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AMPA, NMDA and GABAA receptor mediated network burst dynamics in cortical cultures in vitroFeb 01 2018In this work we study the excitatory AMPA, and NMDA, and inhibitory GABAA receptor mediated dynamical changes in neuronal networks of neonatal rat cortex in vitro. Extracellular network-wide activity was recorded with 59 planar electrodes simultaneously ... More
Analysis and optimal control of an intracellular delayed HIV model with CTL immune responseJan 30 2018A delayed model describing the dynamics of HIV (Human Immunodeficiency Virus) with CTL (Cytotoxic T Lymphocytes) immune response is investigated. The model includes four nonlinear differential equations describing the evolution of uninfected, infected, ... More
Self-organization and chaos in the metabolism of a cellJan 24 2018Aim. To study the dynamics of auto-oscillations arising at the level of enzyme-substrate interaction in a cell and to find the conditions for the self-organization and the formation of chaos in the metabolic process. Methods. A mathematical model of the ... More
Modeling cell size regulation: From single-cell level statistics to molecular mechanisms and population level effectsJan 01 2018Most microorganisms regulate their cell size. We review here some of the mathematical formulations of the problem of cell size regulation. We focus on coarse-grained stochastic models and the statistics they generate. We review the biologically relevant ... More
Addressing current challenges in cancer immunotherapy with mathematical and computational modelingJun 06 2017The goal of cancer immunotherapy is to boost a patient's immune response to a tumor. Yet, the design of an effective immunotherapy is complicated by various factors, including a potentially immunosuppressive tumor microenvironment, immune-modulating effects ... More
Cholesterol impairment contributes to neuroserpin aggregationMay 15 2017Intraneural accumulation of misfolded proteins is a common feature of several neurodegenerative pathologies including Alzheimer's and Parkinson's diseases, and Familial Encephalopathy with Neuroserpin Inclusion Bodies (FENIB). FENIB is a rare disease ... More
Evaporation-driven convective flows in suspensions of non-motile bacteriaApr 08 2017We report a novel form of convection in suspensions of the bioluminiscent marine bacterium $Photobacterium~phosphoreum$. Suspensions of these bacteria placed in a chamber open to the air create persistent luminiscent plumes most easily visible when observed ... More
Ionic Coulomb blockade and anomalous mole fraction effect in NaChBac bacterial ion channelsDec 08 2016We report an experimental study of the influences of the fixed charge and bulk ionic concentrations on the conduction of biological ion channels, and we consider the results within the framework of the ionic Coulomb blockade model of permeation and selectivity. ... More
Chemotaxis and Haptotaxis on Cellular LevelDec 07 2016Chemotaxis and haptotaxis have been a main theme in the macroscopic study of bacterial and cellular motility. In this work we investigate the influence these processes have on the shape and motility of fast migrating cells. We note that despite their ... More
A biology journal that can teach physicists a lesson in peer reviewDec 01 2016This is a Commentary in $Physics~Today$ on the novel review process developed by the biology journal $eLife$, with the suggestion that it be adopted by physics journals.
Lipidomic approach for stratification of Acute Myeloid Leukemia patientsNov 30 2016The pathogenesis and progression of many tumors, including hematologic malignancies is highly dependent on enhanced lipogenesis. De novo fatty-acid synthesis permits accelerated proliferation of tumor cells by providing structural components to build ... More
Phototaxis beyond turning: persistent accumulation and response acclimation of the microalga Chlamydomonas reinhardtiiNov 24 2016Phototaxis is an important reaction to light displayed by a wide range of motile microorganisms. Flagellated eukaryotic microalgae in particular, like the model organism Chlamydomonas reinhardtii, steer either towards or away from light by a rapid and ... More
From cells to tissue: A continuum model for epithelial mechanicsNov 17 2016A continuum model for epithelial tissue mechanics is formulated from cell level mechanical ingredients and morphogenetic cell dynamics, including cell shape changes and cell rearrangements. The model is capable of dealing with finite deformation, and ... More
Bridging the time scales of single-cell and population dynamicsNov 16 2016It is well known that population sizes increase exponentially during balanced growth. Concomitantly, at the single-cell level, the sizes of individual cells themselves increase exponentially; the single-cell exponential growth-rate also determines the ... More
Bridging the time scales of single-cell and population dynamicsNov 16 2016Nov 21 2016It is well known that population sizes increase exponentially during balanced growth. Concomitantly, at the single-cell level, the sizes of individual cells themselves increase exponentially; the single-cell exponential growth-rate also determines the ... More
Defect driven shapes in nematic droplets: analogies with cell divisionNov 15 2016Building on the striking similarity between the structure of the spindle during mitosis in living cells and nematic textures in confined liquid crystals, we use a continuum model of two-dimensional nematic liquid crystal droplets, to examine the physical ... More
Modeling potent pathways for APC/C inhibition: pivotal roles for MCC and BubR1Nov 15 2016The highly conserved spindle assembly checkpoint (SAC) ensures that the sister chromatids of the duplicated genome are not separated and distributed to the spindle poles before all chromosomes have been properly linked to the microtubules of the mitotic ... More
A vertex-based model relating cell shape and mechanical stress in an epitheliumNov 15 2016Using a popular vertex-based model to describe a spatially disordered planar epithelial monolayer, we examine the relationship between cell shape and mechanical stress at the cell and tissue level. Deriving expressions for stress tensors starting from ... More
Clusters of calcium release channels harness the Ising phase transition to confine their elementary intracellular signalsNov 07 2016Intracellular Ca signals represent a universal mechanism of cell function. Messages carried by Ca are local, rapid, and powerful enough to be delivered over the thermal noise. A higher signal to noise ratio is achieved by a cooperative action of Ca release ... More
Clusters of calcium release channels harness the Ising phase transition to confine their elementary intracellular signalsNov 07 2016Jul 05 2017Intracellular Ca signals represent a universal mechanism of cell function. Messages carried by Ca are local, rapid, and powerful enough to be delivered over the thermal noise. A higher signal to noise ratio is achieved by a cooperative action of Ca release ... More
A mathematical model coupling polarity signaling to cell adhesion explains diverse cell migration patternsNov 02 2016Cells crawling through tissues migrate inside a complex fibrous environment called the extracellular matrix (ECM), which provides signals regulating motility. Here we investigate one such well-known pathway, involving mutually antagonistic signalling ... More
Bursts of activity in collective cell migrationOct 25 2016Dense monolayers of living cells display intriguing relaxation dynamics, reminiscent of soft and glassy materials close to the jamming transition, and migrate collectively when space is available, as in wound healing or in cancer invasion. Here we show ... More
Dynamics of single human embryonic stem cells and their pairs: a quantitative analysisOct 24 2016Numerous biological approaches are available to characterise the mechanisms which govern the formation of human embryonic stem cell (hESC) colonies. To understand how the kinematics of single and pairs of hESCs impact colony formation, we study their ... More
Graphitic C3N4 Sensitized TiO2 Nanotube Layers: A Visible Light Activated Efficient Antimicrobial PlatformOct 20 2016In this work, we introduce a facile procedure to graft a thin graphitic C3N4 (g-C3N4) layer on aligned TiO2 nanotube arrays (TiNT) by one-step chemical vapor deposition (CVD) approach. This provides a platform to enhance the visible-light response of ... More
Overcrowding drives the unjamming transition of gap-free monolayersOct 13 2016Collective cell motility plays central roles in various biological phenomena such as inflammatory response, wound healing, cancer metastasis and embryogenesis. These are biological demonstrations of the unjamming transition. However, contradictory to ... More
Dynamical Pattern Selection of Growing Cellular Mosaic in Fish RetinaOct 12 2016A Markovian lattice model for photoreceptor cells is introduced to describe the growth of mosaic patterns on fish retina. The radial stripe pattern observed in wild-type zebrafish is shown to be selected naturally during the retina growth, against the ... More
Elastohydrodynamic Synchronization of Adjacent Beating FlagellaOct 11 2016It is now well established that nearby beating pairs of eukaryotic flagella or cilia typically synchronize in phase. A substantial body of evidence supports the hypothesis that hydrodynamic coupling between the active filaments, combined with waveform ... More
Perspectives on the mathematics of biological patterning and morphogenesisOct 08 2016A central question in developmental biology is how size and position are determined. The genetic code carries instructions on how to control these properties in order to regulate the pattern and morphology of structures in the developing organism. Transcription ... More
Formation and maintenance of nitrogen fixing cell patterns in filamentous cyanobacteriaOct 07 2016Cyanobacteria forming one-dimensional filaments are paradigmatic model organisms of the transition between unicellular and multicellular living forms. Under nitrogen limiting conditions, in filaments of the genus Anabaena, some cells differentiate into ... More
Analysis of a model microswimmer with applications to blebbing cells and mini-robotsOct 06 2016Recent research has shown that motile cells can adapt their mode of propulsion depending on the environment in which they find themselves. One mode is swimming by blebbing or other shape changes, and in this paper we analyze a class of models for movement ... More
A minimal model for spontaneous cell polarization and edge activity in oscillating, rotating and migrating cellsSep 28 2016How the cells break symmetry and organize their edge activity to move directionally is a fun- damental question in cell biology. Physical models of cell motility commonly rely on gradients of regulatory factors and/or feedback from the motion itself to ... More
Stability and Optimal Control of a Delayed HIV ModelSep 24 2016We propose and investigate a delayed model that studies the relationship between HIV and the immune system during the natural course of infection and in the context of antiviral treatment regimes. Sufficient criteria for local asymptotic stability of ... More
On the role of $\rm CD8^+$ T cells in determining recovery time from influenza virus infectionSep 20 2016Myriad experiments have identified an important role for $\rm CD8^+$ T cell response mechanisms in determining recovery from influenza A virus infection. Animal models of influenza infection further implicate multiple elements of the immune response in ... More
Self-tolerance and autoimmunity in a minimal model of the idiotypic networkSep 19 2016We consider self-tolerance and its failure -autoimmunity- in a minimal mathematical model of the idiotypic network. A node in the network represents a clone of B-lymphocytes and its antibodies of the same idiotype which is encoded by a bitstring. The ... More
Multi-dimensional phenotype and long-term dynamics in individual bacteriaSep 18 2016Genetically identical microbial cells typically display significant variability in every measurable property. In particular, highly abundant proteins - which can determine cellular behavior - exhibit large variability in copy number among individuals. ... More
Purification of recombinant human and Drosophila septin hexamers for TIRF assays of actin-septin filament assemblySep 13 2016Septins are guanine nucleotide-binding proteins that are conserved from fungi to humans. Septins assemble into heterooligomeric complexes and higher-order structures with key roles in various cellular functions including cell migration and division. The ... More
An efficient Cellular Potts Model algorithm that forbids cell fragmentationSep 13 2016The Cellular Potts Model (CPM) is a lattice based modeling technique which is widely used for simulating cellular patterns such as foams or biological tissues. Despite its realism and generality, the standard Monte Carlo algorithm used in the scientific ... More
Visualizing septins in early Drosophila embryosSep 13 2016Functional studies in Drosophila have been key for establishing a role for the septin family of proteins in animal cell division and thus extending for the first time observations from the budding yeast to animal cells. Visualizing the distribution of ... More
Mitochondria poised at a fission-fusion balance?: A quantitative assessment of mitochondrial network complexitySep 07 2016Mitochondrial networks have been shown to exhibit a variety of complex behaviors, including cell-wide oscillations of mitochondrial energy states, as well as a phase transition in response to oxidative stress. Since functional status and structural properties ... More
Crawling and turning in a minimal reaction-diffusion cell motility model: coupling cell shape and biochemistrySep 06 2016We study a minimal model of a crawling eukaryotic cell with a chemical polarity controlled by a reaction-diffusion mechanism describing Rho GTPase dynamics. The size, shape, and speed of the cell emerge from the combination of the chemical polarity, which ... More
Enhanced Adhesion of S. Mutans to Hydroxyapatite after Inoculation in SalivaSep 05 2016Streptococcus mutans cells form robust biofilms on human teeth and are strongly related to caries incidents. Hence, understanding the adhesion of S. mutans in the human oral cavity is of major interest for preventive dentistry. In this study, we report ... More
Systemic stability, cell differentiation, and evolution - A dynamical systems perspectiveAug 30 2016Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available substrate. ... More
Stem Cell Therapy for Alzheimer's DiseaseAug 26 2016The loss of neuronal cells in the central nervous system may happen in numerous neurodegenerative illnesses. Alzheimer's Disease (AD) is an intricate, irreversible, dynamic neurodegenerative sickness. It is the main source of age-related dementia, influencing ... More
Modelling the effect of curvature on the collective behaviour of cells growing new tissueAug 25 2016The growth of several biological tissues is known to be controlled in part by local geometrical features, such as the curvature of the tissue interface. This control leads to changes in tissue shape that in turn can affect the tissue's evolution. Understanding ... More
Probing Three-dimensional Collective Cancer Invasion with DIGMEAug 24 2016Multicellular migration and pattern formation play important roles in developmental biology, cancer metastasis and wound healing. To understand the collective cell dynamics in three dimensional extracellular matrix (ECM), we have developed a simple and ... More
Identification of Bifurcations from Observations of Noisy Biological OscillatorsAug 23 2016Hair bundles are biological oscillators that actively transduce mechanical stimuli into electrical signals in the auditory, vestibular, and lateral-line systems of vertebrates. A bundle's function can be explained in part by its operation near a particular ... More
The Role of the Hes1 Crosstalk Hub in Notch-Wnt Interactions of the Intestinal CryptAug 22 2016The Notch pathway plays a vital role in determining whether cells in the intestinal epithelium adopt a secretory or an absorptive phenotype. Cell fate specification is coordinated via Notch's interaction with the canonical Wnt pathway. Here, we propose ... More
The effect of reactions on the formation and readout of the gradient of BicoidAug 11 2016During early development, the establishment of gradients of transcriptional factors determines the patterning of cell fates. The case of Bicoid (Bcd) in {\it Drosophila melanogaster} embryos is well documented and studied. There are still controversies ... More
TLR-exosomes exhibit distinct kinetics and effector functionAug 10 2016The innate immune system is vital to rapidly responding to pathogens and Toll-like receptors (TLRs) are a critical component of this response. Nanovesicular exosomes play a role in immunity, but to date their exact contribution to the dissemination of ... More
Physical limits to biomechanical sensingAug 04 2016Cells actively probe and respond to the stiffness of their surroundings. Since mechanosensory cells in connective tissue are surrounded by a disordered network of biopolymers, their in vivo mechanical environment can be extremely heterogeneous. Here, ... More
Normal and pathological dynamics of platelets in humansJul 29 2016We develop a comprehensive mathematical model of platelet, megakaryocyte, and thrombopoietin dynamics in humans. We show that there is a single stationary solution that can undergo a Hopf bifurcation, and use this information to investigate both normal ... More
The Mechanism Behind Beauty: Golden Ratio Appears in Red Blood Cell ShapeJul 25 2016In the past two decades, under the conditions that both the osmotic pressure $\Delta p$ and tensile stress $\lambda$ equal zero, a rigorous solution (RS) of human red blood cell (RBC) with a minus spontaneous curvature $c_{0}$ has been derived with Helfrich ... More
Multicellular self-organization of P. aeruginosa due to interactions with secreted trailsJul 22 2016Sep 19 2016Guided movement in response to slowly diffusing polymeric trails provides a unique mechanism for self-organization of some microorganisms. To elucidate how this signaling route leads to microcolony formation, we experimentally probe the trajectory and ... More
Bayesian uncertainty analysis for complex systems biology models: emulation, global parameter searches and evaluation of gene functionsJul 21 2016Background: Many mathematical models have now been employed across every area of systems biology. These models increasingly involve large numbers of unknown parameters, have complex structure which can result in substantial evaluation time relative to ... More
Aggregation Dynamics Using Phase Wave Signals and Branching PatternsJul 21 2016The aggregation dynamics of slime mold is studied using coupled equations of phase \phi and cell concentration n. Phase waves work as tactic signals for aggregation. Branching structures appear during the aggregation. A stationary branching pattern appears ... More
Structured Models of Cell Migration Incorporating Molecular Binding ProcessesJul 18 2016The dynamic interplay between collective cell movement and the various molecules involved in the accompanying cell signalling mechanisms plays a crucial role in many biological processes including normal tissue development and pathological scenarios such ... More
Hydrodynamic theory of tissue shear flowJul 12 2016We propose a hydrodynamic theory to describe shear flows in developing epithelial tissues. We introduce hydrodynamic fields corresponding to state properties of constituent cells as well as a contribution to overall tissue shear flow due to rearrangements ... More
Active dynamics of tissue shear flowJul 12 2016Nov 25 2016We present a hydrodynamic theory to describe shear flows in developing epithelial tissues. We introduce hydrodynamic fields corresponding to state properties of constituent cells as well as a contribution to overall tissue shear flow due to rearrangements ... More
Theory for transitions between log and stationary phases: universal laws for lag timeJul 12 2016Quantitative characterization of bacterial growth has gathered substantial attention since Monod's pioneering study. Theoretical and experimental work has uncovered several laws for describing the log growth phase, in which the number of cells grows exponentially. ... More
Filter-feeding, near-field flows, and the morphologies of colonial choanoflagellatesJul 11 2016Efficient uptake of nutrients from the environment is an important component in the fitness of all microorganisms, and its dependence on size may reveal clues to the origins of evolutionary transitions to multicellularity. Because potential benefits in ... More
Dynamic sampling and information encoding in biochemical networksJul 06 2016Cells use biochemical networks to translate environmental information into intracellular responses. These responses can be highly dynamic, but how the information is encoded in these dynamics remains poorly understood. Here we investigate the dynamic ... More
Stochastic multi-scale models of competition within heterogeneous cellular populations: simulation methods and mean-field analysisJul 06 2016We propose a modelling framework to analyse the stochastic behaviour of heterogeneous, multi-scale cellular populations. We illustrate our methodology with a particular example in which we study a population with an oxygen-regulated proliferation rate. ... More
A Macroscopic Mathematical Model For Cell Migration Assays Using A Real-Time Cell AnalysisJul 05 2016Experiments of cell migration and chemotaxis assays have been classically performed in the so-called Boyden Chambers. A recent technology, xCELLigence Real Time Cell Analysis, is now allowing to monitor the cell migration in real time. This technology ... More
Emergence of Lévy Walks in Systems of Interacting IndividualsJun 30 2016Recent experiments (G. Ariel, et al., Nature Comm. 6, 8396 (2015)) revealed an intriguing behavior of swarming bacteria: they fundamentally change their collective motion from simple diffusion into a superdiffusive L\'{e}vy walk dynamics. We introduce ... More
Relevant parameters in models of cell division controlJun 29 2016A recent burst of dynamic single-cell growth-division data makes it possible to characterize the stochastic dynamics of cell division control in bacteria. Different modeling frameworks were used to infer specific mechanisms from such data, but the links ... More
Collective motion of cells crawling on a substrate: roles of cell shape and contact inhibitionJun 24 2016Nov 24 2016Contact inhibition plays a crucial role in the motility of cells, the process of wound healing, and the formation of tumors. By mimicking the mechanical motion of calls crawling on a substrate using a pseudopod, we constructed a minimal model for migrating ... More
Collective motion of cells crawling on a substrate: roles of cell shape and contact inhibitionJun 24 2016Nov 21 2016Contact inhibition plays a crucial role in the motility of cells, the process of wound healing, and the formation of tumors. By mimicking the mechanical motion of calls crawling on a substrate using a pseudopod, we constructed a minimal model for migrating ... More
Collective motion of cells crawling on a substrate: roles of cell shape and contact inhibitionJun 24 2016Jun 27 2016Contact inhibition plays a crucial role in the motility of cells, the process of wound healing, and the formation of tumors. By mimicking the mechanical motion of calls crawling on a substrate using a pseudopod, we constructed a minimal model for migrating ... More
Aerotaxis in the Closest Relatives of AnimalsJun 18 2016As the closest unicellular relatives of animals, choanoflagellates serve as useful model organisms for understanding the evolution of animal multicellularity. An important factor in animal evolution was the increasing ocean oxygen levels in the Precambrian, ... More
A Mathematical Model of Cell Reprogramming due to Intermediate Differential Regulator's RegulationsJun 13 2016In this paper I have given a mathematical model of Cell reprogramming from a different contexts. Here I considered there is a delay in differential regulator rate equations due to intermediate regulator's regulations. At first I gave some basic mathematical ... More
Astrocytic Ion Dynamics: Implications for Potassium Buffering and Liquid FlowJun 09 2016We review modeling of astrocyte ion dynamics with a specific focus on the implications of so-called spatial potassium buffering, where excess potassium in the extracellular space (ECS) is transported away to prevent pathological neural spiking. The recently ... More
MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic modelsJun 09 2016Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Our previous work revealed the potential of analyzing extracellular metabolomic data in the context of the metabolic model ... More
Integrative modeling of sprout formation in angiogenesis: coupling the VEGFA-Notch signaling in a dynamic stalk-tip cell selectionJun 07 2016During angiogenesis, new blood vessels headed by a migrating endothelial tip cell sprout from pre-existing ones. This process is known to be regulated by two signaling pathways concurrently, vascular endothelial growth factor A (VEGFA) and Notch-Delta. ... More
A brief introduction to the model microswimmer {\it Chlamydomonas reinhardtii}Jun 06 2016The unicellular biflagellate green alga {\it Chlamydomonas reinhardtii} has been an important model system in biology for decades, and in recent years it has started to attract growing attention also within the biophysics community. Here we provide a ... More
The Physics of Biofilms -- An IntroductionJun 04 2016Biofilms are complex, self-organized consortia of microorganisms that produce a functional, protective matrix of biomolecules. Physically, the structure of a biofilm can be described as an entangled polymer network which grows and changes under the effect ... More
The load-response of the flagellar beatJun 02 2016Nov 21 2016Cilia and flagella exhibit regular bending waves that perform mechanical work on the surrounding fluid, to propel cellular swimmers and pump fluids inside organisms. Here, we quantify a force-velocity relationship of the beating flagellum, by exposing ... More
The load-response of the flagellar beatJun 02 2016Cilia and flagella exhibit regular bending waves that perform mechanical work on the surrounding fluid, to propel cellular swimmers and pump fluids inside organisms. Here, we quantify a force-velocity relationship of the beating flagellum, by exposing ... More
Conditions for cell size homeostasis: A stochastic hybrid systems approachJun 02 2016A ubiquitous feature of living cells is their growth over time followed by division into daughter cells. How isogenic cell populations maintain size homeostasis, i.e., a narrow distribution of cell size, is an intriguing fundamental problem. We model ... More
Modelling cross-reactivity and memory in the cellular adaptive immune response to influenza infection in the hostJun 01 2016Nov 22 2016The cellular adaptive immune response plays a key role in resolving influenza infection. Experiments where individuals are successively infected with different strains within a short timeframe provide insight into the underlying viral dynamics and the ... More
Modelling cross-reactivity and memory in the cellular adaptive immune response to influenza infection in the hostJun 01 2016The cellular adaptive immune response plays a key role in resolving influenza infection. It can provide cross-protection between subtypes of influenza A which share epitopes; thus, the strength of the immune response to a given strain is dependent upon ... More
An unbiased metric of antiproliferative drug effect in vitroMay 22 2016In vitro cell proliferation assays are widely used in pharmacology, molecular biology, and drug discovery. Using theoretical modeling and experimentation, we show that current antiproliferative drug effect metrics suffer from time-dependent bias, leading ... More
Topological defect launches 3D mound in the active nematic sheet of neural progenitorsMay 20 2016Cultured stem cells have become a standard platform not only for regenerative medicine and developmental biology but also for biophysical studies. Yet, the characterization of cultured stem cells at the level of morphology and macroscopic patterns resulting ... More
Antibiotic resistance: a physicist's viewMay 19 2016The problem of antibiotic resistance poses challenges across many disciplines. One such challenge is to understand the fundamental science of how antibiotics work, and how resistance to them can emerge. This is an area where physicists can make important ... More
Collective migration under hydrodynamic interactions -- a computational approachMay 19 2016Substrate-based cell motility is essential for fundamental biological processes, such as tissue growth, wound healing and immune response. Even if a comprehensive understanding of this motility mode remains elusive, progress has been achieved in its modeling ... More
Shear-Induced Nitric Oxide Production by Endothelial CellsMay 19 2016We present a biochemical model of the wall shear stress (WSS)-induced activation of endothelial nitric oxide synthase (eNOS) in an endothelial cell (EC). The model includes three key mechanotransducers: mechanosensing ion channels, integrins and G-protein-coupled ... More
Cell contractility facilitates alignment of cells and tissues to static uniaxial stretchMay 12 2016During animal development and homeostasis, the structure of tissues, including muscles, blood vessels and connective tissues adapts to mechanical strains in the extracellular matrix (ECM). These strains originate from the differential growth of tissues ... More
Functional Characteristics of Gene Expression Motifs with Single and Dual Strategies of RegulationMay 11 2016Transcriptional regulation by transcription factors and post-transcriptional regulation by microRNAs constitute two major modes of regulation of gene expression. While gene expression motifs incorporating solely transcriptional regulation are well investigated, ... More
Target shape dependence in a simple model of receptor-mediated endocytosis and phagocytosisMay 10 2016Phagocytosis and receptor-mediated endocytosis are vitally important particle uptake mechanisms in many cell types, ranging from single-cell organisms to immune cells. In both processes, engulfment by the cell depends critically on both particle shape ... More
Run and tumble navigation can be very fastMay 10 2016The ability to navigate environmental gradients is often critical for survival. When gradients are shallow or noisy, most organisms move by alternating straight motion (runs) with random reorientations (tumbles). Navigation is achieved by transiently ... More
Rescaling of spatio-temporal sensing in eukaryotic chemotaxisMay 07 2016Eukaryotic cells can detect the direction of a chemoattractant gradient precisely by generating intracellular gradients of signaling molecules that mirror the extracellular gradient ? an ability called directional sensing. Quantitative experiments have ... More
Rescaling of spatio-temporal sensing in eukaryotic chemotaxisMay 07 2016Oct 25 2016Eukaryotic cells respond to a chemoattractant gradient by forming intracellular gradients of signaling molecules that reflect the extracellular chemical gradient - an ability called directional sensing. Quantitative experiments have revealed two characteristic ... More
Immersed Boundary Simulations of Active Fluid DropletsMay 05 2016Aug 03 2016We present numerical simulations of active fluid droplets immersed in an external fluid in 2-dimensions { using} an Immersed Boundary method to simulate the fluid droplet interface as a Lagrangian mesh. We present results from two example systems, firstly ... More
Inferring models of bacterial dynamics toward point sourcesApr 29 2016May 02 2016Experiments have shown that bacteria can be sensitive to small variations in chemoattractant (CA) concentrations. Motivated by these findings, our focus here is on a regime rarely studied in experiments: bacteria tracking point CA sources (such as food ... More
Membrane tension is a key determinant of bud morphology in clathrin-mediated endocytosisApr 28 2016In clathrin-mediated endocytosis (CME), clathrin and various adaptor proteins coat a patch of the plasma membrane, which is reshaped to form a budded vesicle. Experimental studies have demonstrated that elevated membrane tension can inhibit bud formation ... More
Amoeboid swimming in a channelApr 20 2016Aug 28 2016Several micro-organisms, such as bacteria, algae, or spermatozoa, use flagella or cilia to swim in a fluid, while many other micro-organisms instead use ample shape deformation, described as amoeboid, to propel themselves by either crawling on a substrate ... More
A multiscale approach to the migration of cancer stem cells: mathematical modelling and simulationsApr 18 2016We propose a multiscale model of the invasion of the extracellular matrix by two types of cancer cells, the differentiated cancer cells and the cancer stem cells. We assume that the epithelial mesenchymal-like transition between them is driven primarily ... More
Generating Semi-Synthetic Validation Benchmarks for EmbryomicsApr 17 2016Systematic validation is an essential part of algorithm development. The enormous dataset sizes and the complexity observed in many recent time-resolved 3D fluorescence microscopy imaging experiments, however, prohibit a comprehensive manual ground truth ... More
Traveling Pulses for a Two-Species Chemotaxis ModelApr 14 2016Mathematical models have been widely used to describe the collective movement of bacteria by chemotaxis. In particular, bacterial concentration waves traveling in a narrow channel have been experimentally observed and can be precisely described thanks ... More
Biomechanics of epithelial cell islands analyzed by modeling and experimentationApr 13 2016We generated a new computational approach to analyze the biomechanics of epithelial cell islands that combines both vertex and contact-inhibition-of-locomotion models to include both cell-cell and cell-substrate adhesion. Examination of the distribution ... More
Contact inhibition of locomotion and mechanical cross-talk between cell-cell and cell-substrate adhesion determines the pattern of junctional tension in epithelial cell aggregatesApr 13 2016Nov 18 2016We generated a computational approach to analyze the biomechanics of epithelial cell aggregates, either island or stripes or entire monolayers, that combines both vertex and contact-inhibition-of-locomotion models to include both cell-cell and cell-substrate ... More