21 research outputs found
Self-gravitating Brownian particles in two dimensions: the case of N=2 particles
We study the motion of N=2 overdamped Brownian particles in gravitational
interaction in a space of dimension d=2. This is equivalent to the simplified
motion of two biological entities interacting via chemotaxis when time delay
and degradation of the chemical are ignored. This problem also bears some
similarities with the stochastic motion of two point vortices in viscous
hydrodynamics [Agullo & Verga, Phys. Rev. E, 63, 056304 (2001)]. We
analytically obtain the density probability of finding the particles at a
distance r from each other at time t. We also determine the probability that
the particles have coalesced and formed a Dirac peak at time t (i.e. the
probability that the reduced particle has reached r=0 at time t). Finally, we
investigate the variance of the distribution and discuss the proper form
of the virial theorem for this system. The reduced particle has a normal
diffusion behaviour for small times with a gravity-modified diffusion
coefficient =r_0^2+(4k_B/\xi\mu)(T-T_*)t, where k_BT_{*}=Gm_1m_2/2 is a
critical temperature, and an anomalous diffusion for large times
~t^(1-T_*/T). As a by-product, our solution also describes the growth of
the Dirac peak (condensate) that forms in the post-collapse regime of the
Smoluchowski-Poisson system (or Keller-Segel model) for T<T_c=GMm/(4k_B). We
find that the saturation of the mass of the condensate to the total mass is
algebraic in an infinite domain and exponential in a bounded domain.Comment: Revised version (20/5/2010) accepted for publication in EPJ
Guest Charge and Potential Fluctuations in Two-Dimensional Classical Coulomb Systems
A known generalization of the Stillinger-Lovett sum rule for a guest charge
immersed in a two-dimensional one-component plasma (the second moment of the
screening cloud around this guest charge) is more simply retrieved, just by
using the BGY hierarchy for a mixture of several species; the zeroth moment of
the excess density around a guest charge immersed in a two-component plasma is
also obtained. The moments of the electric potential are related to the excess
chemical potential of a guest charge; explicit results are obtained in several
special cases.Comment: 21 pages. Latex. Appendix moved, with changes, to new subsection 2.3.
Description of the Appendix at the end of the Introduction, from an earlier
version, delete
Semi-automated assembly of high-quality diploid human reference genomes
The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements
pavarotti encodes a kinesin-like protein required to organize the central spindle and contractile ring for cytokinesis
Classifying Patterns in Bioinformatics Databases by Using Alpha-Beta Associative Memories
Expanding the phenotype of NUP85 mutations beyond nephrotic syndrome to primary autosomal recessive microcephaly and Seckel syndrome spectrum disorders
Primary autosomal recessive microcephaly and Seckel syndrome spectrum disorders (MCPH-SCKS) include a heterogeneous group of autosomal recessive inherited diseases characterized by primary (congenital) microcephaly, the absence of visceral abnormalities, and a variable degree of cognitive impairment, short stature and facial dysmorphism. Recently, biallelic variants in the nuclear pore complex (NPC) component nucleoporin 85 gene (NUP85) were reported to cause steroid-resistant nephrotic syndrome (SRNS). Here, we report biallelic variants in NUP85 in two pedigrees with an MCPH-SCKS phenotype spectrum without SRNS, thereby expanding the phenotypic spectrum of NUP85-linked diseases. Structural analysis predicts the identified NUP85 variants cause conformational changes that could have an effect on NPC architecture or on its interaction with other NUPs. We show that mutant NUP85 is, however, associated with a reduced number of NPCs but unaltered nucleocytoplasmic compartmentalization, abnormal mitotic spindle morphology, and decreased cell viability and proliferation in one patient's cells. Our results also indicate the link of common cellular mechanisms involved in MCPH-SCKS spectrum disorders and NUP85-associated diseases. In addition to the previous studies, our results broaden the phenotypic spectrum of NUP85-linked human disease and propose a role for NUP85 in nervous system development.SCOPUS: ar.jDecretOANoAutActifinfo:eu-repo/semantics/publishe
3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources.
While scientists can often infer the biological function of proteins from their 3-dimensional quaternary structures, the gap between the number of known protein sequences and their experimentally determined structures keeps increasing. A potential solution to this problem is presented by ever more sophisticated computational protein modeling approaches. While often powerful on their own, most methods have strengths and weaknesses. Therefore, it benefits researchers to examine models from various model providers and perform comparative analysis to identify what models can best address their specific use cases. To make data from a large array of model providers more easily accessible to the broader scientific community, we established 3D-Beacons, a collaborative initiative to create a federated network with unified data access mechanisms. The 3D-Beacons Network allows researchers to collate coordinate files and metadata for experimentally determined and theoretical protein models from state-of-the-art and specialist model providers and also from the Protein Data Bank