arXiv subjects

M. V. Tamm

Publications and source records attributed to M. V. Tamm.

18 recordsLinked to original sources

arXiv2025

Quantifying world geography as seen through the lens of Soviet propaganda

Cultural data typically contains a variety of biases. In particular, geographical locations are unequally portrayed in media, creating a distorted representation of the world. Identifying and measuring such biases is crucial to understand both the data and the socio-cultural processes that have produced them. Here we suggest to measure geographical biases in a large historical news media corpus by studying the representation of cities. Leveraging ideas of quantitative urban science, we develop a mixed quantitative-qualitative procedure, which allows us to get robust quantitative estimates of the biases. These biases can be further qualitatively interpreted resulting in a hermeneutic feedback loop. We apply this procedure to a corpus of the Soviet newsreel series 'Novosti Dnya' (News of the Day) and show that city representation grows super-linearly with city size, and is further biased by city specialization and geographical location. This allows to systematically identify geographical regions which are explicitly or sneakily emphasized by Soviet propaganda and quantify their importance.

physics.soc-ph↗

arXiv2023

Nearest-neighbour directed random hyperbolic graphs

Undirected hyperbolic graph models have been extensively used as models of scale-free small-world networks with high clustering coefficient. Here we presented a simple directed hyperbolic model, where nodes randomly distributed on a hyperbolic disk are connected to a fixed number m of their nearest spatial neighbours. We introduce also a canonical version of this network (which we call "network with varied connection radius"), where maximal length of outgoing bond is space-dependent and is determined by fixing the average out-degree to m. We study local bond length, in-degree and reciprocity in these networks as a function of spatial coordinates of the nodes, and show that the network has a distinct core-periphery structure. We show that for small densities of nodes the overall in-degree has a truncated power law distribution. We demonstrate that reciprocity of the network can be regulated by adjusting an additional temperature-like parameter without changing other global properties of the network.

physics.soc-ph↗

arXiv2021

Polygon-based hierarchical planar networks based on generalized Apollonian construction

Experimentally observed complex networks are often scale-free, small-world and have unexpectedly large number of small cycles. Apollonian network is one notable example of a model network respecting simultaneously having all three of these properties. This network is constructed by a deterministic procedure of consequentially splitting a triangle into smaller and smaller triangles. Here we present a similar construction based on consequential splitting of tetragons and other polygons with even number of edges. The suggested procedure is stochastic and results in the ensemble of planar scale-free graphs, in the limit of large number of splittings the degree distribution of the graph converges to a true power law with exponent, which is smaller than 3 in the case of tetragons, and larger than 3 for polygons with larger number of edges. We show that it is possible to stochastically mix tetragon-based and hexagon-based constructions to obtain an ensemble of graphs with tunable exponent of degree distribution. Other possible planar generalizations of the Apollonian procedure are also briefly discussed.

cond-mat.stat-mech↗

arXiv2020

Analysis of English free association network reveals mechanisms of efficient solution of Remote Association Tests

We study correlations between the structure and properties of a free association network of the English language, and solutions of psycholinguistic Remote Association Tests (RATs). We show that average hardness of individual RATs is largely determined by relative positions of test words (stimuli and response) on the free association network. We argue that the solution of RATs can be interpreted as a first passage search problem on a network whose vertices are words and links are associations between words. We propose different heuristic search algorithms and demonstrate that in "easily-solving" RATs (those that are solved in 15 seconds by more than 64\% subjects) the solution is governed by "strong" network links (i.e. strong associations) directly connecting stimuli and response, and thus the efficient strategy consist in activating such strong links. In turn, the most efficient mechanism of solving medium and hard RATs consists of preferentially following sequence of "moderately weak" associations.

cs.AI↗

arXiv2020

Growth rate of 3D heaps of pieces

We consider configurational statistics of three-dimensional heaps of $N$ pieces ($N\gg 1$) on a simple cubic lattice in a large 3D bounding box of base $n \times n$, and calculate the growth rate, $Λ(n)$, of the corresponding partition function, $Z_N\sim N^θ[Λ(n)]^N$, at $n\gg 1$. Our computations rely on a theorem of G.X. Viennot \cite{viennot-rev}, which connects the generating function of a $(D+1)$-dimensional heap of pieces to the generating function of projection of these pieces onto a $D$-dimensional subspace. The growth rate of a heap of cubic blocks, which cannot touch each other by vertical faces, is thus related to the position of zeros of the partition function describing 2D lattice gas of hard squares. We study the corresponding partition function exactly at low densities on finite $n\times n$ lattice of arbitrary $n$, and extrapolate its behavior to the jamming transition density. This allows us to estimate the limiting growth rate, $Λ=\lim_{n\to\infty}Λ(n)\approx 9.5$. The same method works for any underlying 2D lattice and for various shapes of pieces: flat vertical squares, mapped to an ensemble of repulsive dimers, dominoes mapped to an ensemble of rectangles with hard-core repulsion, etc.

cond-mat.stat-mech↗

arXiv2019

Geometrical selection in growing needles

We investigate the growth of needles from a flat substrate. We focus on the situation when needles suddenly begin to grow from the seeds randomly distributed on the line. The width of needles is ignored and we additionally assume that (i) the growth rate is the same for all needles; (ii) the direction of the growth of each needle is randomly chosen from the same distribution; (iii) whenever the tip of a needle hits the body of another needle, the former needle freezes, while the latter continues to grow. We elucidate the large time behavior by employing an exact analysis and the Boltzmann equation approach. We also analyze the evolution when seeds are located on a half-line, on a finite interval. Needles growing from the two-dimensional substrate are also examined.

cond-mat.stat-mech↗

arXiv2019

Many-body contacts in fractal polymer chains and fBm trajectories

We calculate the probabilities that a trajectory of a fractional Brownian motion with arbitrary fractal dimension $d_f$ visits the same spot $n \ge 3$ times, at given moments $t_1, ..., t_n$, and obtain a determinant expression for these probabilities in terms of a displacement-displacement covariance matrix. Except for the standard Brownian trajectories with $d_f = 2$, the resulting many-body contact probabilities cannot be factorized into a product of single loop contributions. Within a Gaussian network model of a self-interacting polymer chain, which we suggested recently, the probabilities we calculate here can be interpreted as probabilities of multi-body contacts in a fractal polymer conformation with the same fractal dimension $d_f$. This Gaussian approach, which implies a mapping from fractional Brownian motion trajectories to polymer conformations, can be used as a semiquantitative model of polymer chains in topologically-stabilized conformations, e.g., in melts of unconcatenated rings or in the chromatin fiber, which is the material medium containing genetic information. The model presented here can be used, therefore, as a benchmark for interpretation of the data of many-body contacts in genomes, which we expect to be available soon in, e.g., Hi-C experiments.

physics.chem-ph↗

arXiv2018

Effective Hamiltonian of topologically stabilized polymer states

Topologically stabilized polymer conformations observed in melts of nonconcatenated polymer rings and crumpled globules, are considered to be a good candidate for the description of the spatial structure of mitotic chromosomes. Despite significant efforts, the microscopic Hamiltonian capable of describing such systems, remains yet inaccessible. In this paper we consider a Gaussian network - a system with a simple Hamiltonian quadratic in all coordinates - and show that by tuning interactions, one can obtain fractal equilibrium conformations with any fractal dimension between 2 (ideal polymer chain) and 3 (crumpled globule). Monomer-to-monomer distances in topologically stabilized states, according to our analysis of available numerical data, fit very well the Gaussian distribution, giving an additional argument in support of the quadratic Hamiltonian model. Mathematically, the resulting polymer conformations can be mapped onto the trajectories of a subdiffusive fractal Brownian particle. As a by-product of our study, two novel continual integral representations of the fractal Brownian motion are proposed.

cond-mat.stat-mech↗

arXiv2017

Folding and cytoplasm viscoelasticity contribute jointly to chromosome dynamics

The chromosome is a key player of cell physiology, and its dynamics provides valuable information about its physical organization. In both prokaryotes and eukaryotes, the short-time motion of chromosomal loci has been described as a Rouse model in a simple or viscoelastic medium. However, little emphasis has been put on the role played by the folded organization of chromosomes on the local dynamics. Clearly, stress-propagation, and thus dynamics, must be affected by such organization, but a theory allowing to extract such information from data, e.g.\ of two-point correlations, is lacking. Here, we describe a theoretical framework able to answer this general polymer dynamics question, and we provide a general scaling analysis of the stress-propagation time between two loci at a given arclength distance along the chromosomal coordinate. The results suggest a precise way to detect folding information from the dynamical coupling of chromosome segments. Additionally, we realize this framework in a specific theoretical model of a polymer with variable-range interactions in a viscoelastic medium characterized by a tunable scaling exponent, where we derive analytical estimates of the correlation functions.

physics.bio-ph↗

arXiv2017

Paths counting on simple graphs: from escape to localization

We study the asymptotic behavior of the number of paths of length $N$ on several classes of infinite graphs with a single special vertex. This vertex can work as an entropic trap for the path, i.e. under certain conditions the dominant part of long paths become localized in the vicinity of the special point instead of spreading to infinity. We study the conditions for such localization on decorated star graphs, regular trees and regular hyperbolic graphs as a function of the functionality of the special vertex. In all cases the localization occurs for large enough functionality. The particular value of transition point depends on the large-scale topology of the graph. The emergence of localization is supported by the analysis of the spectra of the adjacency matrices of corresponding finite graphs.

cond-mat.stat-mech↗

arXiv2014

Lamplighter model of a random copolymer adsorption on a line

We present a model of an AB-diblock random copolymer sequential self-packaging with local quenched interactions on a one-dimensional infinite sticky substrate. It is assumed that the A-A and B-B contacts are favorable, while A-B are not. The position of a newly added monomer is selected in view of the local contact energy minimization. The model demonstrates a self-organization behavior with the nontrivial dependence of the total energy, $E$ (the number of unfavorable contacts), on the number of chain monomers, $N$: $E\sim N^{3/4}$ for quenched random equally probable distribution of A- and B-monomers along the chain. The model is treated by mapping it onto the "lamplighter" random walk and the diffusion-controlled chemical reaction of $X+X\to 0$ type with the subdiffusive motion of reagents.

cond-mat.stat-mech↗

arXiv2014

Islands of stability in motif distributions of random networks

We consider random non-directed networks subject to dynamics conserving vertex degrees and study analytically and numerically equilibrium three-vertex motif distributions in the presence of an external field, $h$, coupled to one of the motifs. For small $h$ the numerics is well described by the "chemical kinetics" for the concentrations of motifs based on the law of mass action. For larger $h$ a transition into some trapped motif state occurs in Erdős-Rényi networks. We explain the existence of the transition by employing the notion of the entropy of the motif distribution and describe it in terms of a phenomenological Landau-type theory with a non-zero cubic term. A localization transition should always occur if the entropy function is non-convex. We conjecture that this phenomenon is the origin of the motifs' pattern formation in real evolutionary networks.

cond-mat.stat-mech↗

arXiv2013

Statistical model of intra-chromosome contact maps

The statistical properties of intra-chromosome maps obtained by a genome-wide chromosome conformation capture method (Hi-C) are described in the framework of the hierarchical crumpling model of heteropolymer chain with quenched disorder in the primary sequence. We conjecture that the observed Hi-C maps are statistical averages over many different ways of hierarchical genome folding, and show that the existence of quenched primary structure coupled with hierarchical folding can induce the observed fine structure of intra-chromosome contact maps.

q-bio.GN↗

arXiv2012

New alphabet-dependent morphological transition in a random RNA alignment

We study the fraction $f$ of nucleotides involved in the formation of a cactus--like secondary structure of random heteropolymer RNA--like molecules. In the low--temperature limit we study this fraction as a function of the number $c$ of different nucleotide species. We show, that with changing $c$, the secondary structures of random RNAs undergo a morphological transition: $f(c)\to 1$ for $c \le c_{\rm cr}$ as the chain length $n$ goes to infinity, signaling the formation of a virtually "perfect" gapless secondary structure; while $f(c)<1$ for $c>c_{\rm cr}$, what means that a non-perfect structure with gaps is formed. The strict upper and lower bounds $2 \le c_{\rm cr} \le 4$ are proven, and the numerical evidence for $c_{\rm cr}$ is presented. The relevance of the transition from the evolutional point of view is discussed.

q-bio.GN↗

arXiv2010

Sequence matching algorithms and pairing of noncoding RNAs

A new statistical method of alignment of two heteropolymers which can form hierarchical cloverleaf-like secondary structures is proposed. This offers a new constructive algorithm for quantitative determination of binding free energy of two noncoding RNAs with arbitrary primary sequences. The alignment of ncRNAs differs from the complete alignment of two RNA sequences: in ncRNA case we align only the sequences of nucleotides which constitute pairs between two different RNAs, while the secondary structure of each RNA comes into play only by the combinatorial factors affecting the entropc contribution of each molecule to the total cost function. The proposed algorithm is based on two observations: i) the standard alignment problem is considered as a zero-temperature limit of a more general statistical problem of binding of two associating heteropolymer chains; ii) this last problem is generalized onto the sequences with hierarchical cloverleaf-like structures (i.e. of RNA-type). Taking zero-temperature limit at the very end we arrive at the desired "cost function" of the system with account for entropy of side cactus-like loops. Moreover, we have demonstrated in detail how our algorithm enables to solve the "structure recovery" problem. Namely, we can predict in zero-temperature limit the cloverleaf-like (i.e. secondary) structure of interacting ncRNAs by knowing only their primary sequences.

q-bio.QM↗

arXiv2008

Unzipping of two random heteropolymers: Ground state energy and finite size effects

We have analyzed the dependence of average ground state energy per monomer, $e$, of the complex of two random heteropolymers with quenched sequences, on chain length, $n$, in the ensemble of chains with uniform distribution of primary sequences. Every chain monomer is randomly and independently chosen with the uniform probability distribution $p=1/c$ from a set of $c$ different types A, B, C, D, .... Monomers of the first chain could form saturating reversible bonds with monomers of the second chain. The bonds between similar monomer types (like A--A, B--B, C--C, etc.) have the attraction energy $u$, while the bonds between different monomer types (like A--B, A--D, B--D, etc.) have the attraction energy $v$. The main attention is paid to the computation of the normalized free energy $e(n)$ for intermediate chain lengths, $n$, and different ratios $a=\frac{v}{u}$ at sufficiently low temperatures when the entropic contribution of the loop formation is negligible compared to direct energetic interactions between chain monomers and the partition function of the chains is dominated by the ground state. The performed analysis allows one to derive the force, $f$, which is necessary to apply for unzipping of two random heteropolymer chains of equal lengths whose ends are separated by the distance $x$, averaged over all equally distributed primary structures at low temperatures for fixed values $a$ and $c$.

cond-mat.stat-mech↗

arXiv2006

Necklace-Cloverleaf Transition in Associating RNA-like Diblock Copolymers

We consider a ${\rm A}_m{\rm B}_n$ diblock copolymer, whose links are capable of forming local reversible bonds with each other. We assume that the resulting structure of the bonds is RNA--like, i.e. topologically isomorphic to a tree. We show that, depending on the relative strengths of A--A, A--B and B--B contacts, such a polymer can be in one of two different states. Namely, if a self--association is preferable (i.e., A--A and B--B bonds are comparatively stronger than A--B contacts) then the polymer forms a typical randomly branched cloverleaf structure. On the contrary, if alternating association is preferable (i.e. A--B bonds are stronger than A--A and B--B contacts) then the polymer tends to form a generally linear necklace structure (with, probably, some rear side branches and loops, which do not influence the overall characteristics of the chain). The transition between cloverleaf and necklace states is studied in details and it is shown that it is a 2nd order phase transition.

cond-mat.soft↗

arXiv2004

Statistics of randomly branched polymers in a semi-space

We investigate the statistical properties of a randomly branched 3--functional $N$--link polymer chain without excluded volume, whose one point is fixed at the distance $d$ from the impenetrable surface in a 3--dimensional space. Exactly solving the Dyson-type equation for the partition function $Z(N,d)=N^{-θ} e^{γN}$ in 3D, we find the "surface" critical exponent $θ={5/2}$, as well as the density profiles of 3--functional units and of dead ends. Our approach enables to compute also the pairwise correlation function of a randomly branched polymer in a 3D semi-space.

cond-mat.stat-mech↗