28 papers · ranked by Valyu relevance
Gheorghe Ilie, Adrian V. Jaeggi
One of the foundational tenets of evolutionary psychology, the modular view of the mind, offers promising applications for clinical psychiatry. This perspective conceptualizes the mind as a collection of specialized information-processing modules, shaped by natural selection to address adaptive challenges faced by our…
Saúl Huitzil, Cristián Huepe
Modularity, the structuring of systems into discrete, interconnected units, is a fundamental organizing principle in biology across multiple scales. Recent progress in understanding the role of modularity as an evolutionary mechanism and a key driver of biological complexity has highlighted its importance in shaping…
Daniele Della Posta, Jacopo Junio Valerio Branca, Giulia Guarnieri, Cristiana Veltro + 3 more
'Cristiana Veltro' 'Alessandra Pacini' 'Ferdinando Paternostro' 'Nicola Smania'] Introduction: For many years, anatomical studies have been conducted with a shattered view of the body. Although the study of the different apparatuses provides a systemic view of the human body, the reconstruction of the complex network…
Michael Pan, Peter J. Gawthrop, Joseph Cursons, Edmund J. Crampin
It is widely acknowledged that the construction of large-scale dynamic models in systems biology requires complex modelling problems to be broken up into more manageable pieces. To this end, both modelling and software frameworks are required to enable modular modelling. While there has been consistent progress in the…
Claus Kadelka, Matthew Wheeler, Alan Veliz-Cuba, David Murrugarra + 1 more
This paper addresses two topics in systems biology, the hypothesis that biological systems are modular and the problem of relating structure and function of biological systems. The focus here is on gene regulatory networks, represented by Boolean network models, a commonly used tool. Most of the research on gene…
Filip Milisav, Andrea I. Luppi, Laura E. Suárez, Guillaume Lajoie + 1 more
Modularity is a fundamental principle of brain organization, reflected in the presence of segregated sub-networks that enable specialized information processing. These small, densely connected modules are often nested within larger, higher-order modules, giving rise to a hierarchical modular architecture. This…
Michael Pan, Peter J. Gawthrop, Joseph Cursons, Edmund J. Crampin + 1 more
'Anders Wallqvist'] It is widely acknowledged that the construction of large-scale dynamic models in systems biology requires complex modelling problems to be broken up into more manageable pieces. To this end, both modelling and software frameworks are required to enable modular modelling. While there has been…
Melia E. Bonomo, Christof Karmonik, Anthony Brandt, Jessica Frazier
We investigate the use of modularity as a quantifier of whole-brain functional networks. Brain networks are constructed from functional magnetic resonance imaging while subjects listened to auditory pieces that varied in emotivity and cultural familiarity. The results of our analysis reveal high and low modularity…
Libertad Pantoja-Hernández, Juan Carlos Martínez-García
Synthetic biology has intensively promoted the technical implementation of modular strategies in the fabrication of biological devices. Modules are considered as networks of reactions. The behavior displayed by biomolecular systems results from the information processes carried out by the interconnection of the…
Zhenyue Qin, Bob McKay, Tom Gedeon
Wagner's modularity inducing problem domain is a key contribution to the study of the evolution of modularity, including both evolutionary theory and evolutionary computation. We study its behavior under classical genetic algorithms. Unlike what we seem to observe in nature, the emergence of modularity is highly…
Flávia Maria Darcie Marquitti, Paulo R. Guimarães, Mathias M. Pires, Luiz F. Bittencourt
'Luiz F. Bittencourt'] Ecological systems can be seen as networks of interactions between individual, species, or habitat patches. A key feature of many ecological networks is their organization into modules, which are subsets of elements that are more connected to each other than to the other elements in the network.…
Sergi Valverde
The presence of modular organisation is a common property of a wide range of complex systems, from cellular or brain networks to technological graphs. Modularity allows some degree of segregation between different parts of the network and has been suggested to be a prerequisite for the evolvability of biological…
Dirk M. Lorenz, Alice Jeng, Michael W. Deem
In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to explain modular organization of biology, with a focus on explaining how biology may…
Artemy Kolchinsky, Alexander J. Gates, Luís M. Rocha
We propose a method to decompose dynamical systems based on the idea that modules constrain the spread of perturbations. We find partitions of system variables that maximize 'perturbation modularity', defined as the autocovariance of coarse-grained perturbed trajectories. The measure effectively separates the fast…
Hari Sivakumar, Stephen R. Proulx, João P. Hespanha
This paper addresses the decomposition of biochemical networks into functional modules that preserve their dynamic properties upon interconnection with other modules, which permits the inference of network behavior from the properties of its constituent modules. The modular decomposition method developed here also has…
Sergi Valverde
The presence of modular organization is a common property of a wide range of complex systems, from cellular or brain networks to technological graphs. Modularity allows some degree of segregation between different parts of the network and has been suggested to be a prerequisite for the evolvability of biological…
Borja Esteve-Altava
Form is a rich concept that agglutinates information about the proportions and topological arrangement of body parts. Modularity is readily observable in both the variation of proportions (variational modules) and the organization of topology (organizational modules). The study of variational modularity and of…
Borja Esteve-Altava
The modular organization of the phenotype is an emergent property that derives from a semi-independent relation of body parts in their inheritance, development, function, and evolution. Understanding the modular organization of living beings is essential to understand the evolvability and plasticity of organismal form…
Brenden K Petersen, Glen EP Ropella, C Anthony Hunt
Background Currently, most biomedical models exist in isolation. It is often difficult to reuse or integrate models or their components, in part because they are not modular. Modular components allow the modeler to think more deeply about the role of the model and to more completely address a modeling project’s…
Blai Vidiella, Salva Duran‐Nebreda, Sergi Valverde
Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to represent inter-dependencies among many system components, facilitating the study of…
Shuaijian Dai, Yage Zhang, Weichuan Yu, Ning Li
Proteins are organized into modules by both functions and physical interactions within compartments of an eukaryotic cell. The in vivo chemical crosslinking mass spectrometry (XL-MS) data collected from organelles, the whole cells and tissues are able to provide unique information about both protein-protein interaction…
Anna Matuszyńska, Oliver Ebenhöh, Matias D. Zurbriggen, Daniel C. Ducat + 1 more
Synthetic biology designs and constructs new biological parts, devices and systems with predetermined functionalities. With the unlimited ability to synthesise any DNA and RNA and transfer it to almost any organism, we are at the dawn of a new era in which biology is being recreated in ways never before possible. It…
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Despite the promise of self-driving laboratories to accelerate discovery, their widespread implementation is hindered by prohibitive cost and technical complexity. We introduce BrickSDLab, a fully functional self-driving lab platform built entirely from LEGO® components, designed to bridge this accessibility gap.…
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γ-Lactams are crucial scaffolds in many bioactive compounds and pharmaceutical agents, yet their synthesis featuring diverse γ- and N-substitution remains a significant synthetic challenge. Current methods often lack modularity and efficiency, particularly when targeting sterically hindered or highly functionalized…
Abootaleb Sedighi, Tudor Radu, Qirat Ashraf, Balmiki Kumar + 3 more
We developed the Interdisciplinary Science Program in Research and Entrepreneurship (INSPIRE) to address the changing career landscape that students with an interest in Physical Chemistry, Biophysics and Biochemistry face. Third and fourth-year undergraduate Chemistry and Physics students participated in a 4-week…
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Rapid and robust simulation of chemical processes is critical to conduct process design, optimization, techno-economic analysis, and sustainability analysis. Yet, efficiently solving simulation models remains a challenge due to the highly coupled and nonlinear nature of the underlying algebraic equations that capture…
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This paper formally defines an operational isomorphism between spectral damping in molecular vibronic systems and neuromodulatory control in biological sensory systems. Without asserting causal continuity or physical identity across scales, we show that both domains instantiate the same class of output-selective…
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Chemistry curricula often separate “wet” experimental work from “dry” computation, yet modern discovery increasingly demands both. This Perspective offers an instructor-ready roadmap to train “hybrid chemists” within existing courses. We distill recent advances in machine learning, automation, and real-time analytics…