513 research outputs found
Diffusive hidden Markov model characterization of DNA looping dynamics in tethered particle experiments
In many biochemical processes, proteins bound to DNA at distant sites are
brought into close proximity by loops in the underlying DNA. For example, the
function of some gene-regulatory proteins depends on such DNA looping
interactions. We present a new technique for characterizing the kinetics of
loop formation in vitro, as observed using the tethered particle method, and
apply it to experimental data on looping induced by lambda repressor. Our
method uses a modified (diffusive) hidden Markov analysis that directly
incorporates the Brownian motion of the observed tethered bead. We compare
looping lifetimes found with our method (which we find are consistent over a
range of sampling frequencies) to those obtained via the traditional
threshold-crossing analysis (which can vary depending on how the raw data are
filtered in the time domain). Our method does not involve any time filtering
and can detect sudden changes in looping behavior. For example, we show how our
method can identify transitions between long-lived, kinetically distinct states
that would otherwise be difficult to discern
Isospin Purity of T=1 States in the A=38 Nuclei Studied Via Lifetime Measurements in K38
The Doppler Shift Attenuation Method was used to measure lifetimes for levels in 38K at excitation energies of 1698, 2404, 2830, 2996, and 3671 keV, populated using the 40Ca(d, α) 38K reaction at a beam energy of 4.5 MeV. Values of 109(29), 95(22), 457(63), 130(40), and 160(50) fs, respectively, were measured and are compared with previous values obtained using different stopping powers. The matrix element for the transition between the Jπ = 2+ T=1 and 0+ T=1 states in this Tz = 0 nucleus is compared with the analogous transition in the other nuclei in the T = 1 triplet, 38Ca (Tz = −1) and 38Ar (Tz = +1), and with the results of shell-model calculations
Isospin purity of <i>T</i>=1 measurements in the <i>A</i>=38 nuclei studied via lifetime measurements in <sup>38</sup>K
The Doppler Shift Attenuation Method was used to measure lifetimes for levels in 38K at excitation energies of 1698, 2404, 2830, 2996, and 3671 keV, populated using the 40Ca(d, α) 38K reaction at a beam energy of 4.5 MeV. Values of 109(29), 95(22), 457(63), 130(40), and 160(50) fs, respectively, were measured and are compared with previous values obtained using different stopping powers. The matrix element for the transition between the Jπ = 2+ T=1 and 0+ T=1 states in this Tz = 0 nucleus is compared with the analogous transition in the other nuclei in the T = 1 triplet, 38Ca (Tz = −1) and 38Ar (Tz = +1), and with the results of shell-model calculations
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
Spin-rotor Interpretation of Identical Bands and Quantized Alignment in Superdeformed A 190 Nuclei
The ``identical'' bands in superdeformed mercury, thallium, and lead nuclei
are interpreted as examples of orbital angular momentum rotors with the weak
spin-orbit coupling of pseudo- symmetries and supersymmetries.Comment: 15 pages, revtex 3.0, 7 figures available upon request from
[email protected]
\u3cem\u3eγ\u3c/em\u3e-ray Spectroscopy of \u3csup\u3e166\u3c/sup\u3eHf: X(5) in \u3cem\u3eN\u3c/em\u3e \u3e 90?
Excited states in 166Hf were populated in the β+/∈ decay of 166Ta and studied through off-beam γ –ray spectroscopy at the Yale moving tape collector. New coincidence data found no support for two previously reported excited 0+ states and led to a substantially revised level scheme. Similarities between the revised level scheme of 166Hf and the X(5) critical point symmetry are discussed, and the extent of X(5) behavior in this mass region is explored through the W and Os isotopes. Among X(5) candidates with N \u3e 90, good agreement is observed for most energies and interband B(E2) strengths, while all exhibit similar disagreements with other key observables, in particular, yrast B(E2) values and spacing in the excited K = 0+ sequence
Time-odd components in the mean field of rotating superdeformed nuclei
Rotation-induced time-odd components in the nuclear mean field are analyzed
using the Hartree-Fock cranking approach with effective interactions SIII,
SkM*, and SkP. Identical dynamical moments are obtained for
pairs of superdeformed bands Tb(2)--Dy(1) and
Gd(2)--Tb(1). The corresponding relative alignments strongly
depend on which time-odd mean-field terms are taken into account in the
Hartree-Fock equations.Comment: 23 pages, ReVTeX, 6 uuencoded postscript figures include
Measurement of Conversion Coefficients in Normal and Triaxial Strongly Deformed Bands in \u3csup\u3e167\u3c/sup\u3eLu
Internal conversion coefficients have been measured for transitions in both normal deformed and triaxial strongly deformed bands in 167Lu using the Gammasphere and ICE Ball spectrometers. The results for all in-band transitions are consistent with E2 multipolarity. Upper limits are determined for the internal conversion coefficients for linking transitions between TSD Band 2 and TSD Band 1, the nw = 1 and nw = 0 wobbling bands, respectively
Isomeric Decay of \u3csup\u3e208\u3c/sup\u3eRa
Low-energy excited states of 208Ra were investigated using the 182W(30Si, 4n) reaction at the Wright Nuclear Structure Laboratory of Yale University. Fusion evaporation recoils were selected using the gas-filled spectrometer SASSYER. Delayed γ rays, following isomeric decays, were detected at the focal plane of SASSYER with a small array of three clover Ge detectors. Transitions following a proposed J π = 8+ isomer were observed, and the half-life was measured
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