Latest in physics.bio-ph

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Musculoskeletal full-body models including a detailed thoracolumbar spine for children and adolescents aged 6 to 18 yearsJun 13 2019Currently available thoracolumbar spine models are entirely based on data from adults and might therefore not be applicable for simulations in children and adolescents. In addition, these models lack lower extremities, which are required for comprehensive ... More
Self-organized critical balanced networks: a unified frameworkJun 13 2019Asynchronous irregular (AI) and critical states are two competing frameworks proposed to explain spontaneous neuronal activity. Here, we propose a mean-field model with simple stochastic neurons that generalizes the integrate-and-fire network of Brunel ... More
The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growthJun 13 2019Many proteins have the potential to aggregate into amyloid fibrils, which are associated with a wide range of human disorders including Alzheimer's and Parkinson's disease. In contrast to that of folded proteins, the thermodynamic stability of amyloid ... More
An SEIR Epidemic Model where Empirical Distribution of Incubation Period has Approximated by Coxian DistributionJun 13 2019In this work, we have developed a Coxian distributed SEIR model in incorporating an empirical incubation period since Coxian distribution approximately converges to any distribution. A basic reproduction number is found from the model. An application ... More
Self-organized avalanches in globally-coupled phase oscillatorsJun 13 2019Spontaneous desynchronization of coupled oscillators occurs in diverse systems spanning from the mammalian brain to alternating current power grids. Here, we model desynchronization using a generalization of the classical Kuramoto model, which includes ... More
Single frame wide-field Nanoscopy based on Ghost Imaging via Sparsity Constraints (GISC Nanoscopy)Jun 13 2019The applications of present nanoscopy techniques for live cell imaging are limited by the long sampling time and low emitter density. Here we developed a new single frame wide-field nanoscopy based on ghost imaging via sparsity constraints (GISC Nanoscopy), ... More
Identifying and Predicting Parkinson's Disease Subtypes through Trajectory Clustering via Bipartite NetworksJun 12 2019Parkinson's disease (PD) is a common neurodegenerative disease with a high degree of heterogeneity in its clinical features, rate of progression, and change of variables over time. In this work, we present a novel data-driven, network-based Trajectory ... More
Can Life Exist in 2 + 1 Dimensions?Jun 12 2019There are anthropic reasons to suspect that life in more than three spatial dimensions is not possible, and if the same could be said of fewer than three, then one would have an anthropic argument for why we experience precisely three large spatial dimensions. ... More
Mechanics of allostery: contrasting the induced fit and population shift scenariosJun 12 2019In allosteric proteins, binding a ligand can affect function at a distant location, for example by changing the binding affinity of a substrate at the active site. The induced fit and population shift models, which differ by the assumed number of stable ... More
In silico evidence that protein unfolding is as a precursor of the protein aggregationJun 12 2019We present a computational study on the folding and aggregation of proteins in aqueous environment, as function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding of the native ... More
High-resolution Markov state models for the dynamics of Trp-cage miniprotein constructed over slow folding modes identified by state-free reversible VAMPnetsJun 12 2019State-free reversible VAMPnets (SRVs) are a neural network-based framework capable of learning the leading eigenfunctions of the transfer operator of a dynamical system from trajectory data. In molecular dynamics simulations, these data-driven collective ... More
Anomalous diffusion for neuronal growth on surfaces with controlled geometriesJun 11 2019Geometrical cues are known to play a very important role in neuronal growth and the formation of neuronal networks. Here, we present a detailed analysis of axonal growth and dynamics for neuronal cells cultured on patterned polydimethylsiloxane surfaces. ... More
Universal scaling of active nematic turbulenceJun 11 2019A landmark of turbulence is the emergence of universal scaling laws, such as Kolmogorov's $E(q)\sim q^{-5/3}$ scaling of the kinetic energy spectrum of inertial turbulence with the wave vector $q$. In recent years, active fluids have been shown to exhibit ... More
Snapshot projection optical tomographyJun 11 2019We present a new plenoptic microscopy configuration consisting of an objective lens and a micro-lens array (MLA), which is used as a tube lens. The new system that we named as snapshot projection optical tomography (SPOT) can directly record the projection ... More
Iron Embedded Magnetic Nanodiamonds for in vivo MRI Contrast EnhancementJun 11 2019Although nanodiamonds have long being considered as a potential tool for biomedical research, the practical in vivo application of nanodiamonds remains relatively unexplored. In this paper, we present the first application of in vivo MRI contrast enhancement ... More
Gait modeling and optimization for the perturbed Stokes regimeJun 11 2019Many forms of locomotion, both natural and artificial, are dominated by viscous friction in the sense that without power expenditure they quickly come to a standstill. From geometric mechanics, it is known that for swimming at the "Stokesian" (viscous; ... More
Phylogenetic correlations can suffice to infer protein partners from sequencesJun 10 2019Determining which proteins interact together is crucial to a systems-level understanding of the cell. Recently, algorithms based on Direct Coupling Analysis (DCA) pairwise maximum-entropy models have allowed to identify interaction partners among the ... More
Altruism in populations at the extinction transitionJun 10 2019We study the evolution of cooperation as a birth-death process in spatially extended populations. The benefit from the altruistic behavior of a cooperator is implemented by decreasing the death rate of its direct neighbours. The cost of cooperation is ... More
Multiparametric Deep Learning and Radiomics for Tumor Grading and Treatment Response Assessment of Brain Cancer: Preliminary ResultsJun 10 2019Radiomics is an exciting new area of texture research for extracting quantitative and morphological characteristics of pathological tissue. However, to date, only single images have been used for texture analysis. We have extended radiomic texture methods ... More
Dynamic metabolic resource allocation based on the maximum entropy principleJun 10 2019This paper introduces a dynamic metabolic modelling framework that is a synthesis of recent ideas on resource allocation and the powerful optimal control formulation of Ramkrishna and colleagues. In particular, their work is extended based on the hypothesis ... More
Active glassesJun 09 2019Active glassy matter has recently emerged as a novel class of non-equilibrium soft matter, combining energy-driven, active particle movement with dense and disordered glass-like behavior. Here we review the state-of-the-art in this field from an experimental, ... More
Critical phenomena in the temperature-pressure-crowding phase diagram of a proteinJun 09 2019In the cell, proteins fold and perform complex functions through global structural rearrangements. Function requires a protein to be at the brink of stability to be susceptible to small environmental fluctuations, yet stable enough to maintain structural ... More
Identification of nutrient deficiency in bean plants by prompt chlorophyll fluorescence measurements and Artificial Neural NetworksJun 07 2019The deficiency of macro (N, P, S, Ca, Mg and K) and micro (Zn, Cu, B, Mo, Cl, Mn and Fe) minerals has a major effect on plant development. The lack of some nutrient minerals especially of nitrogen, potassium, calcium, phosphorus and iron is a huge problem ... More
Harnessing elasticity to generate self-oscillation via an electrohydrodynamic instabilityJun 07 2019Under a steady DC electric field of sufficient strength, a weakly conducting dielectric sphere in a dielectric solvent with higher conductivity can undergo spontaneous spinning (Quincke rotation) through a pitchfork bifurcation. We design an object composed ... More
Transcription-driven DNA Supercoiling: Non-Equilibrium Dynamics and Action-at-a-distanceJun 07 2019We study the effect of transcription on the kinetics of DNA supercoiling in 3D by means of Brownian dynamics simulations of a single nucleotide resolution coarse-grained model for double stranded DNA. By accounting for the action of a transcribing RNA ... More
OLEDs as models for bird magnetoception: detecting electron spin resonance in geomagnetic fieldsJun 07 2019Certain species of living creatures are known to orientate themselves in the geomagnetic field. Given the small magnitude of approximately 48 {\mu}T, the underlying quantum mechanical phenomena are expected to exhibit coherence times approaching the millisecond ... More
Inhibitory autapse mediates anticipated synchronization between coupled neuronsJun 07 2019Two identical autonomous dynamical systems unidirectionally coupled in a sender-receiver configuration can exhibit anticipated synchronization (AS) if the Receiver neuron (R) also receives a delayed negative self-feedback. Recently, AS was shown to occur ... More
Femoral fracture load and damage localisation pattern prediction based on a quasi-brittle law : linear and non-linear FE meshingJun 07 2019Finite element analysis is one of the most used tool for studying femoral neck fracture. Nerveless, consensus concerning either the choice of material characteristics, damage law and /or geometric models (linear on nonlinear) still remains unreached. ... More
Cytoplasmic streaming in C. elegans: forces that drive oogenesisJun 07 2019Jun 13 2019In the gonad of C. elegans worms, germ cells form the outer lining of the central tube, the rachis, which carries a cytoplasmic flow.
Cytoplasmic streaming in C. elegans: forces that drive oogenesisJun 07 2019In the gonad of C. elegans worms, germ cells form the outer lining of the central tube, the rachis, which carries a cytoplasmic flow. The porous interface between the germ cells and rachis allows a radial flow of cytoplasm across the interface. In the ... More
Patterns of polar domains in a spatiotemporal model of interacting polaritiesJun 06 2019Polarity fields are known to exhibit long distance patterns, in both physical and biological systems. The mechanisms behind such patterns are poorly understood. Here, we describe the dynamics of polarity fields using an original physical model that generalizes ... More
Model of lamellipodium initiation during cell spreadingJun 06 2019Cell spreading requires a major reorganisation of the actin cytoskeleton, from a cortical structure to a lamellipodium where filaments are mostly parallel to the substrate. We propose a model inspired by the physics of nematic liquid crystals and fluid ... More
#neverforget - Photobiomodulation Against Alzheimer's Disease: A Systematic ReviewJun 06 2019Alzheimer's disease affects an ever-increasing number of people in the aging population. Current treatment options are limited to a narrow time frame at the mild to moderate stage of dementia, and patients are confronted with the inevitable progression ... More
Fine-grained simulations of the microenvironment of vascularized tumoursJun 06 2019One of many important features of the tumour microenvironment is that it is a place of active Darwinian selection where different tumour clones become adapted to the variety of ecological niches that make up the microenvironment. These evolutionary processes ... More
Cup-to-vesicle transition of a fluid membrane with spontaneous curvatureJun 06 2019The disk-to-vesicle transition of a fluid membrane with no spontaneous curvature is well described by the competition between edge line and curvature energies. However, the transition of asymmetric membranes with spontaneous curvatures is not yet understood. ... More
OnionNet: a multiple-layer inter-molecular contact based convolutional neural network for protein-ligand binding affinity predictionJun 06 2019Computational drug discovery provides an efficient tool helping large scale lead molecules screening. One of the major tasks of lead discovery is identifying molecules with promising binding affinities towards a target, a protein in general. The accuracies ... More
Readout of fluorescence functional signals through highly scattering tissueJun 05 2019Fluorescence is a powerful mean to probe information processing in the mammalian brain. However, neuronal tissues are highly heterogeneous and thus opaque to light. A wide set of non-invasive or invasive techniques for scattered light rejection, optical ... More
Propulsion driven by self-oscillation via an electrohydrodynamic instabilityJun 05 2019Oscillations of flagella and cilia play an important role in biology, which motivates the idea of functional mimicry as part of bio-inspired applications. Nevertheless, it still remains challenging to drive their artificial counterparts to oscillate via ... More
Bifurcation dynamics of a particle-encapsulating droplet in shear flowJun 05 2019To understand the behavior of composite fluid particles such as nucleated cells and double-emulsions in flow, we study a finite-size particle encapsulated in a deforming droplet under shear flow as a model system. In addition to its concentric particle-droplet ... More
Design and applications of a fluorescent labeling technique for lipid and surfactant preformed vesiclesJun 04 2019Amphiphilic molecules such as surfactants, lipids and block copolymers can be assembled into bilayers and form vesicles. Fluorescent membrane labeling methods require the use of dye molecules that can be inserted in the bilayers at different stages of ... More
Enhancing the performance of DNA surface-hybridization biosensors through target depletionJun 04 2019DNA surface-hybridization biosensors utilize the selective hybridization of target sequences in solution to surface-immobilized probes. In this process, the target is usually assumed to be in excess, so that its concentration does not significantly vary ... More
Chaos and mixing in self-propelled dropletsJun 04 2019We consider self-propelled droplets which are driven by internal flow. Tracer particles, which are advected by the flow, in general follow chaotic trajectories, even though the motion of the autonomous swimmer is completely regular. The flow is mixing, ... More
On numerical modeling of dispersive mechanical waves in lipid bi-layersJun 04 2019We investigate different mechanical effects which accompany the nerve pulse propagation by using mathematical modeling. The propagation process is composed by three connected phenomena: (i) the action potential (electrical signal) which is usually considered ... More
Modelling of processes in nerve fibres at the interface of physiology and mathematicsJun 04 2019The in silico simulations are widely used in contemporary systems biology including the analysis of nerve pulse propagation. As known from numerous experiments, the propagation of an action potential is accompanied by mechanical and thermal effects. This ... More
Interacting contagions are indistinguishable from social reinforcementJun 04 2019From fake news to innovative technologies, many contagions spread via a process of social reinforcement, where multiple exposures are distinct from prolonged exposure to a single source. Contrarily, biological agents such as Ebola or measles are typically ... More
Energy landscapes and dynamics of xylo-nucleic acidsJun 03 2019Artificial analogues of the natural nucleic acids have attracted recent interest as a diverse class of information storage molecules capable of self-replication. In the present study, we use the computational potential energy landscape framework to investigate ... More
Human information processing in complex networksJun 03 2019Humans communicate using systems of interconnected stimuli or concepts -- from language and music to literature and science -- yet it remains unclear how, if at all, the structure of these networks supports the communication of information. Although information ... More
Photo Switching of Protein Dynamical CollectivityJun 03 2019We examine changes in the picosecond structural dynamics with irreversible photobleaching of red fluorescent proteins mCherry, mOrange2 and TagRFP-T. Measurements of the protein dynamical transition using terahertz time-domain spectroscopy show in all ... More
Influence of Initial Residual Stress on Growth and Pattern Creation for a Layered AortaJun 03 2019Residual stress is ubiquitous and indispensable in most biological and artificial materials, where it sustains and optimizes many biological and functional mechanisms. The theory of volume growth, starting from a stress-free initial state, is widely used ... More
The behaviour of information flow near criticalityJun 03 2019Recent experiments have indicated that many biological systems self-organise near their critical point, which hints at a common design principle. While it has been suggested that information transmission is optimized near the critical point, it remains ... More
Loopy Lévy flights enhance tracer diffusion in active suspensionsJun 03 2019Brownian motion is widely used as a paradigmatic model of diffusion in equilibrium media throughout the physical, chemical, and biological sciences. However, many real world systems, particularly biological ones, are intrinsically out-of-equilibrium due ... More
Population stability risks and biophysical benefits of cell-cell fusion in macrophage, osteoclast, and giant multinucleated cellsJun 02 2019Plant and animal cells are commonly understood as acquiring specialized functions through differentiation and asymmetric division. However, unique capabilities are also acquired when two or more cells fuse together, mixing cytoplasmic and genetic material. ... More
Deformation and dynamics of erythrocytes govern their traversal through microfluidic devices with a deterministic lateral displacement architectureJun 02 2019Deterministic lateral displacement (DLD) microfluidic devices promise versatile and precise processing of biological samples. However, this prospect has been realized so far only for rigid spherical particles and remains limited for biological cells due ... More
Improved fragment-based movement with LRFragLib for all-atom Ab initio protein foldingJun 02 2019Fragment-based assembly has been widely used in Ab initio protein folding simulation which can effectively reduce the conformational space and thus accelerate sampling. The efficiency of fragment-based movement as well as the quality of fragment library ... More
Capabilities and Limitations of Time-lagged Autoencoders for Slow Mode Discovery in Dynamical SystemsJun 02 2019Time-lagged autoencoders (TAEs) have been proposed as a deep learning regression-based approach to the discovery of slow modes in dynamical systems. However, a rigorous analysis of nonlinear TAEs remains lacking. In this work, we discuss the capabilities ... More
The pairwise hydrodynamic interactions of synchronized spermatozoaJun 01 2019The journey of mammalian spermatozoa in nature is well-known to be reliant on their individual motility. Often swimming in crowded microenvironments, the progress of any single swimmer is likely dependent on their interactions with other nearby swimmers. ... More
Mesoscopic non-equilibrium measures can reveal intrinsic features of the active drivingMay 31 2019Biological assemblies such as chromosomes, membranes, and the cytoskeleton are driven out of equilibrium at the nanoscale by enzymatic activity and molecular motors. Similar non-equilibrium dynamics can be realized in synthetic systems, such as chemically ... More
Compressing $Θ$-chain in slit geometryMay 31 2019When compressed in a slit of width $D$, a $\Theta$-chain that displays the scaling of size $R_0$ (diameter) with respect to the number of monomers $N$, $R_0\sim aN^{1/2}$, expands in the lateral direction as $R_{\parallel}\sim a N^{\nu}(a/D)^{2\nu-1}$. ... More
Current enhancement in solid-state nanopores depends on three-dimensional DNA structureMay 31 2019The translocation of double-stranded DNA through a solid-state nanopore may either decrease or increase the ionic current depending on the ionic concentration of the surrounding solution. Below a certain crossover ionic concentration, the current change ... More
Linear response in neuronal networks: from neurons dynamics to collective responseMay 31 2019We review two examples where the linear response of a neuronal network submitted to an external stimulus can be derived explicitely, including network parameters dependence. This is done in a statistical physics-like approach where one associates to the ... More
Custom Edge-Element FEM Solver and its Application to Eddy-Current Simulation of Realistic 2M-Element Human Brain PhantomMay 30 2019Extensive research papers of three-dimensional computational techniques are widely used for the investigation of human brain pathophysiology. Eddy current analyzing could provide an indication of conductivity change within a biological body. A significant ... More
Nonlinear analysis of the fluid-solid transition in a model for ordered biological tissuesMay 29 2019The rheology of biological tissues is important for their function, and we would like to better understand how single cells control global tissue properties such as tissue fluidity. A confluent tissue can fluidize when cells diffuse by executing a series ... More
Search and capture efficiency of dynamic microtubules for centrosome relocation during IS formationMay 29 2019Upon contact with antigen presenting cells (APCs) cytotoxic T lymphocytes (T cells) establish a highly organized contact zone denoted as immunological synapse (IS). The formation of the IS implies relocation of the microtubule organizing center (MTOC) ... More
A practical review on the measurement tools for cellular adhesion forceMay 29 2019Cell cell and cell matrix adhesions are fundamental in all multicellular organisms. They play a key role in cellular growth, differentiation, pattern formation and migration. Cell-cell adhesion is substantial in the immune response, pathogen host interactions, ... More
Analysis of evoked EMG using wavelet transformationMay 29 2019Evoked EMG M-responses obtained from the thenar muscle in the palm by electrical stimulation of the median nerve demonstrate a well-established smooth bipolar shape for normal healthy subjects while kinks are observed in certain neurological disorders, ... More
Shot noise limited high speed stimulated Raman microscopyMay 28 2019We report a shot noise limited high speed stimulated Raman microscopy platform allowing to acquire molecular vibrational spectra over \SI{200}{\per \cm} in \SI{12}{\micro \second} at a scan rate of 40kHz. Using spectral focusing together with optimized ... More
Extreme value theory of evolving phenomena in complex dynamical systems: firing cascades in a model of neural networkMay 28 2019We extend the scope of the dynamical theory of extreme values to cover phenomena that do not happen instantaneously, but evolve over a finite, albeit unknown at the onset, time interval. We consider complex dynamical systems, composed of many individual ... More
Geometric effects in random assemblies of ellipsesMay 28 2019Assemblies of anisotropic particles commonly appear in studies of active many-body systems. However, in two dimensions, the geometric ramifications of the finite density of such objects are not entirely understood. To fully characterize these effects, ... More
Role of Ligand Conformation on Nanoparticle-Protein InteractionsMay 28 2019Engineered biomedical nanoparticles (NP) administered via intravenous routes are prone to associate to serum proteins. The protein corona can mask the NP surface functionalization and hamper the delivery of the NP to its biological target. The design ... More
Multiline Orthogonal Scanning Temporal Focusing (mosTF) Microscopy for Scattering Reduction in High-speed in vivo Brain ImagingMay 27 2019Temporal focusing two-photon microscopy enables high resolution imaging of fine structures in vivo over a large volume. A limitation of temporal focusing is that signal-to-background ratio and resolution degrade rapidly with increasing imaging depth. ... More
Task-specific multispectral band selectionMay 27 2019Multispectral imaging provides valuable information on tissue composition such as hemoglobin oxygen saturation. However, the real-time application of this technique in interventional medicine can be challenging because the acquisition time of large amount ... More
Cells exploit a phase transition to establish interconnections in fibrous extracellular matricesMay 27 2019By exerting mechanical forces, biological cells generate striking spatial patterns of localised deformation in the surrounding collagen network. Tethers-paths of high densification and fiber alignment-form between cells, and radial hair-like bands emanate ... More
Optimal localization patterns in bacterial protein synthesisMay 25 2019In $\textit{Escherichia coli}$ bacterium, the molecular compounds involved in protein synthesis, messenger RNAs (mRNAs) and ribosomes, show marked intracellular localization patterns. Yet a quantitative understanding of the physical principles which would ... More
Modeling work-speed-accuracy trade-offs in a stochastic rotary machineMay 25 2019Molecular machines are stochastic systems that catalyze the energetic processes keeping living cells alive and structured. Inspired by the examples of \F1-ATP synthase and the bacterial flagellum, we present a minimal model of a driven stochastic rotary ... More
Stochastic modeling of gene expression: application of ensembles of trajectoriesMay 25 2019It is well established that gene expression can be modeled as a Markovian stochastic process and hence proper observables might be subjected to large fluctuations and rare events. Since dynamics is often more than statics, one can work with ensembles ... More
The pH-dependent electrostatic interaction of a metal nanoparticle with the MS2 virus-like particlesMay 25 2019The electrostatic interaction of metal nanoparticles with viruses is attracting great interest due to their antiviral activity and their role in enhancing the detection of viruses at ultra-low concentrations. We model the MS2 virus devoid of its single ... More
Analytical study on phase transition of shape memory alloy wire under uniaxial tensionMay 24 2019May 30 2019This paper considers the stress-induced phase transitions of shape memory alloy slender cylinder, and analytically studies the phase transition process and the associated instability. A three-dimensional (3D) phenomenological model with an internal variable ... More
Low-dose ionizing radiation exposure during pregnancy induces behavioral impairment and lower weight gain in adult ratsMay 24 2019Low-dose ionizing radiation may induce far-reaching consequences in human, especially regarding intrauterine development. Many studies have documented that the risks of in utero irradiation remain controversial and no effect is reported at doses below ... More
Description of spreading dynamics by microscopic network models and macroscopic branching processes can differ due to coalescenceMay 24 2019Spreading processes are conventionally monitored on a macroscopic level by counting the number of incidences over time. The spreading process can then be modeled either on the microscopic level, assuming an underlying interaction network, or directly ... More
Information parity in complex networksMay 24 2019A growing interest in complex networks theory results in an ongoing demand for new analytical tools. We propose a novel measure based on information theory that provides a new perspective for a better understanding of networked systems: Termed "information ... More
Network properties of healthy and Alzheimer's brainsMay 24 2019Small-world structures are often used to describe structural connections in the brain. In this work, we compare the structural connection of cortical areas of a healthy brain and a brain affected by Alzheimer's disease with artificial small-world networks. ... More
Computing Long Timescale Biomolecular Dynamics using Quasi-Stationary Distribution Kinetic Monte Carlo (QSD-KMC)May 24 2019It is a challenge to obtain an accurate model of the state-to-state dynamics of a complex biological system from molecular dynamics (MD) simulations. Typically, biologically relevant processes occur at time scales on the order of milliseconds while the ... More
Stochastic Yield Catastrophes and Robustness in Self-AssemblyMay 23 2019A guiding principle in self-assembly is that, for high production yield, nucleation of structures must be significantly slower than their growth. However, details of the mechanism that impedes nucleation are broadly considered irrelevant. Here, we analyze ... More
Nonlinear Poisson effect governed by mechanical critical transitionMay 23 2019The Poisson effect describes the tendency of an elastic material stretched along one axis to deform along the transverse axes. Under applied extensional strain, biopolymer gels have been shown to exhibit an unusually large and nonlinear Poisson effect, ... More
Mechanical interplay between cell shape and actin cytoskeleton organizationMay 23 2019We investigate the mechanical interplay between the spatial organization of the actin cytoskeleton and the shape of animal cells adhering on micropillar arrays. Using a combination of analytical work, computer simulations and in vitro experiments, we ... More
A trust model for spreading gossip in social networksMay 23 2019We introduce here a multi-type bootstrap percolation model, which we call T-Bootstrap Percolation (T-BP), and apply it to study information propagation in social networks. In this model, a social network is represented by a graph G whose vertices have ... More
Simple Muscle Architecture Analysis (SMA): an ImageJ macro tool to automate measurements in B-mode ultrasound scansMay 23 2019In vivo measurements of muscle architecture (i.e. the spatial arrangement of muscle fascicles) are routinely included in research and clinical settings to monitor muscle structure, function and plasticity. However, in most cases such measurements are ... More
Simple Muscle Architecture Analysis (SMA): an ImageJ macro tool to automate measurements in B-mode ultrasound scansMay 23 2019May 31 2019In vivo measurements of muscle architecture (i.e. the spatial arrangement of muscle fascicles) are routinely included in research and clinical settings to monitor muscle structure, function and plasticity. However, in most cases such measurements are ... More
Cavity-modified exciton dynamics in photosynthetic unitsMay 22 2019Jun 10 2019Recently, exciton-photon strong coupling has been proposed as a means to control and enhance energy transfer in ensembles of organic molecules. Here, we demonstrate that the exciton dynamics in an archetypal purple bacterial photosynthetic unit, composed ... More
Cavity-modified exciton dynamics in photosynthetic unitsMay 22 2019Recently, exciton-photon strong coupling has been proposed as a means to control and enhance energy transfer in ensembles of organic molecules. Here, we demonstrate that the exciton dynamics in an archetypal purple bacterial photosynthetic unit, composed ... More
Mobile obstacles accelerates and inhibits the bundle formation in two-patch colloidal particleMay 22 2019Aggregation of protein into bundles is responsible for many neurodegenerative diseases. In this work, we show how two-patch colloidal particles self assemble into chains and a sudden transition to bundles takes place by tuning the patch size and solvent ... More
Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsinMay 22 2019Bacteriorhodopsin (bR) is a light-driven proton pump. We use time-resolved crystallography at an X-ray free-electron laser to follow the structural changes in multiphoton-excited bR from 250 femtoseconds to 10 picoseconds. Quantum chemistry and ultrafast ... More
Evolving nature of human contact networks with its impact on epidemic processesMay 21 2019Human contact networks are constituted by a multitude of individuals and pairwise contacts among them. However, the dynamic nature, which generates the evolution of human contact networks, of contact patterns is not known yet. Here, we analyse three empirical ... More
Molecular rules for selectivity in lipase-catalysed acylation of lysineMay 21 2019The selectivity of L-lysine acylation by lauric acid catalysed by Candida antarctica lipase B (CALB) was investigated combining experimental and theoretical methodologies. Experiments showed the near-exclusive acylation of lysine $\epsilon$-amino group; ... More
Effect of Boundary Constraints on the Nonlinear Flapping of Filaments Animated by Follower ForcesMay 21 2019Elastically driven filaments subjected to animating compressive follower forces provide a synthetic way to mimic the oscillatory beating of active biological filaments such as eukaryotic cilia. The dynamics of such active filaments can, under favorable ... More
A unified analysis of nano-to-microscale particle dispersion in tubular blood flowMay 21 2019Transport of solid particles in blood flow exhibits qualitative differences in the transport mechanism when the particle varies from nanoscale to microscale size comparable to the red blood cell (RBC). The effect of microscale particle margination has ... More
A unified analysis of nano-to-microscale particle dispersion in tubular blood flowMay 21 2019Jun 01 2019Transport of solid particles in blood flow exhibits qualitative differences in the transport mechanism when the particle varies from nanoscale to microscale size comparable to the red blood cell (RBC). The effect of microscale particle margination has ... More
Effect of UV radiation on the structure of graphene oxide in water and its impact on cytotoxicity and As(III) adsorptionMay 20 2019Graphene oxide (GO) is widely used in different applications, however once release into the environment it can change its structure and affect the transport of important contaminants such as arsenic. In this work we show that UV radiation, even in the ... More
Stress relaxation in F-actin solutions by severingMay 20 2019Networks of filamentous actin (F-actin) are important for the mechanics of most animal cells. These cytoskeletal networks are highly dynamic, with a variety of actin-associated proteins that control cross-linking, polymerization and force generation in ... More
Fluid pumping and active flexoelectricity can promote lumen nucleation in cell assembliesMay 20 2019We discuss the physical mechanisms that promote or suppress the nucleation of a fluid-filled lumen inside a cell assembly or a tissue. We discuss lumen formation in a continuum theory of tissue material properties in which the tissue is described as a ... More