IMAGING GENOMICS

Imaging genomics is an emerging research field, where integrative analysis of imaging and omics data is performed to provide new insights into the phenotypic characteristics and genetic mechanisms of normal and/or disordered biological structures and functions, and to impact the development of new diagnostic, therapeutic and preventive approaches. The Imaging Genomics Session at PSB 2017 aims to encourage discussion on fundamental concepts, new methods and innovative applications in this young and rapidly evolving field

Functional bosonization with time dependent perturbations

We extend a path-integral approach to bosonization previously developed in the framework of equilibrium Quantum Field Theories, to the case in which time-dependent interactions are taken into account. In particular we consider a non covariant version of the Thirring model in the presence of a dynamic barrier at zero temperature. By using the Closed Time Path (Schwinger-Keldysh) formalism, we compute the Green's function and the Total Energy Density of the system. Since our model contains the Tomonaga Luttinger model as a particular case, we make contact with recent results on non-equilibrium electronic systems.Comment: 21 pages, 8 figure

Solitary Waves of Planar Ferromagnets and the Breakdown of the Spin-Polarized Quantum Hall Effect

A branch of uniformly-propagating solitary waves of planar ferromagnets is identified. The energy dispersion and structures of the solitary waves are determined for an isotropic ferromagnet as functions of a conserved momentum. With increasing momentum, their structure undergoes a transition from a form ressembling a droplet of spin-waves to a Skyrmion/anti-Skyrmion pair. An instability to the formation of these solitary waves is shown to provide a mechanism for the electric field-induced breakdown of the spin-polarized quantum Hall effect.Comment: 5 pages, 3 eps-figures, revtex with epsf.tex and multicol.st

Irreversible reorganization in a supercooled liquid originates from localised soft modes

The transition of a fluid to a rigid glass upon cooling is a common route of transformation from liquid to solid that embodies the most poorly understood features of both phases1,2,3. From the liquid perspective, the puzzle is to understand stress relaxation in the disordered state. From the perspective of solids, the challenge is to extend our description of structure and its mechanical consequences to materials without long range order. Using computer simulations, we show that the localized low frequency normal modes of a configuration in a supercooled liquid are causally correlated to the irreversible structural reorganization of the particles within that configuration. We also demonstrate that the spatial distribution of these soft local modes can persist in spite of significant particle reorganization. The consequence of these two results is that it is now feasible to construct a theory of relaxation length scales in glass-forming liquids without recourse to dynamics and to explicitly relate molecular properties to their collective relaxation.Comment: Published online: 20 July 2008 | doi:10.1038/nphys1025 Available from http://www.nature.com/nphys/journal/v4/n9/abs/nphys1025.htm

Dual Response Models for the Fractional Quantum Hall Effect

It is shown that the Jain mapping between states of integer and fractional quantum Hall systems can be described dynamically as a perturbative renormalization of an effective Chern-Simons field theory. The effects of mirror duality symmetries of toroidally compactified string theory on this system are studied and it is shown that, when the gauge group is compact, the mirror map has the same effect as the Jain map. The extrinsic ingredients of the Jain construction appear naturally as topologically non-trivial field configurations of the compact gauge theory giving a dynamical origin for the Jain hierarchy of fractional quantum Hall states.Comment: 8 pages LaTe

Dual-acting stapled peptides target both HIV-1 entry and assembly

Background: Previously, we reported the conversion of the 12-mer linear and cell-impermeable peptide CAI to a cell-penetrating peptide NYAD-1 by using an i,i + 4 hydrocarbon stapling technique and confirmed its binding to the C-terminal domain (CTD) of the HIV-1 capsid (CA) protein with an improved affinity (Kd ~ 1 μM) compared to CAI (Kd ~ 15 μM). NYAD-1 disrupts the formation of both immature- and mature-like virus particles in in vitro and cell-based assembly assays. In addition, it displays potent anti-HIV-1 activity in cell culture against a range of laboratory-adapted and primary HIV-1 isolates.<p></p> Results: In this report, we expanded the study to i,i + 7 hydrocarbon-stapled peptides to delineate their mechanism of action and antiviral activity. We identified three potent inhibitors, NYAD-36, -66 and -67, which showed strong binding to CA in NMR and isothermal titration calorimetry (ITC) studies and disrupted the formation of mature-like particles. They showed typical α-helical structures and penetrated cells; however, the cell penetration was not as efficient as observed with the i,i + 4 peptides. Unlike NYAD-1, the i,i + 7 peptides did not have any effect on virus release; however, they impaired Gag precursor processing. HIV-1 particles produced in the presence of these peptides displayed impaired infectivity. Consistent with an effect on virus entry, selection for viral resistance led to the emergence of two mutations in the gp120 subunit of the viral envelope (Env) glycoprotein, V120Q and A327P, located in the conserved region 1 (C1) and the base of the V3 loop, respectively.<p></p> Conclusion: The i,i + 7 stapled peptides derived from CAI unexpectedly target both CA and the V3 loop of gp120. This dual-targeted activity is dependent on their ability to penetrate cells as well as their net charge. This mechanistic revelation will be useful in further modifying these peptides as potent anti-HIV-1 agents.<p></p&gt

Non-Equilibrium Large N Yukawa Dynamics: marching through the Landau pole

The non-equilibrium dynamics of a Yukawa theory with N fermions coupled to a scalar field is studied in the large N limit with the goal of comparing the dynamics predicted from the renormalization group improved effective potential to that obtained including the fermionic backreaction. The effective potential is of the Coleman-Weinberg type. Its renormalization group improvement is unbounded from below and features a Landau pole. When viewed self-consistently, the initial time singularity does not arise. The different regimes of the dynamics of the fully renormalized theory are studied both analytically and numerically. Despite the existence of a Landau pole in the model, the dynamics of the mean field is smooth as it passes the location of the pole. This is a consequence of a remarkable cancellation between the effective potential and the dynamical chiral condensate. The asymptotic evolution is effectively described by a quartic upright effective potential. In all regimes, profuse particle production results in the formation of a dense fermionic plasma with occupation numbers nearly saturated up to a scale of the order of the mean field. This can be interpreted as a chemical potential. We discuss the implications of these results for cosmological preheating.Comment: 36 pages, 14 figures, LaTeX, submitted to Physical Review

Non-locality and Medium Effects in the Exclusive Photoproduction of Eta Mesons on Nuclei

A relativistic model for the quasifree exclusive photoproduction of $\eta$ mesons on nuclei is extended to include both non-local and medium effects. The reaction is assumed to proceed via the dominant contribution of the S$_{11}$(1535) resonance. The complicated integrals resulting from the non-locality are simplified using a modified version of a method given by Cooper and Maxwell. The non-locality effects are found to affect the magnitude of the cross section. Some possibilities reflecting the effects of the medium on the propagation and properties of the intermediate S$_{11}$ resonance are studied. The effects of allowing the S$_{11}$ to interact with the medium via mean field scalar and vector potentials are considered. Both broadening of width and reduction in mass of the resonance lead to a suppression of the calculated cross sections.Comment: 19 pages, 7 figure