Localized Dynamics in the Floquet Quantum East Model.

We introduce and study the discrete-time version of the quantum East model, an interacting quantum spin chain inspired by simple kinetically constrained models of classical glasses. Previous work has established that its continuous-time counterpart displays a disorder-free localization transition signaled by the appearance of an exponentially large (in the volume) family of nonthermal, localized eigenstates. Here we combine analytical and numerical approaches to show that (i) the transition persists for discrete times, in fact, it is present for any finite value of the time step apart from a zero measure set; (ii) it is directly detected by following the nonequilibrium dynamics of the fully polarized state. Our findings imply that the transition is currently observable in state-of-the-art platforms for digital quantum simulation.

Scrambling Is Necessary but Not Sufficient for Chaos.

We show that out-of-time-order correlators (OTOCs) constitute a probe for local-operator entanglement (LOE). There is strong evidence that a volumetric growth of LOE is a faithful dynamical indicator of quantum chaos, while OTOC decay corresponds to operator scrambling, often conflated with chaos. We show that rapid OTOC decay is a necessary but not sufficient condition for linear (chaotic) growth of the LOE entropy. We analytically support our results through wide classes of local-circuit models of many-body dynamics, including both integrable and nonintegrable dual-unitary circuits. We show sufficient conditions under which local dynamics leads to an equivalence of scrambling and chaos.

Cohesin and CTCF control the dynamics of chromosome folding.

In mammals, interactions between sequences within topologically associating domains enable control of gene expression across large genomic distances. Yet it is unknown how frequently such contacts occur, how long they last and how they depend on the dynamics of chromosome folding and loop extrusion activity of cohesin. By imaging chromosomal locations at high spatial and temporal resolution in living cells, we show that interactions within topologically associating domains are transient and occur frequently during the course of a cell cycle. Interactions become more frequent and longer in the presence of convergent CTCF sites, resulting in suppression of variability in chromosome folding across time. Supported by physical models of chromosome dynamics, our data suggest that CTCF-anchored loops last around 10 min. Our results show that long-range transcriptional regulation might rely on transient physical proximity, and that cohesin and CTCF stabilize highly dynamic chromosome structures, facilitating selected subsets of chromosomal interactions.

Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data.

Construction of chromosomes 3D models based on single cell Hi-C data constitute an important challenge. We present a reconstruction approach, DPDchrom, that incorporates basic knowledge whether the reconstructed conformation should be coil-like or globular and spring relaxation at contact sites. In contrast to previously published protocols, DPDchrom can naturally form globular conformation due to the presence of explicit solvent. Benchmarking of this and several other methods on artificial polymer models reveals similar reconstruction accuracy at high contact density and DPDchrom advantage at low contact density. To compare 3D structures insensitively to spatial orientation and scale, we propose the Modified Jaccard Index. We analyzed two sources of the contact dropout: contact radius change and random contact sampling. We found that the reconstruction accuracy exponentially depends on the number of contacts per genomic bin allowing to estimate the reconstruction accuracy in advance. We applied DPDchrom to model chromosome configurations based on single-cell Hi-C data of mouse oocytes and found that these configurations differ significantly from a random one, that is consistent with other studies.

Chaos and Ergodicity in Extended Quantum Systems with Noisy Driving.

We study the time-evolution operator in a family of local quantum circuits with random fields in a fixed direction. We argue that the presence of quantum chaos implies that at large times the time-evolution operator becomes effectively a random matrix in the many-body Hilbert space. To quantify this phenomenon, we compute analytically the squared magnitude of the trace of the evolution operator-the generalized spectral form factor-and compare it with the prediction of random matrix theory. We show that for the systems under consideration, the generalized spectral form factor can be expressed in terms of dynamical correlation functions of local observables in the infinite temperature state, linking chaotic and ergodic properties of the systems. This also provides a connection between the many-body Thouless time τ_{th}-the time at which the generalized spectral form factor starts following the random matrix theory prediction-and the conservation laws of the system. Moreover, we explain different scalings of τ_{th} with the system size observed for systems with and without the conservation laws.

HP1 drives de novo 3D genome reorganization in early Drosophila embryos.

Fundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown1,2. Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein 1a (HP1a) is essential for de novo 3D genome organization during Drosophila early development. The binding of HP1a at pericentromeric heterochromatin is required to establish clustering of pericentromeric regions. Moreover, HP1a binding within chromosome arms is responsible for overall chromosome folding and has an important role in the formation of B-compartment regions. However, depletion of HP1a does not affect the A-compartment, which suggests that a different molecular mechanism segregates active chromosome regions. Our work identifies HP1a as an epigenetic regulator that is involved in establishing the global structure of the genome in the early embryo.

Crystallization of semiflexible polymers in melts and solutions.

We studied the crystallization of semiflexible polymer chains in melts and poor-solvent solutions with different concentrations using dissipative particle dynamics (DPD) computer simulation techniques. We used the coarse-grained polymer model to reveal the general principles and microscopic scenario of crystallization in such systems at large time and length scales. It covers both primary and secondary nucleation as well as crystallites' merging. The parameters of the DPD model were chosen appropriately to reproduce the entanglements of polymer chains. We started from an initial homogeneous disordered solution of Gaussian chains and observed the initial stages of crystallization process caused in our model by orientational ordering of polymer chains and polymer-solvent phase separation. We found that the overall crystalline fraction at the end of the crystallization process decreases with the increasing polymer volume fraction while the steady-state crystallization speed at later stages does not depend on the polymer volume fraction. The average crystallite size has a maximal value in the systems with a polymer volume fraction from 0.7 to 0.95. In our model, these polymer concentrations represent an optimal value in the sense of balance between the amount of polymer material available to increase the crystallite size and chain entanglements, that prevent crystallites' growth and merging. On large time scales, our model allows us to observe lamellar thickening linear in logarithmic time scale.

Order and stochasticity in the folding of individual Drosophila genomes.

Mammalian and Drosophila genomes are partitioned into topologically associating domains (TADs). Although this partitioning has been reported to be functionally relevant, it is unclear whether TADs represent true physical units located at the same genomic positions in each cell nucleus or emerge as an average of numerous alternative chromatin folding patterns in a cell population. Here, we use a single-nucleus Hi-C technique to construct high-resolution Hi-C maps in individual Drosophila genomes. These maps demonstrate chromatin compartmentalization at the megabase scale and partitioning of the genome into non-hierarchical TADs at the scale of 100 kb, which closely resembles the TAD profile in the bulk in situ Hi-C data. Over 40% of TAD boundaries are conserved between individual nuclei and possess a high level of active epigenetic marks. Polymer simulations demonstrate that chromatin folding is best described by the random walk model within TADs and is most suitably approximated by a crumpled globule build of Gaussian blobs at longer distances. We observe prominent cell-to-cell variability in the long-range contacts between either active genome loci or between Polycomb-bound regions, suggesting an important contribution of stochastic processes to the formation of the Drosophila 3D genome.

Kinetic mechanisms of crumpled globule formation.

A homopolymer chain with beads forming pairwise reversible bonds is a well-known model in polymer physics. We studied the kinetics of homopolymer chain collapse, which was induced by pairwise reversible bond formation. We compared the kinetic mechanism of this coil-globule transition with the mechanism of collapse in a poor solvent. We discovered that if collapse of a spatially confined chain is induced by formation of long-living pairwise reversible bonds, the transient structures do not resemble classical pearl-necklace conformations formed during collapse in a poor solvent. However, both types of collapse lead to formation of a metastable state of a crumpled globule, which is one of the well-known models of interphase chromatin structure in different organisms. Moreover, we found that the stability and dynamics of this state can be controlled by the fraction of reversible bonds and bond lifetime.

Exact Correlation Functions for Dual-Unitary Lattice Models in 1+1 Dimensions.

We consider a class of quantum lattice models in 1+1 dimensions represented as local quantum circuits that enjoy a particular dual-unitarity property. In essence, this property ensures that both the evolution in time and that in space are given in terms of unitary transfer matrices. We show that for this class of circuits, generically nonintegrable, one can compute explicitly all dynamical correlations of local observables. Our result is exact, nonpertubative, and holds for any dimension d of the local Hilbert space. In the minimal case of qubits (d=2) we also present a classification of all dual-unitary circuits which allows us to single out a number of distinct classes for the behavior of the dynamical correlations. We find noninteracting classes, where all correlations are preserved, the ergodic and mixing one, where all correlations decay, and, interestingly, also classes that are both interacting and nonergodic.

Scent lineups compared across eleven countries: Looking for the future of a controversial forensic technique.

A scent lineup is generally a procedure whereby a dog's alerting behavior is used to establish that the dog detects two scents, one from a crime scene and one from a suspect, as deriving from the same person. The aim of this article is to compare methodologies of using dogs in scent lineups as a means of identifying perpetrators of crimes. It is hoped that this comparative approach, looking at countries where the method is currently or has in the past been used, will help determine what issues should be addressed in order to assure that the scent lineup will have a future as a forensic technique. Participants from eleven countries-Belgium, The Czech Republic, Finland, France, Germany, Hungary, Lithuania, The Netherlands, Poland, Russia, and the U.S.-completed a survey questionnaire regarding key aspects of the scent lineup procedures used by the police in their countries. Although there was broad overlap on certain matters, such as the use of control and zero trials, collection of decoy scents from individuals of similar gender and race as the suspect, materials for holding scent, frequency of cleaning and changing stations, and use and timing of rewards, there were significant differences in the degree of blindness required, who calls an alert (handler or experimenter), and whether handlers can work with more than one dog. The gap between recommendations and results available from the scientific literature and procedures used in police practice was greater for some countries than others, even taking into account that some scientific methodologies might be expensive or impractical given agency resources. The authors make recommendations about how to go forward if scent lineups are to remain a valid forensic technique.

Nuclear lamina integrity is required for proper spatial organization of chromatin in Drosophila.

How the nuclear lamina (NL) impacts on global chromatin architecture is poorly understood. Here, we show that NL disruption in Drosophila S2 cells leads to chromatin compaction and repositioning from the nuclear envelope. This increases the chromatin density in a fraction of topologically-associating domains (TADs) enriched in active chromatin and enhances interactions between active and inactive chromatin. Importantly, upon NL disruption the NL-associated TADs become more acetylated at histone H3 and less compact, while background transcription is derepressed. Two-colour FISH confirms that a TAD becomes less compact following its release from the NL. Finally, polymer simulations show that chromatin binding to the NL can per se compact attached TADs. Collectively, our findings demonstrate a dual function of the NL in shaping the 3D genome. Attachment of TADs to the NL makes them more condensed but decreases the overall chromatin density in the nucleus by stretching interphase chromosomes.

Micellar polymerization: Computer simulations by dissipative particle dynamics.

Nowadays, micellar polymerization is widely used in different fields of industry and research, including modern living polymerization technique. However, this process has many variables and there is no comprehensive model to describe all features. This research presents simulation methodology which describes key properties of such reactions to take a guide through a variety of their modifications. Dissipative particle dynamics is used in addition to Monte Carlo scheme to simulate initiation, propagation, and termination events. Influence of initiation probability and different termination processes on final conversion and molecular-weight distribution are presented. We demonstrate that prolonged initiation leads to increasing in polymer average molecular weight, and surface termination events play major role in conversion limitation, in comparison with recombination. © 2018 Wiley Periodicals, Inc.

Exact Spectral Form Factor in a Minimal Model of Many-Body Quantum Chaos.

The most general and versatile defining feature of quantum chaotic systems is that they possess an energy spectrum with correlations universally described by random matrix theory (RMT). This feature can be exhibited by systems with a well-defined classical limit as well as by systems with no classical correspondence, such as locally interacting spins or fermions. Despite great phenomenological success, a general mechanism explaining the emergence of RMT without reference to semiclassical concepts is still missing. Here we provide the example of a quantum many-body system with no semiclassical limit (no large parameter) where the emergence of RMT spectral correlations is proven exactly. Specifically, we consider a periodically driven Ising model and write the Fourier transform of spectral density's two-point function, the spectral form factor, in terms of a partition function of a two-dimensional classical Ising model featuring a space-time duality. We show that the self-dual cases provide a minimal model of many-body quantum chaos, where the spectral form factor is demonstrated to match RMT for all values of the integer time variable t in the thermodynamic limit. In particular, we rigorously prove RMT form factor for an odd t, while we formulate a precise conjecture for an even t. The results imply ergodicity for any finite amount of disorder in the longitudinal field, rigorously excluding the possibility of many-body localization. Our method provides a novel route for obtaining exact nonperturbative results in nonintegrable systems.

Unraveling the mechanisms of chromatin fibril packaging.

Recent data indicate that eukaryotic chromosomes are organized into Topologically Associating Domains (TADs); however, the mechanisms underlying TAD formation remain obscure. Based on the results of Hi-C analysis performed on 4 Drosophila melanogaster cell lines, we have proposed that specific properties of nucleosomes in active and repressed chromatin play a key role in the formation of TADs. Our computer simulations showed that the ability of "inactive" nucleosomes to stick to each other and the lack of such ability in "active" nucleosomes is sufficient for spatial segregation of these types of chromatin, which is revealed in the Hi-C analysis as TAD/inter-TAD partitioning. However, some Drosophila and mammalian TADs contain both active and inactive chromatin, a fact that does not fit this model. Herein, we present additional arguments for the model by postulating that transcriptionally active chromatin is extruded on the surface of a TAD, and discuss the possible impact of this organization on the enhancer-promoter communication and on the segregation of TADs.

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains.

Recent advances enabled by the Hi-C technique have unraveled many principles of chromosomal folding that were subsequently linked to disease and gene regulation. In particular, Hi-C revealed that chromosomes of animals are organized into topologically associating domains (TADs), evolutionary conserved compact chromatin domains that influence gene expression. Mechanisms that underlie partitioning of the genome into TADs remain poorly understood. To explore principles of TAD folding in Drosophila melanogaster, we performed Hi-C and poly(A)(+) RNA-seq in four cell lines of various origins (S2, Kc167, DmBG3-c2, and OSC). Contrary to previous studies, we find that regions between TADs (i.e., the inter-TADs and TAD boundaries) in Drosophila are only weakly enriched with the insulator protein dCTCF, while another insulator protein Su(Hw) is preferentially present within TADs. However, Drosophila inter-TADs harbor active chromatin and constitutively transcribed (housekeeping) genes. Accordingly, we find that binding of insulator proteins dCTCF and Su(Hw) predicts TAD boundaries much worse than active chromatin marks do. Interestingly, inter-TADs correspond to decompacted inter-bands of polytene chromosomes, whereas TADs mostly correspond to densely packed bands. Collectively, our results suggest that TADs are condensed chromatin domains depleted in active chromatin marks, separated by regions of active chromatin. We propose the mechanism of TAD self-assembly based on the ability of nucleosomes from inactive chromatin to aggregate, and lack of this ability in acetylated nucleosomal arrays. Finally, we test this hypothesis by polymer simulations and find that TAD partitioning may be explained by different modes of inter-nucleosomal interactions for active and inactive chromatin.