36 research outputs found
Solving ill-posed bilevel programs
This paper deals with ill-posed bilevel programs, i.e., problems admitting multiple lower-level solutions for some upper-level parameters. Many publications have been devoted to the standard optimistic case of this problem, where the difficulty is essentially moved from the objective function to the feasible set. This new problem is simpler but there is no guaranty to obtain local optimal solutions for the original optimistic problem by this process. Considering the intrinsic non-convexity of bilevel programs, computing local optimal solutions is the best one can hope to get in most cases. To achieve this goal, we start by establishing an equivalence between the original optimistic problem an a certain set-valued optimization problem. Next, we develop optimality conditions for the latter problem and show that they generalize all the results currently known in the literature on optimistic bilevel optimization. Our approach is then extended to multiobjective bilevel optimization, and completely new results are derived for problems with vector-valued upper- and lower-level objective functions. Numerical implementations of the results of this paper are provided on some examples, in order to demonstrate how the original optimistic problem can be solved in practice, by means of a special set-valued optimization problem
Rapid movement and transcriptional re-localization of human cohesin on DNA
The spatial organization, correct expression, repair, and segregation of eukaryotic genomes depend on cohesin, ring-shaped protein complexes that are thought to function by entrapping DNA It has been proposed that cohesin is recruited to specific genomic locations from distal loading sites by an unknown mechanism, which depends on transcription, and it has been speculated that cohesin movements along DNA could create three-dimensional genomic organization by loop extrusion. However, whether cohesin can translocate along DNA is unknown. Here, we used single-molecule imaging to show that cohesin can diffuse rapidly on DNA in a manner consistent with topological entrapment and can pass over some DNA-bound proteins and nucleosomes but is constrained in its movement by transcription and DNA-bound CCCTC-binding factor (CTCF). These results indicate that cohesin can be positioned in the genome by moving along DNA, that transcription can provide directionality to these movements, that CTCF functions as a boundary element for moving cohesin, and they are consistent with the hypothesis that cohesin spatially organizes the genome via loop extrusion
ARPES: A probe of electronic correlations
Angle-resolved photoemission spectroscopy (ARPES) is one of the most direct
methods of studying the electronic structure of solids. By measuring the
kinetic energy and angular distribution of the electrons photoemitted from a
sample illuminated with sufficiently high-energy radiation, one can gain
information on both the energy and momentum of the electrons propagating inside
a material. This is of vital importance in elucidating the connection between
electronic, magnetic, and chemical structure of solids, in particular for those
complex systems which cannot be appropriately described within the
independent-particle picture. Among the various classes of complex systems, of
great interest are the transition metal oxides, which have been at the center
stage in condensed matter physics for the last four decades. Following a
general introduction to the topic, we will lay the theoretical basis needed to
understand the pivotal role of ARPES in the study of such systems. After a
brief overview on the state-of-the-art capabilities of the technique, we will
review some of the most interesting and relevant case studies of the novel
physics revealed by ARPES in 3d-, 4d- and 5d-based oxides.Comment: Chapter to appear in "Strongly Correlated Systems: Experimental
Techniques", edited by A. Avella and F. Mancini, Springer Series in
Solid-State Sciences (2013). A high-resolution version can be found at:
http://www.phas.ubc.ca/~quantmat/ARPES/PUBLICATIONS/Reviews/ARPES_Springer.pdf.
arXiv admin note: text overlap with arXiv:cond-mat/0307085,
arXiv:cond-mat/020850
Filament Depolymerization Can Explain Chromosome Pulling during Bacterial Mitosis
Chromosome segregation is fundamental to all cells, but the force-generating mechanisms underlying chromosome translocation in bacteria remain mysterious. Caulobacter crescentus utilizes a depolymerization-driven process in which a ParA protein structure elongates from the new cell pole, binds to a ParB-decorated chromosome, and then retracts via disassembly, pulling the chromosome across the cell. This poses the question of how a depolymerizing structure can robustly pull the chromosome that disassembles it. We perform Brownian dynamics simulations with a simple, physically consistent model of the ParABS system. The simulations suggest that the mechanism of translocation is “self-diffusiophoretic”: by disassembling ParA, ParB generates a ParA concentration gradient so that the ParA concentration is higher in front of the chromosome than behind it. Since the chromosome is attracted to ParA via ParB, it moves up the ParA gradient and across the cell. We find that translocation is most robust when ParB binds side-on to ParA filaments. In this case, robust translocation occurs over a wide parameter range and is controlled by a single dimensionless quantity: the product of the rate of ParA disassembly and a characteristic relaxation time of the chromosome. This time scale measures the time it takes for the chromosome to recover its average shape after it is has been pulled. Our results suggest explanations for observed phenomena such as segregation failure, filament-length-dependent translocation velocity, and chromosomal compaction