional binary Lennard-Jones liquids. Distributions of changes of the collective quantities energy, pressure and shear stress become exponential at low temperatures, as does that of the event "size" $S\equiv\sum {d_i}^2$. We show how the $S$-distribution controls the others, while itself following from exponential tails in the distributions of (1) single particle displacements $d$, involving a Lindemann-like length $d_L$ and (2) the number of active particles (with $d>d_L$).Comment: Accepter version (PRL

Spectral methods for the wave equation in second-order form

Current spectral simulations of Einstein's equations require writing the equations in first-order form, potentially introducing instabilities and inefficiencies. We present a new penalty method for pseudo-spectral evolutions of second order in space wave equations. The penalties are constructed as functions of Legendre polynomials and are added to the equations of motion everywhere, not only on the boundaries. Using energy methods, we prove semi-discrete stability of the new method for the scalar wave equation in flat space and show how it can be applied to the scalar wave on a curved background. Numerical results demonstrating stability and convergence for multi-domain second-order scalar wave evolutions are also presented. This work provides a foundation for treating Einstein's equations directly in second-order form by spectral methods.Comment: 16 pages, 5 figure

New Understanding of Large Magellanic Cloud Structure, Dynamics and Orbit from Carbon Star Kinematics

We derive general expressions for the LMC velocity field which we fit to kinematical data for 1041 carbon stars. We demonstrate that all previous studies of LMC kinematics have made unnecessary over-simplifications that have led to incorrect estimates of important structural parameters. We compile and improve LMC proper motion estimates to support our analysis. We find that the kinematically determined position angle of the line of nodes is 129.9 +/- 6.0 deg. The LMC inclination changes at a rate di/dt = -103 +/- 61 deg/Gyr, a result of precession and nutation induced by Milky Way tidal torques. The LMC rotation curve V(R) has amplitude 49.8 +/- 15.9 km/s, 40% lower than what has previously (and incorrectly) been inferred from e.g. HI. The dynamical center of the carbon stars is consistent with the center of the bar and the center of the outer isophotes, but not with the HI kinematical center. The enclosed mass inside 8.9 kpc is (8.7 +/- 4.3) x 10^9 M_sun, more than half of which is due to a dark halo. The LMC has a larger vertical thickness than has traditionally been believed. Its V/sigma is less than the value for the Milky Way thick disk. We discuss the implications for the LMC self-lensing optical depth. We determine the LMC velocity and orbit in the Galactocentric rest frame and find it to be consistent with the range of velocities that has been predicted by models for the Magellanic Stream. The Milky Way dark halo must have mass >4.3 x 10^{11} M_sun and extent >39 kpc for the LMC to be bound. We predict the LMC proper motion velocity field, and discuss techniques for kinematical distance estimation. [ABRIDGED]Comment: 57 pages, LaTeX, with 11 PostScript figures. Submitted to the Astronomical Journa

Synthesis and alkyne-coupling chemistry of cyclomanganated 1- and 3-acetylindoles, 3-formylindole and analogues

The syntheses are reported of new cyclomanganated indole derivatives (1-acetyl-κO-indolyl-κC2)dicarbonylbis(trimethylphosphite)manganese (2), (1-methyl-3-acetyl-κO-indolyl-κC2)tetracarbonylmanganese (4), (3-formyl-κO-indolyl-κC2)tetracarbonylmanganese (5a) and (1-methyl-3-formyl-κO-indolyl-κC2)tetracarbonylmanganese (5b). The unusually complicated crystal structure of 5b has been determined, the first for a cyclomanganated aryl aldehyde. The preparations of a mitomycin-related pyrrolo-indole and related products by thermally promoted and oxidatively (Me3NO) initiated alkyne-coupling reactions of the previously known complex (1-acetyl-κO-indolyl-κC2)tetracarbonylmanganese (1) are reported for different alkynes and solvents. X-ray crystal structures are reported for the dimethyl acetylenedicarboxylate coupling product of 1 (dimethyl 1-methyl-l-hydroxypyrrolo[1,2a]-indole-2,3-dicarboxylate; 6a), and an unusually-cyclised triple insertion product 8 from the coupling of acetylene with 4, in which a cyclopentadiene moiety is η3-allyl-coordinated to Mn through only one double bond and an exocyclic carbon, but which rearranges on heating to an η5-cyclopentadienyl complex

Strong pressure-energy correlations in liquids as a configuration space property: Simulations of temperature down jumps and crystallization

Computer simulations recently revealed that several liquids exhibit strong correlations between virial and potential energy equilibrium fluctuations in the NVT ensemble [U. R. Pedersen {\it et al.}, Phys. Rev. Lett. {\bf 100}, 015701 (2008)]. In order to investigate whether these correlations are present also far from equilibrium constant-volume aging following a temperature down jump from equilibrium was simulated for two strongly correlating liquids, an asymmetric dumbbell model and Lewis-Wahnstr{\"o}m OTP, as well as for SPC water that is not strongly correlating. For the two strongly correlating liquids virial and potential energy follow each other closely during the aging towards equilibrium. For SPC water, on the other hand, virial and potential energy vary with little correlation as the system ages towards equilibrium. Further proof that strong pressure-energy correlations express a configuration space property comes from monitoring pressure and energy during the crystallization (reported here for the first time) of supercooled Lewis-Wahnstr{\"o}m OTP at constant temperature