91 research outputs found
Structure, Stresses and Local Dynamics in Glasses
The interrelations between short range structural and elastic aspects in
glasses and glass forming liquids pose important and yet unresolved questions.
In this paper these relations are analyzed for mono-atomic glasses and stressed
liquids with a short range repulsive-attractive pair potentials. Strong
variations of the local pressure are found even in a zero temperature glass,
whereas the largest values of pressure are the same in both glasses and
liquids. The coordination number z(J) and the effective first peak radius
depend on the local pressures J's. A linear relation was found between
components of site stress tensor and the local elastic constants. A linear
relation was also found between the trace of the squares of the local
frequencies and the local pressures. Those relations hold for glasses at zero
temperature and for liquids. We explain this by a relation between the
structure and the potential terms. A structural similarity between liquids and
solids is manifested by similar dependencies of the coordination number on the
pressures.Comment: 7 pages, 11 figure
Organization of atomic bond tensions in model glasses
In order to understand whether internal stresses in glasses are correlated or
randomly distributed, we study the organization of atomic bond tensions (normal
forces between pairs of atoms). Measurements of the invariants of the atomic
bond tension tensor in simulated 2D and 3D binary Lennard-Jones glasses, reveal
new and unexpected correlations and provide support for Alexander's conjecture
about the non-random character of internal stresses in amorphous solids
Force distributions near the jamming and glass transitions
We calculate the distribution of interparticle normal forces near the
glass and jamming transitions in model supercooled liquids and foams,
respectively. develops a peak that appears near the glass or jamming
transitions, whose height increases with decreasing temperature, decreasing
shear stress and increasing packing density. A similar shape of was
observed in experiments on static granular packings. We propose that the
appearance of this peak signals the development of a yield stress. The
sensitivity of the peak to temperature, shear stress and density lends credence
to the recently proposed generalized jamming phase diagram.Comment: 4 pages, 3 postscript figures;Version 3 replaces figure 1 and removes
figure 2 from version 1. Significant rewording of version 1 to emphasize the
formation of peak in P(F) when these systems jam along five different routes
of the recently proposed jamming phase diagram. Version 2 displayed the
incorrect abstrac
Voronoi-Delaunay analysis of normal modes in a simple model glass
We combine a conventional harmonic analysis of vibrations in a one-atomic
model glass of soft spheres with a Voronoi-Delaunay geometrical analysis of the
structure. ``Structure potentials'' (tetragonality, sphericity or perfectness)
are introduced to describe the shape of the local atomic configurations
(Delaunay simplices) as function of the atomic coordinates. Apart from the
highest and lowest frequencies the amplitude weighted ``structure potential''
varies only little with frequency. The movement of atoms in soft modes causes
transitions between different ``perfect'' realizations of local structure. As
for the potential energy a dynamic matrix can be defined for the ``structure
potential''. Its expectation value with respect to the vibrational modes
increases nearly linearly with frequency and shows a clear indication of the
boson peak. The structure eigenvectors of this dynamical matrix are strongly
correlated to the vibrational ones. Four subgroups of modes can be
distinguished
Nucleocytoplasmic transport: a thermodynamic mechanism
The nuclear pore supports molecular communication between cytoplasm and
nucleus in eukaryotic cells. Selective transport of proteins is mediated by
soluble receptors, whose regulation by the small GTPase Ran leads to cargo
accumulation in, or depletion from the nucleus, i.e., nuclear import or nuclear
export. We consider the operation of this transport system by a combined
analytical and experimental approach. Provocative predictions of a simple model
were tested using cell-free nuclei reconstituted in Xenopus egg extract, a
system well suited to quantitative studies. We found that accumulation capacity
is limited, so that introduction of one import cargo leads to egress of
another. Clearly, the pore per se does not determine transport directionality.
Moreover, different cargo reach a similar ratio of nuclear to cytoplasmic
concentration in steady-state. The model shows that this ratio should in fact
be independent of the receptor-cargo affinity, though kinetics may be strongly
influenced. Numerical conservation of the system components highlights a
conflict between the observations and the popular concept of transport cycles.
We suggest that chemical partitioning provides a framework to understand the
capacity to generate concentration gradients by equilibration of the
receptor-cargo intermediary.Comment: in press at HFSP Journal, vol 3 16 text pages, 1 table, 4 figures,
plus Supplementary Material include
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Individual common variants exert weak effects on the risk for autism spectrum disorders.
While it is apparent that rare variation can play an important role in the genetic architecture of autism spectrum disorders (ASDs), the contribution of common variation to the risk of developing ASD is less clear. To produce a more comprehensive picture, we report Stage 2 of the Autism Genome Project genome-wide association study, adding 1301 ASD families and bringing the total to 2705 families analysed (Stages 1 and 2). In addition to evaluating the association of individual single nucleotide polymorphisms (SNPs), we also sought evidence that common variants, en masse, might affect the risk. Despite genotyping over a million SNPs covering the genome, no single SNP shows significant association with ASD or selected phenotypes at a genome-wide level. The SNP that achieves the smallest P-value from secondary analyses is rs1718101. It falls in CNTNAP2, a gene previously implicated in susceptibility for ASD. This SNP also shows modest association with age of word/phrase acquisition in ASD subjects, of interest because features of language development are also associated with other variation in CNTNAP2. In contrast, allele scores derived from the transmission of common alleles to Stage 1 cases significantly predict case status in the independent Stage 2 sample. Despite being significant, the variance explained by these allele scores was small (Vm< 1%). Based on results from individual SNPs and their en masse effect on risk, as inferred from the allele score results, it is reasonable to conclude that common variants affect the risk for ASD but their individual effects are modest
A genome-wide scan for common alleles affecting risk for autism
Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10−8. When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10−8 threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C
The MLL recombinome of acute leukemias in 2017
Chromosomal rearrangements of the human MLL/KMT2A gene are associated with infant, pediatric, adult and therapy-induced acute leukemias. Here we present the data obtained from 2345 acute leukemia patients. Genomic breakpoints within the MLL gene and the involved translocation partner genes (TPGs) were determined and 11 novel TPGs were identified. Thus, a total of 135 different MLL rearrangements have been identified so far, of which 94 TPGs are now characterized at the molecular level. In all, 35 out of these 94 TPGs occur recurrently, but only 9 specific gene fusions account for more than 90% of all illegitimate recombinations of the MLL gene. We observed an age-dependent breakpoint shift with breakpoints localizing within MLL intron 11 associated with acute lymphoblastic leukemia and younger patients, while breakpoints in MLL intron 9 predominate in AML or older patients. The molecular characterization of MLL breakpoints suggests different etiologies in the different age groups and allows the correlation of functional domains of the MLL gene with clinical outcome. This study provides a comprehensive analysis of the MLL recombinome in acute leukemia and demonstrates that the establishment of patient-specific chromosomal fusion sites allows the design of specific PCR primers for minimal residual disease analyses for all patients
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