2,260 research outputs found
Biophysical Fitness Landscapes for Transcription Factor Binding Sites
Evolutionary trajectories and phenotypic states available to cell populations
are ultimately dictated by intermolecular interactions between DNA, RNA,
proteins, and other molecular species. Here we study how evolution of gene
regulation in a single-cell eukaryote S. cerevisiae is affected by the
interactions between transcription factors (TFs) and their cognate genomic
sites. Our study is informed by high-throughput in vitro measurements of TF-DNA
binding interactions and by a comprehensive collection of genomic binding
sites. Using an evolutionary model for monomorphic populations evolving on a
fitness landscape, we infer fitness as a function of TF-DNA binding energy for
a collection of 12 yeast TFs, and show that the shape of the predicted fitness
functions is in broad agreement with a simple thermodynamic model of two-state
TF-DNA binding. However, the effective temperature of the model is not always
equal to the physical temperature, indicating selection pressures in addition
to biophysical constraints caused by TF-DNA interactions. We find little
statistical support for the fitness landscape in which each position in the
binding site evolves independently, showing that epistasis is common in
evolution of gene regulation. Finally, by correlating TF-DNA binding energies
with biological properties of the sites or the genes they regulate, we are able
to rule out several scenarios of site-specific selection, under which binding
sites of the same TF would experience a spectrum of selection pressures
depending on their position in the genome. These findings argue for the
existence of universal fitness landscapes which shape evolution of all sites
for a given TF, and whose properties are determined in part by the physics of
protein-DNA interactions
Spinons in Conformal Field Theory
We study the conformal field theory in its spinon description,
adapted to the Yangian invariance. By evaluating the action of the Yangian
generators on the primary fields, we find a new connection between this
conformal field theory and the Calogero-Sutherland model with spin. We
use this connection to describe how the spinons are the quasi-particles
spanning the irreducible Yangian multiplet, and also to exhibit operators
creating the -spinon highest weight vectors.Comment: 18 page
Dynamical correlation functions in the Calogero-Sutherland model
We compute the dynamical Green function and density-density correlation in
the Calogero-Sutherland model for all integer values of the coupling constant.
An interpretation of the intermediate states in terms of quasi-particles is
found.Comment: 20pgs, (1 reference added
Yang-Baxter equation in spin chains with long range interactions
We consider the spin chains with long range interactions and the
spin generalization of the Calogero-Sutherland models. We show that their
properties derive from a transfer matrix obeying the Yang-Baxter equation. We
obtain the expression of the conserved quantities and we diagonalize them.Comment: Saclay-t93/00
Integrals of motion of the Haldane Shastry Model
In this letter we develop a method to construct all the integrals of motion
of the Haldane-Shastry model of spins, equally spaced around a circle,
interacting through a exchange interaction. These integrals of motion
respect the Yangian symmetry algebra of the Hamiltonian.Comment: 13 pages, REVTEX v3.
The effect of Fermi surface curvature on low-energy properties of fermions with singular interactions
We discuss the effect of Fermi surface curvature on long-distance/time
asymptotic behaviors of two-dimensional fermions interacting via a gapless mode
described by an effective gauge field-like propagator. By comparing the
predictions based on the idea of multi-dimensional bosonization with those of
the strong- coupling Eliashberg approach, we demonstrate that an agreement
between the two requires a further extension of the former technique.Comment: Latex, 4+ pages. Phys. Rev. Lett., to appea
Quantum Chemistry, Anomalous Dimensions, and the Breakdown of Fermi Liquid Theory in Strongly Correlated Systems
We formulate a local picture of strongly correlated systems as a Feynman sum
over atomic configurations. The hopping amplitudes between these atomic
configurations are identified as the renormalization group charges, which
describe the local physics at different energy scales. For a metallic system
away from half-filling, the fixed point local Hamiltonian is a generalized
Anderson impurity model in the mixed valence regime. There are three types of
fixed points: a coherent Fermi liquid (FL) and two classes of self-similar
(scale invariant) phases which we denote incoherent metallic states (IMS). When
the transitions between the atomic configurations proceed coherently at low
energies, the system is a Fermi liquid. Incoherent transitions between the low
energy atomic configurations characterize the incoherent metallic states. The
initial conditions for the renormalization group flow are determined by the
physics at rather high energy scales. This is the domain of local quantum
chemistry. We use simple quantum chemistry estimates to specify the basin of
attraction of the IMS fixed points.Comment: 12 pages, REVTE
Thermodynamics of an one-dimensional ideal gas with fractional exclusion statistics
We show that the particles in the Calogero-Sutherland Model obey fractional
exclusion statistics as defined by Haldane. We construct anyon number densities
and derive the energy distribution function. We show that the partition
function factorizes in the form characteristic of an ideal gas. The virial
expansion is exactly computable and interestingly it is only the second virial
coefficient that encodes the statistics information.Comment: 10pp, REVTE
Spin nematics in the bilinear-biquadratic S=1 spin chain
We report the existence of an extended critical, nondimerized region in the
phase diagram of the bilinear-biquadratic spin-one chain. The dominant power
law correlations are ferroquadrupolar, i.e. spin nematic in character. Another
known critical region is also characterized by dominant quadrupolar
correlations, although with a different wave vector. Our results show that spin
nematic correlations play an important role in quantum magnets with spin S >= 1
in regions between antiferromagnetic and ferromagnetic phases.Comment: 4 pages, 7 figure
Single particle Green's function in the Calogero-Sutherland model for rational couplings
We derive an exact expression for the single particle Green function in the
Calogero-Sutherland model for all rational values of the coupling . The
calculation is based on Jack polynomial techniques and the results are given in
the thermodynamical limit. Two type of intermediate states contribute. The
firts one consists of a particle propagating out of the Fermi sea and the
second one consists of a particle propagating in one direction, q particles in
the opposite direction and p holes.Comment: 9 pages, RevTeX, epsf.tex, 4 figures, files uuencode
- …