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Long term observation of Magnetospirillum gryphiswaldense in a microfluidic channelFeb 21 2019We controlled and observed individual magnetotactic bacteria (Magnetospirillum gryphiswaldense) inside a 5 {\mu}m high microfluidic channel for over four hours. After a period of constant velocity, the duration of which varied between bacteria, all observed ... More
Asymmetric Oxidation of Giant Vesicles triggers Curvature-associated Shape Transition and Permeabilization. Running title: Oxidation of Vesicles produces CurvatureFeb 18 2019(200 words) Oxidation of unsaturated lipids is a fundamental process involved in cell bioenergetics as well as in cell death. Using giant unilamellar vesicles and a chlorin photosensitizer, we asymmetrically oxidized the outer or inner monolayers of lipid ... More
Actin filaments pushing against a barrier: Comparison between two force generation mechanismsFeb 18 2019To theoretically understand force generation properties of actin filaments, many models consider growing filaments pushing against a movable obstacle or barrier. In order to grow, the filaments need space and hence it is necessary to move the barrier. ... More
Modelling cell reactions to ionizing radiation -- from a lesion to a cancerFeb 16 2019This paper focuses on the analytic modelling of responses of cells in the body to ionizing radiation. The related mechanisms are consecutively taken into account and discussed. A model of the dose- and time-dependent adaptive response is considered, for ... More
Remark on Protein Collapse from a Random WalkFeb 15 2019We use a mean-field approximation to show the rapid collapse of protein-like polymers from random walk size to a much smaller, molten globule state due to hydrophobic interactions, to be followed by a slower annealing process in which there is little ... More
Ion Condensation onto Ribozyme is Site-Specific and Fold-DependentFeb 15 2019The highly charged RNA molecules, with each phosphate carrying a single negative charge, cannot fold into well-defined architectures with tertiary interactions, in the absence of ions. For ribozymes, divalent cations are known to be more efficient than ... More
Circular spectropolarimetric sensing of vegetation in the field; possibilities for the remote detection of extraterrestrial lifeFeb 15 2019Homochirality is a generic and unique property of all biochemical life and the fractional circular polarization it induces therefore constitutes an unambiguous biosignature. However, while high-quality circular polarimetric spectra can be easily and quickly ... More
Assessing the Level of Autonomic Nervous Activity for Effective Biofeedback TrainingFeb 15 2019This paper proposes a prototype of a new biofeedback training based on mathematical models of cardiovascular control. For this purpose we develop a low-cost device that is able to record and process arterial pulse wave via photoplethysmograph and skin ... More
Thermodynamics of force-induced B-DNA melting: single-strand discreteness mattersFeb 15 2019Overstretching of B-DNA is currently understood as force-induced melting. Depending on the geometry of the stretching experiment, the force threshold for the overstretching transition is around 65 or 110 pN. Although the mechanisms behind force-induced ... More
Acoustic scattering mediated single detector optoacoustic tomographyFeb 14 2019Optoacoustic image formation is conventionally based upon ultrasound time-of-flight readings from multiple detection positions. Herein, we exploit acoustic scattering to physically encode the position of optical absorbers in the acquired signals, thus ... More
One-Loop Fluctuation Entropy of Charge Inversion in DNAFeb 14 2019Experiments have revealed correlation-driven behavior of DNA in charged solutions, including charge inversion and condensation. This paper presents calculations of a lattice-gas model of charge inversion for the adsorption of charged dimers on DNA. Each ... More
Understanding the dynamics of biological and neural oscillator networks through mean-field reductions: a reviewFeb 14 2019Many biological and neural system can be seen as networks of interacting periodic processes. Importantly, the function of these networks depends on the collective dynamics: Synchrony of oscillations is probably amongst the most prominent examples of collective ... More
Diffusion through nanopores in connected lipid bilayer networksFeb 13 2019A biomimetic model of cell-cell communication was developed to probe the passive molecular transport across ion channels inserted in synthetic lipid bilayers formed between contacting droplets arranged in a linear array. Diffusion of a fluorescent probe ... More
A stochastic model for bacteria-driven micro-swimmersFeb 13 2019Experiments have recently shown the feasibility of utilising bacteria as micro-scale robotic devices, with special attention paid to the development of bacteria-driven micro-swimmers taking advantage of built-in actuation and sensing mechanisms of cells. ... More
On the selectivity of KcsA potassium channel: asymptotic analysis and computationFeb 12 2019Potassium (K$^+$) channels regulate the flux of K$^+$ ions through cell membranes and plays significant roles in many physiological functions. This work studies the KcsA potassium channel, including the selectivity and current-voltage (IV) relations. ... More
Development of high-sensitivity chip calorimeters for cellular metabolic heat sensingFeb 12 2019Cellular metabolic rate is a good indicator of the physiological state of cells and its changes, which can be measured by total heat flux accompanying metabolism. Chip calorimeters can provide label-free and high throughput measurements of cellular metabolic ... More
Osmotic pressure of compressed lattice knotsFeb 12 2019A numerical simulation shows that the osmotic pressure of compressed lattice knots is a function of knot type, and so of entanglements. The osmotic pressure for the unknot goes through a negative minimum at low concentrations, but in the case of non-trivial ... More
Osmotic pressure of compressed lattice knotsFeb 12 2019Feb 20 2019A numerical simulation shows that the osmotic pressure of compressed lattice knots is a function of knot type, and so of entanglements. The osmotic pressure for the unknot goes through a negative minimum at low concentrations, but in the case of non-trivial ... More
Effects of empathy on the evolution of fairness in group-structured populationsFeb 12 2019The ultimatum game has been a prominent paradigm in studying the evolution of fairness. It predicts that responders should accept any nonzero offer and proposers should offer the smallest possible amount according to orthodox game theory. However, the ... More
Fast consensus clustering in complex networksFeb 11 2019Algorithms for community detection are usually stochastic, leading to different partitions for different choices of random seeds. Consensus clustering has proven to be an effective technique to derive more stable and accurate partitions than the ones ... More
Multi-Season Analysis Reveals the Spatial Structure of Disease SpreadFeb 11 2019Understanding the dynamics of infectious disease spread in a heterogeneous population is an important factor in designing control strategies. Here, we develop a novel tensor-driven multi-compartment version of the classic Susceptible-Infected-Recovered ... More
Interspike interval correlations in networks of inhibitory integrate-and-fire neuronsFeb 11 2019We study temporal correlations of interspike intervals (ISIs), quantified by the network-averaged serial correlation coefficient (SCC), in networks of both current- and conductance-based purely inhibitory integrate-and-fire neurons. Numerical simulations ... More
Classifying attention deficit hyperactivity disorder in children with non-linearities in actigraphyFeb 10 2019Objective This study provides an objective measure based on actigraphy for Attention Deficit Hyperactivity Disorder (ADHD) diagnosis in children. We search for motor activity features that could allow further investigation into their association with ... More
Nonlinear Discovery of Slow Molecular Modes using Hierarchical Dynamics EncodersFeb 09 2019The success of enhanced sampling molecular simulations that accelerate along collective variables (CVs) is predicated on the availability of variables coincident with the slow collective motions governing the long-time conformational dynamics of a system. ... More
Linear Dynamics & Control of Brain NetworksFeb 08 2019The brain is an intricately structured organ responsible for the rich emergent dynamics that support the complex cognitive functions we enjoy as humans. With around $10^{11}$ neurons and $10^{15}$ synapses, understanding how the human brain works has ... More
Efficient sliding locomotion with isotropic frictionFeb 08 2019Snakes' bodies are covered in scales that make it easier to slide in some directions than in others. This frictional anisotropy allows for sliding locomotion with an undulatory gait, one of the most common for snakes. Isotropic friction is a simpler situation ... More
Fractal nature of protein structures affects their Vibrational Energy ExchangeFeb 08 2019Recent vibrational energy exchange experiments on a protein have been explained employing the relation, not new in itself, between protein and fractal structure. The differnce in the scaling exponent of specific part of the protein entails a distinct ... More
Dynamics of a large population of red blood cells under shear flowFeb 08 2019An exhaustive description of the dynamics under shear flow of a large number of red blood cells in dilute regime is proposed, which highlights and takes into account the dispersion in cell properties within a given blood sample. Physiological suspending ... More
Mobile Artificial Intelligence Technology for Detecting Macula Edema and Subretinal Fluid on OCT Scans: Initial Results from the DATUM alpha StudyFeb 08 2019Importance: Artificial Intelligence (AI) is necessary to address the large and growing deficit in retina and healthcare access globally. Mobile AI diagnostic platforms running in the Cloud may effectively and efficiently distribute such AI capability. ... More
Mobile Artificial Intelligence Technology for Detecting Macula Edema and Subretinal Fluid on OCT Scans: Initial Results from the DATUM alpha StudyFeb 08 2019Feb 12 2019Artificial Intelligence (AI) is necessary to address the large and growing deficit in retina and healthcare access globally. And mobile AI diagnostic platforms running in the Cloud may effectively and efficiently distribute such AI capability. Here we ... More
Influence of Bonded Interactions on Structural Phases of Flexible PolymersFeb 07 2019We introduce a novel coarse-grained bead-spring model for flexible polymers to systematically examine the effects of an adjusted bonded potential on the formation and stability of structural macrostates in a thermal environment. The density of states ... More
A minimal model for nematic cell ordering in tissueFeb 07 2019Recent advances mean that samples of artificial tissue can now be grown. Hence there is a need for theoretical understanding of these tissues commensurate with the size of experimental systems. We present a minimal model for predicting cell orientations ... More
Identification of epileptic regions from electroencephalographic data: Feigenbaum graphsFeb 07 2019Diagnosing epilepsy is a problem of crucial importance. So analysing EEG data is of much importance to help this diagnosis. Assembling the Feigenbaum graphs for EEG signals. And calculating their average clustering, average degree, and average shortest ... More
Quantitative analysis of self-organized patterns in ombrotrophic peatlandsFeb 07 2019We numerically investigate a diffusion-reaction model of an ombrotrophic peatland implementing a Turing instability relying on nutrient accumulation. We propose a systematic and quantitative sorting of the vegetation patterns, based on the statistical ... More
Snare machinery is optimized for ultrafast fusionFeb 07 2019SNARE proteins zipper to form SNAREpins that power vesicle fusion with target membranes in a variety of biological processes. A single SNAREpin takes about 1 second to fuse two bilayers, yet a handful can ensure release of neurotransmitters from synaptic ... More
Biochemical feedback and its application to immune cells II: dynamics and critical slowing downFeb 07 2019Near a bifurcation point, the response time of a system is expected to diverge due to the phenomenon of critical slowing down. We investigate critical slowing down in well-mixed stochastic models of biochemical feedback by exploiting a mapping to the ... More
Aggregation dynamics of active cells on non-adhesive substrateFeb 06 2019Cellular self-assembly and organization are fundamental steps for the development of biological tissues. In this paper, within the framework of a cellular automata model, we address how an ordered tissue pattern spontaneously emerges from a randomly migrating ... More
Stick-Slip Dynamics of Migrating Cells on Viscoelastic SubstratesFeb 06 2019Stick-slip motion, a common phenomenon observed during crawling of cells, is found to be strongly sensitive to the substrate stiffness. Stick-slip behaviours have previously been investigated typically using purely elastic substrates. For a more realistic ... More
Molecular motors govern liquid-like ordering and fusion dynamics of bacterial coloniesFeb 06 2019Bacteria can adjust the structure of colonies and biofilms to enhance their survival rate under external stress. Here, we explore the link between bacterial interaction forces and colony structure. We show that the activity of extracellular pilus motors ... More
An open-source multi-person virtual reality framework for interactive molecular dynamics: from quantum chemistry to drug bindingFeb 05 2019Conceptually, the mechanics of nanoscale molecular objects arise through electrostatic forces acting on particles in non-uniform fields, and are relatively well characterized owing to decades of study. Nevertheless, because dynamics at this scale differ ... More
An open-source multi-person virtual reality framework for interactive molecular dynamics: from quantum chemistry to drug bindingFeb 05 2019Feb 12 2019Conceptually, the mechanics of nanoscale molecular objects arise through electrostatic forces acting on particles in non-uniform fields, and are relatively well characterized owing to decades of study. Nevertheless, because dynamics at this scale differ ... More
Substrate Roughness Significantly Affects Bilayer Phase SeparationFeb 05 2019Supported Lipid Bilayers (SLBs) are model membranes formed at solid substrate surfaces. This architecture renders membranes experimentally accessible to surface sensitive techniques used to study their properties, including Atomic Force Microscopy (AFM), ... More
Crawling in a fluidFeb 05 2019There is increasing evidence that mammalian cells not only crawl on substrates but can also swim in fluids. To elucidate the mechanisms of the onset of motility of cells in suspension, a model which couples actin and myosin kinetics to fluid flow is proposed ... More
Direct observation of the cell-wall remodeling in adhering Staphylococcus aureus 27217: an AFM study supported by SEM and TEMFeb 05 2019We took benefit from Atomic Force Microscopy (AFM) in the force spectroscopy mode to describe the time evolution-over 24h-of the surface nanotopography and mechanical properties of the strain Staphylococcus aureus 27217 from bacterial adhesion to the ... More
Gd(III)-Gd(III) RIDME for In-Cell EPR Distance DeterminationFeb 04 2019In-cell distance determination by EPR reveals essential structural information about biomacromolecules under native conditions. We demonstrate that the pulsed EPR technique RIDME (relaxation induced dipolar modulation enhancement) can be utilized for ... More
Sex-ratio bias induced by mutationFeb 04 2019A question in evolutionary biology is why the number of males is approximately equal to that of females in many species, and Fisher's theory of equal investment answers that it is the evolutionarily stable state. The Fisherian mechanism can be given a ... More
Lateral inhibition provides a unifying framework for spatiotemporal pattern formation in media comprising relaxation oscillatorsFeb 04 2019The collective dynamics seen in a wide variety of chemical, biological and ecological systems involve interactions between relaxation oscillators that typically involve fast activation process coupled with a slower inactivation. In this paper, we show ... More
A general model of focal adhesion orientation dynamics in response to static and cyclic stretchFeb 03 2019Understanding cellular response to mechanical forces is immensely important for a plethora of biological processes. Focal adhesions are multi-molecular protein assemblies that connect the cell to the extracellular matrix and play a pivotal role in cell ... More
New combinational therapies for cancer using modern statistical mechanicsFeb 02 2019We investigate a new dynamical system that describes tumor-host interaction. The equation that describes the untreated tumor growth is based on non-extensive statistical mechanics. Recently, this model has been shown to fit successfully exponential, Gompertz, ... More
A model for meme popularity growth in social networking systems based on biological principle and human interest dynamicsFeb 01 2019We analyze five big data sets from a variety of online social networking (OSN) systems and find that the growth dynamics of meme popularity exhibit characteristically different behaviors. For example, there is linear growth associated with online recommendation ... More
Ensembles, Dynamics, and Cell Types: Revisiting the Statistical Mechanics Perspective on Cellular RegulationFeb 01 2019Genetic regulatory networks control ontogeny. For fifty years Boolean networks have served as models of such systems, ranging from ensembles of random Boolean networks as models for generic properties of gene regulation to working dynamical models of ... More
Spectral content of a single non-Brownian trajectoryFeb 01 2019Time-dependent processes are often analysed using the power spectral density (PSD), calculated by taking an appropriate Fourier transform of individual trajectories and finding the associated ensemble-average. Frequently, the available experimental data ... More
Optimal power generation using dark states in dimers strongly coupled to their environmentJan 31 2019Dark state protection has been proposed as a mechanism to increase the power output of light harvesting devices by reducing the rate of radiative recombination. Indeed many theoretical studies have reported increased power outputs in dimer systems which ... More
Mathematics of nerve signalsJan 31 2019Mathematical models describing the signals propagating in nerve fibres are described. The emphasis is on the mathematical structures of governing equations while the extremely rich physiological aspects are here not analysed. Based on models of single ... More
Ligand-induced oligomerization of the human GPCR neurotensin receptor 1 monitored in living HEK293T cellsJan 31 2019The human neurotensin receptor 1 (NTSR1) is a G protein-coupled receptor that can be expressed in HEK293T cells by stable transfection. Its ligand is a 13-amino-acid peptide that binds with nanomolar affinity from the extracellular side to NTSR1. Ligand ... More
Direct three-dimensional measurement of refractive index via dual photon-phonon scatteringJan 30 2019We developed a microscopy technique that can measure the local refractive index without sampling the optical phase delay of the electromagnetic radiation. To do this, we designed and experimentally demonstrated a setup with two co-localized Brillouin ... More
\textit{C. elegans} collectively forms dynamical networksJan 30 2019Understanding physical rules underlying collective motions requires perturbation of controllable parameters in self-propelled particles. However, controlling parameters in animals is generally not easy, which makes collective behaviours of animals elusive. ... More
Charge Transport in Bifidobacterium animalis subsp. lactis BB-12 under the various AtmosphereJan 30 2019The influence of relative humidity (RH) on quasistatic current-voltage ${(I-V)}$ characteristics of Bifidobacterium animalis subsp. lactis BB-12 thin layers have been studied for the first time. The value of electrical conductivity in 75$ \%$ RH was found ... More
Dense Fiber Modeling for 3D-Polarized Light Imaging SimulationsJan 29 20193D-Polarized Light Imaging (3D-PLI) is a neuroimaging technique used to study the structural connectivity of the human brain at the meso- and microscale. In 3D-PLI, the complex nerve fiber architecture of the brain is characterized by 3D orientation vector ... More
Facilitation of DNA loop formation by protein-DNA non-specific interactionsJan 29 2019Complex DNA topological structures, including polymer loops, are frequently observed in biological processes when protein molecules simultaneously bind to several distant sites on DNA. However, the molecular mechanisms of formation of these systems remain ... More
A Mechano-Chemical model for tumors growthJan 28 2019In this paper we present a study of local dynamics of the growth of cancer tumor and healthy cells considering the presence of nutrients in the system. We also analyze the evolution of system if we take indirectly into account the level of alkalinity ... More
Magic numbers in polymer phase separation - the importance of being rigidJan 27 2019Cells possess non-membrane-bound bodies, many of which are now understood as phase-separated condensates. One class of such condensates is composed of two polymer species, where each consists of repeated binding sites that interact in a one-to-one fashion ... More
Enhanced propagation of motile bacteria on surfaces due to forward scatteringJan 24 2019How motile bacteria move near a surface is a problem of fundamental biophysical interest and is key to the emergence of several phenomena of biological, ecological and medical relevance, including biofilm formation. Solid boundaries can strongly influence ... More
Spontaneous formation of chaotic protrusions in a polymerizing active gel layerJan 24 2019The actin cortex is a thin layer of actin filaments and myosin motors beneath the outer membrane of animal cells. It determines the cells' mechanical properties and forms important morphological structures. Physical descriptions of the cortex as a contractile ... More
Fixation in Fluctuating PopulationsJan 24 2019We investigate the dynamics of the voter model in which the population itself changes endogenously via the birth-death process. There are two species of voters, labeled A and B, and the population of each species can grow or shrink by the birth-death ... More
Stability of arrays of bottom-heavy spherical squirmersJan 24 2019The incessant swimming motion of microbes in dense suspensions can give rise to striking collective motions and coherent structures. However, theoretical investigations of these structures typically utilize either computationally demanding numerical simulations, ... More
Renormalization of radiobiological response functions by energy loss fluctuations and complexities in chromosome aberration induction: deactivation theory for proton therapy from cells to tumor controlJan 24 2019We employ a multi-scale mechanistic approach to investigate radiation induced cell toxicities and deactivation mechanisms as a function of linear energy transfer in hadron therapy. Our theoretical model consists of a system of Markov chains in microscopic ... More
Bacterial range expansions on a growing front: Roughness, Fixation, and Directed PercolationJan 23 2019Directed Percolation (DP) is a classic model for nonequilibrium phase transitions into a single absorbing state (fixation). It has been extensively studied by analytical and numerical techniques in diverse contexts. Recently, DP has appeared as a generic ... More
Knowing the past improves cooperation in the futureJan 22 2019Cooperation is the cornerstone of human evolutionary success. Like no other species, we champion the sacrifice of personal benefits for the common good, and we work together to achieve what we are unable to achieve alone. Knowledge and information from ... More
Built-in Fluorescence Anisotropy: an in vivo Imaging Probe for bis-Retinoid Products in RetinaJan 21 2019Non-degradable fluorophores that accumulate as Lipofuscin in retinal pigment epithelium (RPE) cells has been a major source of intrinsic biomarker for quantifying the progression of several diseases, including age-related macular degeneration, Stargardt ... More
Ti2NiCu Based Composite Nanotweezers with a Shape Memory Effect and its Use for DNA Bunches 3D ManipulationJan 21 2019Jan 24 2019The DNA molecules were controllable deposited on graphene and thin graphite films and visualized using AFM. The mechanical micro- and nanotools, such as nanotweezers with shape memory effect controlled by heating were designed and tested. A technique ... More
Can all-atom protein dynamics be reconstructed from the knowledge of C-alpha time evolution?Jan 21 2019We inquire to what extent protein peptide plane and side chain dynamics can be reconstructed from knowledge of C-alpha dynamics. Due to lack of experimental data we analyze all atom molecular dynamics trajectories from Anton supercomputer, and for clarity ... More
Horizontal transfer between loose compartments stabilizes replication of fragmented ribozymesJan 21 2019The emergence of replicases that can replicate themselves is a central issue in the origin of life. Recent experiments suggest that such replicases can be realized if an RNA polymerase ribozyme is divided into fragments short enough to be replicable by ... More
Spontaneous Spatiotemporal Ordering of Shape Oscillations Enhances Cell MigrationJan 20 2019The migration of cells is relevant for processes such as morphogenesis, wound healing, and invasion of cancer cells. In order to move, single cells deform cyclically. However, it is not understood how these shape oscillations influence collective properties. ... More
Abrupt efficiency collapse in real-world complex weighted networks: robustness decrease with link weights heterogeneityJan 18 2019Here we report a comprehensive analysis of the robustness of five high-quality real-world complex weighted networks to errors and attacks of nodes and links. We analyze C. Elegans, Cargo ship, E. Coli, Us Airports and Human brain real-world complex weighted ... More
Centre-finding in E. coli and the role of mathematical modelling: past, present and futureJan 18 2019We review the key role played by mathematical modelling in elucidating two centre-finding patterning systems in E. coli: midcell division positioning by the MinCDE system and DNA partitioning by the ParABS system. We focus particularly on how, despite ... More
Flagellar number governs bacterial spreading and transport efficiencyJan 16 2019Peritrichous bacteria synchronize and bundle their flagella to actively swim while disruption of the bundle leads to tumbling. It is still not known whether the number of flagella represents an evolutionary adaptation towards optimizing bacterial navigation. ... More
Trapping in and escape from branched structures of neuronal dendritesJan 16 2019We present a coarse-grained model for stochastic transport of noninteracting chemical signals inside neuronal dendrites and show how first-passage properties depend on the key structural factors affected by neurodegenerative disorders or aging: the extent ... More
Predicting Growth Rate from Gene ExpressionJan 15 2019Growth rate is one of the most important and most complex phenotypic characteristics of unicellular microorganisms, which determines the genetic mutations that dominate at the population level, and ultimately whether the population will survive. Translating ... More
Assessment of wall stresses and mechanical heart power in the left ventricle: Finite element modeling versus Laplace analysisJan 15 2019Introduction: Stenotic aortic valve disease (AS) causes pressure overload of the left ventricle (LV) that may trigger adverse remodeling and precipitate progression towards heart failure (HF). As myocardial energetics can be impaired during AS, LV wall ... More
Towards a Computational Framework for Modeling the Impact of Aortic Coarctations upon Left Ventricular LoadJan 15 2019Computational fluid dynamics (CFD) models of blood flow in the left ventricle (LV) and aorta are important tools for analyzing the mechanistic links between myocardial deformation and flow patterns. Typically, the use of image-based kinematic CFD models ... More
Universal motion patterns in confluent cell monolayersJan 15 2019Epithelial cell monolayers show remarkable long-range displacement and velocity correlations reminiscent of supercooled liquids and active nematics. Here we show that many of the observed features can be understood within the framework of active matter ... More
Dynamics of growth and form in prebiotic vesiclesJan 14 2019The growth, form, and division of prebiotic vesicles, membraneous bags of fluid of varying components and shapes, served as the substrate for the origin of life. The dynamics of these out-of-equilibrium structures is controlled by physicochemical processes ... More
Game theoretic modelling of infectious disease dynamics and intervention methods: a mini-reviewJan 14 2019We review research papers which use game theory to model the decision making of individuals during an epidemic, attempting to classify the literature and identify the emerging trends in this field. We show that the literature can be classified based on ... More
Influence of image segmentation on pulse wave propagation models of the pulmonary circulationJan 14 2019Computational fluid dynamics (CFD) models are emerging as mathematical tools to assist in the diagnostic assessment of cardiovascular disease. Recent advances in medical imaging and computational algorithms for analyzing said images have made subject-specific ... More
Competition for Stem Cell Fate Determinants as a Mechanism for Tissue HomeostasisJan 12 2019Jan 20 2019Stem cells maintain tissues by generating differentiated cell types while simultaneously self-renewing their own population. The mechanisms that allow stem cell populations to function collectively to control their density, maintain robust homeostasis ... More
Sharp-edged geometric obstacles in microfluidics promote deformability-based sorting of cellsJan 12 2019Sorting cells based on their intrinsic properties is a highly desirable objective, since changes in cell deformability are often associated with various stress conditions and diseases. Deterministic lateral displacement (DLD) devices offer high precision ... More
Sorting of particles suspended in whole bloodJan 11 2019An important step in diagnostics is the isolation of specific cells and microorganisms of interest from blood. Since such bioparticles are often present at very low concentrations, throughput needs to be as high as possible. In addition, to ensure simplicity, ... More
Non-ideal rheology of semidilute bacterial suspensionsJan 11 2019Jan 29 2019The rheology of semidilute bacterial suspensions is studied with the tools of kinetic theory, considering binary interactions, going beyond the ideal gas approximation. Two models for the interactions are considered, which encompass both the steric and ... More
An open source Etextile VR glove for real-time manipulation of molecular simulationsJan 11 2019With VR finding increasing application in scientific research, we are beginning to better understand the domains in which it brings the most benefit, as well as the sorts of gestures which scientific workers find most useful as they navigate simulated ... More
Scaling behavior of non-equilibrium measures in internally driven elastic assembliesJan 10 2019Detecting and quantifying non-equilibrium activity is essential for studying internally driven assemblies, including synthetic active matter and complex living systems such as cells or tissue. We discuss a non-invasive approach of measuring non-equilibrium ... More
A Martini coarse-grained model of the calcein fluorescent dyeJan 10 2019Calcein leakage assays are a standard experimental set-up for probing the extent of damage induced by external agents on synthetic lipid vesicles. The fluorescence signal associated with calcein release from liposomes is the signature of vesicle disruption, ... More
Pearl-Necklace-Like Local Ordering Drives Polypeptide CollapseJan 10 2019Collapse of the polypeptide backbone is an integral part of protein folding. Using polyglycine as a probe, we explore the nonequilibrium pathways of protein collapse in water. We find that the collapse depends on the competition between hydration effects ... More
Evolution of instabilities in filament buckling processesJan 09 2019In this work we study the dynamical buckling process of a thin filament immersed in a high viscous medium. We perform an experimental study to track the shape evolution of the filament during a constant velocity compression. Numerical simulations reproduce ... More
Exact solution of generalized cooperative SIR dynamicsJan 09 2019In this paper, we introduce a general framework for co-infection as cooperative SIR dynamics. We first solve analytically CGCG model [1] and then the generalized model in symmetric scenarios. We calculate transition points, order parameter, i.e. total ... More
Synchronization transitions through metastable state on structured networksJan 08 2019Recently, we considered the fully connected competing Kuramoto model with uniform intrinsic frequency distribution $g(\omega)$. This competing Kuramoto model assigns two opposite-sign coupling constants $K_1 < 0$ and $K_2 > 0$ to $1-p$ and $p$ fractions ... More
Spectral Properties of Effective Dynamics from Conditional ExpectationsJan 06 2019The reduction of high-dimensional systems to effective models on a smaller set of variables is an essential task in many areas of science. For stochastic dynamics governed by diffusion processes, a general procedure to find effective equations has recently ... More
The peculiarities of dynamic current-voltage and charge-voltage loops and transient currents of melanin under pulse hydrationJan 06 2019Melanin is a biopolymer with unique set of applicable physical and chemical properties. The impact of a moisture-saturated air pulse (~1 s) on dynamic current-voltage (I-V-), charge-voltage (Q-V-) and transient (I-t-) characteristics of fungal melanin ... More
Phoretic and hydrodynamic interactions of weakly-confined autophoretic particlesJan 04 2019Phoretic particles self-propel using self-generated physico-chemical gradients at their surface. Within a suspension, they interact hydrodynamically by setting the fluid around them into motion, and chemically by modifying the chemical background seen ... More
Fourier analysis of a delayed Rulkov neuron networkJan 04 2019We have analyzed the synchronization of a small-world network of chaotic Rulkov neurons with an electrical coupling that contains a delay. We have developed an algorithm to compute a certain delay whose result is to improve the synchronization of the ... More