arXiv subjects

S. Kelly

Publications and source records attributed to S. Kelly.

5 recordsLinked to original sources

arXiv2020

Simulating topological domains in human chromosomes with a fitting-free model

We discuss a polymer model for the 3D organization of human chromosomes. A chromosome is represented by a string of beads, with each bead being "colored" according to 1D bioinformatic data (e.g., chromatin state, histone modification, GC content). Individual spheres (representing bi- and multi-valent transcription factors) can bind reversibly and selectively to beads with the appropriate color. During molecular dynamics simulations, the factors bind, and the string spontaneously folds into loops, rosettes, and topologically-associating domains (TADs). This organization occurs in the absence of any specified interactions between distant DNA segments, or between transcription factors. A comparison with Hi-C data shows that simulations predict the location of most boundaries between TADs correctly. The model is "fitting-free" in the sense that it does not use Hi-C data as an input; consequently, one of its strengths is that it can -- in principle -- be used to predict the 3D organization of any region of interest, or whole chromosome, in a given organism, or cell line, in the absence of existing Hi-C data. We discuss how this simple model might be refined to include more transcription factors and binding sites, and to correctly predict contacts between convergent CTCF binding sites.

physics.bio-ph↗

arXiv2015

Binding of bivalent transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and domains

Biophysicists are modeling conformations of interphase chromosomes, often basing the strengths of interactions between segments distant on the genetic map on contact frequencies determined experimentally. Here, instead, we develop a fitting-free, minimal model: bivalent red and green "transcription factors" bind to cognate sites in runs of beads ("chromatin") to form molecular bridges stabilizing loops. In the absence of additional explicit forces, molecular dynamic simulations reveal that bound "factors' spontaneously cluster -- red with red, green with green, but rarely red with green -- to give structures reminiscent of transcription factories. Binding of just two transcription factors (or proteins) to active and inactive regions of human chromosomes yields rosettes, topological domains, and contact maps much like those seen experimentally. This emergent "bridging-induced attraction" proves to be a robust, simple, and generic force able to organize interphase chromosomes at all scales.

q-bio.BM↗

arXiv2009

Correlations between the morphology and the electronic structure at the surface of thin film manganites, investigated with STM

Thin-film colossal magnetoresistance manganites such as La$_{0.67}$Ca$_{0.33}$MnO$_{3}$ (LCMO) have now been intensely studied for more than a decade, but the issue of possible nanoscale electronic phase separation is not fully solved. Scanning Tunneling Microscopy / Spectroscopy (STS) has been pivotal in studying phase separation, but is hindered by being surface- rather than bulk-sensitive. For our sputtered LCMO films the data indicates a strong correlation between surface morphology and signatures of phase separation; rough films show phase separation while atomically flat films are electronically homogeneous but have a more or less inactive surface layer. Regardless of surface morphology, the film bulk is electronically and magnetically active. Many of the reported conclusions about electronic inhomogeneities measured by STS have been confused by this issue. We study both strained and unstrained films and find no correlation between substrate-induced strain and either electronic phase separation or dead layers.

cond-mat.str-el↗

arXiv2008

Debye relaxation in high magnetic fields

Dielectric relaxation is universal in characterizing polar liquids and solids, insulators, and semiconductors, and the theoretical models are well developed. However, in high magnetic fields, previously unknown aspects of dielectric relaxation can be revealed and exploited. Here, we report low temperature dielectric relaxation measurements in lightly doped silicon in high dc magnetic fields B both parallel and perpendicular to the applied ac electric field E. For B//E, we observe a temperature and magnetic field dependent dielectric dispersion e(w)characteristic of conventional Debye relaxation where the free carrier concentration is dependent on thermal dopant ionization, magnetic freeze-out, and/or magnetic localization effects. However, for BperpE, anomalous dispersion emerges in e(w) with increasing magnetic field. It is shown that the Debye formalism can be simply extended by adding the Lorentz force to describe the general response of a dielectric in crossed magnetic and electric fields. Moreover, we predict and observe a new transverse dielectric response EH perp B perp E not previously described in magneto-dielectric measurements. The new formalism allows the determination of the mobility and the ability to discriminate between magnetic localization/freeze out and Lorentz force effects in the magneto-dielectric response.

cond-mat.mtrl-sci↗

arXiv2002

Does the Charm Flow at RHIC?

Recent PHENIX Au+Au -> e- + X data from open charm decay are shown to be consistent with two extreme opposite dynamical scenarios of ultra-relativistic nuclear reactions. Perturbative QCD without final state interactions was previously shown to be consistent with the data. However, we show that the data are also consistent with zero mean free path hydrodynamics characterized by a common transverse flow velocity field. The surprising coincidence of both D and B hydrodynamic flow spectra with pQCD up to p_T ~ 3 and 5 GeV, respectively, suggests that heavy quarks may be produced essentially at rest in the rapidly expanding gluon plasma. Possible implications and further tests of collective heavy quark dynamics are discussed.

nucl-th↗