Excluded-Volume Effects in Tethered-Particle Experiments: Bead Size Matters

The tethered-particle method is a single-molecule technique that has been used to explore the dynamics of a variety of macromolecules of biological interest. We give a theoretical analysis of the particle motions in such experiments. Our analysis reveals that the proximity of the tethered bead to a nearby surface (the microscope slide) gives rise to a volume-exclusion effect, resulting in an entropic force on the molecule. This force stretches the molecule, changing its statistical properties. In particular, the proximity of bead and surface brings about intriguing scaling relations between key observables (statistical moments of the bead) and parameters such as the bead size and contour length of the molecule. We present both approximate analytic solutions and numerical results for these effects in both flexible and semiflexible tethers. Finally, our results give a precise, experimentally-testable prediction for the probability distribution of the distance between the polymer attachment point and the center of the mobile bead.Comment: 4 pages, 3 figure

Coherent Control for a Two-level System Coupled to Phonons

The interband polarizations induced by two phase-locked pulses in a semiconductor show strong interference effects depending on the time tau_1 separating the pulses. The four-wave mixing signal diffracted from a third pulse delayed by tau is coherently controlled by tuning tau_1. The four-wave mixing response is evaluated exactly for a two-level system coupled to a single LO phonon. In the weak coupling regime it shows oscillations with the phonon frequency which turn into sharp peaks at multiples of the phonon period for a larger coupling strength. Destructive interferences between the two phase-locked pulses produce a splitting of the phonon peaks into a doublet. For fixed tau but varying tau_1 the signal shows rapid oscillations at the interband-transition frequency, whose amplitude exhibits bursts at multiples of the phonon period.Comment: 4 pages, 4 figures, RevTex, content change

Effects of thermal fluctuation and the receptor-receptor interaction in bacterial chemotactic signalling and adaptation

Bacterial chemotaxis is controlled by the conformational changes of the receptors, in response to the change of the ambient chemical concentration. In a statistical mechanical approach, the signalling due to the conformational changes is a thermodynamic average quantity, dependent on the temperature and the total energy of the system, including both ligand-receptor interaction and receptor-receptor interaction. This physical theory suggests to biology a new understanding of cooperation in ligand binding and receptor signalling problems. How much experimental support of this approach can be obtained from the currently available data? What are the parameter values? What is the practical information for experiments? Here we make comparisons between the theory and recent experimental results. Although currently comparisons can only be semi-quantitative or qualitative, consistency is clearly shown. The theory also helps to sort a variety of data.Comment: 26 pages, revtex. Journal version. Analysis on another set of data on adaptation time is adde

From sensorimotor dependencies to perceptual practices: making enactivism social

Proponents of enactivism should be interested in exploring what notion of action best captures the type of action-perception link that the view proposes, such that it covers all the aspects in which our doings constitute and are constituted by our perceiving. This article proposes and defends the thesis that the notion of sensorimotor dependencies is insufficient to account for the reality of human perception, and that the central enactive notion should be that of perceptual practices. Sensorimotor enactivism is insufficient because it has no traction on socially dependent perceptions, which are essential to the role and significance of perception in our lives. Since the social dimension is a central desideratum in a theory of human perception, enactivism needs a notion that accounts for such an aspect. This article sketches the main features of the Wittgenstein-inspired notion of perceptual practices as the central notion to understand perception. Perception, I claim, is properly understood as woven into a type of social practices that includes food, dance, dress, music, etc. More specifically, perceptual practices are the enactment of culturally structured, normatively rich techniques of commerce of meaningful multi- and inter-modal perceptible material. I argue that perceptual practices explain three central features of socially dependent perception: attentional focus, aspects’ saliency, and modal-specific harmony-like relations

Impact of time-ordered measurements of the two states in a niobium superconducting qubit structure

Measurements of thermal activation are made in a superconducting, niobium Persistent-Current (PC) qubit structure, which has two stable classical states of equal and opposite circulating current. The magnetization signal is read out by ramping the bias current of a DC SQUID. This ramping causes time-ordered measurements of the two states, where measurement of one state occurs before the other. This time-ordering results in an effective measurement time, which can be used to probe the thermal activation rate between the two states. Fitting the magnetization signal as a function of temperature and ramp time allows one to estimate a quality factor of 10^6 for our devices, a value favorable for the observation of long quantum coherence times at lower temperatures.Comment: 14 pages, 4 figure

Increased accuracy of ligand sensing by receptor internalization

Many types of cells can sense external ligand concentrations with cell-surface receptors at extremely high accuracy. Interestingly, ligand-bound receptors are often internalized, a process also known as receptor-mediated endocytosis. While internalization is involved in a vast number of important functions for the life of a cell, it was recently also suggested to increase the accuracy of sensing ligand as the overcounting of the same ligand molecules is reduced. Here we show, by extending simple ligand-receptor models to out-of-equilibrium thermodynamics, that internalization increases the accuracy with which cells can measure ligand concentrations in the external environment. Comparison with experimental rates of real receptors demonstrates that our model has indeed biological significance.Comment: 9 pages, 4 figures, accepted for publication in Physical Review

Diffraction in low-energy electron scattering from DNA: bridging gas phase and solid state theory

Using high-quality gas phase electron scattering calculations and multiple scattering theory, we attempt to gain insights on the radiation damage to DNA induced by secondary low-energy electrons in the condensed phase, and to bridge the existing gap with the gas phase theory and experiments. The origin of different resonant features (arising from single molecules or diffraction) is discussed and the calculations are compared to existing experiments in thin films.Comment: 40 pages preprint, 12 figures, submitted to J. Chem. Phy

Optimal transport on wireless networks

We present a study of the application of a variant of a recently introduced heuristic algorithm for the optimization of transport routes on complex networks to the problem of finding the optimal routes of communication between nodes on wireless networks. Our algorithm iteratively balances network traffic by minimizing the maximum node betweenness on the network. The variant we consider specifically accounts for the broadcast restrictions imposed by wireless communication by using a different betweenness measure. We compare the performance of our algorithm to two other known algorithms and find that our algorithm achieves the highest transport capacity both for minimum node degree geometric networks, which are directed geometric networks that model wireless communication networks, and for configuration model networks that are uncorrelated scale-free networks.Comment: 5 pages, 4 figure

Electronic structure of superconducting graphite intercalate compounds: The role of the interlayer state

Although not an intrinsic superconductor, it has been long--known that, when intercalated with certain dopants, graphite is capable of exhibiting superconductivity. Of the family of graphite--based materials which are known to superconduct, perhaps the most well--studied are the alkali metal--graphite intercalation compounds (GIC) and, of these, the most easily fabricated is the C${}_8$K system which exhibits a transition temperature $\bm{T_c\simeq 0.14}$K. By increasing the alkali metal concentration (through high pressure fabrication techniques), the transition temperature has been shown to increase to as much as $\bm 5$K in C${}_2$Na. Lately, in an important recent development, Weller \emph{et al.} have shown that, at ambient conditions, the intercalated compounds \cyb and \cca exhibit superconductivity with transition temperatures $\bm{T_c\simeq 6.5}$K and $\bm{11.5}$K respectively, in excess of that presently reported for other graphite--based compounds. We explore the architecture of the states near the Fermi level and identify characteristics of the electronic band structure generic to GICs. As expected, we find that charge transfer from the intercalant atoms to the graphene sheets results in the occupation of the $\bm\pi$--bands. Yet, remarkably, in all those -- and only those -- compounds that superconduct, we find that an interlayer state, which is well separated from the carbon sheets, also becomes occupied. We show that the energy of the interlayer band is controlled by a combination of its occupancy and the separation between the carbon layers.Comment: 4 Figures. Please see accompanying experimental manuscript "Superconductivity in the Intercalated Graphite Compounds C6Yb and C6Ca" by Weller et a

First principles study of the origin and nature of ferromagnetism in (Ga,Mn)As

The properties of diluted Ga$_{1-x}$Mn$_x$As are calculated for a wide range of Mn concentrations within the local spin density approximation of density functional theory. M\"ulliken population analyses and orbital-resolved densities of states show that the configuration of Mn in GaAs is compatible with either 3d$^5$ or 3d$^6$, however the occupation is not integer due to the large $p$-$d$ hybridization between the Mn $d$ states and the valence band of GaAs. The spin splitting of the conduction band of GaAs has a mean field-like linear variation with the Mn concentration and indicates ferromagnetic coupling with the Mn ions. In contrast the valence band is antiferromagnetically coupled with the Mn impurities and the spin splitting is not linearly dependent on the Mn concentration. This suggests that the mean field approximation breaks down in the case of Mn-doped GaAs and corrections due to multiple scattering must be considered. We calculate these corrections within a simple free electron model and find good agreement with our {\it ab initio} results if a large exchange constant ($N\beta=-4.5$eV) is assumed.Comment: 15 pages, 14 figure