Rigorous results on the local equilibrium kinetics of a protein folding model

A local equilibrium approach for the kinetics of a simplified protein folding model, whose equilibrium thermodynamics is exactly solvable, was developed in [M. Zamparo and A. Pelizzola, Phys. Rev. Lett. 97, 068106 (2006)]. Important properties of this approach are (i) the free energy decreases with time, (ii) the exact equilibrium is recovered in the infinite time limit, (iii) the equilibration rate is an upper bound of the exact one and (iv) computational complexity is polynomial in the number of variables. Moreover, (v) this method is equivalent to another approximate approach to the kinetics: the path probability method. In this paper we give detailed rigorous proofs for the above results.Comment: 25 pages, RevTeX 4, to be published in JSTA

Theory of temperature dependence of the Fermi surface-induced splitting of the alloy diffuse-scattering intensity peak

The explanation is presented for the temperature dependence of the fourfold intensity peak splitting found recently in diffuse scattering from the disordered Cu3Au alloy. The wavevector and temperature dependence of the self-energy is identified as the origin of the observed behaviour. Two approaches for the calculation of the self-energy, the high-temperature expansion and the alpha-expansion, are proposed. Applied to the Cu3Au alloy, both methods predict the increase of the splitting with temperature, in agreement with the experimental results.Comment: 4 pages, 3 EPS figures, RevTeX, submitted to J. Phys. Condens. Matter (Letter to the Editor

Deficient calcium, zinc, and iron intake on absorption of cadmium from diet

Background/Aim: In vitro and in vivo studies have demonstrated that deficient calcium, zinc, and iron dietary intake upregulates metal ion transporters to increase intestinal absorption. However, these gut transporters are not specific and bind to other metals, including cadmium. Few human studies have investigated whether deficient calcium, zinc, and iron intake increases intestinal absorption of dietary cadmium. Methods: We used enrollment data (2010-2012) from the Study of Environment, Lifestyle & Fibroids, a cohort of 1693 African American women ages 23-35 who reside in the Detroit, Michigan area. Whole blood cadmium concentrations (proxy for cadmium absorption) were measured in 1548 participants. Dietary and supplemental calcium, zinc, and iron intake was estimated using Block 2005 Food Frequency Questionnaire data; deficient intake was defined as <80% of the recommended daily allowance. Daily dietary intake of total grains was used as the proxy for dietary cadmium intake as grains are a major source of cadmium exposure in U.S. diet. We estimated the percent difference in blood cadmium concentrations per median daily intake of total grains (4.55 ounce equivalents) using multivariable linear regression, stratified by deficient and sufficient calcium, zinc, and/or iron intake. We restricted the analyses to never smokers with plausible values for total energy intake (>400 and <5000 kcal/day) (n=1087). We adjusted for age at enrollment, total energy intake, body mass index, height, education, and natural log-transformed blood lead concentrations. Results: The observed percent difference in blood cadmium concentrations in relation to intake of total grains was stronger among those with deficient intake of calcium, zinc, and/or iron (28%, 95% CI; 6, 53%) than among those with sufficient intake of all 3 essential nutrients (5%, 95% CI: -7, 19%). Conclusions: Our preliminary findings suggest that women with deficient calcium, zinc, and/or iron intake have increased absorption of cadmium from the diet

Kinetostatics of Wheel Vehicle in the Category of Spiral-Screw Routes

International audienceDeterministic mathematical model of kinetostatics of wheel vehicle in terms of different modes of spatial motion in the context of curved route is proposed. Earth-based coordinate system is introduced which pole and axial orientation are determined by the convenience of route description as well as vehicle-related coordinates which pole axial orientation are determined within inertial space with the help of natural trihedral. Turn of the natural trihedral within inertial coordinates is described by means of quaternion matrices in the context of Rodrigues-Hamilton parameters. Rodrigues-Hamilton parameters are in matrix form in direct accordance with specified hodograph. Kinetostatics of wheel vehicle is considered in terms of spatial motion with an allowance for three-dimensional aerodynamic forces, gravity, and tangential and centrifugal inertial forces. In the context of spiral-screw lines deterministic mathematical model of wheel vehicle kinetostatics is proposed in the form of hodograph in terms of uniform motion, accelerated motion, and decelerated motion within following route sections: straight and horizontal; in terms of vertical grade; in terms of horizontal plane. Analytical approach to determine animated contact drive-control forces of wheel vehicle for structural diagrams having one and two support points involving of a driving-driven wheel characteristic is proposed based on kinetostatics equations. Mathematical model of wheel vehicle kinetostatics in terms of spatial motion is constructed on the basis of nonlinear differential Euler-Lagrange equations; it is proposed to consider physically implemented motion trajectories of wheel vehicles in the context of spiral-screw lines; hodograph determines spatial displacement; Rodrigues-Hamilton parameters determines spatial turn; Varignon theorem is applied to identify components of drive (control) force. The obtained results make it possible to solve a wide range of problems connected with dynamic design of wheel vehicles involving controllability, and estimation of dynamic load of both system and support surface

Interaction of Saturn's magnetosphere and its moons: 2. Shape of the Enceladus plume

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95207/1/jgra20314.pd

Influence of the radio frequency ponderomotive force on anomalous impurity transport in tokamaks

Trace impurity transport in tokamaks is studied using an electrostatic, collisionless fluid model for ion-temperature-gradient and trapped-electron mode driven turbulence in the presence of radio frequency (rf) fields, and the results are compared with neoclassical predictions. It is shown that the inward impurity convective velocity (pinch) that is usually obtained can be reduced by the rf fields, in particular close to the wave resonance location where the rf ponderomotive force may be significant. However, the impurity diffusivity and convective velocity are usually similarly affected by the ponderomotive force, and hence the steady-state impurity density peaking factor -∇nz/nz is only moderately affected by the rf fields

Electron-acoustic plasma waves: oblique modulation and envelope solitons

Theoretical and numerical studies are presented of the amplitude modulation of electron-acoustic waves (EAWs) propagating in space plasmas whose constituents are inertial cold electrons, Boltzmann distributed hot electrons and stationary ions. Perturbations oblique to the carrier EAW propagation direction have been considered. The stability analysis, based on a nonlinear Schroedinger equation (NLSE), reveals that the EAW may become unstable; the stability criteria depend on the angle $\theta$ between the modulation and propagation directions. Different types of localized EA excitations are shown to exist.Comment: 10 pages, 5 figures; to appear in Phys. Rev.

An Introductory Guide to Aligning Networks Using SANA, the Simulated Annealing Network Aligner.

Sequence alignment has had an enormous impact on our understanding of biology, evolution, and disease. The alignment of biological networks holds similar promise. Biological networks generally model interactions between biomolecules such as proteins, genes, metabolites, or mRNAs. There is strong evidence that the network topology-the "structure" of the network-is correlated with the functions performed, so that network topology can be used to help predict or understand function. However, unlike sequence comparison and alignment-which is an essentially solved problem-network comparison and alignment is an NP-complete problem for which heuristic algorithms must be used.Here we introduce SANA, the Simulated Annealing Network Aligner. SANA is one of many algorithms proposed for the arena of biological network alignment. In the context of global network alignment, SANA stands out for its speed, memory efficiency, ease-of-use, and flexibility in the arena of producing alignments between two or more networks. SANA produces better alignments in minutes on a laptop than most other algorithms can produce in hours or days of CPU time on large server-class machines. We walk the user through how to use SANA for several types of biomolecular networks