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1. A particle-field approach bridges phase separation and collective motion in active matter

   https://doi.org/10.1038/s41467-020-18978-5  

   Großmann, Robert; Aranson, Igor S.; Peruani, Fernando (December 2020, Nature Communications)

   null (Ed.)

   Abstract Whereas self-propelled hard discs undergo motility-induced phase separation, self-propelled rods exhibit a variety of nonequilibrium phenomena, including clustering, collective motion, and spatio-temporal chaos. In this work, we present a theoretical framework representing active particles by continuum fields. This concept combines the simplicity of alignment-based models, enabling analytical studies, and realistic models that incorporate the shape of self-propelled objects explicitly. By varying particle shape from circular to ellipsoidal, we show how nonequilibrium stresses acting among self-propelled rods destabilize motility-induced phase separation and facilitate orientational ordering, thereby connecting the realms of scalar and vectorial active matter. Though the interaction potential is strictly apolar, both, polar and nematic order may emerge and even coexist. Accordingly, the symmetry of ordered states is a dynamical property in active matter. The presented framework may represent various systems including bacterial colonies, cytoskeletal extracts, or shaken granular media. 

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2. Does number of rods matter? 4-, 5-, and 6-rods across a lumbar pedicle subtraction osteotomy: a finite element analysis

   https://doi.org/10.1007/s43390-022-00627-0  

   Shekouhi, Niloufar; Vosoughi, Ardalan S.; Goel, Vijay K.; Theologis, Alekos A. (May 2023, Spine Deformity)

   Abstract PurposeTo assess biomechanics of a lumbar PSO stabilized with different multi-rod constructs (4-, 5-, 6-rods) using satellite and accessory rods. MethodsA validated spinopelvic finite element model with a L3 PSO was used to evaluate the following constructs: 2 primary rods T10-pelvis (“Control”), two satellite rods (4-rod), two satellite rods + one accessory rod (5-rod), or two satellite rods + two accessory rods (6-rod). Data recorded included: ROM T10-S1 and L2-L4, von Mises stresses on primary, satellite, and accessory rods, factor of safety yield stress, and force across the PSO surfaces. Percent differences relative to Control were calculated. ResultsCompared to Control, 4-rods increased PSO flexion and extension. Lower PSO ROMs were observed for 5- and 6-rods compared to 4-rods. However, 4-rod (348.6 N) and 5-rod (343.2 N) showed higher PSO forces than 2-rods (336 N) and 6-rods had lower PSO forces (324.2 N). 5- and 6-rods led to the lowest rod von Mises stresses across the PSO. 6-rod had the maximum factor of safety on the primary rods. ConclusionsIn this finite element analysis, 4-rods reduced stresses on primary rods across a lumbar PSO. Although increased rigidity afforded by 5- and 6-rods decreased rod stresses, it resulted in less load transfer to the anterior vertebral column (particularly for 6-rod), which may not be favorable for the healing of the anterior column. A balance between the construct’s rigidity and anterior load sharing is essential. 

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3. Self-consistent dynamical field theory of kernel evolution in wide neural networks ^*

   https://doi.org/10.1088/1742-5468/ad01b0  

   Bordelon, Blake; Pehlevan, Cengiz (November 2023, Journal of Statistical Mechanics: Theory and Experiment)

   Abstract We analyze feature learning in infinite-width neural networks trained with gradient flow through a self-consistent dynamical field theory. We construct a collection of deterministic dynamical order parameters which are inner-product kernels for hidden unit activations and gradients in each layer at pairs of time points, providing a reduced description of network activity through training. These kernel order parameters collectively define the hidden layer activation distribution, the evolution of the neural tangent kernel (NTK), and consequently, output predictions. We show that the field theory derivation recovers the recursive stochastic process of infinite-width feature learning networks obtained by Yang and Hu with tensor programs. For deep linear networks, these kernels satisfy a set of algebraic matrix equations. For nonlinear networks, we provide an alternating sampling procedure to self-consistently solve for the kernel order parameters. We provide comparisons of the self-consistent solution to various approximation schemes including the static NTK approximation, gradient independence assumption, and leading order perturbation theory, showing that each of these approximations can break down in regimes where general self-consistent solutions still provide an accurate description. Lastly, we provide experiments in more realistic settings which demonstrate that the loss and kernel dynamics of convolutional neural networks at fixed feature learning strength are preserved across different widths on a image classification task. 

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4. Involvement of ArlI, ArlJ, and CirA in archaeal type IV pilin-mediated motility regulation

   https://doi.org/10.1128/jb.00089-24  

   Chatterjee, Priyanka; Garcia, Marco A; Cote, Jacob A; Yun, Kun; Legerme, Georgio P; Habib, Rumi; Tripepi, Manuela; Young, Criston; Kulp, Daniel; Dyall-Smith, Mike; et al (June 2024, Journal of Bacteriology)

   Maupin-Furlow, Julie A (Ed.)

   ABSTRACT Many prokaryotes use swimming motility to move toward favorable conditions and escape adverse surroundings. Regulatory mechanisms governing bacterial flagella-driven motility are well-established; however, little is yet known about the regulation underlying swimming motility propelled by the archaeal cell surface structure, the archaella. Previous research showed that the deletion of the adhesion pilins (PilA1-6), subunits of the type IV pili cell surface structure, renders the model archaeonHaloferax volcaniinon-motile. In this study, we used ethyl methanesulfonate mutagenesis and a motility assay to identify motile suppressors of the ∆pilA[1-6] strain. Of the eight suppressors identified, six contain missense mutations in archaella biosynthesis genes,arlIandarlJ. In transexpression ofarlIandarlJmutant constructs in the respective multi-deletion strains ∆pilA[1-6]∆arlIand ∆pilA[1-6]∆arlJconfirmed their role in suppressing the ∆pilA[1-6] motility defect. Additionally, three suppressors harbor co-occurring disruptive missense and nonsense mutations incirA, a gene encoding a proposed regulatory protein. A deletion ofcirAresulted in hypermotility, whilecirAexpressionin transin wild-type cells led to decreased motility. Moreover, quantitative real-time PCR analysis revealed that in wild-type cells, higher expression levels ofarlI,arlJ, and the archaellin genearlA1were observed in motile early-log phase rod-shaped cells compared to non-motile mid-log phase disk-shaped cells. Conversely, ∆cirAcells, which form rods during both early- and mid-log phases, exhibited similar expression levels ofarlgenes in both growth phases. Our findings contribute to a deeper understanding of the mechanisms governing archaeal motility, highlighting the involvement of ArlI, ArlJ, and CirA in pilin-mediated motility regulation.IMPORTANCEArchaea are close relatives of eukaryotes and play crucial ecological roles. Certain behaviors, such as swimming motility, are thought to be important for archaeal environmental adaptation. Archaella, the archaeal motility appendages, are evolutionarily distinct from bacterial flagella, and the regulatory mechanisms driving archaeal motility are largely unknown. Previous research has linked the loss of type IV pili subunits to archaeal motility suppression. This study reveals threeHaloferax volcaniiproteins involved in pilin-mediated motility regulation, offering a deeper understanding of motility regulation in this understudied domain while also paving the way for uncovering novel mechanisms that govern archaeal motility. Understanding archaeal cellular processes will help elucidate the ecological roles of archaea as well as the evolution of these processes across domains. 

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5. Biomechanical evaluation of multi-rod constructs to stabilize an S1 pedicle subtraction osteotomy (PSO): a finite element analysis

   https://doi.org/10.1007/s43390-023-00784-w  

   Shekouhi, Niloufar; Tripathi, Sudharshan; Goel, Vijay K; Theologis, Alekos A (March 2024, Spine Deformity)

   Abstract PurposeTo develop and validate a finite element (FE) model of a sacral pedicle subtraction osteotomy (S1-PSO) and to compare biomechanical properties of various multi-rod configurations to stabilize S1-PSOs. MethodsA previously validated FE spinopelvic model was used to develop a 30° PSO at the sacrum. Five multi-rod techniques spanning the S1-PSO were made using 4 iliac screws and a variety of primary rods (PR) and accessory rods (AR; lateral: Lat-AR or medial: Med-AR). All constructs, except one, utilized a horizontal rod (HR) connecting the iliac bolts to which PRs and Med-ARs were connected. Lat-ARs were connected to proximal iliac bolts. The simulation was performed in two steps with the acetabula fixed. For each model, PSO ROM and maximum stress on the PRs, ARs, and HRs were recorded and compared. The maximum stress on the L5–S1 disc and the PSO forces were captured and compared. ResultsHighest PSO ROMs were observed for 4-Rods (HR + 2 Med-AR). Constructs consisting of 5-Rods (HR + 2 Lat-ARs + 1 Med-AR) and 6-Rods (HR + 2 Lat-AR + 2 Med-AR) had the lowest PSO ROM. The least stress on the primary rods was seen with 6-Rods, followed by 5-Rods and 4-Rods (HR + 2 Lat-ARs). Lowest PSO forces and lowest L5–S1 disc stresses were observed for 4-Rod (Lat-AR), 5-Rod, and 6-Rod constructs, while 4-Rods (HR + Med-AR) had the highest. ConclusionIn this first FE analysis of an S1-PSO, the 4-Rod construct (HR + Med-AR) created the least rigid environment and highest PSO forces anteriorly. While 5- and 6-Rods created the stiffest constructs and lowest stresses on the primary rods, it also jeopardized load transfer to the anterior column, which may not be favorable for healing anteriorly. A balance between the construct’s rigidity and anterior load sharing is essential. 

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