A5041646890- Genomics and Chromatin Dynamics
- Advanced Materials and Mechanics
- Theoretical and Computational Physics
- Cellular Mechanics and Interactions
- Gene Regulatory Network Analysis
- Structural Analysis and Optimization
- RNA Research and Splicing
- Black Holes and Theoretical Physics
- Algebraic structures and combinatorial models
- Nonlinear Waves and Solitons
- Genetics, Aging, and Longevity in Model Organisms
- Corporate Finance and Governance
- Light effects on plants
- Stochastic processes and statistical mechanics
- Protein Structure and Dynamics
- Microtubule and mitosis dynamics
- Plant Molecular Biology Research
- Diffusion and Search Dynamics
- Random Matrices and Applications
- Bioinformatics and Genomic Networks
- Advanced Thermodynamics and Statistical Mechanics
- Gene expression and cancer classification
- Phase Equilibria and Thermodynamics
- Material Dynamics and Properties
- Complex Network Analysis Techniques
Independent University of Moscow
2024
Skolkovo Institute of Science and Technology
2017-2023
Interdisciplinary Scientific Center J.-V. Poncelet
2018-2022
Centre National de la Recherche Scientifique
2022
Massachusetts Institute of Technology
2020-2022
Sorbonne Université
2022
Institut Curie
2022
Université Paris Sciences et Lettres
2022
Lomonosov Moscow State University
2016-2019
Moscow State University
2018
The topological state of chromosomes determines their mechanical properties, dynamics, and function. Recent work indicated that interphase are largely free entanglements. Here, we use Hi-C, polymer simulations, multi-contact 3C find that, by contrast, mitotic self-entangled. We explore how a self-entangled is converted into an unentangled during exit. Most entanglements removed anaphase/telophase, with remaining ones early G1, in topoisomerase-II-dependent process. Polymer models suggest...
Abstract 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 a population. Here, we use single-nucleus Hi-C technique construct high-resolution maps individual genomes. These demonstrate...
Chromosomes are exceedingly long topologically-constrained polymers compacted in a cell nucleus. We recently suggested that chromosomes organized into loops by an active process of loop extrusion. Yet remain elusive to direct observations living cells; detection and characterization myriads such is major challenge. The lack tractable physical model polymer folded limits our ability interpret experimental data detect loops. Here, we introduce new - sequence loops, solve it analytically. Our...
Chromosomes are key players of cell physiology, their dynamics provides valuable information about its physical organization. In both prokaryotes and eukaryotes, the short-time motion chromosomal loci has been described with a Rouse model in simple or viscoelastic medium. However, little emphasis put on influence folded organization chromosomes local dynamics. Clearly, stress propagation, thus dynamics, must be affected by such organization, but theory allowing us to extract from data, e.g.,...
Chromosomes are crumpled polymer chains further folded into a sequence of stochastic loops via loop extrusion. While extrusion has been verified experimentally, the particular means by which extruding complexes bind DNA remains controversial. Here we analyze behavior contact probability function for with two possible modes cohesin binding, topological and nontopological mechanisms. As show, in model chain resembles comb-like that can be solved analytically using quenched disorder approach....
Chromosomes are exceedingly long topologically-constrained polymers compacted in a cell nucleus. We recently suggested that chromosomes organized into loops by an active process of loop extrusion. Yet remain elusive to direct observations living cells; detection and characterization myriads such is major challenge. The lack tractable physical model polymer folded limits our ability interpret experimental data detect loops. Here, we introduce new – sequence loops, solve it analytically. Our...
We propose a universal method of relating the Calogero model to set decoupled particles on real line, which can be uniformly applied both conformal and nonconformal versions as well supersymmetric extensions. For models simplification is achieved at price nonlocal realization full symmetry in Hilbert space resulting free theory. As an application, we construct two different N=2 superconformal
Topologically stabilized polymer conformations in melts of nonconcatenated rings and crumpled globules are considered to be a good candidate for the description spatial structure mitotic chromosomes. Despite significant efforts, microscopic Hamiltonian capable describing such systems still remains unknown. We describe conformation by Gaussian network - system with quadratic all coordinates show that tuning interaction constants, one can obtain equilibrium any fractal dimension between 2 (an...
The following question is the subject of our work: could a two-dimensional random path pushed by some constraints to an improbable "large deviation regime", possess extreme statistics with one-dimensional Kardar-Parisi-Zhang (KPZ) fluctuations? answer positive, though non-universal, since fluctuations depend on underlying geometry. We consider in details two examples 2D systems for which imposed external force stationary stochastic process stay atypical regime anomalous statistics. first...
Abstract Chromatin communities stabilized by protein machinery play essential role in gene regulation and refine global polymeric folding of the chromatin fiber. However, treatment these framework classical network theory (stochastic block model, SBM) does not take into account intrinsic linear connectivity loci. Here we propose polymer paving way for community detection networks. On basis this new model modify non-backtracking flow operator suggest first protocol annotation compartmental...
We calculate the probabilities that a trajectory of fractional Brownian motion with arbitrary fractal dimension $d_f$ visits same spot $n \ge 3$ times, at given moments $t_1, ..., t_n$, and obtain determinant expression for these in terms displacement-displacement covariance matrix. Except standard trajectories $d_f = 2$, resulting many-body contact cannot be factorized into product single loop contributions. Within Gaussian network model self-interacting polymer chain, which we suggested...
Optimal buckling of a tissue, e.g. plant leaf, growing by means exponential division its peripheral cells, is considered in the framework conformal approach. It shown that boundary profile tissue described 2D eikonal equation, which provides geometric optic approximation for wavefront propagating medium with an inhomogeneous refraction coefficient. A variety optimal surfaces embedded 3D controlled spatial dependence coefficient which, turn, dictated local growth protocol.
Micelle formation of amphiphilic block copolymers various architectures comprising both flexible and rodlike blocks were studied in a selective solvent via dissipative particle dynamics (DPD) simulations. Peculiarities self-assembly Y-shaped (insoluble rigid two soluble arms) comblike (soluble backbone with insoluble side chains) are compared those equivalent rod–coil diblock copolymers. We have shown that aggregation the into dense core micelles is accompanied by their nematic ordering....
SUMMARY The topological state of chromosomes determines their mechanical properties, dynamics, and function. Recent work indicated that interphase are largely free entanglements. Here, we use Hi-C, polymer simulations multi-contact 3C, propose that, in contrast, mitotic self-entangled. We explore how a self-entangled is converted into an unentangled during exit. Most entanglements removed anaphase/telophase, with remaining ones early G1, Topoisomerase II-dependent process. Polymer models...
We predict morphology-controlled nanopumping of a nonselective solvent in the swollen lamellae-forming diblock copolymer systems under applied uniaxial deformation sample. Normal compression lamellae at conditions that is not extruded (evaporated) from sample (so-called "sealed" sample) leads to flow lamellar interior AB interfaces. On contrary, normal expansion results increase concentration interfaces which practically accompanied by interior. The physical reason for shown be related...
Knowledge of beneficial owners companies is key to monitoring and managing wealth inequality in any country. Here we propose a robust scalable network-based algorithm reveal hidden ultimate public ownership data. Our approach based on the idea Katz centrality complex networks circumvents problem cyclic used obscure effective control through closed chains intermediaries. When applied country-scale directed network with 6 million nodes, identifies holders every organisation 2021’s Russia. The...