Subcellular Processes
Assembly and control of subcellular structures (channels, organelles, cytoskeletons, capsules, etc.); molecular motors, transport, subcellular localization; mitosis and meiosis
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Thermal fluctuations from discrete ions set a hard bound on 10 microsecond gating timescales close to observed performance.
· “Thermal fluctuations set fundamental limits on ion channel function”
Theory: the compact-cell approximation emerges at late times, not from the start, on a microsecond scale.
· “Voltage dynamics of spherical membranes from single ion channel currents”
Slopes of reactive-equilibrium curves replace unknown reaction rates in stability analysis of cell polarity networks.
· “Classification of Intracellular Protein Patterns from Reactive Equilibria”
A new smooth-muscle model shows ERα modulation only retunes Ca2+ handling; bifurcation structure stays the same across 7–700 pg/mL…
· “The role of estrogen receptor alpha on calcium transport during smooth muscle contractions”
The same one-or-two paused particles set the maximum for lattice lengths 50 to 500.
· “Low-frequency output fluctuations in an open exclusion process with particle pausing”
Viscoelastic time-scale matching predicts adhesion size, stability, and Piezo1 calcium signaling.
· “Active wetting/de-wetting of focal adhesions on viscoelastic substrates”
Slightly stronger retrograde persistence equalizes travel times; anterograde bias makes them grow linearly with distance.
· “A persistent random-walk model of molecular transport in neuronal dendritic trees”
If the spread of initial-stage dwell times exceeds the transient-stage mean, a system splits into two modes—no bistability needed.
Kinetic phase diagram from the Onsager principle explains how crowding gets viruses to the membrane and why HIV-1 sits at the sweet spot.
Locus-specific editors are now required for both safer therapy and high-resolution research
· “Targeting DNA Methylation: New Paradigms and the Advent of Gene-Selective Tools”
Simulations reveal how emergent properties create two gates that decide flat, stalled or closed fates and match experiments without fitting.
Review links loss of precise membrane proximity to sarcopenia and weighs ways to keep the contacts intact.
Analytical separatrices reveal a region where omitting division yields wrong stable-state predictions.
· “Cell Division Changes Fate Decisions in a Genetic Toggle Switch”
A yeast genome model shows that uneven replication speeds explain both average timing spreads and rare long events under stress.
· “DNA Replication under Thermal, Chemical, and Genotoxic Stress”
Agent-based simulations of Gram-negative outer membrane growth suggest bursty protein incorporation and complex collaboration.
· “An agent-based model of outer membrane biogenesis in Gram-negative bacteria”
Random parallel filament arrays create effective traps for active particles that switch between diffusion and directed motion, strongest at
· “Localization of Active Particles on Random Arrays of Parallel Filaments”
The quasi-steady state assumption ignores these effects and gets transition durations and onset points wrong in models of cells, metabolism,
Progressive cross-linking restricts basal body motion from diffusive to confined, enabling even spacing needed for aligned motile cilia and
· “Actin cross-linking organizes basal body patterning through anomalous diffusion transitions”
Identical average release rates can yield sharply different first-passage times to threshold
· “Activation in Vesicle-Mediated Signaling Shaped by Batch Arrival Statistics”
Bacterial chemotaxis has long been viewed as operating near the physical limits of sensing, as originally articulated by Berg and Purcell. Recent information-theoretic analyses challenge this view, suggesting that Escherichia coli uses only a small fraction of the information available in ligand arrival statistics to bias its motion. How should such low information efficiency be interpreted at the level of behavior? Here, I argue that chemotactic performance is shaped not only by information transmission and noise, but by the strategy of movement itself. Using simple scaling arguments and minimal models, I show how run-and-tumble chemotaxis can remain robust to noise through symmetry and temporal averaging, even when internal information processing is inefficient. Comparing bacterial and eukaryotic chemotaxis highlights how different sensing strategies convert physical limits into observable behavior. These considerations suggest that low information efficiency need not imply poor performance, but may instead reflect an evolved balance between robustness, simplicity, and function.
Statistical tomography shows alternative spatial strategies likely key to transduction success.
One reaction-transport equation for electron-holding potential explains spikes, speed, and heat
Murburn electron-holding potential yields voltage waveforms and conduction velocity from first principles
Fusion-fission cycles breaking detailed balance produce stable, cycling and progressing cisternae with embedded size control.
· “Building and maintaining a System of Intracellular Compartments”
Hydrodynamic model maps how compressibility, friction and turnover produce stresses that amplify small surface corrugations.
· “Mechanical stress induced by the polymerisation of an active gel near a surface”
A simple model links equal abundances of ATP, GTP and related currencies to better independent regulation at higher thermodynamic cost.
· “Thermodynamic cost-controllability tradeoff in metabolic currency coupling”
A general mapping shows when single-cell capture noise can be absorbed into effective kinetic rates — and when it cannot.
Negative feedback from shared pool competition leads to steady states or selection without extra regulators.
Necessary and sufficient conditions bracket the exact boundary, explaining discontinuous, nonmonotonic onset.
· “Theoretical Analysis of Resource-Induced Phase Transitions in Estimation Strategies”
Surviving HEI10 droplets on the synaptonemal complex explain crossover counts, interference, assurance, and mutant data.
Attractant, repellent, growth, and reaction terms all recoverable from boundary and final-time data.
A model shows Dictyostelium can read very dilute cAMP without losing sensing precision.
· “Limitations to Chemotactic Concentration Sensing during Ca²⁺ Signaling”
Nanoscale layers hold all free charge, so the long-time response maps to a cable-theory circuit.
A six-state receptor model with a pre-activated state reproduces Ca2+ oscillations and sets sharp start and stop thresholds.
· “A Novel Nonlinear IP₃R State Transition Model and Calcium Oscillation”
A ribosome-traffic model reproduces chloramphenicol's short-vs-long expression gap and points to initiation rate as a shield.
A drug-gated sodium channel makes adrenal cells secrete aldosterone while slowing their growth
Spatial-network simulations reproduce 20 ms sparks and split CSQ's roles into buffering and receptor regulation.
· “Formation and Regulation of Calcium Sparks on a Nonlinear Spatial Network of Ryanodine Receptors”
A chromosome-localized poleward slide driven by kinesin KLP-18 overturns the earlier no-flux result.
Picosecond dehydration-translocation-hydration spikes may add up to the large signals fluorescent probes see.
Self-consistent equations keep fluctuation-dissipation balance and reproduce heat-driven escape and gradient sensing.
Incoming and outgoing light obey a duality law, so cell shape redistributes light without changing a cell's average gain.
A stochastic model of Drosophila dendrites shows local nucleation feedback alone can lock in either orientation.
A review of immunotherapy, gene editing, and cell therapy for CADASIL maps several paths against this inherited stroke disorder.
Fragmented networks mix by encounters; fused ones by diffusion—half-filling times differ sevenfold across cells.
· “Diffusive Spreading Across Dynamic Mitochondrial Network Architectures”
A length-resistance energy explains the angle and the bands; it also predicts new patterns.
· “Active Matter under Cyclic Stretch: Modeling Microtubule Alignment and Bundling”
Eight clusters and two axes emerge from LLM scoring of 68 definitions—there is no one right answer.
· “What Lives? A meta-analysis of diverse opinions on the definition of life”
ODE models combine ion-channel block data to flag dangerous drugs early; the FDA now uses the result.
· “Using mathematical models of heart cells to assess the safety of new pharmaceutical drugs”
Sequence, image, and hybrid methods compared; fusion is promising but not yet built.
· “A Comprehensive Review on RNA Subcellular Localization Prediction”
Hydrodynamic model links mechanical forces and transcription fluctuations to chromatin organization under nuclear confinement.
· “Active Hydrodynamic Theory of Euchromatin and Heterochromatin”
A torque tug-of-war replaces conformational spread and buys faster, equally sharp switching at the cost of dissipation.
Voltage dependence of Piezo1 may explain why mechanical pacing succeeds, then stops, at high rates.
Review argues motor-driven diffusion, spatial stiffness variation, and viscoelasticity shape organelle placement and reaction rates.
· “Active Intracellular Mechanics: A Key to Cellular Function and Organization”
A new review maps life-science problems in three tiers and tells which AI fixes are ready now.
· “Applications and Challenges of AI and Microscopy in Life Science Research: A Review”
One fluorescence channel plus AEMS-Net replaces two-channel sequential acquisition, halving staining and light exposure for live cells.
Narrow windows and curvature set local voltage via solutions of electro-diffusion equations.
· “Voltage laws in nanodomains revealed by asymptotics and simulations of electro-diffusion equations”
Trees, networks and static landscapes miss randomness and time-dependence; one framework covers all current model forms.
· “Towards a mathematical framework for modelling cell fate dynamics”
A dynamic model of the endomembrane system fits classic transferrin kinetics and reveals hidden heterogeneity.
· “Re-visiting the intracellular pathway of transferrin on board of a mathematical simulation”
Water's hydrogen-bond web feeds molecules order until a hidden entropy reservoir reverses the flow, delaying equilibrium.
Sarcomere length randomness sets a binding-energy ceiling, explaining why nonmuscle cells remodel more easily.
· “Adaptive flexibility of cells through nonequilibrium entropy production”
Model shows this position emerges from the transport cycle itself and increases nuclear content of Ran.
· “Spatio-Temporal Dynamics of Nucleo-Cytoplasmic Transport”
Delay distributions and protection metrics depend on elongation, pausing, and binding parameters.
· “Stochastic dynamics and ribosome-RNAP interactions in Transcription-Translation Coupling”
As mRNA length grows, the average output is set by the slowest possible rate, not by noise.
· “Variability in mRNA Translation: A Random Matrix Theory Approach”
A spherical-cell model shows that the binding-to-diffusion ratio decides whether actin stays central or reaches the cortex.
· “Microtubule-based actin transport and localization in a spherical cell”
A mutation can flip from beneficial to harmful only if fitness tracks ribosome travel time, not protein output.
A synthesis of brain energetics, mitochondria, and TBI proposes a testable rule for how injury cascades unfold.
· “Brain Energetics, Mitochondria, and Traumatic Brain Injury”
Active transport on an unordered microtubule mesh redistributes bicoid mRNA in minutes, the simulation shows.
Coarse-grained Markov models explain in vitro data and put universal bounds on the energy cost of precision.
In growth-limited cells, severed filaments multiply only above a rescue-after-severing threshold that theory can predict.
· “Critical threshold for microtubule amplification through templated severing”
A closed-form spectral-efficiency formula shows receptor structure determines which frequencies get through.
· “Linear Noise Approximation of Intensity-Driven Signal Transduction Channels”
A deformable-cell model shows size changes can erase polarity and set a single GTPase oscillating.
· “Cell size, mechanical tension, and GTPase signaling in the Single Cell”
Mixed catch-slip bonds make free-integrin mobility a non-invasive readout of load, the paper argues.
· “Evolving roles and dynamics for catch and slip bonds during adhesion cluster maturation”
A measurable randomness pattern could end the debate over whether kinesin waits with one or two heads attached.
· “How kinesin waits for ATP affects the nucleotide and load dependence of the stepping kinetics”
Simulations show how self-deposited mark trails let repair proteins dive into collapsed chromatin and reach lesions fast.
· “A nonequilibrium strategy for fast target search on the genome”
Two nucleosome populations with correlated motion form domains whose sizes sit near loop domains and TADs.
· “Organization of fast and slow chromatin revealed by single-nucleosome dynamics”
The result ties a measurable recruitment rate to spatial clustering on the cell surface.
· “Stability Analysis of a Bulk-Surface Reaction Model for Membrane-Protein Clustering”
A wandering ligand concentration sets a weaker error bound than the static limit; a simple circuit reaches it.
· “Physical limit to concentration sensing in a changing environment”
A two-protein model shows a mid-strength bond can beat both strong and weak sticking.
· “Target search on DNA by interacting molecules: First-passage approach”
In an otherwise symmetric simulation, only a big length gap breaks symmetry and feeds the longer neurite.
· “On the Role of Vesicle Transport in Neurite Growth: Modelling and Experiments”
It extracts oligomer states from fluorescence data even when proteins are distributed unevenly across the cell surface.
· “Molecular Brightness analysis of GPCR oligomerization in the presence of spatial heterogeneity”
Model shows residence time peaks at specific lengths, allowing tunable sequestration controlled by network geometry.
· “Cytoskeletal filament length controlled dynamic sequestering of intracellular cargo”
