19,765 research outputs found
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>
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
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(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 resonance are
studied. The effects of allowing the S 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
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