Modeling collective cell migration in geometric confinement.


:Monolayer expansion has generated great interest as a model system to study collective cell migration. During such an expansion the culture front often develops 'fingers', which we have recently modeled using a proposed feedback between the curvature of the monolayer's leading edge and the outward motility of the edge cells. We show that this model is able to explain the puzzling observed increase of collective cellular migration speed of a monolayer expanding into thin stripes, as well as describe the behavior within different confining geometries that were recently observed in experiments. These comparisons give support to the model and emphasize the role played by the edge cells and the edge shape during collective cell motion.


Phys Biol


Physical biology


Tarle V,Gauquelin E,Vedula SRK,D'Alessandro J,Lim CT,Ladoux B,Gov NS




Has Abstract


2017-05-03 00:00:00












  • ENVIRONMENT: a computational platform to stochastically simulate reacting and self-reproducing lipid compartments.

    abstract::'ENVIRONMENT' is a computational platform that has been developed in the last few years with the aim to simulate stochastically the dynamics and stability of chemically reacting protocellular systems. Here we present and describe some of its main features, showing how the stochastic kinetics approach can be applied to...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Mavelli F,Ruiz-Mirazo K

    更新日期:2010-08-11 00:00:00

  • From analog to digital models of gene regulation.

    abstract::Recently, major progress has been made to develop computational models to predict and explain the mechanisms and behaviors of gene regulation. Here, we review progress on how these mechanisms and behaviors have been interpreted with analog models, where cell properties continuously modulate transcription, and digital ...

    journal_title:Physical biology

    pub_type: 杂志文章,评审


    authors: Munsky B,Neuert G

    更新日期:2015-06-18 00:00:00

  • On the general concept of buoyancy in sedimentation and ultracentrifugation.

    abstract::Gravity or ultracentrifuge settling of colloidal particles and macromolecules usually involves several disperse species, either because natural and industrial colloids display a large size polydispersity, or because additives are put in on purpose to allow for density-based fractionation of the suspension. Such 'macro...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Piazza R,Buzzaccaro S,Secchi E,Parola A

    更新日期:2013-08-01 00:00:00

  • Mechanical model of Golgi apparatus.

    abstract::The Golgi apparatus has intrigued researchers since its discovery and despite the advances, there are still many open questions in regards to its shape and function. We propose a mechanical model of Golgi apparatus stack and explain its most elementary geometrical properties: the equilibrium number of cisternae, the s...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Jelerčič U

    更新日期:2019-09-05 00:00:00

  • Caenorhabditis elegans vulval cell fate patterning.

    abstract::The spatial patterning of three cell fates in a row of competent cells is exemplified by vulva development in the nematode Caenorhabditis elegans. The intercellular signaling network that underlies fate specification is well understood, yet quantitative aspects remain to be elucidated. Quantitative models of the netwo...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Félix MA

    更新日期:2012-08-01 00:00:00

  • Motions of leaves and stems, from growth to potential use.

    abstract::The study on aerial plant organs (leaves and stems) motions is reviewed. The history of observations and studies is put in the perspective of the ideas surrounding them, leading to a presentation of the current classification of these motions. After showing the shortcomings of such a classification, we present, follow...

    journal_title:Physical biology

    pub_type: 历史文章,杂志文章,评审


    authors: Rivière M,Derr J,Douady S

    更新日期:2017-08-21 00:00:00

  • A minimal model for household effects in epidemics.

    abstract::Shelter-in-place and other confinement strategies implemented in the current COVID-19 pandemic have created stratified patterns of contacts between people: close contacts within households and more distant contacts between the households. The epidemic transmission dynamics is significantly modified as a consequence. W...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Huber G,Kamb M,Kawagoe K,Li LM,Veytsman B,Yllanes D,Zigmond D

    更新日期:2020-10-21 00:00:00

  • Control of ribosome traffic by position-dependent choice of synonymous codons.

    abstract::Messenger RNA (mRNA) encodes a sequence of amino acids by using codons. For most amino acids, there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for changing the ribosome speed while keeping the amino acid sequence and hence...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Mitarai N,Pedersen S

    更新日期:2013-10-01 00:00:00

  • 'Dicty dynamics': Dictyostelium motility as persistent random motion.

    abstract::We model the motility of Dictyostelium cells in a systematic data-driven manner. We deduce a minimal dynamical model that reproduces the statistical features of experimental trajectories. These are trajectories of the centroid of the cell perimeter, which is more sensitive to pseudopod activity than the usual tracking...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Li L,Cox EC,Flyvbjerg H

    更新日期:2011-08-01 00:00:00

  • Cost-benefit theory and optimal design of gene regulation functions.

    abstract::Cells respond to the environment by regulating the expression of genes according to environmental signals. The relation between the input signal level and the expression of the gene is called the gene regulation function. It is of interest to understand the shape of a gene regulation function in terms of the environme...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Kalisky T,Dekel E,Alon U

    更新日期:2007-11-07 00:00:00

  • Effect of ribosome shielding on mRNA stability.

    abstract::Based on the experimental evidence that translating ribosomes stabilize the mRNAs, we introduce and study a theoretical model for the dynamic shielding of mRNA by ribosomes. We present an improved fitting of published decay assay data in E. coli and show that only one third of the decay patterns are exponential. Our n...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Deneke C,Lipowsky R,Valleriani A

    更新日期:2013-08-01 00:00:00

  • Effect of co-transporter blockers on non-synaptic epileptiform activity-computational simulation.

    abstract::The important role of cation-chloride co-transporters in epilepsy is being supported by an increasing number of investigations. However, enormous complexity is involved since the action of these co-transporters has effects on the ionic homeostasis influencing directly the neuronal excitability and the tissue propensit...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Lopes MR,Santos LE,Rodrigues AM,Duarte MA,Infantosi AF,Scorza FA,Arida RM,Madureira AP,da Silveira GA,dos Santos IC,Cavalheiro EA,de Almeida AC

    更新日期:2013-10-01 00:00:00

  • Temperature response of the neuronal cytoskeleton mapped via atomic force and fluorescence microscopy.

    abstract::Neuronal cells change their growth properties in response to external physical stimuli such as variations in external temperature, stiffness of the growth substrate, or topographical guidance cues. Detailed knowledge of the mechanisms that control these biomechanical responses is necessary for understanding the basic ...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Spedden E,Kaplan DL,Staii C

    更新日期:2013-10-01 00:00:00

  • Capacitance fluctuations causing channel noise reduction in stochastic Hodgkin-Huxley systems.

    abstract::Voltage-dependent ion channels determine the electric properties of axonal cell membranes. They not only allow the passage of ions through the cell membrane, but also contribute to an additional charging of the cell membrane resulting in the so-called capacitance loading. The switching of the channel gates between an ...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Schmid G,Goychuk I,Hänggi P

    更新日期:2006-11-22 00:00:00

  • Modeling synaptic transmission of the tripartite synapse.

    abstract::The tripartite synapse denotes the junction of a pre- and postsynaptic neuron modulated by a synaptic astrocyte. Enhanced transmission probability and frequency of the postsynaptic current-events are among the significant effects of the astrocyte on the synapse as experimentally characterized by several groups. In thi...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Nadkarni S,Jung P

    更新日期:2007-01-09 00:00:00

  • A stochastic spatiotemporal model of a response-regulator network in the Caulobacter crescentus cell cycle.

    abstract::The asymmetric cell division cycle in Caulobacter crescentus is controlled by an elaborate molecular mechanism governing the production, activation and spatial localization of a host of interacting proteins. In previous work, we proposed a deterministic mathematical model for the spatiotemporal dynamics of six major r...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Li F,Subramanian K,Chen M,Tyson JJ,Cao Y

    更新日期:2016-06-25 00:00:00

  • Shaping up synthetic cells.

    abstract::How do the cells in our body reconfigure their shape to achieve complex tasks like migration and mitosis, yet maintain their shape in response to forces exerted by, for instance, blood flow and muscle action? Cell shape control is defined by a delicate mechanical balance between active force generation and passive mat...

    journal_title:Physical biology

    pub_type: 杂志文章,评审


    authors: Mulla Y,Aufderhorst-Roberts A,Koenderink GH

    更新日期:2018-04-30 00:00:00

  • Folding pathways explored with artificial potential functions.

    abstract::This paper considers the generation of trajectories to a given protein conformation and presents a novel approach based on artificial potential functions--originally proposed for multi-robot navigation. The artificial potential function corresponds to a simplified energy model, but with the novelty that--motivated by ...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Ulutaş B,Haliloglu T,Bozma I

    更新日期:2009-05-14 00:00:00

  • Elastic and damping forces generated by confined arrays of dynamic microtubules.

    abstract::In addition to serving as structural elements and as tracks for motor proteins, microtubules use chemical energy derived from the hydrolysis of GTP to generate forces when growing and shrinking. These forces are used to push or pull on organelles such as chromosomes and the mitotic spindle. If an array of microtubules...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Howard J

    更新日期:2006-02-28 00:00:00

  • Resting potential, oncogene-induced tumorigenesis, and metastasis: the bioelectric basis of cancer in vivo.

    abstract::Cancer may result from localized failure of instructive cues that normally orchestrate cell behaviors toward the patterning needs of the organism. Steady-state gradients of transmembrane voltage (V(mem)) in non-neural cells are instructive, epigenetic signals that regulate pattern formation during embryogenesis and mo...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Lobikin M,Chernet B,Lobo D,Levin M

    更新日期:2012-12-01 00:00:00

  • Folate and S-adenosylmethionine modulate synaptic activity in cultured cortical neurons: acute differential impact on normal and apolipoprotein-deficient mice.

    abstract::Folate deficiency is accompanied by a decline in the cognitive neurotransmitter acetylcholine and a decline in cognitive performance in mice lacking apolipoprotein E (ApoE-/- mice), a low-density lipoprotein that regulates aspects of lipid metabolism. One direct consequence of folate deficiency is a decline in S-adeno...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Serra M,Chan A,Dubey M,Gilman V,Shea TB

    更新日期:2008-12-19 00:00:00

  • Toward the modeling of mucus draining from the human lung: role of the geometry of the airway tree.

    abstract::Mucociliary clearance and cough are the two main natural mucus draining methods in the bronchial tree. If they are affected by a pathology, they can become insufficient or even ineffective, then therapeutic draining of mucus plays a critical role to keep mucus levels in the lungs acceptable. The manipulations of physi...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Mauroy B,Fausser C,Pelca D,Merckx J,Flaud P

    更新日期:2011-10-01 00:00:00

  • Spin symmetry transitions make DNA strands separate. New insight into the mechanism of transcription.

    abstract::The DFT:B3LYP (6-31G** basis set) method, including the hyperfine and spin-orbit couplings (HFC and SOC, respectively), is used to study the separation of two complementary trinucleotide sequences, (dC-dG-dA)-(dG-dC-dT), upon the action of two Mg(2+) cofactors (a simplified model). The computations reveal a crossing o...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Tulub AA,Stefanov VE

    更新日期:2015-12-10 00:00:00

  • Robustness of the division symmetry in Escherichia coli and functional consequences of symmetry breaking.

    abstract::The morphological symmetry of the division process of Escherichia coli is well-known. Recent studies verified that, in optimal growth conditions, most divisions are symmetric, although there are exceptions. We investigate whether such morphological asymmetries in division introduce functional asymmetries between siste...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Gupta A,Lloyd-Price J,Oliveira SM,Yli-Harja O,Muthukrishnan AB,Ribeiro AS

    更新日期:2014-11-10 00:00:00

  • Rayleigh instability of the inverted one-cell amphibian embryo.

    abstract::The one-cell amphibian embryo is modeled as a rigid spherical shell containing equal volumes of two immiscible fluids with different densities and viscosities and a surface tension between them. The fluids represent denser yolk in the bottom hemisphere and clearer cytoplasm and the germinal vesicle in the top hemisphe...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Nouri C,Luppes R,Veldman AE,Tuszynski JA,Gordon R

    更新日期:2008-04-10 00:00:00

  • On the origin of the tensile strength of insect swarms.

    abstract::Traditionally animal groups have been characterized by the macroscopic patterns that they form. It is now recognised that such patterns convey limited information about the nature of the aggregation as a whole. Aggregate properties cannot be determined by passive observations alone; instead one must interact with them...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Reynolds AM

    更新日期:2019-04-23 00:00:00

  • FtsZ rings and helices: physical mechanisms for the dynamic alignment of biopolymers in rod-shaped bacteria.

    abstract::In many bacterial species, the protein FtsZ forms a cytoskeletal ring that marks the future division site and scaffolds the division machinery. In rod-shaped bacteria, most frequently membrane-attached FtsZ rings or ring fragments are reported and occasionally helices. By contrast, axial FtsZ clusters have never been ...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Fischer-Friedrich E,Friedrich BM,Gov NS

    更新日期:2012-02-01 00:00:00

  • Ligand-receptor binding kinetics in surface plasmon resonance cells: a Monte Carlo analysis.

    abstract::Surface plasmon resonance (SPR) chips are widely used to measure association and dissociation rates for the binding kinetics between two species of chemicals, e.g., cell receptors and ligands. It is commonly assumed that ligands are spatially well mixed in the SPR region, and hence a mean-field rate equation descripti...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Carroll J,Raum M,Forsten-Williams K,Täuber UC

    更新日期:2016-12-06 00:00:00

  • Dressed neurons: modeling neural-glial interactions.

    abstract::Based on recent experimental data, we design a model for neuronal membrane potentials that incorporates the influence of the surrounding glia (dressed neurons). A neurotransmitter released into the synaptic cleft triggers a Ca(2+) response in nearby glial cells that spreads as a Ca(2+) wave and interacts with other sy...

    journal_title:Physical biology

    pub_type: 杂志文章


    authors: Nadkarni S,Jung P

    更新日期:2004-06-01 00:00:00

  • Manipulation of in vitro collagen matrix architecture for scaffolds of improved physiological relevance.

    abstract::Type I collagen is a versatile biomaterial that is widely used in medical applications due to its weak antigenicity, robust biocompatibility, and its ability to be modified for a wide array of applications. As such, collagen has become a major component of many tissue engineering scaffolds, drug delivery platforms, an...

    journal_title:Physical biology

    pub_type: 杂志文章,评审


    authors: Hapach LA,VanderBurgh JA,Miller JP,Reinhart-King CA

    更新日期:2015-12-21 00:00:00