Extracellular vesicles (EVs) hold great promise in drug delivery, disease diagnosis, and treatment; however, the inability to control EVs biogenesis critically limits their therapeutic and diagnostic potential. Although regulatory mechanisms for biochemical cues have been extensively studied, the pr…

[Phys. Rev. E 114, 014407] Published Tue Jul 14, 2026

A mechanism for the biological effects of the hypomagnetic field is proposed, based on the rotational motion of a molecule as a whole within a cavity in an enzyme. It has been shown previously that a molecular rotator about 1 nm in size can have a decoherence time of up to tens of milliseconds. On s…

[Phys. Rev. E 114, 014406] Published Mon Jul 13, 2026

The self-organization of microbial ecosystems involves a large variety of mechanisms, ranging from biochemical signaling to population dynamics. Among these, the role of motility regulation has been little studied, despite the importance of active migration processes. Here we show how weak, random m…

[Phys. Rev. E 114, 014404] Published Tue Jul 07, 2026

Biological membranes are dynamic surfaces whose shape and function are critically influenced by protein inclusions (PIs). While membrane deformations induced by PIs have been extensively studied in the small-deformation regime, a variety of processes involve strong membrane deformations. We investig…

[Phys. Rev. E 114, 014405] Published Tue Jul 07, 2026

The height of viral particles adsorbed on solid substrates is governed by the equilibrium between adhesion energy and capsid elasticity. While the resulting height distribution has been proposed as a noninvasive proxy for viral stiffness, the physical origin of its broadening is unknown. In this wor…

[Phys. Rev. E 114, 014401] Published Mon Jul 06, 2026

Cells interpret noisy biochemical signals with remarkable precision, raising fundamental questions about the limits of sensing. While receptor-level constraints in chemosensing are well characterized, the role of intracellular signaling remains underexplored. We develop a theoretical framework combi…

[Phys. Rev. E 114, 014402] Published Mon Jul 06, 2026

Protein complexes play crucial roles in cellular functions. The work focuses on the prediction of interchain ternary residue contacts in protein complexes. We first constructed a homotrimeric dataset from the PDB and developed DTC (Deep Ternary Contact predictor), a hybrid deep learning framework fo…

[Phys. Rev. E 114, 014403] Published Mon Jul 06, 2026

Layers composed of lateral connections are ubiquitous in biological systems from subcellular membranes to epithelial sheets. Such layers are often found in nonflat environments, such as the ellipsoidal Drosophila embryo. Here we build on Lou et al. [Phys. Rev. Lett. 130, 108401 (2023)] to provide a …

[Phys. Rev. E 113, 064412] Published Tue Jun 30, 2026

Understanding the mechanisms that shape bacterial community composition has implications in the ecology and evolution of both natural and synthetic microbial communities. Quorum sensing (QS), the regulation of cellular activity through signal exchange as a response to cell density, is a common mecha…

[Phys. Rev. E 113, 064411] Published Mon Jun 29, 2026

Cellular Potts model (CPM) simulations display significant variation in dynamics, structural ordering, and observed phase transitions. Such differences may emerge, at least in part, because CPM simulations are not implemented in a uniform manner, specifically in terms of the definitions of cell peri…

[Phys. Rev. E 113, 064410] Published Mon Jun 22, 2026

Control of transcription presides over a vast array of biological processes, including those mediated by gene regulatory circuits that exhibit multistability. Within these circuits, two- and three-gene network motifs are particularly critical to the repertoire of metabolic and developmental pathways…

[Phys. Rev. E 113, 064408] Published Wed Jun 17, 2026

This study investigates the influence of visual field offset—a restricted field of vision positioned at a fixed angle from an agent's heading direction—on collective behavior using the Vicsek model. This offset shapes an agent's ability to perceive and respond to neighbors, thereby impacting overall…

[Phys. Rev. E 113, 064409] Published Wed Jun 17, 2026

Knotted proteins embed a physical (i.e., open) knot within their native structures. For decades, significant effort has been devoted to elucidating the functional role of knots in proteins, yet no consensus has been reached. Here, using extensive Monte Carlo off-lattice simulations of a simple struc…

[Phys. Rev. E 113, L062402] Published Wed Jun 17, 2026

In any ecosystem, the conditions of the environment and the characteristics of the species that inhabit it are entangled, coevolving in space and time. We introduce a model that couples active agents with a dynamic environment, interpreted as a nutrient source. Agents are persistent random walkers t…

[Phys. Rev. E 113, 064406] Published Mon Jun 15, 2026

Designing a miniature microscale engine that can override the role of thermal fluctuations has remained elusive and is an important open challenge. Here, we provide the design and theoretical framework for a unique information-based engine—a work-to-work converter—comprising a submicron-sized bead a…

[Phys. Rev. E 113, 064407] Published Mon Jun 15, 2026

Biomolecular condensates are cellular phase-separated droplets that usually exhibit a viscoelastic mechanical response, a behavior rationalized by modeling the complex molecules that make up a condensate as stickers and spacers, which assemble into a network-like structure. Condensates usually exhib…

[Phys. Rev. E 113, 064405] Published Tue Jun 09, 2026

We present a $Q$-learning framework for optimizing chemotherapy dosing schedules in a stochastic finite-cell model of tumor evolution under drug-induced selection. The tumor consists of three competing subpopulations: a chemosensitive lineage, $S$, and two single-drug-resistant lineages, $R_1$ and $R_2$, each…

[Phys. Rev. E 113, 064404] Published Fri Jun 05, 2026

The authors tested the response of natural killer cells cocultured with cancer cells and with fibroblasts. They found that natural killer cells targeted the cancer cells, but not fibroblasts. The natural killer cells clustered around cancer cells and promoted apoptosis, whereas they scouted around fibroblasts and did not form large aggregates. Generality of these responses could be established by testing additional normal cell types and tumor lines.

#BiophysicsSpotlight #BroadlyAccessible #Interdisciplinary

[Phys. Rev. E 113, L062401] Published Thu Jun 04, 2026

Detecting Lévy flights of cells has been a challenging problem in experiments. The challenge lies in accessing data in spatiotemporal scales across orders of magnitude, which is necessary for reliably extracting a power-law scaling. Differential dynamic microscopy has been shown to be a powerful met…

[Phys. Rev. E 113, 064403] Published Tue Jun 02, 2026

Due to cell destruction in sequencing, time-series data yield unpaired snapshots, obscuring lineages and gene dynamics in individual cells. Current data-driven methods rely on single-variate expression, ignoring cell types and rotational effects in nonsteady states, limiting interpretability and acc…

[Phys. Rev. E 113, 064401] Published Mon Jun 01, 2026

Allosteric regulation in proteins arises from collective dynamics distributed over networks of residue contacts, but how multiple communication pathways contribute to signal transmission and noise suppression remains unclear. Here we develop a spanning-tree-based framework to quantify allosteric com…

[Phys. Rev. E 113, 064402] Published Mon Jun 01, 2026

Polymer physics models have been employed to elucidate the 3D organization of chromosomes in the cell nucleus. However, how well they capture chromatin architectures at the single-molecule level remains poorly understood. Here, we consider a minimal polymer model where folding is driven by sequence-…

[Phys. Rev. E 113, 054416] Published Thu May 28, 2026

An important goal of computational studies of protein-protein interfaces (PPIs) is to predict the binding site between two monomers that form a heterodimer. The simplest version of this problem is to rigidly redock the bound forms of the monomers, which involves generating computational models of th…

[Phys. Rev. E 113, 054417] Published Thu May 28, 2026

Using a mathematical model, this manuscript investigates the effect of cell-cell communication on bacterial chemotaxis. The authors find that self-secreted chemoattractants can either promote or hinder chemotaxis, depending on parameters. Analytical results identify which parameters are critical to collective migration and offer insights for future experiments.

#BiophysicsSpotlight #Interdisciplinary #ClearMotivation

[Phys. Rev. E 113, 054415] Published Tue May 26, 2026

Turing patterns are a well-studied model of reaction-diffusion equations for developmental patterning. Their applicability has often been limited by the difficulty in identifying candidate molecules that satisfy the requisite criteria for patterning. Here, we build on recent work on geometric models…

[Phys. Rev. E 113, 054413] Published Wed May 20, 2026

The authors investigated interactions in groups of freshwater shrimp confined to a circular space. They introduced a model in which the orientation of each shrimp is mapped with spin aligned or antialigned with the boundary. They identified a distinct progression in network organization with increasing group size. Shrimp were selected as examples of active particles in a nonequilibrium system. The authors expect that collective behavior in other systems could be studied with the framework presented here.

#BiophysicsSpotlight #ClearMotivation #Interdisciplinary

[Phys. Rev. E 113, 054414] Published Wed May 20, 2026

This paper investigates maintenance of biodiversity in a spatial rock-paper-scissors game. The authors use reinforcement learning at the species level, rather than at an individual level, so that mobility in this model operates on “collective wisdom” of the species. Survival of biodiversity depends on the balance between two prominent tendencies: survival-priority (escaping from predators) and predation-priority (remaining near prey).

#ClearMotvation

[Phys. Rev. E 113, 054411] Published Mon May 18, 2026

Vegetation in arid and semi-arid ecosystems often exhibits self-organized spatial patterns as a collective adaptation to water limitation. While reaction-diffusion models have successfully captured such pattern formation, the influence of individual-level traits, particularly root phenotypic plastic…

[Phys. Rev. E 113, 054412] Published Mon May 18, 2026

Filamentous actin, a species of dynamic protein polymers, is one of the main components of the cytoskeleton of eukaryotic cells. We formulate a class of models that predict the possibility of bistable steady states in populations of dynamic actin filaments. They are built upon a basic model of actin…

[Phys. Rev. E 113, 054410] Published Fri May 15, 2026

The experimental use of micropatterned quasi-one-dimensional substrates has emerged as a useful experimental tool to study the nature of cell-cell interactions and gain insight on collective behavior of cell colonies. Inspired by these experiments, we propose an active spin model to investigate the …

[Phys. Rev. E 113, 054408] Published Thu May 14, 2026

At the intersection of population ecology and statistical physics, this study addresses how two factors, demographic stochasticity and migration, govern the emergence of large-scale synchronization in predator-prey metapopulations. The authors demonstrate that the collective phase dynamics of coupled ecological oscillators can be rigorously mapped onto a theoretical framework analogous to the classic $XY$ model of statistical mechanics.

#BiophysicsSpotlight #Interdisciplinary

[Phys. Rev. E 113, 054409] Published Wed May 13, 2026

The Nuclear Pore Complex (NPC) is an ancestral feature of eukaryotic cells, essential for the exchange of material and information between cytoplasm and nucleoplasm. While typical eukaryotic cells harbor thousands of NPCs covering the nuclear surface, a quantitative characterization of their spatial…

[Phys. Rev. E 113, 054407] Published Tue May 12, 2026

The Peyrard-Bishop-Dauxois (PBD) model of DNA denaturation, although successful in the description of melting profiles, fails to predict melting entropies, unzipping forces, and dynamical properties, e.g., hairpin dynamics. The paper presents an atomistic “toy model” of the intra-base-pair motion wh…

[Phys. Rev. E 113, 054405] Published Mon May 11, 2026

Inhibitory interneurons in the cortex are classified into cell types differing in their morphology, electrophysiology, and connectivity. Although it is known that parvalbumin (PV), somatostatin (SST), and vasoactive intestinal polypeptide-expressing neurons (VIP), the major inhibitory neuron subtype…

[Phys. Rev. E 113, 054406] Published Mon May 11, 2026

Microbial adaptation to extreme stress, such as starvation, antimicrobial exposure, or freezing, often reveals fundamental trade-offs between survival and proliferation. Understanding how populations navigate these trade-offs in fluctuating environments remains a central challenge. We develop a quan…

[Phys. Rev. E 113, 054403] Published Fri May 08, 2026

Antimicrobial resistance (AMR) threatens global health. A promising and underexplored strategy to tackle this problem is sequential therapies exploiting collateral sensitivity (CS), whereby resistance to one drug increases sensitivity to another. Here, we develop a four-genotype stochastic birth-dea…

[Phys. Rev. E 113, 054404] Published Fri May 08, 2026

Recent advances in microscopy techniques has uncovered unique aspects of flagella-driven motility in bacteria. A remarkable example is the discovery of flagellar wrapping, a phenomenon whereby a bacterium wraps its flagellum (or flagellar bundle) around its cell body and propels itself like a corksc…

[Phys. Rev. E 113, 054402] Published Wed May 06, 2026

We present a theory for the effects of osmotic pressure exerted by macromolecular crowders on a double-stranded DNA or other semiflexible polymer extended by tension. Our results predict the force and crowder-density dependence of the polymer extension. The lowest-order effect is a crowder-dependent…

[Phys. Rev. E 113, L052401] Published Wed May 06, 2026

Promoter-proximal pausing is a key regulatory checkpoint in RNA polymerase II transcription, yet current models lack a unified description of how arrival-state-dependent pause heterogeneity shapes nascent transcriptional occupancy, completion flux, and steady-state mature mRNA levels. We introduce a…

[Phys. Rev. E 113, 054401] Published Tue May 05, 2026

Simplified stochastic models are widely used in the study of frequency-resolved noise propagation in biochemical reaction networks, a common measure being the coherence between random fluctuations in molecule number trajectories. Such models have also found widespread application in the quantificati…

[Phys. Rev. E 113, 044416] Published Wed Apr 29, 2026

We consider populations evolving according to natural selection, mutation, and recombination and assume that the genomes of all or a representative selection of individuals are known. We pose the problem of whether it is possible to infer fitness parameters and genotype fitness order from such data.…

[Phys. Rev. E 113, 044415] Published Wed Apr 22, 2026

Active matter systems comprise self-propelled particles that move on a substrate while leaving chemical trails that influence other particles through chemotaxis (e.g., slime-depositing bacteria). Orientational chemotaxis manifests as a torque that steers the particle toward the chemical gradient. As…

[Phys. Rev. E 113, 044413] Published Fri Apr 17, 2026

This study introduces a theoretical model explaining how eukaryotic cells can achieve perfect adaptation in chemical gradient sensing through cooperative allosteric regulation of receptor activity.

#AdvancingField #BiophysicsSpotlight

[Phys. Rev. E 113, 044414] Published Fri Apr 17, 2026

By pairing a fly-eye-inspired camera with motion signals, this study shows that characteristic perceptual biases arise from input statistics. From camera data sampled in nature, the authors construct optimal motion estimators, suggesting that biological performance is limited more by environmental statistics than physiology.

#BiophysicsSpotlight #ElegantVisuals #TheoryExperiment

[Phys. Rev. E 113, 044412] Published Tue Apr 14, 2026

Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches and oscillators of various kinds. And, yet, there is more to t…

[Phys. Rev. E 113, 044409] Published Mon Apr 13, 2026

The locomotion of microorganisms near solid-liquid interfaces is of significant scientific interest due to its relevance in various natural and industrial contexts, including biofilm formation and marine biofouling. In this study, we investigate the swimming behavior of $C.\mathit{reinhardtii}$ near a sinusoid…

[Phys. Rev. E 113, 044410] Published Mon Apr 13, 2026

Neurons are notably rich in structure and functioning, so rather diverse in their response to stimuli. Consequently, the proper characterization of their dynamical response to external signals is a crucial step in understanding stimulation mechanisms. In particular, kilohertz (kHz) neuronal electric…

[Phys. Rev. E 113, 044411] Published Mon Apr 13, 2026

Regulation of contraction in striated muscle is controlled by a dual mechanism involving both thin filaments containing actin and thick filaments containing myosin. The thin filament is activated by calcium ions binding to troponin, leading to tropomyosin azimuthal displacement, which allows the act…

[Phys. Rev. E 113, 044408] Published Fri Apr 10, 2026

Nanoscale molecular systems such as DNA require an atomistic quantum treatment to accurately capture their electrical properties, owing to their small dimensions. A central challenge in modeling transport through these systems is the inclusion of phase-breaking scattering. Decoherence-probe methods …

[Phys. Rev. E 113, 044407] Published Wed Apr 08, 2026

In this paper, we explore the features of a genetic network where the transcription factors, namely, activators and repressors bind to the promoter in a competitive way. We have developed an analytical method to find the most probable set of parameter values that are unavailable in experiments. We s…

[Phys. Rev. E 113, 044406] Published Tue Apr 07, 2026

We present a model of a crawler consisting of several suction units distributed along a straight line and connected by springs. The suction units are rudimentary proprioceptors-actuators, which sense binary states of compression versus elongation of the springs and can either adhere or remain idle. …

[Phys. Rev. E 113, 044404] Published Fri Apr 03, 2026

Epiboly, during which a tissue closes around the surface of the egg, pervades animal development. This epithelial gap closure involves cell intercalations at the edge of the gap, but the interplay between these plastic cell rearrangements and the elasticity of the tissue is not understood. Here, ins…

[Phys. Rev. E 113, 044405] Published Fri Apr 03, 2026

We examine how heterogeneous swarms, mixing exploratory and exploitative agents with distinct decision rules, consistently outperform homogeneous ones where each agent balances exploration and exploitation individually, performing experiments in two contrasting deployment scenarios. Using odor field…

[Phys. Rev. E 113, 044401] Published Thu Apr 02, 2026

Membrane structures play a central role in cellular processes, adopting morphologies such as sheetlike cisternae of the endoplasmic reticulum and mitochondrial cristae, tubular extensions of the ER and neurons, and cup-shaped double membranes of autophagosomes. Theoretical descriptions of these fund…

[Phys. Rev. E 113, 044402] Published Thu Apr 02, 2026

This is a study of swarming in three different biological systems, honey bees, midges, and jackdaws. The authors combine three complementary network identification approaches with anisotropy analysis to identify task-dependent interaction neighborhood size. The work provides a framework for uncovering emergence of collective motion in different biological systems.

#BiophysicsSpotlight #ClearMotivation #WellStructured

[Phys. Rev. E 113, 044403] Published Thu Apr 02, 2026

We study the genetic interfaces between two species of an expanding colony that consists of individual microorganisms that reproduce and undergo diffusion, both at the frontier and in the interior. Within the bulk of the colony, the genetic interface is controlled in a simple way via interspecies in…

[Phys. Rev. E 113, 034408] Published Mon Mar 30, 2026

Plants often exhibit regular arrangements of seeds or leaves, known as phyllotaxis, and can famously exhibit Fibonacci spirals, as in sunflower heads or on pine cones. While there are many models which can reproduce a spiral formation, the actual mechanism of arrangement remains unclear. Here, we te…

[Phys. Rev. E 113, 034407] Published Fri Mar 27, 2026

Cells navigating multiple chemoattractant gradients prioritize signals according to how accurately each can be sensed, leading to diverse migration behaviors and spatial patterns in complex environments.

#BiophysicsSpotlight #ClearMotivation

[Phys. Rev. E 113, 034406] Published Mon Mar 23, 2026

Groups of cells, including clusters of cancerous cells, multicellular organisms, and developing organs, may both grow and break apart. What physical factors control these fractures? In these processes, what sets the eventual size of clusters? We first develop a one-dimensional framework for understa…

[Phys. Rev. E 113, 034405] Published Wed Mar 18, 2026

The inner membrane of mitochondria presents folds, the cristae, which are the production place of ATP. This synthesis is catalized by transmembrane proteins and relies on a flow of protons confined to the surface of the membrane. We posit that, in turn, the proton flux shapes the crista membrane in …

[Phys. Rev. E 113, 034404] Published Tue Mar 10, 2026

Bulges in the plasma membrane of cells known as blebs can form spontaneously in a wide range of biological processes, but what controls their shape and stability remains incompletely understood. To address this we introduce a dual phase-field model with coupled order parameters representing the cell…

[Phys. Rev. E 113, 034403] Published Mon Mar 09, 2026

Reaction-diffusion equations describe various spatially extended processes that unfold as traveling fronts moving at constant velocity. We introduce and solve analytically a model that, besides such fronts, supports solutions advancing as the square root of time. These sublinear fronts preserve an i…

[Phys. Rev. E 113, L032401] Published Thu Mar 05, 2026

In typical models of collective motion, each individual takes the average direction of multiple neighbors, resulting in the ordered movement of large flocks. Alternatively, interactions with only one random neighbor at a time can also lead to order, referred to as noise-induced order, but only in sm…

[Phys. Rev. E 113, 034402] Published Tue Mar 03, 2026

Experimental evidence indicates that intracellular chloride concentration regulates the excitation–inhibition (EI) balance, yet the mechanisms by which activity-dependent chloride dynamics drive seizure evolution and stage transitions remain unclear. We present a conductance-based neuronal network i…

[Phys. Rev. E 113, 034401] Published Mon Mar 02, 2026

In RNA world scenarios, pools of RNA oligomers form strongly interacting, dynamic systems, which enable molecular evolution. In such pools, RNA oligomers hybridize and dehybridize, ligate, and break, ultimately generating longer RNA molecules, which may fold into catalytically active ribozymes. A ke…

[Phys. Rev. E 113, 024407] Published Fri Feb 27, 2026

Learning to detect, identify, or select stimuli is an essential requirement of many behavioral tasks. In real-life situations, relevant and nonrelevant stimuli are often embedded in a continuous sensory stream, presumably represented by different segments of neural activity. Here we introduce a spik…

[Phys. Rev. E 113, 024406] Published Wed Feb 25, 2026

The collective behavior of numerous animal species, including insects, exhibits scale-free behavior indicative of the critical (second-order) phase transition. Previous research uncovered such phenomena in the behavior of honeybees, most notably the long-range correlations in space and time. Further…

[Phys. Rev. E 113, 024405] Published Fri Feb 20, 2026

Given an evolutionary model, such as Wright-Fisher or Moran, the $n\text{−}\mathrm{coalescent}$ problem consists of going backward in time to find, for example, the time to the most recent common ancestor (MRCA) and the topology of the tree. In the literature, this problem is mainly addressed by directly computing th…

[Phys. Rev. E 113, 024404] Published Thu Feb 19, 2026

The growth of biological tissue is sensitive to the physical properties of the environment. For example, the growth rate of contractile tissue under geometric confinement is proportional to local curvature as a result of tissue surface tension. It is not known how local cell behavior is coordinated …

[Phys. Rev. E 113, 024403] Published Thu Feb 12, 2026

Chromosomal translocations, arising from unresolved double-stranded DNA breaks (DSBs), play a central role in genome instability and evolution. A prevailing hypothesis suggests that the probability of translocation between two chromatin segments depends on both their spatial proximity and the likeli…

[Phys. Rev. E 113, 024402] Published Mon Feb 09, 2026

Nearly a decade ago, it was discovered that the spherical cell body of the alga Chlamydomonas reinhardtii can act as a lens to concentrate incoming light onto the cell's membrane-bound photoreceptor and thereby affect phototaxis. Since many nearly transparent cells in marine environments have comple…

[Phys. Rev. E 113, 024401] Published Wed Feb 04, 2026

Many bacteria share the fascinating ability to sense Earth's magnetic field—a process known as magnetotaxis. These bacteria synthesize magnetic nanoparticles, called magnetosomes, within their own cell body and arrange them to form a linear magnetic chain. The chain, which behaves like a compass nee…

[Phys. Rev. E 113, 014408] Published Fri Jan 30, 2026

The segmentation clock is an emergent embryonic oscillator that controls the periodic formation of vertebrae precursors (or somites). It relies on the self-organization at the presomitic mesoderm (PSM) level of multiple coupled cellular oscillators. Dissociation-reaggregation experiments have furthe…

[Phys. Rev. E 113, 014405] Published Tue Jan 27, 2026

Neural processing in animals facilitates sensory adaptation by eliciting appropriate responses to changing environmental stimuli. Although sensory adaptation is well recognized, the specific role of individual neurons in these adaptive mechanisms remains poorly understood from a theoretical standpoi…

[Phys. Rev. E 113, 014406] Published Tue Jan 27, 2026

Several external factors are known to influence active cell movement, but little is known about the impact of the porous structure of the extracellular matrix. This work combines computational modeling and theory to show how such porous environments determine cell migration dynamics, and how spatial heterogeneities effectively guide cell movement towards regions of low porosity.

#BiophysicsSpotlight #AdvancingField #Interdisciplinary

[Phys. Rev. E 113, 014407] Published Tue Jan 27, 2026

Assembling reacting molecules (“targets”) into clusters slows down the kinetics of their reactions with mobile particles from a solution due to competition between the targets. Recently, we used a simple probabilistic approach to predict the dependence of this slowing down on the structures of clust…

[Phys. Rev. E 113, 014404] Published Mon Jan 26, 2026

Dense, microbial communities are shaped by local interactions between cells. Both the nature of interactions, spanning antagonistic to cooperative, and the strength of interactions vary between and across microbial species and strains. These local interactions can influence the emergence and mainten…

[Phys. Rev. E 113, 014402] Published Thu Jan 22, 2026

Applied electric fields precisely steer protein crystallization pathways, inducing distinct multiarm morphologies such as flowerlike and triconic structures. This field-driven control over angular ordering and phase behavior offers new insights into engineering complex protein architectures.

#BiophysicsSpotlight #TheoryExperiment

[Phys. Rev. E 113, 014403] Published Thu Jan 22, 2026

The use of statistical physics models to investigate real-world networks and reveal their underlying dynamics has shown promising results and acquired increasing attention. Here, we show how exponential random-graph (ERG) models can be suitably adopted to characterize how Alzheimer's disease (AD) af…

[Phys. Rev. E 113, 014401] Published Tue Jan 20, 2026

Radiation therapy is one of the most common cancer treatments, and dose optimization and targeting of radiation are crucial since both cancerous and healthy cells are affected. Different mathematical and computational approaches have been developed for this task. The most common mathematical approac…

[Phys. Rev. E 112, 064413] Published Tue Dec 23, 2025

The brain's synaptic network, characterized by parallel connections and feedback loops, drives interaction pathways between neurons through a large system with infinitely many degrees of freedom. This system is best modeled by the graph C*-algebra of the underlying directed graph, the Toeplitz-Cuntz…

[Phys. Rev. E 112, 064412] Published Thu Dec 18, 2025

Protein nanoclustering is a characteristic feature of their activated state and is essential for forming numerous subcellular structures. The formation of these nanoclusters is highly dependent on a series of posttranslational modifications, such as mono- and multiphosphorylation and dephosphorylati…

[Phys. Rev. E 112, 064411] Published Wed Dec 10, 2025

Metastasis of cancer cells is closely associated with their ability to undergo mechanical softening under shear stress. A statistical-thermodynamic model has been developed to demonstrate the crucial role of entropic effects in this process. The model establishes a quantitative relationship between …

[Phys. Rev. E 112, L062402] Published Wed Dec 10, 2025

The aggregation of amyloid-$\beta 42$ ($\mathrm{A}\beta 42$) peptide, a key pathological event in Alzheimer's disease, is strongly influenced by its solvent environment. While cosolvents are often used in experimental studies, their specific role in modulating the conformational stability and aggregation propensity of $\mathrm{A}\beta \mathrm{4\dots }$

[Phys. Rev. E 112, 064409] Published Tue Dec 09, 2025

Biomolecular condensates are essential for cellular organization and result from phase separation in systems far from thermodynamic equilibrium. Among various models, chemically active droplets play a significant role, and consist of proteins that switch between attractive and repulsive states via n…

[Phys. Rev. E 112, 064410] Published Tue Dec 09, 2025

Feedback in cellular processes is typically inferred through cellular responses to experimental perturbations. Modular response analysis provides a theoretical framework for translating specific perturbations into feedback sensitivities between cellular modules. However, in large-scale drug perturba…

[Phys. Rev. E 112, 064404] Published Mon Dec 08, 2025

1-alkanols are well known to have anesthetic and penetration properties, though the mode of operation remains enigmatic. We perform extensive atomistic molecular dynamics simulation to study the penetration of 1-alkanols of different chain lengths in the dioleoyl-phosphatidylcholine (DOPC) bilayer m…

[Phys. Rev. E 112, 064405] Published Mon Dec 08, 2025

The vertex model with homogeneous cell properties is known to exhibit a parameter degeneracy in which the system's dynamics is independent of the target area. Here, we show, for the heterogeneous vertex model where cells differ in size and stiffness, that degeneracy is also present with the average …

[Phys. Rev. E 112, 064406] Published Mon Dec 08, 2025

The sorting of cell mixtures is fundamental to biological processes such as embryonic development, wound healing, and cancer metastasis. Previous studies have overlooked the unique nonmotile activities of cells, such as self-pulsating. In a 2D bidisperse confluent biological tissue lacking heterogen…

[Phys. Rev. E 112, 064407] Published Mon Dec 08, 2025

Bacteria benefit from cellular heterogeneity: cells differentiate into diverse gene expression states. As colonies grow, cellular phenotypes arrange into spatial patterns. To uncover the functional role of these emergent patterns, we must understand how they arise from cellular growth and mechanical…

[Phys. Rev. E 112, 064408] Published Mon Dec 08, 2025

In eukaryotic cells, the nucleolus is a pivotal subnuclear organelle, instrumental in ribosomal RNA synthesis and nuclear organization. Although the unique viscoelastic properties of the nucleolus are associated with transient interactions between chromatin and regulatory proteins, the specific mech…

[Phys. Rev. E 112, 064403] Published Fri Dec 05, 2025

Self-organized Turing patterns, arising from the dynamic interplay of reaction and diffusion processes, are instrumental in modeling natural morphogenesis and deciphering the biological functions of diverse structures. These patterns exhibit complex spatial arrangements that can be analyzed through …

[Phys. Rev. E 112, L062401] Published Tue Dec 02, 2025

The “criticality hypothesis,” based on observed scale-free correlations in neural activity, posits that the brain operates at a critical point of transition between two phases. However, the validity of this hypothesis is still debated. Here, employing a commonly used model of cortical dynamics, we f…

[Phys. Rev. E 112, 064401] Published Mon Dec 01, 2025

The active transfer of phospholipids between membrane leaflets (flip-flop), mediated by (adenosine triphosphate) ATP-dependent enzymes such as flippases and floppases, is a key regulator of membrane asymmetry and curvature. However, the theoretical understanding of curvature generation driven by fli…

[Phys. Rev. E 112, 064402] Published Mon Dec 01, 2025

This study explores the application of elongated particle interaction models, traditionally used in liquid crystal phase research, in the context of early bacterial biofilm development. Through computer simulations using an agent-based model, we have investigated the possibilities and limitations of…

[Phys. Rev. E 112, 054411] Published Mon Nov 24, 2025

Effective clearance of amyloid-$\beta$ ($\mathrm{A}\beta$) from the brain is essential for preventing neurodegenerative diseases such as Alzheimer's. A significant portion of this clearance occurs through the blood-brain barrier (BBB) via receptor-mediated transport. However, current models fail to capture the complex k…

[Phys. Rev. E 112, 054410] Published Fri Nov 21, 2025

When taking place under fluctuating environments, some classical results of evolutionary dynamics in fitness landscapes need to be reconsidered. Under such nonequilibrium conditions, the properties of adaptive evolution might escape from the expectations grounded in equilibrium systems. Here, an imp…

[Phys. Rev. E 112, 054409] Published Mon Nov 17, 2025

The linear stability of a lipid membrane under a dc electric field, applied perpendicularly to the interface, is investigated in the electrokinetic framework, taking into account the dynamics of the Debye layers formed near the membrane. The perturbed charge in the Debye layers redistributes and gen…

[Phys. Rev. E 112, 054408] Published Thu Nov 13, 2025

Autochemotaxis, the directed movement of cells along gradients in chemicals they secrete, is central to the formation of complex spatiotemporal patterns in biological systems. Since the introduction of the Keller-Segel model, numerous variants have been analyzed, revealing phenomena such as coarseni…

[Phys. Rev. E 112, 054406] Published Mon Nov 10, 2025

Individual bacterial cells grow and divide stochastically. Yet they maintain their characteristic sizes across generations within a tightly controlled range. What rules ensure intergenerational stochastic homeostasis of individual cell sizes? Valuable clues have emerged from high-precision long-term…

[Phys. Rev. E 112, 054407] Published Mon Nov 10, 2025