A model for hand-over-hand motion of molecular motors

A simple flashing ratchet model in two dimensions is proposed to simulate the hand-over-hand motion of two head molecular motors like kinesin. Extensive Langevin simulations of the model are performed. Good qualitative agreement with the expected behavior is observed. We discuss different regimes of motion and efficiency depending of model parameters.Comment: 8 pages, Phys. Rev. E (in press

Linear response of a grafted semiflexible polymer to a uniform force field

We use the worm-like chain model to analytically calculate the linear response of a grafted semiflexible polymer to a uniform force field. The result is a function of the bending stiffness, the temperature, the total contour length, and the orientation of the field with respect to that of the grafted end. We also study the linear response of a worm-like chain with a periodic alternating sequence of positive and negative charges. This can be considered as a model for a polyampholyte with intrinsic bending siffness and negligible intramolecular interactions. We show how the finite intrinsic persistence length affects the linear response to the external field.Comment: 6 pages, 3 figure

Buckling instability for a charged and fluctuating semiflexible polymer

In this article we address the problem of Euler's buckling instability in a charged semi-flexible polymer that is under the action of a compressive force. We consider this instability as a phase transition and investigate the role of thermal fluctuations in the buckling critical force. By performing molecular dynamic simulations, we show that the critical force decreases when the temperature increases. Repulsive electrostatic interaction in the finite temperature is in competition with thermal fluctuations to increase the buckling threshold

Sequence heterogeneity and the dynamics of molecular motors

The effect of sequence heterogeneity on the dynamics of molecular motors is reviewed and analyzed using a set of recently introduced lattice models. First, we review results for the influence of heterogenous tracks such as a single-strand of DNA or RNA on the dynamics of the motors. We stress how the predicted behavior might be observed experimentally in anomalous drift and diffusion of motors over a wide range of parameters near the stall force and discuss the extreme limit of strongly biased motors with one-way hopping. We then consider the dynamics in an environment containing a variety of different fuels which supply chemical energy for the motor motion, either on a heterogeneous or on a periodic track. The results for motion along a periodic track are relevant to kinesin motors in a solution with a mixture of different nucleotide triphosphate fuel sources.Comment: To appear in a JPhys special issue on molecular motor

Potential structural material problems in a hydrogen energy system

Potential structural material problems that may be encountered in the three components of a hydrogen energy system - production, transmission/storage, and utilization - were identified. Hydrogen embrittlement, corrosion, oxidation, and erosion may occur during the production of hydrogen. Hydrogen embrittlement is of major concern during both transmission and utilization of hydrogen. Specific materials research and development programs necessary to support a hydrogen energy system are described

An Empirically Derived Three-Dimensional Laplace Resonance in the Gliese 876 Planetary System

We report constraints on the three-dimensional orbital architecture for all four planets known to orbit the nearby M dwarf Gliese 876 based solely on Doppler measurements and demanding long-term orbital stability. Our dataset incorporates publicly available radial velocities taken with the ELODIE and CORALIE spectrographs, HARPS, and Keck HIRES as well as previously unpublished HIRES velocities. We first quantitatively assess the validity of the planets thought to orbit GJ 876 by computing the Bayes factors for a variety of different coplanar models using an importance sampling algorithm. We find that a four-planet model is preferred over a three-planet model. Next, we apply a Newtonian MCMC algorithm to perform a Bayesian analysis of the planet masses and orbits using an n-body model in three-dimensional space. Based on the radial velocities alone, we find that a 99% credible interval provides upper limits on the mutual inclinations for the three resonant planets ($\Phi_{cb}<6.20^\circ$ for the "c" and "b" pair and $\Phi_{be}<28.5^\circ$ for the "b" and "e" pair). Subsequent dynamical integrations of our posterior sample find that the GJ 876 planets must be roughly coplanar ($\Phi_{cb}<2.60^\circ$ and $\Phi_{be}<7.87^\circ$), suggesting the amount of planet-planet scattering in the system has been low. We investigate the distribution of the respective resonant arguments of each planet pair and find that at least one argument for each planet pair and the Laplace argument librate. The libration amplitudes in our three-dimensional orbital model supports the idea of the outer-three planets having undergone significant past disk migration.Comment: 19 pages, 11 figures, 8 tables. Accepted to MNRAS. Posterior samples available at https://github.com/benelson/GJ87

"If chemists don’t do it, who is going to?" Peer-driven occupational change and the emergence of green chemistry

Occupational membership guides what people do, how they think of themselves, and how they interact in organizations and with society. While a rich literature explains how occupations adapt in response to external triggers for change, we have limited insight into how occupational incumbents, absent external triggers, work to influence how their peers do their work. We investigate the emergence and growth of “green chemistry,” an effort by chemists to encourage other chemists to reduce the health, safety, and environmental impacts of chemical products and processes. We find that advocates simultaneously advanced normalizing, moralizing, and pragmatizing frames for green chemistry and that each frame resonated differently with chemists in their various occupational roles. While this pluralistic approach generated broad acceptance of the change effort, it also exposed tensions, which threatened the coherence of the change. Divergent responses of advocates to these tensions contribute to a persistent state of pluralism and dynamism in the change effort. We discuss implications for theory on occupational change arising from our attention to internally-generated peer-driven change, heterogeneity within occupations, and change efforts that moralize occupational work.Meyer Fund for Sustainability grant (University of Oregon

The 55 Cancri Planetary System: Fully Self-Consistent N-body Constraints and a Dynamical Analysis

We present an updated study of the planets known to orbit 55 Cancri A using 1,418 high-precision radial velocity observations from four observatories (Lick, Keck, Hobby-Eberly Telescope, Harlan J. Smith Telescope) and transit time/durations for the inner-most planet, 55 Cancri "e" (Winn et al. 2011). We provide the first posterior sample for the masses and orbital parameters based on self-consistent n-body orbital solutions for the 55 Cancri planets, all of which are dynamically stable (for at least $10^8$ years). We apply a GPU version of Radial velocity Using N-body Differential evolution Markov Chain Monte Carlo (RUN DMC; B. Nelson et al. 2014) to perform a Bayesian analysis of the radial velocity and transit observations. Each of the planets in this remarkable system has unique characteristics. Our investigation of high-cadence radial velocities and priors based on space-based photometry yields an updated mass estimate for planet "e" ($8.09\pm0.26$ M$_\oplus$), which affects its density ($5.51\pm^{1.32}_{1.00}$ g cm$^{-3}$) and inferred bulk composition. Dynamical stability dictates that the orbital plane of planet "e" must be aligned to within $60^o$ of the orbital plane of the outer planets (which we assume to be coplanar). The mutual interactions between the planets "b" and "c" may develop an apsidal lock about $180^o$. We find 36-45% of all our model systems librate about the anti-aligned configuration with an amplitude of $51^o\pm^{6^o}_{10^o}$. Other cases showed short-term perturbations in the libration of $\varpi_b-\varpi_c$, circulation, and nodding, but we find the planets are not in a 3:1 mean-motion resonance. A revised orbital period and eccentricity for planet "d" pushes it further toward the closest known Jupiter analog in the exoplanet population.Comment: 12 pages, 5 figures, 4 tables, accepted to MNRAS. Figure 2 (left) is updated from published version. Posterior samples available at http://www.personal.psu.edu/ben125/Downloads.htm