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

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

Isospin purity of <i>T</i>=1 measurements in the <i>A</i>=38 nuclei studied via lifetime measurements in ³⁸K

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

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 ${{\cal J}^{(2)}}$ are obtained for pairs of superdeformed bands $^{151}$Tb(2)--$^{152}$Dy(1) and $^{150}$Gd(2)--$^{151}$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

To the Continuum and Beyond: Structure of U Nuclei

An experiment was performed at the 88-inch cyclotron at LBNL to investigate the structure of uranium isotopes and concurrently test the so-called surrogate ratio method. A 28 MeV proton beam was used to bombard 236U and 238U targets and the outgoing light ions were detected using the STARS silicon telescope allowing isotopic assignments and the excitation energy of the compound nucleus to be measured. A fission detector was placed at backward angles to give particle-fission coincidences, while the six clover germanium detectors of the LIBERACE array were used for particle-γ coincidences. The (p,d) reaction channels on 236U and 238U targets were used as a surrogate to measure the σ(234U(n,f))/σ(236U(n,f)) cross section ratio. The results give reasonable agreement with literature values over an equivalent neutron energy range between 0 MeV and 6 MeV. Structure results in 235U include a new (3/2−) level at 1035 keV, that is tentatively assigned as the 3/2−[501] Nilsson state. The analogue 3/2−[501] state in 237U may be associated with a previously observed level at 1201 keV, whose spin/parity is restricted to Jπ = 3/2− on the basis of newly observed decays to the ground band

Spin-rotor Interpretation of Identical Bands and Quantized Alignment in Superdeformed A ≈\approx 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-$SU(3)$ symmetries and supersymmetries.Comment: 15 pages, revtex 3.0, 7 figures available upon request from [email protected]

Utilizing (\u3cem\u3ep,d\u3c/em\u3e) and (\u3cem\u3ep,t\u3c/em\u3e) Reactions to Obtain (\u3cem\u3en,f\u3c/em\u3e) Cross Sections in Uranium Nuclei Via the Surrogate-Ratio Method

The surrogate ratio method has been tested for (p,d) and (p,t) reactions on uranium nuclei. 236U and 238U targets were bombarded with 28-MeV protons and the light ion recoils and fission fragments were detected using the Silicon Telescope Array for Reaction Studies detector array at the 88-Inch Cyclotron at Lawrence Berkeley National Laboratory. The (p,df) reaction channels on 236U and 238U targets were used as a surrogate to determine the σ[236U(n,f)]/σ[234U(n,f)] cross-section ratio. The (p,tf) reaction channels were also measured with the same targets as a surrogate for the σ[235U(n,f)]/σ[(233U(n,f)] ratio. For the (p,df) and (p,tf) surrogate measurements, there is good agreement with accepted (n,f) values over equivalent neutron energy ranges of En=0–7 MeV and En=0–5.5 MeV, respectively. An internal surrogate ratio method comparing the (p,d) and (p,t) reaction channels on a single target is also discussed. The σ[234U(n,f)]/σ[233U(n,f)] and σ[236U(n,f)]/σ[235U(n,f)] cross-section ratios are extracted using this method for the 236U and 238U targets, respectively. The resulting fission cross-section ratios show relatively good agreement with accepted values up to En∼5 MeV

Triplet energy differences and the low lying structure of Ga 62

Background: Triplet energy differences (TED) can be studied to yield information on isospin-non-conserving interactions in nuclei. Purpose: The systematic behavior of triplet energy differences (TED) of T=1, J\u3c0=2+ states is examined. The A=62 isobar is identified as having a TED value that deviates significantly from an otherwise very consistent trend. This deviation can be attributed to the tentative assignments of the pertinent states in Ga62 and Ge62. Methods: An in-beam \u3b3-ray spectroscopy experiment was performed to identify excited states in Ga62 using Gamma-Ray Energy Tracking In-Beam Nuclear Array with the S800 spectrometer at NSCL using a two-nucleon knockout approach. Cross-section calculations for the knockout process and shell-model calculations have been performed to interpret the population and decay properties observed. Results: Using the systematics as a guide, a candidate for the transition from the T=1, 2+ state is identified. However, previous work has identified similar states with different J\u3c0 assignments. Cross-section calculations indicate that the relevant T=1, 2+ state should be one of the states directly populated in this reaction. Conclusions: As spins and parities were not measurable, it is concluded that an unambiguous identification of the first T=1, 2+ state is required to reconcile our understanding of TED systematics