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

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

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]

Relative \u3csup\u3e235\u3c/sup\u3eU(\u3cem\u3en,γ\u3c/em\u3e) and (\u3cem\u3en,f\u3c/em\u3e) Cross Sections From \u3csup\u3e235\u3c/sup\u3eU(\u3cem\u3ed,pγ\u3c/em\u3e) and (\u3cem\u3ed,pf\u3c/em\u3e)

The internal surrogate ratio method allows for the determination of an unknown cross section, such as (n,γ), relative to a better-known cross section, such as (n,f), by measuring the relative exit-channel probabilities of a surrogate reaction that proceeds through the same compound nucleus. The validity of the internal surrogate ratio method is tested by comparing the relative γ and fission exit-channel probabilities of a 236U∗ compound nucleus, formed in the 235U(d,p) reaction, to the known 235U(n,γ) and (n,f) cross sections. A model-independent method for measuring the γ-channel yield is presented and used

Gd-149:What's confirmed? What's new?

A long run performed with EUROGAM II allowed remeasuring the Gd-149 superdeformed (SD) band 1. The Delta I = 4 bifurcation in band 1 is confirmed and two resolved gamma-ray transitions linking the SD band 1 and the normal deformed states have been observed

Gd-149:What's confirmed? What's new?

A long run performed with EUROGAM II allowed remeasuring the Gd-149 superdeformed (SD) band 1. The Delta I = 4 bifurcation in band 1 is confirmed and two resolved gamma-ray transitions linking the SD band 1 and the normal deformed states have been observed