Functionally relevant protein motions: extracting basin-specific collective coordinates from molecular dynamics trajectories

Functionally relevant motion of proteins has been associated with a number of atoms moving in a concerted fashion along so-called "collective coordinates." We present an approach to extract collective coordinates from conformations obtained from molecular dynamics simulations. The power of this technique for differentiating local structural fluctuations between classes of conformers obtained by clustering is illustrated by analyzing nanosecond-long trajectories for the response regulator protein Spo0F of Bacillus subtilis, generated both in vacuo and using an implicit-solvent representation. Conformational clustering is performed using automated histogram filtering of the inter-C(alpha) distances. Orthogonal (varimax) rotation of the vectors obtained by principal component analysis of these interresidue distances for the members of individual clusters is key to the interpretation of collective coordinates dominating each conformational class. The rotated loadings plots isolate significant variation in interresidue distances, and these are associated with entire mobile secondary structure elements. From this we infer concerted motions of these structural elements. For the Spo0F simulations employing an implicit-solvent representation, collective coordinates obtained in this fashion are consistent with the location of the protein's known active sites and experimentally determined mobile regions.     

Unbiased expectation values from diffusion quantum Monte Carlo simulations with a fixed number of walkers

We append forward walking to a diffusion Monte Carlo algorithm which maintains a fixed number of walkers. This removes the importance sampling bias of expectation values of operators which do not commute with the Hamiltonian. We demonstrate the effectiveness of this approach by employing three importance sampling functions for the hydrogen atom ground state, two very crude. We estimate moments of the electron-nuclear distance, static polarizabilities, and high-order hyperpolarizabilites up to the fourth power in the electric field, where no use is made of the finite field approximation. The results agree with the analytical values, with a statistical error which increases substantially with decreasing overlap of the guiding function with the exact wave function.     

Reduced local energy as a criterion for the accuracy of approximate H2 wave-functions

The goodness of the local fit of an approximate wave-function, \documentclass{article}\pagestyle{empty}\begin{document}$ \tilde \psi $\end{document}, to the exact function, ψ₀, is \documentclass{article}\pagestyle{empty}\begin{document}$ |\tilde \psi - \psi _0 | $\end{document}. From this quantity the global accuracy of \documentclass{article}\pagestyle{empty}\begin{document}$ \tilde \psi $\end{document} is defined and a “working supposition” is presented, which quantitatively relates the global accuracy to the accuracy of expectation values. Two criteria based on the accuracy of the reduced local energy and the density respectively, are presented as alternatives to \documentclass{article}\pagestyle{empty}\begin{document}$ |\tilde \psi - \psi _0 | $\end{document}. The relative global accuracies of eight wave-functions for H₂ are determined using the two criteria. The ‘working supposition’ is applied and predictions are made concerning the relative accuracies of the expectation values of the following operators: z², r², x² + y², 3z² ?; r², ξ, r, r, and E_L (the reduced local energy). The success rate is high (>90%) except for those operators which are sensitive to interelectron coordinates or derivatives of the wave-function.     

Robust Optimal Service Analysis of Single-Server Re-Entrant Queues

We generalize the analysis of J.A. Ball, M.V. Day, and P. Kachroo (Mathematics of Control, Signals, and Systems, vol. 12, pp. 307–345, 1999) to a fluid model of a single server re-entrant queue. The approach is to solve the Hamilton-Jacobi-Isaacs equation associated with optimal robust control of the system. The method of staged characteristics is generalized from Ball et al. (1999) to construct the solution explicitly. Formulas are developed allowing explicit calculations for the Skorokhod problem involved in the system equations. Such formulas are particularly important for numerical verification of conditions on the boundary of the nonnegative orthant. The optimal control (server) strategy is shown to be of linear-index type. Dai-type stability properties are discussed. A modification of the model in which new customers are allowed only at a specified entry queue is considered in 2 dimensions. The same optimal strategy is found in that case as well.     

Precision model independent determination of |Vub| from B --> pilnu

A precision method for determining |V(ub)| using the full range in q(2) of B --> pilnu data is presented. At large q(2) the form factor is taken from unquenched lattice QCD, at q(2) = 0 we impose a model independent constraint obtained from B --> pipi using the soft-collinear effective theory, and the shape is constrained using QCD dispersion relations. We find |V(ub)| = (3.54 +/- 0.170 +/- 0.44) x 10(-3). With 5% experimental error and 12% theory error, this is competitive with inclusive methods. Theory error is dominated by the input points, with negligible uncertainty from the dispersion relations.     

Method for extracting the quark mixing parameter cosalpha via B+/- -->pi(+/-)e(+)e(-)

We show that it is possible to extract the weak mixing angle alpha via a measurement of the rate for B+/--->pi(+/-)e(+)e(-). The sensitivity to cosalpha results from the interference between the long and short distance contributions. The short distance contribution is given in terms of semileptonic form factors. The long distance contribution can be calculated using Ward identities and a short distance operator product expansion if the invariant mass of the lepton pair, q(2), is larger than Lambda(2)(QCD). For q(2)>/=2 GeV2 the branching fraction is approximately 1x10(-8)|V(td)/0.008|(2). The shape of dgamma/dq(2) is very sensitive to the value of cosalpha at small values of q(2) and varies by 50% when -1相似文献   

The effect of pre-shear on the extensional rheology of wormlike micelle solutions

The effect of initial microstructural deformation, alignment, and morphology on the response of wormlike micelle solutions in transient uniaxial extensional flows is investigated using a pre-shear device attached to a filament stretching rheometer. In filament stretching experiments, increasing the strength and the duration of the pre-shear just before stretch is found to delay the onset of strain hardening. In these experiments, the wormlike micelle solution filaments fail through a rupture near the axial midplane. The value of the elastic tensile stress at rupture is found to decrease with increasing pre-shear rate and duration. The most dramatic effects are observed at shear rates for which shear banding has been independently observed. The reduction in the strain hardening suggests that pre-shear before filament stretching might break down the wormlike micelles reducing their size before stretch. Strain hardening is also observed in capillary breakup rheometry experiments; however, the pre-sheared wormlike micelle solutions strain harden faster, achieve larger steady-state extensional viscosities and an increase in the extensional relaxation time with increasing shear rate and duration. The difference between the response of the wormlike micelles in filament stretching and capillary breakup experiments demonstrates the sensitivity of these self-assembling micelle networks to pre-conditioning.