arXiv subjects

Y. Zhan

Publications and source records attributed to Y. Zhan.

5 recordsLinked to original sources

arXiv2023

Locality of contacts determines the subdiffusion exponents in polymeric models of chromatin

Loop extrusion by motor proteins mediates the attractive interactions in chromatin on the length scale of megabases, providing the polymer with a well-defined structure and at the same time determining its dynamics. The mean square displacement of chromatin loci varies from a Rouse-like scaling to a more constrained subdiffusion, depending on cell type, genomic region and time scale. With a simple polymeric model, we show that such a Rouse-like dynamics occurs when the parameters of the model are chosen so that contacts are local along the chain, while in presence of non-local contacts, we observe subdiffusion at short time scales with exponents smaller than 0.5. Such exponents are independent of the detailed choice of the parameters and build a master curve that depends only on the mean locality of the resulting contacts. We compare the loop-extrusion model with a polymeric model with static links, showing that also in this case only the presence of nonlocal contacts can produce low-exponent subdiffusion. We interpret these results in terms of a simple analytical model.

q-bio.BM↗

arXiv2020

Effective Model of Loop Extrusion Predicts Chromosomal Domains

An active loop-extrusion mechanism is regarded as the main out--of--equilibrium mechanism responsible for the structuring of megabase-sized domains in chromosomes. We developed a model to study the dynamics of the chromosome fibre by solving the kinetic equations associated with the motion of the extruder. By averaging out the position of the extruder along the chain, we build an effective equilibrium model capable of reproducing experimental contact maps based solely on the positions of extrusion--blocking proteins. We assessed the quality of the effective model using numerical simulations of chromosomal segments and comparing the results with explicit-extruder models and experimental data.

q-bio.BM↗

arXiv2016

The looping probability of random heteropolymers helps to understand the scaling properties of biopolymers

Random heteropolymers are a minimal description of biopolymers and can provide a theoretical framework to the investigate the formation of loops in biophysical experiments. A two--state model provides a consistent and robust way to study the scaling properties of loop formation in polymers of the size of typical biological systems. Combining it with self--adjusting simulated--tempering simulations, we can calculate numerically the looping properties of several realizations of the random interactions within the chain. Differently from homopolymers, random heteropolymers display at different temperatures a continuous set of scaling exponents. The necessity of using self--averaging quantities makes finite--size effects dominant at low temperatures even for long polymers, shadowing the length--independent character of looping probability expected in analogy with homopolymeric globules. This could provide a simple explanation for the small scaling exponents found in experiments, for example in chromosome folding.

q-bio.QM↗

arXiv2015

An independent test of the photometric selection of white dwarf candidates using LAMOST DR3

In Gentile Fusillo et al. (2015) we developed a selection method for white dwarf candidates which makes use of photometry, colours and proper motions to calculate a probability of being a white dwarf (Pwd). The application of our method to the Sloan Digital Sky Survey (SDSS) data release 10 resulted in nearly 66,000 photometrically selected objects with a derived Pwd, approximately 21000 of which are high confidence white dwarf candidates. Here we present an independent test of our selection method based on a sample of spectroscopically confirmed white dwarfs from the LAMOST (Large Sky Area Multi-Fiber Spectroscopic Telescope) survey. We do this by cross matching all our $\sim$66,000 SDSS photometric white dwarf candidates with the over 4 million spectra available in the third data release of LAMOST. This results in 1673 white dwarf candidates with no previous SDSS spectroscopy, but with available LAMOST spectra. Among these objects we identify 309 genuine white dwarfs. We find that our Pwd can efficiently discriminate between confirmed LAMOST white dwarfs and contaminants. Our white dwarf candidate selection method can be applied to any multi-band photometric survey and in this work we conclusively confirm its reliability in selecting white dwarfs without recourse to spectroscopy. We also discuss the spectroscopic completeness of white dwarfs in LAMOST, as well as deriving effective temperatures, surface gravities and masses for the hydrogen-rich atmosphere white dwarfs in the newly identified LAMOST sample.

astro-ph.SR↗

arXiv2007

Negative Spin Valve effects in manganite/organic based devices

We report detailed investigations of hybrid organic-inorganic vertical spin valves. Spin polarized injection in tris(8-hydroxyquinoline) aluminum (Alq3) organic semiconductor (OS) was performed using La0.7Sr0.3MnO3 manganite as the bottom electrode and Co as the top electrode. While manganite was directly connected to the organic semiconductor layer, a thin tunnel barrier was placed between the OS and the Co electrode. A clear negative spin valve effect - low resistance for antiparallel electrodes configuration - was observed below 210 K in various devices using two different tunnel barriers: LiF and Al2O3. The magnetoresistance effect was found to be strongly asymmetric with respect to the bias voltage. Photoelectron Spectroscopy (PES) investigation of the interface between manganite and Alq3 revealed a strong interface dipole, which leads to a better matching of the metal Fermi level with Alq3 LUMO (1.1 eV) rather than with HOMO level (1.7 eV). This unequivocally indicates that the current in these devices is dominated by the electron channel, and not by holes as previously suggested. The knowledge of the energy diagram at the bottom interface allowed us to work out a semi- quantitative model explaining both negative spin valve effect and strong voltage asymmetry. This model involves a sharp energy selection of the moving charges by the very narrow LUMO level of the organic material leading to peculiar resonant effects.

cond-mat.mtrl-sci↗