Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2112.08651

Dynamic Density Functional Theory of Multicomponent Cellular Membranes

Liam G. Stanton·Tomas Oppelstrup·Timothy S. Carpenter·Helgi I. Ingólfsson·Michael P. Surh·Felice C. Lightstone·James N. Glosli
View original source ↗Read source document ↗Export metadata ↓

Abstract

We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be extended to include features such as the presence of proteins and membrane deformations. This framework represents a paradigm shift by enabling simulations that can access length scales on the order of microns and time scales on the order of seconds, all while maintaining near fidelity to the underlying MD models. These length and time scales are significant for accessing biological processes associated with signaling pathways within cells. Membrane interactions with RAS, a protein implicated in roughly 30% of human cancers, are considered as an application. Simulation results are presented and verified with MD simulations, and implications of this new capability are discussed.

Explore related subjects

physics.bio-phcond-mat.stat-mech

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Liam G. Stanton, Tomas Oppelstrup, Timothy S. Carpenter, Helgi I. Ingólfsson, Michael P. Surh, Felice C. Lightstone, James N. Glosli. 2023-03-13. Dynamic Density Functional Theory of Multicomponent Cellular Membranes. https://doi.org/10.1103/physrevresearch.5.013080

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Navigation driven by bidirectional information transmission between sensing and actuation

A wide variety of biological functions are driven by feedback between sensing and actuation. A paradigmatic example is cellular navigation. During navigation, the sensory system maps the environmental input signal onto a sensory output, which then drives an actuation response, thereby changing the future sensory input. How the accuracy of this bidirectional information transmission controls navigation is not currently understood. Here, we study how information controls navigation by analytically solving two generic models that describe two major classes of biological navigators: spatial- and temporal-sensing cells. We find that, in the linear-response regime of shallow gradients, navigation performance is fully determined by bidirectional information transmission alone, as quantified by feedforward and feedback transfer entropies. Elementary system parameters affect navigation performance only through their effect on these information flows. We call these relations Behavioral Equations of State (BESTs): equalities that map information to function in a system-independent way. BESTs predict an experimentally testable data collapse for the performance of navigators with different sensing and actuation parameters. We test the validity of our theory by performing stochastic simulations of chemotaxis of the bacterium Escherichia coli, computing the relevant transfer entropies exactly with the TE-PWS algorithm. The observed performance obeys the BEST without any fitting or scaling parameters. Thus, our theory identifies bidirectional information transmission between sensing and actuation as an organizing principle for navigation.

physics.bio-ph↗
arXiv2026

Multiflagellarity facilitates bacterial upstream motility

Upstream swimming drives bacterial spreading and surface colonization. Many pathogens encounter fluid flows as they infect the intestines, lungs, and urinary tract, so how bacteria use their flagella to counter these flows matters for disease and treatment. Yet how morphology and flagellar arrangement govern motility against flow remains unknown. Here, we investigate the biophysical determinants of rheotaxis by combining microfluidics, directed evolution, genetics, holography, and hydrodynamics simulations. Using upstream swimming competitions, we find that peritrichous E. coli and S. enterica rapidly outcompete monotrichous P. aeruginosa and V. cholerae, accumulating upstream at densities up to five orders of magnitude higher, even though Vibrio swims three times as fast. Motility selection experiments show that rheotaxis increases with flagellar number and length, confirmed by overexpressing the master regulator flhD/C. Three-dimensional holography and single-cell tracking reveal that multiflagellarity stabilizes surface residence and promotes the weathervane effect that reorients cells upstream, a mechanism further supported by simulations that fully resolve flagellar arrangement and fluid-structure interactions. These results establish multiflagellarity as a key facilitator of upstream navigation, governed by near-wall residence and shear-driven reorientation rather than by swimming speed.

physics.bio-ph↗
arXiv2026

Multiscale retinal flow on a spherical cap of varying aperture

Modelling retinal haemodynamics is crucial for understanding retinal microcirculation but is computationally demanding because it involves coupling between the vasculature and surrounding tissue across multiple scales. This computational burden has been substantially alleviated by a recent analytic solution on the planar disc that enables lumping the capillary bed and surrounding tissue into an effective resistor. However, that formulation treats the retina as a flat surface, whereas the retina is a curved surface with a finite anterior aperture. In this work, we develop a nontrivial and physiologically necessary extension to spherical-cap tissue domains with varying apertures, where surface curvature and finite-aperture boundaries complicate solving coupled Darcy equations on a curved manifold. Using a stereographic projection and a decoupling transformation, we derive an analytic solution for the capillary-tissue system on the spherical cap that represents flow in both the capillary bed and interstitial tissue more realistically while retaining the efficient resistor formulation, a key advantage of the planar-disc formulation. This solution is coupled to one-dimensional (1D) arteriolar and venular flows to obtain a multiscale description of retinal haemodynamics. Using a vasculature model designed to capture retinal vascular features, we show that the multiscale model's predictions are consistent with experimental data. We further explore aperture effects using both a fixed hemispherical vasculature and aperture-dependent vasculature. The aperture affects retinal haemodynamics mainly through changes in the constructed vasculature itself, whereas the surface-averaged pressures and relative terminal flow distributions remain nearly unchanged. This framework provides a foundation for studying retinal pathophysiology on more anatomically realistic domains.

physics.bio-ph↗