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"Rocks, Jason W."
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Supervised Learning in Physical Networks: From Machine Learning to Learning Machines
by
Stern, Menachem
,
Rocks, Jason W.
,
Hexner, Daniel
in
Collective behavior in networks
,
Disordered systems
,
Handwriting
2021
Materials and machines are often designed with particular goals in mind, so that they exhibit desired responses to given forces or constraints. Here we explore an alternative approach, namely physical coupled learning. In this paradigm, the system is not initially designed to accomplish a task, but physically adapts to applied forces to develop the ability to perform the task. Crucially, we require coupled learning to be facilitated by physically plausible learning rules, meaning that learning requires only local responses and no explicit information about the desired functionality. We show that such local learning rules can be derived for any physical network, whether in equilibrium or in steady state, with specific focus on two particular systems, namely disordered flow networks and elastic networks. By applying and adapting advances of statistical learning theory to the physical world, we demonstrate the plausibility of new classes of smart metamaterials capable of adapting to users’ needs in situ.
Journal Article
Designing allostery-inspired response in mechanical networks
by
Rocks, Jason W.
,
Pashine, Nidhi
,
Liu, Andrea J.
in
allostery
,
ATOMIC AND MOLECULAR PHYSICS
,
Biomechanics
2017
Recent advances in designing metamaterials have demonstrated that global mechanical properties of disordered spring networks can be tuned by selectively modifying only a small subset of bonds. Here, using a computationally efficient approach, we extend this idea to tune more general properties of networks. With nearly complete success, we are able to produce a strain between any two target nodes in a network in response to an applied source strain on any other pair of nodes by removing only ∼1% of the bonds. We are also able to control multiple pairs of target nodes, each with a different individual response, from a single source, and to tune multiple independent source/target responses simultaneously into a network. We have fabricated physical networks in macroscopic 2D and 3D systems that exhibit these responses. This work is inspired by the long-range coupled conformational changes that constitute allosteric function in proteins. The fact that allostery is a common means for regulation in biological molecules suggests that it is a relatively easy property to develop through evolution. In analogy, our results show that long-range coupled mechanical responses are similarly easy to achieve in disordered networks.
Journal Article
Emergent competition shapes top-down versus bottom-up control in multi-trophic ecosystems
by
Feng, Zhijie
,
Rocks, Jason W.
,
Marsland, Robert
in
Biology and Life Sciences
,
Carnivores
,
Competition
2024
Ecosystems are commonly organized into trophic levels—organisms that occupy the same level in a food chain (e.g., plants, herbivores, carnivores). A fundamental question in theoretical ecology is how the interplay between trophic structure, diversity, and competition shapes the properties of ecosystems. To address this problem, we analyze a generalized Consumer Resource Model with three trophic levels using the zero-temperature cavity method and numerical simulations. We derive the corresponding mean-field cavity equations and show that intra-trophic diversity gives rise to an effective “emergent competition” term between species within a trophic level due to feedbacks mediated by other trophic levels. This emergent competition gives rise to a crossover from a regime of top-down control (populations are limited by predators) to a regime of bottom-up control (populations are limited by primary producers) and is captured by a simple order parameter related to the ratio of surviving species in different trophic levels. We show that our theoretical results agree with empirical observations, suggesting that the theoretical approach outlined here can be used to understand complex ecosystems with multiple trophic levels.
Journal Article
Mechanical signaling coordinates the embryonic heartbeat
by
Chiou, Kevin K.
,
Tewari, Manorama
,
Prosser, Benjamin L.
in
Animals
,
Biological Sciences
,
Biophysics and Computational Biology
2016
In the beating heart, cardiac myocytes (CMs) contract in a coordinated fashion, generating contractile wave fronts that propagate through the heart with each beat. Coordinating this wave front requires fast and robust signaling mechanisms between CMs. The primary signaling mechanism has long been identified as electrical: gap junctions conduct ions between CMs, triggering membrane depolarization, intracellular calcium release, and actomyosin contraction. In contrast, we propose here that, in the early embryonic heart tube, the signaling mechanism coordinating beats is mechanical rather than electrical. We present a simple biophysical model in which CMs are mechanically excitable inclusions embedded within the extracellular matrix (ECM), modeled as an elastic-fluid biphasic material. Our model predicts strong stiffness dependence in both the heartbeat velocity and strain in isolated hearts, as well as the strain for a hydrogel-cultured CM, in quantitative agreement with recent experiments. We challenge our model with experiments disrupting electrical conduction by perfusing intact adult and embryonic hearts with a gap junction blocker, β-glycyrrhetinic acid (BGA). We find this treatment causes rapid failure in adult hearts but not embryonic hearts—consistent with our hypothesis. Last, our model predicts a minimum matrix stiffness necessary to propagate a mechanically coordinated wave front. The predicted value is in accord with our stiffness measurements at the onset of beating, suggesting that mechanical signaling may initiate the very first heartbeats.
Journal Article
Limits of multifunctionality in tunable networks
by
Ronellenfitsch, Henrik
,
Rocks, Jason W.
,
Liu, Andrea J.
in
allostery
,
Biological evolution
,
CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY
2019
Nature is rife with networks that are functionally optimized to propagate inputs to perform specific tasks. Whether via genetic evolution or dynamic adaptation, many networks create functionality by locally tuning interactions between nodes. Here we explore this behavior in two contexts: strain propagation in mechanical networks and pressure redistribution in flow networks. By adding and removing links, we are able to optimize both types of networks to perform specific functions. We define a single function as a tuned response of a single “target” link when another, predetermined part of the network is activated. Using network structures generated via such optimization, we investigate how many simultaneous functions such networks can be programed to fulfill. We find that both flow and mechanical networks display qualitatively similar phase transitions in the number of targets that can be tuned, along with the same robust finite-size scaling behavior. We discuss how these properties can be understood in the context of constraint–satisfaction problems.
Journal Article
Correlation of plastic events with local structure in jammed packings across spatial dimensions
by
Rocks, Jason W.
,
Liu, Andrea J.
,
Ridout, Sean A.
in
CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS
,
Coordination numbers
,
Correlation
2022
In frictionless jammed packings, existing evidence suggests a picture in which localized physics dominates in low spatial dimensions, d = 2, 3, but quickly loses relevance as d rises, replaced by spatially extended mean-field behavior. For example, quasilocalized low-energy vibrational modes and low-coordination particles associated with deviation from mean-field behavior (rattlers and bucklers) all vanish rapidly with increasing d. These results suggest that localized rearrangements, which are associated with low-energy vibrational modes, correlated with local structure, and dominant in low dimensions, should give way in higher d to extended rearrangements uncorrelated with local structure. Here, we use machine learning to analyze simulations of jammed packings under athermal, quasistatic shear, identifying a local structural variable, softness, that correlates with rearrangements in dimensions d = 2 to d = 5. We find that softness—and even just the local coordination number Z—is essentially equally predictive of rearrangements in all d studied. This result provides direct evidence that local structure plays an important role in higher d, suggesting a modified picture for the dimensional cross-over to mean-field theory.
Journal Article
A universal niche geometry governs the response of ecosystems to environmental perturbations
2024
How ecosystems respond to environmental perturbations is a fundamental question in ecology, made especially challenging due to the strong coupling between species and their environment. Here, we introduce a theoretical framework for calculating the steady-state response of ecosystems to environmental perturbations in generalized consumer-resource. Our construction is applicable to a wide class of systems, including models with non-reciprocal interactions, cross-feeding, and non-linear growth/consumption rates. Within our framework, all ecological variables are embedded into four distinct vector spaces and ecological interactions are represented by geometric transformations between these spaces. We show that near a steady state, such geometric transformations directly map environmental perturbations - in resource availability and mortality rates - to shifts in niche structure. We illustrate these ideas in a variety of settings including a minimal model for pH-induced toxicity in bacterial denitrification. We end by discussing the biological implications of our framework. In particular, we show that it is extremely difficult to distinguish cooperative and competitive interactions by measuring species' responses to external perturbations.
Journal Article
Emergent competition shapes top-down versus bottom-up control in multi-trophic ecosystems
2024
Ecosystems are commonly organized into trophic levels-organisms that occupy the same level in a food chain (e.g., plants, herbivores, carnivores). A fundamental question in theoretical ecology is how the interplay between trophic structure, diversity, and competition shapes the properties of ecosystems. To address this problem, we analyze a generalized Consumer Resource Model with three trophic levels using the zero-temperature cavity method and numerical simulations. We derive the corresponding mean-field cavity equations and show that intra-trophic diversity gives rise to an effective \"emergent competition\" term between species within a trophic level due to feedbacks mediated by other trophic levels. This emergent competition gives rise to a crossover from a regime of top-down control (populations are limited by predators) to a regime of bottom-up control (populations are limited by primary producers) and is captured by a simple order parameter related to the ratio of surviving species in different trophic levels. We show that our theoretical results agree with empirical observations, suggesting that the theoretical approach outlined here can be used to understand complex ecosystems with multiple trophic levels.
Journal Article
A universal niche geometry governs the response of ecosystems to environmental perturbations
2024
How ecosystems respond to environmental perturbations is a fundamental question in ecology, made especially challenging due to the strong coupling between species and their environment. Here, we introduce a theoretical framework for calculating the linear response of ecosystems to environmental perturbations in generalized consumer-resource models. Our construction is applicable to a wide class of systems, including models with non-reciprocal interactions, cross-feeding, and non-linear growth/consumption rates. Within our framework, all ecological variables are embedded into four distinct vector spaces and ecological interactions are represented by geometric transformations between these spaces. We show that near a steady state, such geometric transformations directly map environmental perturbations - in resource availability and mortality rates - to shifts in niche structure. We illustrate these ideas in a variety of settings including a minimal model for pH-induced toxicity in bacterial denitrification.
Journal Article
Correlation of plastic events with local structure in jammed packings across spatial dimensions
Significance Mean-field theories, exact in the limit of infinite spatial dimensions, succeed in describing many features of glasses and amorphous solids in low dimensions, leading to considerable effort to understand how behavior evolves with dimension. Until now, all evidence has supported a picture in which “localized physics,” responsible for deviations from mean-field behavior in low dimensions, fades away with rising dimension. Our work shows that rearrangements, in which particles change relative positions leading to fluid-like response, reveal a different picture of dimensional cross-over. We find that rearrangements, which are localized in two- and three-dimensional systems and correlated with local structure, remain just as correlated with local structure up to five dimensions, suggesting that local structure is important even in high dimensions.
Journal Article