arXiv subjects

Orr Levy

Publications and source records attributed to Orr Levy.

6 recordsLinked to original sources

arXiv2026

The mechanistic origin of branching-driven nucleation in abrupt phase transitions

Phase transitions are the macroscopic manifestation of microscopic processes that drive a system towards a new state. The detailed evolution of these processes, particularly in abrupt phase transitions, are currently not fully understood. Here, we introduce a theoretical framework based on internal node dependencies within a single-layer lattice. Crucially, we demonstrate that the fundamental mechanism underlying abrupt transitions is nucleation propagation preceded by a slow cascading process which scales with the range of dependencies. Our findings show that the synergy between these two distinct stages is essential for the occurrence of an abrupt transition. The first stage of a slow cascading mechanism was recently observed experimentally in superconducting layered materials, where heat acts as the dependency links, for the limit of infinite dependency range. Our model thus generalizes the framework to include finite dependency ranges, revealing previously unobserved mechanisms that could be experimentally verified through controlling the range of thermal diffusion in the material. As a universal mechanism, our model provides a robust method to test nucleation-controlled phase transitions in multiple systems, providing a path to discover and understand microscopic mechanisms in phase transitions.

physics.soc-ph↗

arXiv2025

Stable Emotional Co-occurrence Patterns Revealed by Network Analysis of Social Media

Examining emotion interactions as an emotion network in social media offers key insights into human psychology, yet few studies have explored how fluctuations in such emotion network evolve during crises and normal times. This study proposes a novel computational approach grounded in network theory, leveraging large-scale Japanese social media data spanning varied crisis events (earthquakes and COVID-19 vaccination) and non-crisis periods over the past decade. Our analysis identifies and evaluates links between emotions through the co-occurrence of emotion-related concepts (words), revealing a stable structure of emotion network across situations and over time at the population level. We find that some emotion links (represented as link strength) such as emotion links associated with Tension are significantly strengthened during earthquake and pre-vaccination periods. However, the rank of emotion links remains highly intact. These findings challenge the assumption that emotion co-occurrence is context-based and offer a deeper understanding of emotions' intrinsic structure. Moreover, our network-based framework offers a systematic, scalable method for analyzing emotion co-occurrence dynamics, opening new avenues for psychological research using large-scale textual data.

cs.SI↗

arXiv2025

Predicting cell-specific gene expression profile and knockout impact through deep learning

Gene expression data is essential for understanding how genes are regulated and interact within biological systems, providing insights into disease pathways and potential therapeutic targets. Gene knockout has proven to be a fundamental technique in molecular biology, allowing the investigation of the function of specific genes in an organism, as well as in specific cell types. However, gene expression patterns are quite heterogeneous in single-cell transcriptional data from a uniform environment, representing different cell states, which produce cell-type and cell-specific gene knockout impacts. A computational method that can predict the single-cell resolution knockout impact is still lacking. Here, we present a data-driven framework for learning the mapping between gene expression profiles derived from gene assemblages, enabling the accurate prediction of perturbed expression profiles following knockout (KO) for any cell, without relying on prior perturbed data. We systematically validated our framework using synthetic data generated from gene regulatory dynamics models, two mouse knockout single-cell datasets, and high-throughput in vitro CRISPRi Perturb-seq data. Our results demonstrate that the framework can accurately predict both expression profiles and KO effects at the single-cell level. Our approach provides a generalizable tool for inferring gene function at single-cell resolution, offering new opportunities to study genetic perturbations in contexts where large-scale experimental screens are infeasible.

q-bio.GN↗

arXiv2023

Gene regulatory interactions limit the gene expression diversity

The diversity of expressed genes plays a critical role in cellular specialization, adaptation to environmental changes, and overall cell functionality. This diversity varies dramatically across cell types and is orchestrated by intricate, dynamic, and cell type-specific gene regulatory networks (GRNs). Despite extensive research on GRNs, their governing principles, as well as the underlying forces that have shaped them, remain largely unknown. Here, we investigated whether there is a tradeoff between the diversity of expressed genes and the intensity of GRN interactions. We have developed a computational framework that evaluates GRN interaction intensity from scRNA-seq data and used it to analyze simulated and real scRNA-seq data collected from different tissues in humans, mice, fruit flies, and C. elegans. We find a significant tradeoff between diversity and interaction intensity, driven by stability constraints, where the GRN could be stable up to a critical level of complexity - a product of gene expression diversity and interaction intensity. Furthermore, we analyzed hematopoietic stem cell differentiation data and find that the overall complexity of unstable transition states cells is higher than that of stem cells and fully differentiated cells. Our results suggest that GRNs are shaped by stability constraints which limit the diversity of gene expression.

physics.bio-ph↗

arXiv2023

A complexity perspective on the geographical location of companies: How distance reduce trade between firms

Geometrical distance is an important constraining factor underpinning the emergence of social and economic interactions of complex systems. Yet, agent-based studies supported by granular analysis of distances are limited. Here, we develop a complexity method that places the real physical world, represented by the actual geographical location of individual firms in Japan, at the epicentre of our research. By combining methods derived from network science (to evaluate the emerging properties of the agents) together with information theory measures (to capture the strength of interaction among these agents), we can systematically analyse a comprehensive dataset of Japanese inter-firm business transactions network and evaluate the effects of spatial features on the structural patterns of the economy. We find that the normalised probability distributions of distances between interacting firms show a power law like decay concomitant to the sizes of firms and regions, with slower decays in major cities. Furthermore, small firms would reach large distances to become a customer of large firms while trading between either only small firms, or only large firms, tends to be at smaller distances. However, a time evolution analysis suggests that a level of market optimisation occurs over time as a reduction in the overall average trading distances in last 20 years can be observed. Lastly, our analysis concerning the trading dynamics among prefectures indicate that the preference to trade with neighbouring prefectures tends to be more pronounced at rural regions as opposed to the larger central conurbations, leading to the formation of three distinct types of regional geographical clusters.

physics.soc-ph↗

arXiv2023

Nucleation phenomena and extreme vulnerability of spatial k-core systems

K-core percolation is a fundamental dynamical process in complex networks with applications that span numerous real-world systems. Earlier studies focus primarily on random networks without spatial constraints and reveal intriguing mixed-order transitions. However, real-world systems, ranging from transportation and communication networks to complex brain networks, are not random but are spatially embedded. Here, we study k-core percolation on two-dimensional spatially embedded networks and show that, in contrast to regular percolation, the length of connections can control the transition type, leading to four different types of phase transitions associated with novel phenomena and a rich phase diagram. A key finding is the existence of a metastable phase in which microscopic localized damage, independent of system size, can cause a macroscopic phase transition, a result which cannot be achieved in traditional percolation. In this case, local failures can spontaneously propagate the damage radially until the system entirely collapses, a phenomenon analogous to the nucleation process. These findings suggest novel features and extreme vulnerabilities of spatially embedded k-core network systems, and highlight the necessity to take into account the characteristic length of links when designing robust spatial networks. Furthermore, our insight about the microscopic processes and their origin during the mixed order and first order abrupt transitions in k-core networks could shed light on the mechanisms of many systems where such transitions occur.

physics.soc-ph↗