Calibration of Tethered Particle Motion Experiments

The Tethered Particle Motion (TPM) method has been used to observe and characterize a variety of protein-DNA interactions including DNA loping and transcription. TPM experiments exploit the Brownian motion of a DNA-tethered bead to probe biologically relevant conformational changes of the tether. In these experiments, a change in the extent of the bead’s random motion is used as a reporter of the underlying macromolecular dynamics and is often deemed sufficient for TPM analysis. However, a complete understanding of how the motion depends on the physical properties of the tethered particle complex would permit more quantitative and accurate evaluation of TPM data. For instance, such understanding can help extract details about a looped complex geometry (or multiple coexisting geometries) from TPM data. To better characterize the measurement capabilities of TPM experiments involving DNA tethers, we have carried out a detailed calibration of TPM magnitude as a function of DNA length and particle size. We also explore how experimental parameters such as acquisition time and exposure time affect the apparent motion of the tethered particle. We vary the DNA length from 200 bp to 2.6 kbp and consider particle diameters of 200, 490 and 970 nm. We also present a systematic comparison between measured particle excursions and theoretical expectations, which helps clarify both the experiments and models of DNA conformation

Possible origins of macroscopic left-right asymmetry in organisms

I consider the microscopic mechanisms by which a particular left-right (L/R) asymmetry is generated at the organism level from the microscopic handedness of cytoskeletal molecules. In light of a fundamental symmetry principle, the typical pattern-formation mechanisms of diffusion plus regulation cannot implement the "right-hand rule"; at the microscopic level, the cell's cytoskeleton of chiral filaments seems always to be involved, usually in collective states driven by polymerization forces or molecular motors. It seems particularly easy for handedness to emerge in a shear or rotation in the background of an effectively two-dimensional system, such as the cell membrane or a layer of cells, as this requires no pre-existing axis apart from the layer normal. I detail a scenario involving actin/myosin layers in snails and in C. elegans, and also one about the microtubule layer in plant cells. I also survey the other examples that I am aware of, such as the emergence of handedness such as the emergence of handedness in neurons, in eukaryote cell motility, and in non-flagellated bacteria.Comment: 42 pages, 6 figures, resubmitted to J. Stat. Phys. special issue. Major rewrite, rearranged sections/subsections, new Fig 3 + 6, new physics in Sec 2.4 and 3.4.1, added Sec 5 and subsections of Sec

Observation of γ vibrations and alignments built on non-ground-state configurations in Dy 156

The exact nature of the lowest Kπ=2+ rotational bands in all deformed nuclei remains obscure. Traditionally they are assumed to be collective vibrations of the nuclear shape in the γ degree of freedom perpendicular to the nuclear symmetry axis. Very few such γ bands have been traced past the usual backbending rotational alignments of high-j nucleons. We have investigated the structure of positive-parity bands in the N=90 nucleus Dy156, using the Nd148(C12,4n)Dy156 reaction at 65 MeV, observing the resulting γ-ray transitions with the Gammasphere array. The even- and odd-spin members of the Kπ=2+γ band are observed up to 32+ and 31+, respectively. This rotational band faithfully tracks the ground-state configuration to the highest spins. The members of a possible γ vibration built on the aligned yrast S band are observed up to spins 28+ and 27+. An even-spin positive-parity band, observed up to spin 24+, is a candidate for an aligned S band built on the seniority-zero configuration of the 02+ state at 676 keV. The crossing of this band with the 02+ band is at ?ωc=0.28(1)MeV and is consistent with the configuration of the 02+ band not producing any blocking of the monopole pairing

Investigation of negative-parity states in Dy 156: Search for evidence of tetrahedral symmetry

An experiment populating low/medium-spin states in Dy156 was performed to investigate the possibility of tetrahedral symmetry in this nucleus. In particular, focus was placed on the low-spin, negative-parity states since recent theoretical studies suggest that these may be good candidates for this high-rank symmetry. The states were produced in the Nd148(C12,4n) reaction and the Gammasphere array was utilized to detect the emitted γ rays. B(E2)/B(E1) ratios of transition probabilities from the low-spin, negative-parity bands were determined and used to interpret whether these structures are best associated with tetrahedral symmetry or, as previously assigned, to octupole vibrations. In addition, several other negative-parity structures were observed to higher spin and two new sequences were established

Velocity-space sensitivity of the time-of-flight neutron spectrometer at JET

The velocity-space sensitivities of fast-ion diagnostics are often described by so-called weight functions. Recently, we formulated weight functions showing the velocity-space sensitivity of the often dominant beam-target part of neutron energy spectra. These weight functions for neutron emission spectrometry (NES) are independent of the particular NES diagnostic. Here we apply these NES weight functions to the time-of-flight spectrometer TOFOR at JET. By taking the instrumental response function of TOFOR into account, we calculate time-of-flight NES weight functions that enable us to directly determine the velocity-space sensitivity of a given part of a measured time-of-flight spectrum from TOFOR

Relationship of edge localized mode burst times with divertor flux loop signal phase in JET

A phase relationship is identified between sequential edge localized modes (ELMs) occurrence times in a set of H-mode tokamak plasmas to the voltage measured in full flux azimuthal loops in the divertor region. We focus on plasmas in the Joint European Torus where a steady H-mode is sustained over several seconds, during which ELMs are observed in the Be II emission at the divertor. The ELMs analysed arise from intrinsic ELMing, in that there is no deliberate intent to control the ELMing process by external means. We use ELM timings derived from the Be II signal to perform direct time domain analysis of the full flux loop VLD2 and VLD3 signals, which provide a high cadence global measurement proportional to the voltage induced by changes in poloidal magnetic flux. Specifically, we examine how the time interval between pairs of successive ELMs is linked to the time-evolving phase of the full flux loop signals. Each ELM produces a clear early pulse in the full flux loop signals, whose peak time is used to condition our analysis. The arrival time of the following ELM, relative to this pulse, is found to fall into one of two categories: (i) prompt ELMs, which are directly paced by the initial response seen in the flux loop signals; and (ii) all other ELMs, which occur after the initial response of the full flux loop signals has decayed in amplitude. The times at which ELMs in category (ii) occur, relative to the first ELM of the pair, are clustered at times when the instantaneous phase of the full flux loop signal is close to its value at the time of the first ELM

Physical Basis for the Maximum Thermal Radiation Emission between Materials

An analytic basis for the limit on intra-media thermal radiation transport has been obtained as a simple function of temperature and material optical properties (n,k). It is shown that optical parameters determine the maximum radiative energy transfer rate by altering media radiative state density and energy density. Quantitative analysis shows that intra-media radiative transfer rates may exceed the radiation into free space as described by the Stephan-Boltzmann equation by several orders of magnitude. The frequency dependence of the optical properties further alters the expected blackbody spectral dependence. This generalized formulation of the limit to thermal radiation transfer in terms of media optical properties expands the understanding and future potential of radiative processes

The high-spin single-particle structure of 121I

The high-spin level structure of 121I has been established above the first yrast 'band termination state', which occurs at an excitation energy of 5.43 MeV with Ipi =39/2-, using data from the Eurogam array. The high-spin structure exhibits an irregular set of levels consistent with non-collective behaviour. A band terminating state at 9.24 MeV with Ipi =55/2- has been identified. Comparison with total Routhian surface cranking calculations suggest a maximally aligned ( pi h112/g72/2)(23/2-) (X)( nu h112/4)(16+) oblate configuration for this state relative to the 114Sn core

High-spin structure of 121Xe: Triaxiality and band termination

High-spin states of the odd-neutron 121Xe nucleus have been studied with Eurogam using the 96Zr(30Si,5n)121Xe fusion-evaporation reaction. The level scheme has been extended up to 67/2h(cross) and an excitation energy of approximately 14 MeV. Several new rotational bands have been observed and the previously known bands extended. Two of the bands lose their regular character at high spins, which may be interpreted as a transition from collective behaviour to a regime of noncollective oblate states. The deduced high-spin structure is compared with Woods-Saxon TRS cranking and CSM calculations. Configurations of the bands have been suggested on the basis of the measured routhians, aligned angular momenta and B(M1)/B(E2) ratios. The yrast nu h(cross)11/2 band is interpreted as having a triaxial shape. Neutron (h(cross)11/2)2 alignments have been found at the frequencies predicted by the TRS and CSM calculations. The B(M1)/B(E2) ratios for one of the bands show deviation from the predictions of the geometrical model. Enhanced E1 transitions have been observed between bands built on nu d5/2 and nu h(cross)11/2 orbitals

First observation of collective dipole rotational bands in the neutron-deficient bismuth nuclei

The nucleus 202Bi was populated via the 196Pt(11B,5n)202Bi reaction at a beam energy of 75 MeV. Three regular sequences of magnetic dipole transitions have been found. A comparison is made with the known Delta I=1 rotational bands seen in the neighbouring Pb nuclei. An interpretation in terms of collective oblate configurations involving high-K proton and alignable neutron orbitals is suggested