Discrete elastic model for stretching-induced flagellar polymorphs

Force-induced reversible transformations between coiled and normal polymorphs of bacterial flagella have been observed in recent optical-tweezer experiment. We introduce a discrete elastic rod model with two competing helical states governed by a fluctuating spin-like variable that represents the underlying conformational states of flagellin monomers. Using hybrid Brownian dynamics Monte-Carlo simulations, we show that a helix undergoes shape transitions dominated by domain wall nucleation and motion in response to externally applied uniaxial tension. A scaling argument for the critical force is presented in good agreement with experimental and simulation results. Stretching rate-dependent elasticity including a buckling instability are found, also consistent with the experiment

Collective exchange processes reveal an active site proton cage in bacteriorhodopsin

Proton translocation across membranes is vital to all kingdoms of life. Mechanistically, it relies on characteristic proton flows and modifications of hydrogen bonding patterns, termed protonation dynamics, which can be directly observed by fast magic angle spinning (MAS) NMR. Here, we demonstrate that reversible proton displacement in the active site of bacteriorhodopsin already takes place in its equilibrated dark-state, providing new information on the underlying hydrogen exchange processes. In particular, MAS NMR reveals proton exchange at D85 and the retinal Schiff base, suggesting a tautomeric equilibrium and thus partial ionization of D85. We provide evidence for a proton cage and detect a preformed proton path between D85 and the proton shuttle R82. The protons at D96 and D85 exchange with water, in line with ab initio molecular dynamics simulations. We propose that retinal isomerization makes the observed proton exchange processes irreversible and delivers a proton towards the extracellular release site

Creation of ventricular septal defects on the beating heart in a new pig model

Background/ Aims: So far, surgical and interventional therapies for muscular ventricular septal defects ( mVSDs) beyond the moderator band have had their limitations. Thus, alternative therapeutic strategies should be developed. We present a new animal model for the evaluation of such strategies. Methods: In a pig model ( n = 9), anterolateral thoracotomy was performed for exposure of the left ventricle. mVSDs were created under two- and three- dimensional echocardiography with a 7.5- mm sharp punch instrument, which was forwarded via a left ventricular puncture without extracorporeal circulation. Results: Creation of mVSDs was successful in all animals ( n = 9) confirmed by echocardiography, hemodynamic measurements and autopsy. The defects were located in the midmuscular ( n = 4), apical ( n = 1), inlet ( n = 2) and anterior part ( n = 2) of the muscular septum. All animals were hemodynamically stable for further procedures. The diameter and shunt volume of the mVSDs were 4.8 - 7.3 mm ( mean: 5.9 mm) and 12.9 - 41.3% ( mean: 22.1%), respectively. Autopsy confirmed in all animals the creation of a substantial defect. Conclusion: The described new technique for creation of an mVSD on the beating heart in a pig model is suitable for the evaluation of new therapeutic strategies for mVSD closure. Copyright (C) 2008 S. Karger AG, Basel

The Selection of High-Skilled Emigrants

We measure selection among high-skilled emigrants from Germany using predicted earnings. Migrants to less equal countries are positively selected relative to nonmigrants, while migrants to more equal countries are negatively selected, consistent with the prediction in Borjas (1987). Positive selection to less equal countries reflects university quality and grades, and negative selection to more equal countries reflects university subject and gender. Migrants to the United States are highly positively selected and concentrated in STEM fields. Our results highlight the relevance of the Borjas model for high-skilled individuals when credit constraints and other migration barriers are unlikely to be binding

Barrier-crossing times for different non-Markovian friction in well and barrier: A numerical study

We introduce a generalized Langevin model system for different non-Markovian effects in the well and barrier regions of a potential, and use it to numerically study the barrier-crossing time. In the appropriate limits, our model interpolates between the theoretical barrier-crossing-time predictions by Grote and Hynes (GH), as well as by Pollak et al., which for a single barrier memory time can differ by several orders of magnitude. Our model furthermore allows one to test an analytic rate theory for space-inhomogeneous memory, which disagrees with our numerical results in the long well-memory regime. In this regime, we find that short barrier memory decreases the barrier-crossing time as compared to long barrier memory. This is in contrast with the short well-memory regime, where both our numerical results and the GH theory predict an acceleration of the barrier crossing time with increasing barrier memory time. Both effects, the “Markovian-barrier acceleration” and GH “non-Markovian-barrier acceleration,” can be understood from a committor analysis. Our model combines finite relaxation times of orthogonal degrees of freedom with a space-inhomogeneous coupling to such degrees and represents a step towards more realistic modeling of reaction coordinates

Pair-Reaction Dynamics in Water: Competition of Memory, Potential Shape, and Inertial Effects

When described by a one-dimensional reaction coordinate, pair-reaction rates in a solvent depend, in addition to the potential barrier height and the friction coefficient, on the potential shape, the effective mass, and the friction relaxation spectrum, but a rate theory that accurately accounts for all of these effects does not exist. After a review of classical reaction-rate theories, we show how to extract all parameters of the generalized Langevin equation (GLE) and, in particular, the friction memory function from molecular dynamics (MD) simulations of two prototypical pair reactions in water, the dissociation of NaCl and of two methane molecules. The memory exhibits multiple time scales and, for NaCl, pronounced oscillatory components. Simulations of the GLE by Markovian embedding techniques accurately reproduce the pair-reaction kinetics from MD simulations without any fitting parameters, which confirms the accuracy of the approximative form of the GLE and of the parameter extraction techniques. By modification of the GLE parameters, we investigate the relative importance of memory, mass, and potential shape effects. Neglect of memory slows down NaCl and methane dissociation by roughly a factor of 2; neglect of mass accelerates reactions by a similar factor, and the harmonic approximation of the potential shape gives rise to slight acceleration. This partial error cancellation explains why Kramers’ theory, which neglects memory effects and treats the potential shape in harmonic approximation, describes reaction rates better than more sophisticated theories. In essence, all three effects, friction memory, inertia, and the potential shape nonharmonicity, are important to quantitatively describe pair-reaction kinetics in water

Field theory fo charged fluids and colloids

A systematic field theory is presented for charged systems. The one-loop level corresponds to the classical Debye-H\"uckel (DH) theory, and exhibits the full hierarchy of multi-body correlations determined by pair-distribution functions given by the screened DH potential. Higher-loop corrections can lead to attractive pair interactions between colloids in asymmetric ionic environments. The free energy follows as a loop-wise expansion in half-integer powers of the density; the resulting two-phase demixing region shows pronounced deviations from DH theory for strongly charged colloids.Comment: 4 pages, 2 ps figs; new version corrects some minor typo

Lateral diffusion of a protein on a fluctuating membrane

Measurements of lateral diffusion of proteins in a membrane typically assume that the movement of the protein occurs in a flat plane. Real membranes, however, are subject to thermal fluctuations, leading to movement of an inclusion into the third dimension. We calculate the magnitude of this effect by projecting real three-dimensional diffusion onto an effective one on a flat plane. We consider both a protein that is free to diffuse in the membrane and one that also couples to the local curvature. For a freely diffusing inclusion the measured projected diffusion constant is up to 15% smaller than the actual value. Coupling to the curvature enhances diffusion significantly up to a factor of two.Comment: 6 pages, 4 figure

Butane dihedral angle dynamics in water is dominated by internal friction

The dihedral dynamics of butane in water is known to be rather insensitive to the water viscosity; possible explanations for this involve inertial effects or Kramers’ turnover, the finite memory time of friction, and the presence of so-called internal friction. To disentangle these factors, we introduce a method to directly extract the friction memory function from unconstrained simulations in the presence of an arbitrary free-energy landscape. By analysis of the dihedral friction in butane for varying water viscosity, we demonstrate the existence of an internal friction contribution that does not scale linearly with water viscosity. At normal water viscosity, the internal friction turns out to be eight times larger than the solvent friction and thus completely dominates the effective friction. By comparison with simulations of a constrained butane molecule that has the dihedral as the only degree of freedom, we show that internal friction comes from the six additional degrees of freedom in unconstrained butane that are orthogonal to the dihedral angle reaction coordinate. While the insensitivity of butane’s dihedral dynamics to water viscosity is solely due to the presence of internal friction, inertial effects nevertheless crucially influence the resultant transition rates. In contrast, non-Markovian effects due to the finite memory time are present but do not significantly influence the dihedral barrier-crossing rate of butane. These results not only settle the character of dihedral dynamics in small solvated molecular systems such as butane, they also have important implications for the folding of polymers and proteins

Reentrant Phase Transitions of the Blume-Emery-Griffiths Model for a Simple Cubic Lattice on the Cellular Automaton

The spin-1 Ising (BEG) model with the nearest-neighbour bilinear and biquadratic interactions and single-ion anisotropy is simulated on a cellular automaton which improved from the Creutz cellular automaton(CCA) for a simple cubic lattice. The simulations have been made for several sets of parameters $K/J$ and $D/J$ in the $-3<D/J\leq 0$ and $-1\leq K/J\leq 0$ parameter regions. The re-entrant and double re-entrant phase transitions of the BEG model are determined from the temperature variations of the thermodynamic quantities ($M$, $Q$ and $\chi$). The phase diagrams characterizing phase transitions are compared with those obtained from other methods.Comment: 12 pages 7 figure