Molecular dynamics simulations of microscopic structural transition and macroscopic mechanical properties of magnetic gels.

Magnetic gels with embedded micro-/nano-sized magnetic particles in cross-linked polymer networks can be actuated by external magnetic fields, with changes in their internal microscopic structures and macroscopic mechanical properties. We investigate the responses of such magnetic gels to an external magnetic field, by means of coarse-grained molecular dynamics simulations. We find that the dynamics of magnetic particles are determined by the interplay of magnetic dipole-dipole interactions, polymer elasticity, and thermal fluctuations.

Scaling Transition of Active Turbulence from Two to Three Dimensions.

Turbulent flows are observed in low-Reynolds active fluids, which display similar phenomenology to the classical inertial turbulence but are of a different nature. Understanding the dependence of this new type of turbulence on dimensionality is a fundamental challenge in non-equilibrium physics. Real-space structures and kinetic energy spectra of bacterial turbulence are experimentally measured from two to three dimensions.

The microbiome-derived antibacterial lugdunin acts as a cation ionophore in synergy with host peptides.

Unlabelled: Lugdunin is a microbiome-derived antibacterial agent with good activity against Gram-positive pathogens and in animal models of nose colonization and skin infection. We have previously shown that lugdunin depletes bacterial energy resources by dissipating the membrane potential of . Here, we explored the mechanism of action of lugdunin in more detail and show that lugdunin quickly depolarizes cytoplasmic membranes of different bacterial species and acidifies the cytoplasm of within minutes due to protonophore activity.

Near-field hydrodynamic interactions determine travelling wave directions of collectively beating cilia.

Cilia can beat collectively in the form of a metachronal wave, and we investigate how near-field hydrodynamic interactions between cilia can influence the collective response of the beating cilia. Based on the theoretical framework developed in the work of Meng . (Meng .

Probabilistic neural transfer function estimation with Bayesian system identification.

Neural population responses in sensory systems are driven by external physical stimuli. This stimulus-response relationship is typically characterized by receptive fields, which have been estimated by neural system identification approaches. Such models usually require a large amount of training data, yet, the recording time for animal experiments is limited, giving rise to epistemic uncertainty for the learned neural transfer functions.

Lagrangian Irreversibility and Energy Exchanges in Rotating-Stratified Turbulent Flows.

Turbulence in stratified and rotating turbulent flows is characterized by an interplay between waves and eddies, resulting in continuous exchanges between potential and kinetic energy. Here, we study how these processes affect the turbulent energy cascade from large to small scales, which manifests itself by an irreversible evolution of the relative kinetic energy between two tracer particles. We find that when r_{0}, the separation between particles, is below a characteristic length ℓ_{t}, potential energy is on average transferred to kinetic energy, reducing time irreversibility, and conversely when r_{0}>ℓ_{t}.

Escaping Kinetic Traps Using Nonreciprocal Interactions.

Kinetic traps are a notorious problem in equilibrium statistical mechanics, where temperature quenches ultimately fail to bring the system to low energy configurations. Using multifarious self-assembly as a model system, we introduce a mechanism to escape kinetic traps by utilizing nonreciprocal interactions between components. Introducing nonequilibrium effects offered by broken action-reaction symmetry in the system pushes the trajectory of the system out of arrested dynamics.

Power-law growth models explain incidences and sizes of pancreatic cancer precursor lesions and confirm spatial genomic findings.

Pancreatic ductal adenocarcinoma is a rare but lethal cancer. Recent evidence suggests that pancreatic intraepithelial neoplasia (PanIN), a microscopic precursor lesion that gives rise to pancreatic cancer, is larger and more prevalent than previously believed. Better understanding of the growth-law dynamics of PanINs may improve our ability to understand how a miniscule fraction makes the transition to invasive cancer.

Retrospective for the Dynamic Sensorium Competition for predicting large-scale mouse primary visual cortex activity from videos.

Understanding how biological visual systems process information is challenging because of the nonlinear relationship between visual input and neuronal responses. Artificial neural networks allow computational neuroscientists to create predictive models that connect biological and machine vision. Machine learning has benefited tremendously from benchmarks that compare different model on the same task under standardized conditions.

Chaos control in cardiac dynamics: terminating chaotic states with local minima pacing.

Current treatments of cardiac arrhythmias like ventricular fibrillation involve the application of a high-energy electric shock, that induces significant electrical currents in the myocardium and therefore involves severe side effects like possible tissue damage and post-traumatic stress. Using numerical simulations on four different models of 2D excitable media, this study demonstrates that low energy pulses applied shortly after local minima in the mean value of the transmembrane potential provide high success rates. We evaluate the performance of this approach for ten initial conditions of each model, ten spatially different stimuli, and different shock amplitudes.

Early mutational signatures and transmissibility of SARS-CoV-2 Gamma and Lambda variants in Chile.

Genomic surveillance (GS) programmes were crucial in identifying and quantifying the mutating patterns of SARS-CoV-2 during the COVID-19 pandemic. In this work, we develop a Bayesian framework to quantify the relative transmissibility of different variants tailored for regions with limited GS. We use it to study the relative transmissibility of SARS-CoV-2 variants in Chile.

Pore-spanning membranes as a tool to investigate lateral lipid membrane heterogeneity.

Over the years, it has become more and more obvious that lipid membranes show a very complex behavior. This behavior arises in part from the large number of different kinds of lipids and proteins and how they dynamically interact with each other. In vitro studies using artificial membrane systems have shed light on the heterogeneity based on lipid-lipid interactions in multicomponent bilayer mixtures.

Optimized PAR-2 RING dimerization mediates cooperative and selective membrane binding for robust cell polarity.

Cell polarity networks are defined by quantitative features of their constituent feedback circuits, which must be tuned to enable robust and stable polarization, while also ensuring that networks remain responsive to dynamically changing cellular states and/or spatial cues during development. Using the PAR polarity network as a model, we demonstrate that these features are enabled by the dimerization of the polarity protein PAR-2 via its N-terminal RING domain. Combining theory and experiment, we show that dimer affinity is optimized to achieve dynamic, selective, and cooperative binding of PAR-2 to the plasma membrane during polarization.

Pulling on grafted flexible polymers can cause twisted bundles.

Bundles of semiflexible polymers can twist at low temperatures to balance energy gain from attraction and energy cost from bending. This raises the question whether twisting can be also observed for bundles of rather flexible grafted polymers stretched out by pulling force. Here, we address this question using Monte Carlo computer simulations of small bundles.

Quantifying gliding forces of filamentous cyanobacteria by self-buckling.

Filamentous cyanobacteria are one of the oldest and today still most abundant lifeforms on earth, with manifold implications in ecology and economics. Their flexible filaments, often several hundred cells long, exhibit gliding motility in contact with solid surfaces. The underlying force generating mechanism is not yet understood.

Heterogeneous nucleation and growth of sessile chemically active droplets.

Droplets are essential for spatially controlling biomolecules in cells. To work properly, cells need to control the emergence and morphology of droplets. On the one hand, driven chemical reactions can affect droplets profoundly.

Nanocrystal Assemblies: Current Advances and Open Problems.

We explore the potential of nanocrystals (a term used equivalently to nanoparticles) as building blocks for nanomaterials, and the current advances and open challenges for fundamental science developments and applications. Nanocrystal assemblies are inherently multiscale, and the generation of revolutionary material properties requires a precise understanding of the relationship between structure and function, the former being determined by classical effects and the latter often by quantum effects. With an emphasis on theory and computation, we discuss challenges that hamper current assembly strategies and to what extent nanocrystal assemblies represent thermodynamic equilibrium or kinetically trapped metastable states.

Diverse task-driven modeling of macaque V4 reveals functional specialization towards semantic tasks.

Responses to natural stimuli in area V4-a mid-level area of the visual ventral stream-are well predicted by features from convolutional neural networks (CNNs) trained on image classification. This result has been taken as evidence for the functional role of V4 in object classification. However, we currently do not know if and to what extent V4 plays a role in solving other computational objectives.

Threshold current density for diffusion-controlled stability of electrolytic surface nanobubbles.

Understanding the stability mechanism of surface micro/nanobubbles adhered to gas-evolving electrodes is essential for improving the efficiency of water electrolysis, which is known to be hindered by the bubble coverage on electrodes. Using molecular simulations, the diffusion-controlled evolution of single electrolytic nanobubbles on wettability-patterned nanoelectrodes is investigated. These nanoelectrodes feature hydrophobic islands as preferential nucleation sites and allow the growth of nanobubbles in the pinning mode.

Turbulent Properties of Stationary Flows in Porous Media.

In this study, we investigate the flow dynamics in a fixed bed of hydrogel beads using particle tracking velocimetry to compute the velocity field in the middle of the bed for moderate Reynolds numbers (Re=[124,169,203,211]). We discover that even though the flow is stationary at the larger scales, it exhibits complex multiscale spatial dynamics reminiscent of those observed in classical turbulence. We find evidence of the presence of an inertial range and a direct energy cascade, and are able to obtain a value for a "porous" Kolmogorov constant of C_{2}=3.

The antimicrobial fibupeptide lugdunin forms water-filled channel structures in lipid membranes.

Recently, a novel cyclo-heptapeptide composed of alternating D,L-amino acids and a unique thiazolidine heterocycle, called lugdunin, was discovered, which is produced by the nasal and skin commensal Staphylococcus lugdunensis. Lugdunin displays potent antimicrobial activity against a broad spectrum of Gram-positive bacteria, including challenging-to-treat methicillin-resistant Staphylococcus aureus (MRSA). Lugdunin specifically inhibits target bacteria by dissipating their membrane potential.

Slow kinesin-dependent microtubular transport facilitates ribbon synapse assembly in developing cochlear inner hair cells.

Sensory synapses are characterized by electron-dense presynaptic specializations, so-called synaptic ribbons. In cochlear inner hair cells (IHCs), ribbons play an essential role as core active zone (AZ) organizers, where they tether synaptic vesicles, cluster calcium channels and facilitate the temporally-precise release of primed vesicles. While a multitude of studies aimed to elucidate the molecular composition and function of IHC ribbon synapses, the developmental formation of these signalling complexes remains largely elusive to date.

Chemotactic particles as strong electrolytes: Debye-Hückel approximation and effective mobility law.

We consider a binary mixture of chemically active particles that produce or consume solute molecules and that interact with each other through the long-range concentration fields they generate. We analytically calculate the effective phoretic mobility of these particles when the mixture is submitted to a constant, external concentration gradient, at leading order in the overall concentration. Relying on an analogy with the modeling of strong electrolytes, we show that the effective phoretic mobility decays with the square root of the concentration: our result is, therefore, a nonequilibrium counterpart to the celebrated Kohlrausch and Debye-Hückel-Onsager conductivity laws for electrolytes, which are extended here to particles with long-range nonreciprocal interactions.

Most discriminative stimuli for functional cell type clustering.

Identifying cell types and understanding their functional properties is crucial for unraveling the mechanisms underlying perception and cognition. In the retina, functional types can be identified by carefully selected stimuli, but this requires expert domain knowledge and biases the procedure towards previously known cell types. In the visual cortex, it is still unknown what functional types exist and how to identify them.

Waste paper-derived porous carbon via microwave-assisted activation for energy storage and water purification.

The reuse of waste papers by conversion into valuable carbon materials has received considerable attention for diverse applications such as energy storage and water purification. However, traditional methods for converting waste papers into materials with suitable properties for specific applications are often complex and ineffective, involving consecutive carbonization and activation steps. Herein, we propose a simple one-step microwave (MW)-assisted synthesis for preparing waste paper-derived porous carbons (WPCs) for energy storage and water purification.