Latest in physics.bio-ph

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Quantification of Nematic Cell Polarity in Three-dimensional TissuesApr 18 2019How epithelial cells coordinate their polarity to form complex tissues and organs remains a fundamental question in biology. Here, we characterize a unique type of polarity found in liver tissue - nematic cell polarity, which is different from the common ... More
Wrinkle patterns in active viscoelastic thin sheetsApr 18 2019We show that a viscoelastic thin sheet driven out of equilibrium by active structural remodelling develops a rich variety of shapes as a result of a competition between viscous relaxation and activity. In the regime where active processes are faster than ... More
Random coefficient autoregressive processes describe Brownian yet non-Gaussian diffusion in heterogeneous systemsApr 18 2019Many studies on biological and soft matter systems report the joint presence of a linear mean-squared displacement and a non-Gaussian probability density exhibiting, for instance, exponential or stretched-Gaussian tails. This phenomenon is ascribed to ... More
The lubricity of mucin solutions is robust against changes in physiological conditionsApr 18 2019Solutions of manually purified gastric mucins have been shown to be promising lubricants for biomedical purposes, where they can efficiently reduce friction and wear. However, so far, such mucin solutions have been mostly tested in specific settings, ... More
Spike-burst chimera states in an adaptive exponential integrate-and-fire neuronal networkApr 17 2019Chimera states are spatiotemporal patterns in which coherence and incoherence coexist. We observe the coexistence of synchronous (coherent) and desynchronous (incoherent) domains in a neuronal network. The network is composed of coupled adaptive exponential ... More
Mechanical Interaction Between Cells Facilitates Molecular TransportApr 17 2019In vivo, eukaryotic cells are embedded in a matrix environment, where they grow and develop. Generally, this extracellular matrix (ECM) is an anisotropic fibrous structure, through which macromolecules and biochemical signaling molecules at the nanometer ... More
Active Lévy Matter: Anomalous Diffusion, Hydrodynamics and Linear StabilityApr 17 2019Anomalous diffusion, manifest as a nonlinear relationship between the position mean square displacement and the temporal duration, and/or non-Gaussian features of the position statistics, is prevalent in biological transport processes. Likewise, collective ... More
Topological sensitivity of microbial flow fields under tight confinementApr 17 2019Despite their importance in many biological, ecological and physical processes, microorganismal fluid flows under tight confinement have not been investigated experimentally. Strong screening of Stokelets in this geometry suggests that the flow fields ... More
Exactly solvable model of gene expression in proliferating bacterial cell population with stochastic protein bursts and protein partitioningApr 17 2019Many of the existing stochastic models of gene expression contain the first-order decay reaction term that may describe active protein degradation or dilution. If the model variable is interpreted as the molecule number, and not concentration, the decay ... More
Toughening in a nacre-like soft-hard layered structure due to weak nonlinearity in the soft layerApr 17 2019Recently, it has been found experimentally that hydrated nacre exhibits a nonlinear mechanical response. While mechanical nonlinearity has been shown to be important in other biological structures, such as spider webs, the implications of mechanical nonlinearity ... More
A precise relationship among Buller's drop, ballistospore and gill morphology enables maximal packing of spores within gilled mushroomsApr 17 2019Basidiomycete fungi eject spores using a surface tension catapult; a fluid drop forms at the base of each spore and after reaching a critical size, coalesces with the spore and launches it from the gill surface. Although basidiomycetes function within ... More
Impaired coronary blood flow at higher heart rates during atrial fibrillation: investigation via multiscale modellingApr 16 2019Background. Different mechanisms have been proposed to relate atrial fibrillation (AF) and coronary flow impairment, even in absence of relevant coronary artery disease (CAD). However, the underlying hemodynamics remains unclear. Aim of the present work ... More
Lagrangian transport and chaotic advection in three-dimensional laminar flowsApr 16 2019Transport and mixing of scalar quantities in fluid flows is ubiquitous in industry and Nature. Turbulent flows promote efficient transport and mixing by their inherent randomness. Laminar flows lack such a natural mixing mechanism and efficient transport ... More
Interferometric scattering enables fluorescence-free electrokinetic trapping of single nanoparticles in free solutionApr 15 2019Anti-Brownian traps confine single particles in free solution by closed-loop feedback forces that directly counteract Brownian motion. The extended-duration measurement of trapped objects allows detailed characterization of photophysical and transport ... More
Coarse-graining Molecular Systems by Spectral MatchingApr 15 2019Coarse-graining has become an area of tremendous importance within many different research fields. For molecular simulation, coarse-graining bears the promise of finding simplified models such that long-time simulations of large-scale systems become computationally ... More
Conformal symmetry breaking and self-similar spiralsApr 15 2019Self-similar curves are shown to arise naturally as tension-free stationary states of conformally invariant energies. Planar logarithmic spirals are associated with the simplest such energy, the conformal arc-length, and their remarkable properties follow ... More
Uneven rock-paper-scissors models: patterns and coexistenceApr 15 2019We study a class of the stochastic May-Leonard models, with three species dominating each other in a cyclic nonhierarchical way, according to the rock-paper-scissors game. We introduce an unevenness in the system, by considering that one the species is ... More
Shedding light on the dark matter of the biomolecular structural universe: Progress in RNA 3D structure predictionApr 13 2019Structured RNA plays many functionally relevant roles in molecular life. Structural information, while required to understand the functional cycles in detail, is challenging to gather. Computational methods promise to complement experimental efforts by ... More
Nanoparticle diffusion in sheared cellular blood flowApr 13 2019Using a multiscale blood flow solver, the complete diffusion tensor of nanoparticle (NP) in sheared cellular blood flow is calculated over a wide range of shear rate and haematocrit. In the short-time regime, NPs exhibit anomalous dispersive behaviors ... More
Molecular simulations have boosted knowledge of CRISPR/Cas9: A ReviewApr 12 2019Genome editing allows scientists to change an organism's DNA. One promising genome editing protocol, already validated in living organisms, is based on clustered regularly interspaced short palindromic repeats (CRISPR)/Cas protein-nucleic acid complexes. ... More
High-speed in vitro intensity diffraction tomographyApr 12 2019We demonstrate a label-free, scan-free intensity diffraction tomography technique utilizing annular illumination (aIDT) to rapidly characterize large-volume 3D refractive index distributions in vitro. By optimally matching the illumination geometry to ... More
Partial covariance two-dimensional mass spectrometry for determination of biomolecular primary structureApr 11 2019Mass spectrometry (MS) is used widely in biomolecular structural analysis and is particularly dominant in the study of proteins. Despite its considerable power, state-of-the-art protein MS frequently suffers from limited reliability of spectrum-to-structure ... More
Load-dependent adaptation near zero load in the bacterial flagellar motorApr 11 2019The bacterial flagellar motor is an ion-powered transmembrane protein complex which drives swimming in many bacterial species. The motor consists of a cytoplasmic 'rotor' ring and a number of 'stator' units, which are rooted to the cell wall of the bacterium. ... More
Non-locally Encoder-Decoder Convolutional Network for Whole Brain QSM InversionApr 11 2019Quantitative Susceptibility Mapping (QSM) reconstruction is a challenging inverse problem driven by ill conditioning of its field-to -susceptibility transformation. State-of-art QSM reconstruction methods either suffer from image artifacts or long computation ... More
Doppler Fluctuation Spectroscopy of Intracellular Dynamics in Living TissueApr 10 2019Intracellular dynamics in living tissue are dominated by active transport driven by bioenergetic processes far from thermal equilibrium. Intracellular constituents typically execute persistent walks. In the limit of long mean-free paths, the persistent ... More
A generalized kinetic framework applied to whole-cell catalysis in biofilm flow reactors clarifies performance enhancementsApr 10 2019A common kinetic framework for studies of whole-cell catalysis is vital for understanding and optimizing bioflow reactors. In this work, we demonstrate the applicability of a flow-adapted version of Michaelis-Menten kinetics to a catalytic bacterial biofilm. ... More
Combining Mathematical Morphology and the Hilbert Transform for Fully Automatic Nuclei Detection in Fluorescence MicroscopyApr 10 2019Accurate and reliable nuclei identification is an essential part of quantification in microscopy. A range of mathematical and machine learning approaches are used but all methods have limitations. Such limitations include sensitivity to user parameters ... More
Efficient cruising for swimming and flying animals is dictated by fluid dragApr 10 2019Many swimming and flying animals are observed to cruise in a narrow range of Strouhal numbers, where the Strouhal number ${St = 2fA/U}$ is a dimensionless parameter that relates stroke frequency $f$, amplitude $A$, and forward speed $U$. Dolphins, sharks, ... More
Helical and oscillatory microswimmer motility statistics from differential dynamic microscopyApr 10 2019The experimental characterisation of the swimming statistics of populations of microorganisms or artificially propelled particles is essential for understanding the physics of active systems and their exploitation. Here, we construct a theoretical framework ... More
Elastic response of poly(ethylene glycol) polymer chains studied using dynamic atomic force microscopyApr 10 2019Stretching response of polymer chains under external force is crucial in understanding polymer dynamics under equilibrium and non-equilibrium conditions. Here we measure the elastic response of poly(ethylene glycol) using a lock-in based amplitude modulation-AFM ... More
Accelerated Nuclear Magnetic Resonance Spectroscopy with Deep LearningApr 09 2019Nuclear magnetic resonance (NMR) spectroscopy serves as an indispensable tool in chemistry and biology but often suffers from long experimental time. We present a proof-of-concept of harnessing deep learning and neural network for high-quality, reliable, ... More
Buckling Soft Tensegrities: Fickle Elasticity and Configurational Switching in Living CellsApr 09 2019Tensegrity structures are special architectures made by floating compressed struts kept together by a continuous system of tensed cables. The multiplicity of shapes that tensegrity structures can assume and their intrinsic capability to be deployable ... More
Ionic Electro active Polymer-Based Soft Actuators and Their Applications in Microfluidic Micropumps, Microvalves, and Micromixers: A ReviewApr 09 2019This paper provides a detailed review on applications of ionic electroactive polymer (i-EAP) soft actuators as active elements of microfluidic micropumps, microvalves, and micromixers. The related works that have so far been presented by various research ... More
Globular bundles and entangled network of proteins (CorA) by a coarse-grained Monte Carlo simulationApr 09 2019Using a coarse-grained model, self-organized assembly of proteins (e.g. CorA and its inner segment iCorA) is studied by examining quantities such as contact profile, radius of gyration, and structure factor as a function of protein concentration at a ... More
Refractive index measurements of multicellular tumour spheroids using optical coherence tomography: dependence on growth phase and sizeApr 08 2019Knowledge of optical properties, such as the refractive index (RI), of biological tissues is important in optical imaging, as they influence the distribution and propagation of light in tissue. To accurately study the response of cancerous cells to drugs, ... More
Mechanical constraints influence microtubule orientation in plant cellsApr 08 2019In growing plant cells, parallel ordering of microtubules (MTs) along the inner surface of the cell membrane influences the direction of cell expansion and thereby plant morphology. For correct expansion of organs that primarily grow by elongating, such ... More
Uncertainty relation in the presence of information measurement and feedback controlApr 08 2019Thermodynamic uncertainty relation, which provides a universal bound for relative fluctuation of arbitrary currents in nonequilibrium systems, has been developed for various systems. Here we study the uncertainty of dynamical observables for classical ... More
maze: Heterogeneous Ligand Unbinding along Transient Protein TunnelsApr 08 2019Recent developments in enhanced sampling methods showed that it is possible to reconstruct ligand unbinding pathways with spatial and temporal resolution inaccessible to experiments. Ideally, such techniques should provide an atomistic definition of possibly ... More
The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networksApr 08 2019Motivation: Network visualizations of complex biological datasets usually result in 'hairball' images, which do not discriminate network modules. Results: We present the EntOptLayout Cytoscape plug-in based on a recently developed network representation ... More
Acinetobacter baumannii Deactivation by Means of DBD-Based Helium Plasma JetApr 07 2019Acinetobacter baumannii is a typically short, almost round, rod-shaped (coccobacillus) Gram-negative bacterium. It can be an opportunistic pathogen in humans, affecting people with compromised immune systems, and it is becoming increasingly important ... More
Electric-induced reversal of morphogenesis in Hydra regenerationApr 07 2019Morphogenesis in whole-body regeneration requires the dynamic interplay of three types of processes: biochemical, mechanical and electrical, which span all scales from the molecular to the entire organism. Despite significant progress in elucidating the ... More
Does it Swing? Microtiming Deviations and Swing Feeling in JazzApr 06 2019Jazz music that swings has the fascinating power to elicit a pleasant sensation of flow in listeners and the desire to synchronize body movements with the music. Whether microtiming deviations (MTDs), i.e. small timing deviations below the bar or phrase ... More
Translational control of gene expression via interacting feedback loopsApr 05 2019Translation is a key step in the synthesis of proteins. Accordingly, cells have evolved an intricate array of control mechanisms to regulate this process. By constructing a multi-component mathematical framework for translation we uncover how translation ... More
Cell motility, synchronization, and cell traction orientational orderApr 05 2019Suspensions of swimming micro-organisms provide examples of coordinated active dynamics. That has stimulated the study of a phenomenological theory combining synchronization and polar order in active matter. Here, we consider another example inspired ... More
E. coli "super-contaminates" narrow ducts fostered by broad run-time distributionApr 04 2019One striking feature of bacterial motion is their ability to swim upstream along corners and crevices, by leveraging hydrodynamic interactions. This motion through anatomic ducts or medical devices might be at the origin of serious infections. However, ... More
Noninvasive linear fluorescence imaging through scattering media via wavefront shapingApr 04 2019We demonstrate focusing and imaging through a scattering medium noninvasively by using wavefront shaping. Our concept is based on utilizing the spatial fluorescence contrast which naturally exists in the hidden target object. By scanning the angle of ... More
Molecular Self-Organization of Three-Component Lipid MembranesApr 03 2019By constructing a Landau-like energy functional, we investigate the molecular organization of a three-component mixture in cell membranes. In the strongly interacting limit, we model the interaction between molecules using pseudospin variables and convert ... More
Review on methods of solving the refractive index-thickness coupling problem in digital holographic microscopy of biological cellsApr 02 2019Digital holographic microscopy is a thriving imaging modality that attracted considerable research interest in quantitative biological cell imaging due to its ability to not only create excellent label-free contrast, but also supply valuable physical ... More
The N-flagella problem: Elastohydrodynamic motility transition of multi-flagellated bacteriaApr 02 2019Peritrichous bacteria such as Escherichia coli swim in viscous fluids by forming a helical bundle of flagellar filaments. The filaments are spatially distributed around the cell body to which they are connected via a flexible hook. To understand how the ... More
Melting transitions in biomembranesApr 02 2019We investigated melting transitions in biological membranes in their native state that include their membrane proteins. These membranes originated from \textit{E. coli}, \textit{B. subtilis}, lung surfactant and nerve tissue from the spinal cord of several ... More
Strategies that enforce linear payoff relationships under observation errors in Repeated Prisoner's Dilemma gameApr 02 2019The theory of repeated games analyzes the long-term relationship of interacting players and mathematically reveals the condition of how cooperation is achieved, which is not achieved in a one-shot game. In the repeated prisoner's dilemma (RPD) game with ... More
Diverse communities behave like typical random ecosystemsApr 01 2019With a brief letter to Nature in 1972, Robert May triggered a worldwide research program in theoretical ecology and complex systems that continues to this day. Building on powerful mathematical results about large random matrices, he argued that systems ... More
Timing of fungal spore release dictates survival during atmospheric transportApr 01 2019The fungi disperse spores to move across landscapes and spore liberation takes different patterns. While many species release spores intermittently, others release spores at specific times of day or night according to intrinsic rhythms. Despite intriguing ... More
Bayesian inference for nanopore data analysisApr 01 2019Nanopore sensors detect the substructure of individual molecules from modulations in an ion current as molecules pass through them. In this work, we present the classification of features in the substructure as a case study to illustrate the power of ... More
A Center Manifold Reduction Technique for a System of Randomly Coupled OscillatorsApr 01 2019In dynamical systems theory, a fixed point of the dynamics is called nonhyperbolic if the linearization of the system around the fixed point has at least one eigenvalue with zero real part. The center manifold existence theorem guarantees the local existence ... More
Self-organization of swimmers drives long-range fluid transport in bacterial coloniesApr 01 2019Bacteria commonly live in structured communities that affect human health and influence ecological systems. Heterogeneous populations, such as motile and non-motile populations, often coexist in bacteria communities. Motile subpopulations in microbial ... More
Accessible quantitative phase imaging in confocal microscopy with sinusoidal-phase synthetic optical holographyApr 01 2019We present a technically simple implementation of quantitative phase imaging in confocal microscopy based on synthetic optical holography with sinusoidal-phase reference waves. Using a Mirau interference objective and low-amplitude vertical sample vibration ... More
Biophysics-based critique of the assisted discharge mechanism hypothesisApr 01 2019Cell experiments with large, short electric field pulses of opposite polarity reveal a remarkable phenomenon: Bipolar cancellation (BPC). Typical defining experiments involve quantitative observation of tracer molecule influx at times of order 100 s post ... More
Observation of protein thermodynamics in ice by passive millimeter-wave microscopyApr 01 2019The study of protein functions attributed to the conformation and fluctuation that are ruled by both the amino acid sequence and thermodynamics, requires thermodynamic quantities given by calorimetry using thermometric techniques. The increased need for ... More
Long-range temporal correlation in Auditory Brainstem Responses to Spoken Syllable /da/Mar 31 2019The speech auditory brainstem response (sABR) is an objective clinical tool to diagnose particular impairments along the auditory brainstem pathways. We explore the scaling behavior of the brainstem in response to synthetic /da/ stimuli using a proposed ... More
Dynamics from elastic neutron-scattering via direct measurement of the running time-integral of the van Hove distribution functionMar 30 2019We present a new neutron-scattering approach to access the van Hove distribution function directly in the time domain, I(t), which reflects the system dynamics. Currently, I(t) is always determined from neutron energy-exchange. Our method consists of ... More
The physical parameters of neuronal cargo transport regulated by autoinhibition of kinesin UNC-104Mar 29 2019In this review, we focus on the kinesin-3 family molecular motor protein UNC-104 and its regulatory protein ARL-8. UNC-104, originally identified in Caenorhabditis elegans (C. elegans), has a primary role transporting synaptic vesicle precursors (SVPs). ... More
Strand displacement: a fundamental mechanism in RNA biology?Mar 28 2019DNA and RNA are generally regarded as central molecules in molecular biology. Recent advancements in the field of DNA/RNA nanotechnology successfully used DNA/RNA as programmable molecules to construct molecular machines and nanostructures with predefined ... More
Single-exposure full-field multi-depth imaging using low-coherence holographic multiplexingMar 28 2019We present a new interferometric imaging approach that allows for multiple-depth imaging in a single acquisition, using off-axis low-coherence holographic multiplexing. This technique enables sectioned imaging of multiple slices within a thick sample, ... More
Codifference can detect ergodicity breaking and non-GaussianityMar 28 2019We show that the codifference is a useful tool in studying the ergodicity breaking and non-Gaussianity properties of stochastic time series. While the codifference is a measure of dependence that was previously studied mainly in the context of stable ... More
Genetic drift in range expansions is very sensitive to density feedback in dispersal and growthMar 27 2019Theory predicts rapid genetic drift during invasions, yet many expanding populations maintain high genetic diversity. We find that genetic drift is dramatically suppressed when dispersal rates increase with the population density because many more migrants ... More
Bio-energy Transport as a Phonon Dressed Vibrational Exciton in Protein MoleculesMar 27 2019Following the ideas of Davydov's soliton theory, we study the bio-energy transport in protein molecules. By using a quantum Brownian motion model for a phonon dressed vibrational exciton, we calculate the time-dependence on the mean square distance, diffusion ... More
Why understanding multiplex social network structuring processes will help us better understand the evolution of human behaviorMar 26 2019Anthropologists have long appreciated that single-layer networks are insufficient descriptions of human interactions---individuals are embedded in complex networks with dependencies. One debate explicitly about this surrounds food sharing. Some argue ... More
GTPase cascades provide a motif for both robust switches and oscillatorsMar 26 2019GTPases regulate a wide range of cellular processes, such as intracellular vesicular transport, signal transduction, and protein translation. These hydrolase enzymes operate as biochemical switches by toggling between an active guanosine triphosphate ... More
On the possible mechanisms of the selective effect of a non-equilibrium plasma on healthy and cancer cells in a physiological solutionMar 26 2019This paper discusses possible mechanisms for the selective effect of weakly ionized non-equilibrium plasma and currents in electrolyte on healthy and cancerous cells in physiological saline in a Petri dish. The interaction with the plasma source leads ... More
Hole-closing model reveals exponents for nonlinear degenerate diffusivity functions in cell biologyMar 26 2019Continuum mathematical models for collective cell motion normally involve reaction-diffusion equations, such as the Fisher-KPP equation, with a linear diffusion term to describe cell motility and a logistic term to describe cell proliferation. While the ... More
Photoswitchable Single-Walled Carbon Nanotubes for Super-Resolution Microscopy in the Near-InfraredMar 26 2019The design of single-molecule photoswitchable emitters was the first milestone toward the advent of single-molecule localization microscopy that sets a new paradigm in the field of optical imaging. Several photoswitchable emitters have been developed ... More
Stiffening and Inelastic Fluidization in Vimentin Intermediate Filament NetworksMar 25 2019Intermediate filaments are cytoskeletal proteins that are key regulators of cell mechanics, a role which is intrinsically tied to their hierarchical structure and their unique ability to accommodate large axial strains. However, how the single-filament ... More
Elastic Property of Membranes Self-assembled from Diblock and Triblock CopolymersMar 25 2019The elastic property of membranes self-assembled from AB diblock and ABA triblock copolymers, as coarse-grained model of lipids and the bolalipids, are studied using the self-consistent field theory (SCFT). Specifically, solutions of the SCFT equations, ... More
Single-cell approaches to cell competition: high-throughput imaging, machine learning and simulationsMar 25 2019Cell competition is a quality control mechanism in tissues that results in the elimination of less fit cells. Over the past decade, the phenomenon of cell competition has been identified in many physiological and pathological contexts, driven either by ... More
Influence of photic perturbations on circadian rhythmsMar 25 2019The circadian clock is the molecular mechanism responsible for the adaptation to daily rhythms in living organisms. Oscillations and fluctuations in environmental conditions regulate the circadian clock through signaling pathways. We study the response ... More
Does electronic coherence enhance anticorrelated pigment vibrations under realistic conditions?Mar 25 2019The light-harvesting efficiency of a photoactive molecular complex is largely determined by the properties of its electronic quantum states. Those, in turn, are influenced by molecular vibrational states of the nuclear degrees of freedom. Here, we reexamine ... More
Fluctuation Theorem of Information Exchange between Subsystems that Co-Evolve in TimeMar 25 2019Sagawa and Ueda established a fluctuation theorem of information exchange by revealing the role of correlations in stochastic thermodynamics and unified the non-equilibrium thermodynamics of measurement and feedback control [T. Sagawa and M. Ueda, Phys. ... More
Flagella-like beating of a single microtubuleMar 23 2019Kinesin motors can induce a buckling instability in a microtubule with a fixed minus end. Here we show that by modifying the surface with a protein-repellent functionalization and using clusters of kinesin motors, the microtubule can exhibit persistent ... More
Active Materials: Biological Benchmarks and Transport LimitationsMar 22 2019These lecture notes were prepared for the 2018 Summer School on `Active Matter and Non-equilibrium Statistical Physics' at l'\'{E}cole de Physique des Houches. They survey metabolic activity across a wide range of living organisms, and consider size limitations ... More
Roles of mutation rate and co-existence of multiple strategy updating rules in evolutionary prisoner's dilemma gamesMar 22 2019The emergence and maintenance of co-operation has attracted intensive scholarly interest and has been analysed within the framework of evolutionary game theory. The role of innovation, which introduces novel strategies into the population, is a relatively ... More
Collapse of orthotropic spherical shellsMar 22 2019We report on the buckling and subsequent collapse of orthotropic elastic spherical shells under volume and pressure control. Going far beyond what is known for isotropic shells, a rich morphological phase space with three distinct regimes emerges upon ... More
Consensus and diversity in multi-state noisy voter modelsMar 21 2019We study a variant of the voter model with multiple opinions; individuals can imitate each other and also change their opinion randomly in mutation events. We focus on the case of a population with all-to-all interaction. A noise-driven transition between ... More
Biotransformation and biological impact of graphene and graphene oxide during simulated oral ingestionMar 21 2019Graphene is an innovative nanomaterial, made of two-dimensional honeycomb-like carbon lattice, with potential in many different applications. Studying the behaviour of graphene-related materials (GRMs) in biological systems is, therefore, crucial to assess ... More
Fractional Brownian motion in a finite interval: correlations effect depletion or accretion zones of particles near boundariesMar 21 2019Fractional Brownian motion is a Gaussian stochastic process with stationary, long-time correlated increments and is frequently used to model anomalous diffusion processes. We study numerically fractional Brownian motion confined to a finite interval with ... More
How the brain transitions from conscious to subliminal perceptionMar 21 2019We study the transition in the functional networks that characterize the human brains' conscious-state to an unconscious subliminal state of perception by using k-core percolation. We find that the most inner core (i.e., the most connected kernel) of ... More
Scaling methods for accelerating kinetic Monte Carlo simulations of chemical reaction networksMar 20 2019Various kinetic Monte Carlo algorithms become inefficient when some of the population sizes in a system are large, which gives rise to a large number of reaction events per unit time. Here, we present a new acceleration algorithm based on adaptive and ... More
Computational modeling of active deformable membranes embedded in 3D flowsMar 20 2019Active gel theory has recently been very successful in describing biologically active materials such as actin filaments or moving bacteria in temporally fixed and simple geometries such as cubes or spheres. Here we develop a computational algorithm to ... More
Turing-like patterns in an asymmetric dynamic Ising modelMar 20 2019To investigate novel aspects of pattern formation in spin systems, we propose a mapping between reactive concentrations in a reaction-diffusion system and spin orientations in a dynamic multiple-spin Ising model. This specifically designed Ising model ... More
An increase in membrane cholesterol by graphene oxide disrupts calcium homeostasis in primary astrocytesMar 20 2019The use of graphene nanomaterials (GNMs) for biomedical applications targeted to the central nervous system is exponentially increasing, although precise information on their effects on brain cells is lacking. In this work, we addressed the molecular ... More
Interfacing Graphene-Based Materials With Neural CellsMar 20 2019The scientific community has witnessed an exponential increase in the applications of graphene and graphene-based materials in a wide range of fields. For what concerns neuroscience, the interest raised by these materials is two-fold. On one side, nanosheets ... More
Exact Distributions of Currents and Frenesy for Markov BridgesMar 19 2019We consider discrete-time Markov bridges, chains whose initial and final states coincide. We derive an exact finite-time formula for the full probability distribution of additive functionals of trajectories. We apply our theory to time-integrated currents ... More
Layer-specific connectivity revealed by diffusion-weighted functional MRI in the rat thalamocortical pathwayMar 19 2019Investigating neural activity from a global brain perspective in-vivo has been in the domain of functional Magnetic Resonance Imaging (fMRI) over the past few decades. The intricate neurovascular couplings that govern fMRI's blood-oxygenation-level-dependent ... More
Principal component analysis of nonequilibrium molecular dynamics simulationsMar 19 2019Principal component analysis (PCA) represents a standard approach to identify collective variables $\{x_i\}\!=\!\boldsymbol{x}$, which can be used to construct the free energy landscape $\Delta G(\boldsymbol{x})$ of a molecular system. While PCA is routinely ... More
Emergent regularities and scaling in armed conflict dataMar 18 2019Mar 30 2019Large-scale armed conflict is a characteristic feature of modern societies. The statistics of conflict show remarkable regularities like power law distributions of fatalities and duration, but lack a unifying framework. We explore a large, detailed data ... More
Emergent regularities and scaling in armed conflict dataMar 18 2019Large-scale armed conflict is a characteristic feature of modern civilization. The statistics of conflict show remarkable regularities like power law distributions of fatalities and durations, but these properties have remained disparate, albeit prominent, ... More
Local details versus effective medium approximation: A study of diffusion in microfluidic random networks made from Voronoi tessellationsMar 18 2019We measured the effective diffusion coefficient in microfluidic networks of controlled geometry using the FRAP (Fluorescence Recovery After Photobleaching) technique. The geometry of the networks was based on Voronoi tesellations, and had varying size ... More
Hydrodynamics of Active Lévy MatterMar 18 2019Collective motion emerges spontaneously in many biological systems such as bird flocks, insect swarms and tissue under dynamic reorganization. This phenomenon is often modeled within the framework of active fluids, where the constituent active particles, ... More
Hydrodynamics of Active Lévy MatterMar 18 2019Apr 17 2019Collective motion emerges spontaneously in many biological systems such as bird flocks, insect swarms and tissue under dynamic reorganization. This phenomenon is often modeled within the framework of active fluids, where the constituent active particles, ... More
Efficient vaccination strategies for epidemic control using network informationMar 18 2019Network-based interventions against epidemic spread are most powerful when the full network structure is known. However, in practice, resource constraints require decisions to be made based on partial network information. We investigated how the accuracy ... More