arXiv subjects

Bernat Corominas-Murtra

Publications and source records attributed to Bernat Corominas-Murtra.

At least 19 recordsLinked to original sources

arXiv2026

A hyperbolic cell cycle law for early embryonic developmental timing

Across metazoans, early embryos exhibit a strikingly conserved slowing down of their cell duplication speed, despite widely varying developmental paces and underlying molecular mechanisms. Here we show that this common behavior arises because early development unfolds along a biochemical rather than a chronological timescale, resulting from the coupling of finite maternal resource consumption to the Michaelis-Menten-like kinetics governing the rates of the biochemical reactions involved in cell duplication. This leads to a hyperbolic growth of the Cell Cycle Length (CCL), approaching a mathematical singularity, which would correspond to developmental arrest. Data from a wide range of organisms -- cnidarians, nematodes, arthropods, molluscs, echinoderms, tunicates, amphibians, and fish -- collapse on a single curve, quantitatively capturing not only a universal CCL dynamical behaviour, but also key hallmarks of early metazoan development, including cell-number temporal evolution, the dependency of CCL on cell size, and, remarkably, gastrulation timing at the predicted singularity. Crucially, experimental modulation of resource availability and consumption rates validate the model and further demonstrate that a source of heterochrony in early development is an altered biochemical timescale of resource depletion. Overall, this work reveals resource consumption rates as a fundamental mechanism driving developmental timing in early embryogenesis across species.

physics.bio-ph↗

arXiv2026

A dialog between cell adhesion and topology at the core of morphogenesis

During the development of an organism, cells must coordinate and organize to generate the correct shape, structure, and spatial patterns of tissues and organs, a process known as morphogenesis. The morphogenesis of embryonic tissues is supported by multiple processes that induce the precise physical deformations required for tissues to ultimately form organs with complex geometries. Among the most active players shaping the morphogenetic path are fine-tuned changes in cell adhesion. We review here recent advances showing that changes on cell adhesion, a local, pair-wise property defined at the cell-cell contact level has important global consequences for embryonic tissue topology, being determinant in defining both the geometric and material properties of early embryo tissues.

q-bio.TO↗

arXiv2025

Typicality, entropy and the generalization of statistical mechanics

When at equilibrium, large-scale systems obey conventional thermodynamics because they belong to microscopic configurations (or states) that are typical. Crucially, the typical states usually represent only a small fraction of the total number of possible states, and yet the characterization of the set of typical states -- the typical set -- alone is sufficient to describe the macroscopic behavior of a given system. Consequently, the concept of typicality, and the associated Asymptotic Equipartition Property allow for a drastic reduction of the degrees of freedom needed for system's statistical description. The mathematical rationale for such a simplification in the description is due to the phenomenon of concentration of measure. The later emerges for equilibrium configurations thanks to very strict constraints on the underlying dynamics, such as weekly interacting and (almost) independent system constituents. The question naturally arises as to whether the concentration of measure and related typicality considerations can be extended and applied to more general complex systems, and if so, what mathematical structure can be expected in the ensuing generalized thermodynamics. In this paper we illustrate the relevance of the concept of typicality in the toy model context of the "thermalized" coin and show how this leads naturally to Shannon entropy. We also show an intriguing connection: The characterization of typical sets in terms of Renyi and Tsallis entropies naturally leads to the free energy and partition function, respectively, and makes their relationship explicit. Finally, we propose potential ways to generalize the concept of typicality to systems where the standard microscopic assumptions do not hold.

cond-mat.stat-mech↗

arXiv2022

The typical set and entropy in stochastic systems with arbitrary phase space growth

The existence of the {\em typical set} is key for data compression strategies and for the emergence of robust statistical observables in macroscopic physical systems. Standard approaches derive its existence from a restricted set of dynamical constraints. However, given the enormous consequences for the understanding of the system's dynamics, and its role underlying the presence of stable, almost deterministic statistical patterns, a question arises whether typical sets exist in much more general scenarios. We demonstrate here that the typical set can be defined and characterized from general forms of entropy for a much wider class of stochastic processes than it was previously thought. This includes processes showing arbitrary path dependence, long range correlations or dynamic sampling spaces; suggesting that typicality is a generic property of stochastic processes, regardless of their complexity. Our results impact directly in the understanding of the stability of complex systems, open the door to new data compression strategies and points to the existence of statistical mechanics-like approaches to systems arbitrarily away from equilibrium with dynamic phase spaces. We argue that the potential emergence of robust properties in complex stochastic systems provided by the existence of typical sets has special relevance to biological systems.

cond-mat.stat-mech↗

arXiv2020

A morphospace of functional configuration to assess configural breadth based on brain functional networks

The best approach to quantify human brain functional reconfigurations in response to varying cognitive demands remains an unresolved topic in network neuroscience. We propose that such functional reconfigurations may be categorized into three different types: i) Network Configural Breadth, ii) Task-to-Task transitional reconfiguration, and iii) Within-Task reconfiguration. In order to quantify these reconfigurations, we propose a mesoscopic framework focused on functional networks (FNs) or communities. To do so, we introduce a 2D network morphospace that relies on two novel mesoscopic metrics, Trapping Efficiency (TE) and Exit Entropy (EE), which capture topology and integration of information within and between a reference set of FNs. In this study, we use this framework to quantify the Network Configural Breadth across different tasks. We show that the metrics defining this morphospace can differentiate FNs, cognitive tasks and subjects. We also show that network configural breadth significantly predicts behavioral measures, such as episodic memory, verbal episodic memory, fluid intelligence and general intelligence. In essence, we put forth a framework to explore the cognitive space in a comprehensive manner, for each individual separately, and at different levels of granularity. This tool that can also quantify the FN reconfigurations that result from the brain switching between mental states.

q-bio.NC↗

arXiv2020

Stem cell lineage survival as a noisy competition for niche access

Understanding to what extent stem cell potential is a cell-intrinsic property, or an emergent behavior coming from global tissue dynamics and geometry, is a key outstanding question of systems and stem cell biology. Here, we propose a theory of stem cell dynamics as a stochastic competition for access to a spatially-localized niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce a steady cellular stream which advects cells away from the niche, while random rearrangements enable cells away from the niche to be favourably repositioned. Importantly, even when assuming that all cells in a tissue are molecularly equivalent, we predict a common ("universal") functional dependence of the long-term clonal survival probability on distance from the niche, as well as the emergence of a well-defined number of functional stem cells, dependent only on the rate of random movements vs. mitosis-driven advection. We test the predictions of this theory on datasets on pubertal mammary gland tips, embryonic kidney tips as well homeostatic intestinal crypt. Importantly, we find good agreement for the predicted functional dependency of the competition as a function of position, and thus functional stem cell number in each organ. This argues for a key role of positional fluctuations in dictating stem cell number and dynamics, and we discuss the applicability of this theory to other settings.

cond-mat.dis-nn↗

arXiv2020

Decomposing information into copying versus transformation

In many real-world systems, information can be transmitted in two qualitatively different ways: by copying or by transformation. Copying occurs when messages are transmitted without modification, e.g., when an offspring receives an unaltered copy of a gene from its parent. Transformation occurs when messages are modified systematically during transmission, e.g., when mutational biases occur during genetic replication. Standard information-theoretic measures do not distinguish these two modes of information transfer, although they may reflect different mechanisms and have different functional consequences. Starting from a few simple axioms, we derive a decomposition of mutual information into the information transmitted by copying versus the information transmitted by transformation. We begin with a decomposition that applies when the source and destination of the channel have the same set of messages and a notion of message identity exists. We then generalize our decomposition to other kinds of channels, which can involve different source and destination sets and broader notions of similarity. In addition, we show that copy information can be interpreted as the minimal work needed by a physical copying process, which is relevant for understanding the physics of replication. We use the proposed decomposition to explore a model of amino acid substitution rates. Our results apply to any system in which the fidelity of copying, rather than simple predictability, is of critical relevance.

cs.IT↗

arXiv2018

Thermodynamics of duplication thresholds in synthetic protocell systems

Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy gradients and entropic contributions that underlie duplication. The study of synthetic, feasible systems reproducing part of the key ingredients of living entities but overcoming major sources of biological complexity is of great relevance to deepen the comprehension of the fundamental thermodynamic processes underlying life and its prevalence. In this paper an abstract -- yet realistic -- synthetic system made of small synthetic protocell aggregates is studied in detail. A fundamental relation between free energy and entropic gradients is derived for a general, non-equilibrium scenario, setting the thermodynamic conditions for the occurrence and prevalence of duplication phenomena. This relation sets explicitly how the energy gradients invested in creating and maintaining structural -- and eventually, functional -- elements of the system must always compensate the entropic gradients, whose contributions come from changes in the translational, configurational and macrostate entropies, as well as from dissipation due to irreversible transitions. Work/energy relations are also derived, defining lower bounds on the energy required for the duplication event to take place. A specific example including real ternary emulsions is provided in order to grasp the orders of magnitude involved in the problem. It is found that the minimal work invested over the system to trigger a duplication event is around $\sim 10^{-13}{\rm J}$. Without aiming to describe a truly biological process of duplication, this theoretical contribution seeks to explicitly define and identify the key actors that participate in it.

cond-mat.stat-mech↗

arXiv2018

Zipf's law, unbounded complexity and open-ended evolution

A major problem for evolutionary theory is understanding the so called {\em open-ended} nature of evolutionary change, from its definition to its origins. Open-ended evolution (OEE) refers to the unbounded increase in complexity that seems to characterise evolution on multiple scales. This property seems to be a characteristic feature of biological and technological evolution and is strongly tied to the generative potential associated with combinatorics, which allows the system to grow and expand their available state spaces. Interestingly, many complex systems presumably displaying OEE, from language to proteins, share a common statistical property: the presence of Zipf's law. Given an inventory of basic items (such as words or protein domains) required to build more complex structures (sentences or proteins) Zipf's law tells us that most of these elements are rare whereas a few of them are extremely common. Using Algorithmic Information Theory, in this paper we provide a fundamental definition for open-endedness, which can be understood as {\em postulates}. Its statistical counterpart, based on standard Shannon Information theory, has the structure of a variational problem which is shown to lead to Zipf's law as the expected consequence of an evolutionary process displaying OEE. We further explore the problem of information conservation through an OEE process and we conclude that statistical information (standard Shannon information) is not conserved, resulting into the paradoxical situation in which the increase of information content has the effect of erasing itself. We prove that this paradox is solved if we consider non-statistical forms of information. This last result implies that standard information theory may not be a suitable theoretical framework to explore the persistence and increase of the information content in OEE systems.

q-bio.PE↗

arXiv2018

Chromatic transitions in the emergence of syntax networks

The emergence of syntax during childhood is a remarkable example of how complex correlations unfold in nonlinear ways through development. In particular, rapid transitions seem to occur as children reach the age of two, which seems to separate a two-word, tree-like network of syntactic relations among words from a scale-free graphs associated to the adult, complex grammar. Here we explore the evolution of syntax networks through language acquisition using the {\em chromatic number}, which captures the transition and provides a natural link to standard theories on syntactic structures. The data analysis is compared to a null model of network growth dynamics which is shown to display nontrivial and sensible differences. In a more general level, we observe that the chromatic classes define independent regions of the graph, and thus, can be interpreted as the footprints of incompatibility relations, somewhat as opposed to modularity considerations.

q-bio.NC↗

arXiv2018

How driving rates determine the statistics of driven non-equilibrium systems with stationary distributions

Sample space reducing (SSR) processes offer a simple analytical way to understand of the origin and ubiquity of power-laws in many path-dependent complex systems. SRR processes show a wide range of applications that range from fragmentation processes, language formation to cascading pro- cesses. Here we argue that they also offer a natural framework to understand stationary distributions of generic driven non-equilibrium systems that are composed of a driving and a relaxing process. We show that the statistics of driven non-equilibrium systems can be derived from the understanding of the nature of the underlying driving process. For constant driving rates exact power-laws emerge with exponents that are related to the driving rate. If driving rates become state-dependent, or if they vary across the life-span of the process, the functional form of the state-dependence determines the statistics. Constant driving rates lead to exact power-laws, a linear state-dependence function yields exponential or Gamma distributions, a quadratic function gives the normal distribution. Logarithmic and power-law state dependence leads to log-normal and stretched exponential distribution functions, respectively. Also Weibull, Gompertz and Tsallis-Pareto distributions arise naturally from simple state-dependent driving rates. We discuss a simple physical example of consecutive elastic collisions that exactly represents a SSR process.

cond-mat.dis-nn↗

arXiv2017

Sample space reducing cascading processes produce the full spectrum of scaling exponents

Sample Space Reducing (SSR) processes are simple stochastic processes that offer a new route to understand scaling in path-dependent processes. Here we define a cascading process that generalises the recently defined SSR processes and is able to produce power laws with arbitrary exponents. We demonstrate analytically that the frequency distributions of states are power laws with exponents that coincide with the multiplication parameter of the cascading process. In addition, we show that imposing energy conservation in SSR cascades allows us to recover Fermi's classic result on the energy spectrum of cosmic rays, with the universal exponent -2, which is independent of the multiplication parameter of the cascade. Applications of the proposed process include fragmentation processes or directed cascading diffusion on networks, such as rumour or epidemic spreading.

cond-mat.stat-mech↗

arXiv2017

The three faces of entropy for complex systems -- information, thermodynamics and the maxent principle

There are three ways to conceptualize entropy: entropy as an extensive thermodynamic quantity of physical systems (Clausius, Boltzmann, Gibbs), entropy as a measure for information production of ergodic sources (Shannon), and entropy as a means for statistical inference on multinomial Bernoulli processes (Jaynes maximum entropy principle). Even though these notions are fundamentally different concepts, the functional form of the entropy for thermodynamic systems in equilibrium, for ergodic sources in information theory, and for independent sampling processes in statistical systems, is degenerate, $H(p)=-\sum_i p_i\log p_i$. For many complex systems, which are typically history-dependent, non-ergodic and non-multinomial, this is no longer the case. Here we show that for such processes the three entropy concepts lead to different functional forms of entropy. We explicitly compute these entropy functionals for three concrete examples. For Polya urn processes, which are simple self-reinforcing processes, the source information rate is $S_{\rm IT}=\frac{1}{1-c}\frac1N \log N$, the thermodynamical (extensive) entropy is $(c,d)$-entropy, $S_{\rm EXT}=S_{(c,0)}$, and the entropy in the maxent principle (MEP) is $S_{\rm MEP}(p)=-\sum_i \log p_i$. For sample space reducing (SSR) processes, which are simple path-dependent processes that are associated with power law statistics, the information rate is $S_{\rm IT}=1+ \frac12 \log W$, the extensive entropy is $S_{\rm EXT}=H(p)$, and the maxent result is $S_{\rm MEP}(p)=H(p/p_1)+H(1-p/p_1)$. Finally, for multinomial mixture processes, the information rate is given by the conditional entropy $\langle H\rangle_f$, with respect to the mixing kernel $f$, the extensive entropy is given by $H$, and the MEP functional corresponds one-to-one to the logarithm of the mixing kernel.

cond-mat.stat-mech↗

arXiv2016

Analytical computation of frequency distributions of path-dependent processes by means of a non-multinomial maximum entropy approach

Path-dependent stochastic processes are often non-ergodic and observables can no longer be computed within the ensemble picture. The resulting mathematical difficulties pose severe limits to the analytical understanding of path-dependent processes. Their statistics is typically non-multinomial in the sense that the multiplicities of the occurrence of states is not a multinomial factor. The maximum entropy principle is tightly related to multinomial processes, non-interacting systems, and to the ensemble picture; It loses its meaning for path-dependent processes. Here we show that an equivalent to the ensemble picture exists for path-dependent processes, such that the non-multinomial statistics of the underlying dynamical process, by construction, is captured correctly in a functional that plays the role of a relative entropy. We demonstrate this for self-reinforcing Pólya urn processes, which explicitly generalise multinomial statistics. We demonstrate the adequacy of this constructive approach towards non-multinomial pendants of entropy by computing frequency and rank distributions of Pólya urn processes. We show how microscopic update rules of a path-dependent process allow us to explicitly construct a non-multinomial entropy functional, that, when maximized, predicts the time-dependent distribution function.

cond-mat.stat-mech↗

arXiv2016

Fitting Power-laws in empirical data with estimators that work for all exponents

It has been repeatedly stated that maximum likelihood (ML) estimates of exponents of power-law distributions can only be reliably obtained for exponents smaller than minus one. The main argument that power laws are otherwise not normalizable, depends on the underlying sample space the data is drawn from, and is true only for sample spaces that are unbounded from above. Here we show that power-laws obtained from bounded sample spaces (as is the case for practically all data related problems) are always free of such limitations and maximum likelihood estimates can be obtained for arbitrary powers without restrictions. Here we first derive the appropriate ML estimator for arbitrary exponents of power-law distributions on bounded discrete sample spaces. We then show that an almost identical estimator also works perfectly for continuous data. We implemented this ML estimator and discuss its performance with previous attempts. We present a general recipe of how to use these estimators and present the associated computer codes.

physics.data-an↗

arXiv2016

Extreme robustness of scaling in sample space reducing processes explains Zipf's law in diffusion on directed networks

It has been shown recently that a specific class of path-dependent stochastic processes, which reduce their sample space as they unfold, lead to exact scaling laws in frequency and rank distributions. Such Sample Space Reducing processes (SSRP) offer an alternative new mechanism to understand the emergence of scaling in countless processes. The corresponding power law exponents were shown to be related to noise levels in the process. Here we show that the emergence of scaling is not limited to the simplest SSRPs, but holds for a huge domain of stochastic processes that are characterized by non-uniform prior distributions. We demonstrate mathematically that in the absence of noise the scaling exponents converge to $-1$ (Zipf's law) for almost all prior distributions. As a consequence it becomes possible to fully understand targeted diffusion on weighted directed networks and its associated scaling laws law in node visit distributions. The presence of cycles can be properly interpreted as playing the same role as noise in SSRPs and, accordingly, determine the scaling exponents. The result that Zipf's law emerges as a generic feature of diffusion on networks, regardless of its details, and that the exponent of visiting times is related to the amount of cycles in a network could be relevant for a series of applications in traffic-, transport- and supply chain management.

physics.soc-ph↗

arXiv2015

Understanding Zipf's law of word frequencies through sample-space collapse in sentence formation

The formation of sentences is a highly structured and history-dependent process. The probability of using a specific word in a sentence strongly depends on the 'history' of word-usage earlier in that sentence. We study a simple history-dependent model of text generation assuming that the sample-space of word usage reduces along sentence formation, on average. We first show that the model explains the approximate Zipf law found in word frequencies as a direct consequence of sample-space reduction. We then empirically quantify the amount of sample-space reduction in the sentences of ten famous English books, by analysis of corresponding word-transition tables that capture which words can follow any given word in a text. We find a highly nested structure in these transition tables and show that this `nestedness' is tightly related to the power law exponents of the observed word frequency distributions. With the proposed model it is possible to understand that the nestedness of a text can be the origin of the actual scaling exponent, and that deviations from the exact Zipf law can be understood by variations of the degree of nestedness on a book-by-book basis. On a theoretical level we are able to show that in case of weak nesting, Zipf's law breaks down in a fast transition. Unlike previous attempts to understand Zipf's law in language the sample-space reducing model is not based on assumptions of multiplicative, preferential, or self-organised critical mechanisms behind language formation, but simply used the empirically quantifiable parameter 'nestedness' to understand the statistics of word frequencies.

physics.soc-ph↗

arXiv2015

Understanding scaling through history-dependent processes with collapsing sample space

History-dependent processes are ubiquitous in natural and social systems. Many such stochastic processes, especially those that are associated with complex systems, become more constrained as they unfold, meaning that their sample-space, or their set of possible outcomes, reduces as they age. We demonstrate that these sample-space reducing (SSR) processes necessarily lead to Zipf's law in the rank distributions of their outcomes. We show that by adding noise to SSR processes the corresponding rank distributions remain exact power-laws, $p(x)\sim x^{-λ}$, where the exponent directly corresponds to the mixing ratio of the SSR process and noise. This allows us to give a precise meaning to the scaling exponent in terms of the degree to how much a given process reduces its sample-space as it unfolds. Noisy SSR processes further allow us to explain a wide range of scaling exponents in frequency distributions ranging from $α= 2$ to $\infty$. We discuss several applications showing how SSR processes can be used to understand Zipf's law in word frequencies, and how they are related to diffusion processes in directed networks, or ageing processes such as in fragmentation processes. SSR processes provide a new alternative to understand the origin of scaling in complex systems without the recourse to multiplicative, preferential, or self-organised critical processes.

physics.soc-ph↗