Proton network flexibility enables robustness and large electric fields in the ketosteroid isomerase active site

Hydrogen bond networks play vital roles in biological functions ranging from protein folding to enzyme catalysis. Here we combine electronic structure calculations and ab initio path integral molecular dynamics simulations, which incorporate both nuclear and electronic quantum effects, to show why the network of short hydrogen bonds in the active site of ketosteroid isomerase is remarkably robust to mutations along the network and how this gives rise to large local electric fields. We demonstrate that these properties arise from the network's ability to respond to a perturbation by shifting proton positions and redistributing electronic charge density. This flexibility leads to small changes in properties such as the partial ionization of residues and $pK_a$ isotope effects upon mutation of the residues, consistent with recent experiments. This proton flexibility is further enhanced when an extended hydrogen bond network forms in the presence of an intermediate analog, which allows us to explain the chemical origins of the large electric fields in the enzyme's active site observed in recent experiments.Comment: 13 pages, 10 figures (7 main text and 3 SI

Pure sea-quark contributions to the magnetic form factors of Σ\Sigma baryons

We propose the pure sea-quark contributions to the magnetic form factors of $\Sigma$ baryons, $G_{\Sigma^-}^u$ and $G_{\Sigma^+}^d$, as priority observables for the examination of sea-quark contributions to baryon structure, both in present lattice QCD simulations and possible future experimental measurement. $G_{\Sigma^-}^u$, the $u$-quark contribution to the magnetic form factor of $\Sigma^-$, and $G_{\Sigma^+}^d$, the $d$-quark contribution to the magnetic form factor of $\Sigma^+$, are similar to the strange quark contribution to the magnetic form factor of the nucleon, but promise to be larger by an order of magnitude. We explore the size of this quantity within chiral effective field theory, including both octet and decuplet intermediate states. The finite range regularization approach is applied to deal with ultraviolet divergences. Drawing on an established connection between quenched and full QCD, this approach makes it possible to predict the sea quark contribution to the magnetic form factor purely from the meson loop. In the familiar convention where the quark charge is set to unity $G_{\Sigma^-}^u = G_{\Sigma^+}^d$. We find a value of $-0.38^{+0.16}_{-0.17}\ \mu_N$, which is about seven times larger than the strange magnetic moment of the nucleon found in the same approach. Including quark charge factors, the $u$-quark contribution to the $\Sigma^-$ magnetic moment exceeds the strange quark contribution to the nucleon magnetic moment by a factor of 14.Comment: 5 pages, 3 figures. arXiv admin note: text overlap with arXiv:1312.337

Electromagnetic contribution to charge symmetry violation in parton distributions

We report a calculation of the combined effect of photon radiation and quark mass differences on charge symmetry violation (CSV) in the parton distribution functions of the nucleon. Following a recent suggestion of Martin and Ryskin, the initial photon distribution is calculated in terms of coherent radiation from the proton as a whole, while the effect of the quark mass difference is based on a recent lattice QCD simulation. The distributions are then evolved to a scale at which they can be compared with experiment by including both QCD and QED radiation. Overall, at a scale of 5 GeV$^2$, the total CSV effect on the phenomenologically important difference between the $d$ and $u$-quark distributions is some 20\% larger than the value based on quark mass differences alone. In total these sources of CSV account for approximately 40\% of the NuTeV anomaly.Comment: 5 pages, 2 figure

The free energy of biomembrane and nerve excitation and the role of anesthetics

In the electromechanical theory of nerve stimulation, the nerve impulse consists of a traveling region of solid membrane in a liquid environment. Therefore, the free energy necessary to stimulate a pulse is directly related to the free energy difference necessary to induce a phase transition in the nerve membrane. It is a function of temperature and pressure, and it is sensitively dependent on the presence of anesthetics which lower melting transitions. We investigate the free energy difference of solid and liquid membrane phases under the influence of anesthetics. We calculate stimulus-response curves of electromechanical pulses and compare them to measured stimulus-response profiles in lobster and earthworm axons. We also compare them to stimulus-response experiments on human median nerve and frog sciatic nerve published in the literature.Comment: 10 pages, 6 figure

Liquid-gas phase transition in nuclear matter including strangeness

We apply the chiral SU(3) quark mean field model to study the properties of strange hadronic matter at finite temperature. The liquid-gas phase transition is studied as a function of the strangeness fraction. The pressure of the system cannot remain constant during the phase transition, since there are two independent conserved charges (baryon and strangeness number). In a range of temperatures around 15 MeV (precise values depending on the model used) the equation of state exhibits multiple bifurcates. The difference in the strangeness fraction $f_s$ between the liquid and gas phases is small when they coexist. The critical temperature of strange matter turns out to be a non-trivial function of the strangeness fraction.Comment: 15 pages, 7 figure

Chiral extrapolation of nucleon magnetic form factors

The extrapolation of nucleon magnetic form factors calculated within lattice QCD is investigated within a framework based upon heavy baryon chiral effective-field theory. All one-loop graphs are considered at arbitrary momentum transfer and all octet and decuplet baryons are included in the intermediate states. Finite range regularisation is applied to improve the convergence in the quark-mass expansion. At each value of the momentum transfer ($Q^2$), a separate extrapolation to the physical pion mass is carried out as a function of $m_\pi$ alone. Because of the large values of $Q^2$ involved, the role of the pion form factor in the standard pion-loop integrals is also investigated. The resulting values of the form factors at the physical pion mass are compared with experimental data as a function of $Q^2$ and demonstrate the utility and accuracy of the chiral extrapolation methods presented herein.Comment: 19 pages, 10 figure

Neutron stars and strange stars in the chiral SU(3) quark mean field model

We investigate the equations of state for pure neutron matter and strange hadronic matter in $\beta$-equilibrium, including $\Lambda$, $\Sigma$ and $\Xi$ hyperons. The masses and radii of pure neutron stars and strange hadronic stars are obtained. For a pure neutron star, the maximum mass is about $1.8 M_{\mathrm{sun}}$, while for a strange hadronic star, the maximum mass is around $1.45 M_{\mathrm{sun}}$. The typical radii of pure neutron stars and strange hadronic stars are about 11.0-12.3 km and 10.7-11.7 km, respectively.Comment: 18 pages, 7 figure