Reducing model uncertainty effects in flexible manipulators through the addition of passive damping

An important issue in the control of practical systems is the effect of model uncertainty on closed loop performance. This is of particular concern when flexible structures are to be controlled, due to the fact that states associated with higher frequency vibration modes are truncated in order to make the control problem tractable. Digital simulations of a single-link manipulator system are employed to demonstrate that passive damping added to the flexible member reduces adverse effects associated with model uncertainty. A controller was designed based on a model including only one flexible mode. This controller was applied to larger order systems to evaluate the effects of modal truncation. Simulations using a Linear Quadratic Regulator (LQR) design assuming full state feedback illustrate the effect of control spillover. Simulations of a system using output feedback illustrate the destabilizing effect of observation spillover. The simulations reveal that the system with passive damping is less susceptible to these effects than the untreated case

Unifying model of driven polymer translocation

We present a Brownian dynamics model of driven polymer translocation, in which non-equilibrium memory effects arising from tension propagation (TP) along the cis side subchain are incorporated as a time-dependent friction. To solve the effective friction, we develop a finite chain length TP formalism, expanding on the work of Sakaue [Sakaue, PRE 76, 021803 (2007)]. The model, solved numerically, yields results in excellent agreement with molecular dynamics simulations in a wide range of parameters. Our results show that non-equilibrium TP along the cis side subchain dominates the dynamics of driven translocation. In addition, the model explains the different scaling of translocation time w.r.t chain length observed both in experiments and simulations as a combined effect of finite chain length and pore-polymer interactions.Comment: 7 pages, 3 figure

Model for the unidirectional motion of a dynein molecule

Cytoplasmic dyneins transport cellular organelles by moving on a microtubule filament. It has been found recently that depending on the applied force and the concentration of the adenosine triphosphate (ATP) molecules, dynein's step size varies. Based on these studies, we propose a simple model for dynein's unidirectional motion taking into account the variations in its step size. We study how the average velocity and the relative dispersion in the displacement vary with the applied load. The model is amenable to further extensions by inclusion of details associated with the structure and the processivity of the molecule.Comment: 10 pages, 5 figure

Lateral phase separation of confined membranes

We consider membranes interacting via short, intermediate and long stickers. The effects of the intermediate stickers on the lateral phase separation of the membranes are studied via mean-field approximation. The critical potential depth of the stickers increases in the presence of the intermediate sticker. The lateral phase separation of the membrane thus suppressed by the intermediate stickers. Considering membranes interacting with short and long stickers, the effect of confinement on the phase behavior of the membranes is also investigated analytically

Time scale of entropic segregation of flexible polymers in confinement: Implications for chromosome segregation in filamentous bacteria

We report molecular dynamics simulations of the segregation of two overlapping chains in cylindrical confinement. We find that the entropic repulsion between the chains can be sufficiently strong to cause segregation on a time scale that is short compared to the one for diffusion. This result implies that entropic driving forces are sufficiently strong to cause rapid bacterial chromosome segregation.Comment: Minor changes. Added some references, corrected the labels in figure 6 and reformatted in two columns. Also added reference to published version in PR

Fluctuation-Driven Molecular Transport in an Asymmetric Membrane Channel

Channel proteins, that selectively conduct molecules across cell membranes, often exhibit an asymmetric structure. By means of a stochastic model, we argue that channel asymmetry in the presence of non-equilibrium fluctuations, fueled by the cell's metabolism as observed recently, can dramatically influence the transport through such channels by a ratchet-like mechanism. For an aquaglyceroporin that conducts water and glycerol we show that a previously determined asymmetric glycerol potential leads to enhanced inward transport of glycerol, but for unfavorably high glycerol concentrations also to enhanced outward transport that protects a cell against poisoning.Comment: REVTeX4, 4 pages, 3 figures; Accepted for publication in Phys. Rev. Let

Nematic and Polar order in Active Filament Solutions

Using a microscopic model of interacting polar biofilaments and motor proteins, we characterize the phase diagram of both homogeneous and inhomogeneous states in terms of experimental parameters. The polarity of motor clusters is key in determining the organization of the filaments in homogeneous isotropic, polarized and nematic states, while motor-induced bundling yields spatially inhomogeneous structures.Comment: 4 pages. 3 figure

The Spectral Energy Distribution and Infrared Luminosities of z ≈ 2 Dust-obscured Galaxies from Herschel and Spitzer

Dust-obscured galaxies (DOGs) are a subset of high-redshift (z ≈ 2) optically-faint ultra-luminous infrared galaxies (ULIRGs, e.g., L_(IR) > 10^(12) L_☉). We present new far-infrared photometry, at 250, 350, and 500 μm (observed-frame), from the Herschel Space Telescope for a large sample of 113 DOGs with spectroscopically measured redshifts. Approximately 60% of the sample are detected in the far-IR. The Herschel photometry allows the first robust determinations of the total infrared luminosities of a large sample of DOGs, confirming their high IR luminosities, which range from 10^(11.6) L_☉ 10^(13) L_☉. The rest-frame near-IR (1-3 μm) spectral energy distributions (SEDs) of the Herschel-detected DOGs are predictors of their SEDs at longer wavelengths. DOGs with "power-law" SEDs in the rest-frame near-IR show observed-frame 250/24 μm flux density ratios similar to the QSO-like local ULIRG, Mrk 231. DOGs with a stellar "bump" in their rest-frame near-IR show observed-frame 250/24 μm flux density ratios similar to local star-bursting ULIRGs like NGC 6240. None show 250/24 μm flux density ratios similar to extreme local ULIRG, Arp 220; though three show 350/24 μm flux density ratios similar to Arp 220. For the Herschel-detected DOGs, accurate estimates (within ~25%) of total IR luminosity can be predicted from their rest-frame mid-IR data alone (e.g., from Spitzer observed-frame 24 μm luminosities). Herschel-detected DOGs tend to have a high ratio of infrared luminosity to rest-frame 8 μm luminosity (the IR8 = L_(IR)(8-1000 μm)/νL_ν(8 μm) parameter of Elbaz et al.). Instead of lying on the z = 1-2 "infrared main sequence" of star-forming galaxies (like typical LIRGs and ULIRGs at those epochs) the DOGs, especially large fractions of the bump sources, tend to lie in the starburst sequence. While, Herschel-detected DOGs are similar to scaled up versions of local ULIRGs in terms of 250/24 μm flux density ratio, and IR8, they tend to have cooler far-IR dust temperatures (20-40 K for DOGs versus 40-50 K for local ULIRGs) as measured by the rest-frame 80/115 μm flux density ratios (e.g., observed-frame 250/350 μm ratios at z = 2). DOGs that are not detected by Herschel appear to have lower observed-frame 250/24 μm ratios than the detected sample, either because of warmer dust temperatures, lower IR luminosities, or both

Stability of Localized Wave Fronts in Bistable Systems

Localized wave fronts are a fundamental feature of biological systems from cell biology to ecology. Here, we study a broad class of bistable models subject to self-activation, degradation, and spatially inhomogeneous activating agents. We determine the conditions under which wave-front localization is possible and analyze the stability thereof with respect to extrinsic perturbations and internal noise. It is found that stability is enhanced upon regulating a positional signal and, surprisingly, also for a low degree of binding cooperativity. We further show a contrasting impact of self-activation to the stability of these two sources of destabilization. DOI: 10.1103/PhysRevLett.110.03810

Particle Dispersion on Rapidly Folding Random Hetero-Polymers

We investigate the dynamics of a particle moving randomly along a disordered hetero-polymer subjected to rapid conformational changes which induce superdiffusive motion in chemical coordinates. We study the antagonistic interplay between the enhanced diffusion and the quenched disorder. The dispersion speed exhibits universal behavior independent of the folding statistics. On the other hand it is strongly affected by the structure of the disordered potential. The results may serve as a reference point for a number of translocation phenomena observed in biological cells, such as protein dynamics on DNA strands.Comment: 4 pages, 4 figure