21 research outputs found
Looping and Clustering: a statistical physics approach to protein-DNA complexes in bacteria
International audienceThe DNA shows a high degree of spatial and dynamical organization over a broad range of length scales. It interacts with different populations of proteins and can form protein-DNA complexes that underlie various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, an essential component of a widely spread mechanism for DNA segregation in bacteria. Recent studies suggest that DNA-bound ParB proteins interact with each other and condense into large clusters with multiple extruding DNA-loops. In my talk, I present the Looping and Clustering model [1], a simple statistical physics approach to describe how proteins assemble into a protein-DNA cluster with multiple loops. Our analytic model predicts binding profiles of ParB proteins in good agreement with data from high precision ChIP-sequencing – a biochemical technique to analyze the interaction between DNA and proteins at the level of the genome. The Looping and Clustering framework provides a quantitative tool that could be exploited to interpret further experimental results of ParB-like protein complexes and gain some new insights into the organization of DNA.[1] Walter, J.-C., Walliser, N.-O., ... & Broedersz, C. P., New J. Phys. 20, 035002 (2018)
Restrictions on infinite sequences of type IIB vacua
Ashok and Douglas have shown that infinite sequences of type IIB flux vacua
with imaginary self-dual flux can only occur in so-called D-limits,
corresponding to singular points in complex structure moduli space. In this
work we refine this no-go result by demonstrating that there are no infinite
sequences accumulating to the large complex structure point of a certain class
of one-parameter Calabi-Yau manifolds. We perform a similar analysis for
conifold points and for the decoupling limit, obtaining identical results.
Furthermore, we establish the absence of infinite sequences in a D-limit
corresponding to the large complex structure limit of a two-parameter
Calabi-Yau. In particular, our results demonstrate analytically that the series
of vacua recently discovered by Ahlqvist et al., seemingly accumulating to the
large complex structure point, are finite. We perform a numerical study of
these series close to the large complex structure point using appropriate
approximations for the period functions. This analysis reveals that the series
bounce out from the large complex structure point, and that the flux eventually
ceases to be imaginary self-dual. Finally, we study D-limits for F-theory
compactifications on K3\times K3 for which the finiteness of supersymmetric
vacua is already established. We do find infinite sequences of flux vacua which
are, however, identified by automorphisms of K3.Comment: 35 pages. v2. Typos corrected, ref. added. Matches published versio
PALP - a User Manual
This article provides a complete user's guide to version 2.1 of the toric
geometry package PALP by Maximilian Kreuzer and others. In particular,
previously undocumented applications such as the program nef.x are discussed in
detail. New features of PALP 2.1 include an extension of the program mori.x
which can now compute Mori cones and intersection rings of arbitrary dimension
and can also take specific triangulations of reflexive polytopes as input.
Furthermore, the program nef.x is enhanced by an option that allows the user to
enter reflexive Gorenstein cones as input. The present documentation is
complemented by a Wiki which is available online.Comment: 71 pages, to appear in "Strings, Gauge Fields, and the Geometry
Behind - The Legacy of Maximilian Kreuzer". PALP Wiki available at
http://palp.itp.tuwien.ac.at/wiki/index.php/Main_Pag
Signature of (anti)cooperativity in the stochastic fluctuations of small systems: application to the bacterial flagellar motor
The cooperative binding of molecular agents onto a substrate is pervasive in
living systems. To study whether a system shows cooperativity, one can rely on
a fluctuation analysis of quantities such as the number of substrate-bound
units and the residence time in an occupancy state. Since the relative standard
deviation from the statistical mean monotonically decreases with the number of
binding sites, these techniques are only suitable for small enough systems,
such as those implicated in stochastic processes inside cells. Here, we present
a general-purpose grand canonical Hamiltonian description of a small
one-dimensional (1D) lattice gas with either nearest-neighbor or long-range
interactions as prototypical examples of cooperativity-influenced adsorption
processes. First, we elucidate how the strength and sign of the interaction
potential between neighboring bound particles on the lattice determine the
intensity of the fluctuations of the mean occupancy. We then employ this
relationship to compare the theoretical predictions of our model to data from
single molecule experiments on bacterial flagellar motors (BFM) of E. coli. In
this way, we find evidence that cooperativity controls the mechano-sensitive
dynamical assembly of the torque-generating units, the so-called stator units,
onto the BFM. Furthermore, in an attempt to quantify fluctuations and the
adaptability of the BFM, we estimate the stator-stator interaction potential.
Finally, we conclude that the system resides in a sweet spot of the parameter
space (phase diagram) suitable for a smoothly adaptive system while minimizing
fluctuations.Comment: 35 pages, 18 figures, 4 table
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Looping and clustering model for the organization of protein-DNA complexes on the bacterial genome
The bacterial genome is organized by a variety of associated proteins inside a structure called the nucleoid. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the looping and clustering model, which employs a statistical physics approach to describe protein-DNA complexes. The looping and clustering model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins that is organized around a single high-affinity binding site. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and loop closure entropy of this protein-DNA cluster on the one hand, and the positional entropy for placing loops within the cluster on the other. Indeed, we show that the protein interaction strength determines the 'tightness' of the loopy protein-DNA complex. Thus, our model provides a theoretical framework for quantitatively computing the binding profiles of ParB-like proteins around a cognate (parS) binding site
Four-modulus "Swiss Cheese" chiral models
We study the 'Large Volume Scenario' on explicit, new, compact, four-modulus
Calabi-Yau manifolds. We pay special attention to the chirality problem pointed
out by Blumenhagen, Moster and Plauschinn. Namely, we thoroughly analyze the
possibility of generating neutral, non-perturbative superpotentials from
Euclidean D3-branes in the presence of chirally intersecting D7-branes. We find
that taking proper account of the Freed-Witten anomaly on non-spin cycles and
of the Kaehler cone conditions imposes severe constraints on the models.
Nevertheless, we are able to create setups where the constraints are solved,
and up to three moduli are stabilized.Comment: 40 pages, 10 figures, clarifying comments added, minor mistakes
correcte
Toric Construction of Global F-Theory GUTs
We systematically construct a large number of compact Calabi-Yau fourfolds
which are suitable for F-theory model building. These elliptically fibered
Calabi-Yaus are complete intersections of two hypersurfaces in a six
dimensional ambient space. We first construct three-dimensional base manifolds
that are hypersurfaces in a toric ambient space. We search for divisors which
can support an F-theory GUT. The fourfolds are obtained as elliptic fibrations
over these base manifolds. We find that elementary conditions which are
motivated by F-theory GUTs lead to strong constraints on the geometry, which
significantly reduce the number of suitable models. The complete database of
models is available at http://hep.itp.tuwien.ac.at/f-theory/. We work out
several examples in more detail.Comment: 35 pages, references adde
Looping and Clustering model for the organization of protein-DNA complexes on the bacterial genome
The bacterial genome is organized by a variety of associated proteins inside a structure called the nucleoid. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the Looping and Clustering (LC) model, which employs a statistical physics approach to describe protein-DNA complexes. The LC model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins that is organized around a single high-affinity binding site. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and the configurational and loop entropy of this protein-DNA cluster. Indeed, we show that the protein interaction strength determines the "tightness" of the loopy protein-DNA complex. Thus, our model provides a theoretical framework to quantitatively compute the binding profiles of ParB-like proteins around a cognate parS binding site