# Browsing by Subject "physics.bio-ph"

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Item Open Access Diffraction tomography with a deep image priorZhou, Kevin C; Horstmeyer, RoarkeWe present a tomographic imaging technique, termed Deep Prior Diffraction Tomography (DP-DT), to reconstruct the 3D refractive index (RI) of thick biological samples at high resolution from a sequence of low-resolution images collected under angularly varying illumination. DP-DT processes the multi-angle data using a phase retrieval algorithm that is extended by a deep image prior (DIP), which reparameterizes the 3D sample reconstruction with an untrained, deep generative 3D convolutional neural network (CNN). We show that DP-DT effectively addresses the missing cone problem, which otherwise degrades the resolution and quality of standard 3D reconstruction algorithms. As DP-DT does not require pre-captured data or pre-training, it is not biased towards any particular dataset. Hence, it is a general technique that can be applied to a wide variety of 3D samples, including scenarios in which large datasets for supervised training would be infeasible or expensive. We applied DP-DT to obtain 3D RI maps of bead phantoms and complex biological specimens, both in simulation and experiment, and show that DP-DT produces higher-quality results than standard regularization techniques. We further demonstrate the generality of DP-DT, using two different scattering models, the first Born and multi-slice models. Our results point to the potential benefits of DP-DT for other 3D imaging modalities, including X-ray computed tomography, magnetic resonance imaging, and electron microscopy.Item Open Access Emergence of irregular activity in networks of strongly coupled conductance-based neuronsSanzeni, Alessandro; Histed, Mark H; Brunel, NicolasCortical neurons are characterized by irregular firing and a broad distribution of rates. The balanced state model explains these observations with a cancellation of mean excitatory and inhibitory currents, which makes fluctuations drive firing. In networks of neurons with current-based synapses, the balanced state emerges dynamically if coupling is strong, i.e. if the mean number of synapses per neuron $K$ is large and synaptic efficacy is of order $1/\sqrt{K}$. When synapses are conductance-based, current fluctuations are suppressed when coupling is strong, questioning the applicability of the balanced state idea to biological neural networks. We analyze networks of strongly coupled conductance-based neurons and show that asynchronous irregular activity and broad distributions of rates emerge if synapses are of order $1/\log(K)$. In such networks, unlike in the standard balanced state model, current fluctuations are small and firing is maintained by a drift-diffusion balance. This balance emerges dynamically, without fine tuning, if inputs are smaller than a critical value, which depends on synaptic time constants and coupling strength, and is significantly more robust to connection heterogeneities than the classical balanced state model. Our analysis makes experimentally testable predictions of how the network response properties should evolve as input increases.Item Open Access Mean-field equation for a stochastic many-particle model of quorum-sensing microbial populationsFrey, Erwin; Knebel, Johannes; Pickl, PeterWe prove a mean-field equation for the dynamics of quorum-sensing microbial populations. In the stochastic many-particle process, individuals of a population produce public good molecules to different degrees. Individual production is metabolically costly such that non-producers replicate faster than producers. In addition, individuals sense the average production level in the well-mixed population and adjust their production in response ("quorum sensing"). Here we prove that the temporal evolution of such quorum-sensing populations converges to a macroscopic mean-field equation for increasing population sizes. To prove convergence, we introduce an auxiliary stochastic mean-field process that mimics the dynamics of the mean-field equation and that samples independently the individual's production degrees between consecutive update steps. This way, the law of large numbers is separated from the propagation of errors due to correlations. Our developed method of an auxiliary stochastic mean-field process may help to prove mean-field equations for other stochastic many-particle processes.Item Open Access Quantitative Jones matrix imaging using vectorial Fourier ptychography(2021-09-30) Dai, Xiang; Xu, Shiqi; Yang, Xi; Zhou, Kevin C; Glass, Carolyn; Konda, Pavan Chandra; Horstmeyer, RoarkeThis paper presents a microscopic imaging technique that uses variable-angle illumination to recover the complex polarimetric properties of a specimen at high resolution and over a large field-of-view. The approach extends Fourier ptychography, which is a synthetic aperture-based imaging approach to improve resolution with phaseless measurements, to additionally account for the vectorial nature of light. After images are acquired using a standard microscope outfitted with an LED illumination array and two polarizers, our vectorial Fourier Ptychography (vFP) algorithm solves for the complex 2x2 Jones matrix of the anisotropic specimen of interest at each resolved spatial location. We introduce a new sequential Gauss-Newton-based solver that additionally jointly estimates and removes polarization-dependent imaging system aberrations. We demonstrate effective vFP performance by generating large-area (29 mm$^2$), high-resolution (1.24 $\mu$m full-pitch) reconstructions of sample absorption, phase, orientation, diattenuation, and retardance for a variety of calibration samples and biological specimens.Item Open Access Rapid local compression in active gels is caused by nonlinear network response.(Soft matter, 2020-10) Mizuno, D; Tardin, C; Schmidt, CFThe actin cytoskeleton in living cells generates forces in conjunction with myosin motor proteins to directly and indirectly drive essential cellular processes. The semiflexible filaments of the cytoskeleton can respond nonlinearly to the collective action of motors. We here investigate mechanics and force generation in a model actin cytoskeleton, reconstituted in vitro, by observing the response and fluctuations of embedded micron-scale probe particles. Myosin mini-filaments can be modeled as force dipoles and give rise to deformations in the surrounding network of cross-linked actin. Anomalously correlated probe fluctuations indicate the presence of rapid local compression or draining of the network that emerges in addition to the ordinary linear shear elastic (incompressible) response to force dipoles. The anomalous propagation of compression can be attributed to the nonlinear response of actin filaments to the microscopic forces, and is quantitatively consistent with motor-generated large-scale stiffening of the gels.Item Open Access Storage capacity of networks with discrete synapses and sparsely encoded memoriesFeng, Yu; Brunel, NicolasAttractor neural networks (ANNs) are one of the leading theoretical frameworks for the formation and retrieval of memories in networks of biological neurons. In this framework, a pattern imposed by external inputs to the network is said to be learned when this pattern becomes a fixed point attractor of the network dynamics. The storage capacity is the maximum number of patterns that can be learned by the network. In this paper, we study the storage capacity of fully-connected and sparsely-connected networks with a binarized Hebbian rule, for arbitrary coding levels. Our results show that a network with discrete synapses has a similar storage capacity as the model with continuous synapses, and that this capacity tends asymptotically towards the optimal capacity, in the space of all possible binary connectivity matrices, in the sparse coding limit. We also derive finite coding level corrections for the asymptotic solution in the sparse coding limit. The result indicates the capacity of network with Hebbian learning rules converges to the optimal capacity extremely slowly when the coding level becomes small. Our results also show that in networks with sparse binary connectivity matrices, the information capacity per synapse is larger than in the fully connected case, and thus such networks store information more efficiently.Item Open Access Temperature-dependent non-covalent protein-protein interactions explain normal and inverted solubility in a mutant of human gamma D-crystallinKhan, Amir R; James, Susan; Quinn, Michelle K; Altan, Irem; Charbonneau, Patrick; McManus, Jennifer JProtein crystal production is a major bottleneck for the structural characterisation of proteins. To advance beyond large-scale screening, rational strategies for protein crystallization are crucial. Understanding how chemical anisotropy (or patchiness) of the protein surface due to the variety of amino acid side chains in contact with solvent, contributes to protein protein contact formation in the crystal lattice is a major obstacle to predicting and optimising crystallization. The relative scarcity of sophisticated theoretical models that include sufficient detail to link collective behaviour, captured in protein phase diagrams, and molecular level details, determined from high-resolution structural information is a further barrier. Here we present two crystals structures for the P23TR36S mutant of gamma D-crystallin, each with opposite solubility behaviour, one melts when heated, the other when cooled. When combined with the protein phase diagram and a tailored patchy particle model we show that a single temperature dependent interaction is sufficient to stabilise the inverted solubility crystal. This contact, at the P23T substitution site, relates to a genetic cataract and reveals at a molecular level, the origin of the lowered and retrograde solubility of the protein. Our results show that the approach employed here may present an alternative strategy for the rationalization of protein crystallization.