arXiv subjects

Margaret E. Johnson

Publications and source records attributed to Margaret E. Johnson.

4 recordsLinked to original sources

arXiv2026

Hybrid Dynamical Simulation Reveals Apparent Stiffening of Flexible Protein Lattices Driving Membrane Bending

Membrane-deforming protein lattices play a central role in essential and pathogenic remodeling processes, including clathrin-mediated endocytosis and viral budding. Simulating these systems at biologically relevant length and time scales requires mesoscale approaches that preserve structural detail while avoiding the computational cost of atomistic resolution. Here, we present a hybrid simulation framework that couples a particle-based flexible protein lattice to a continuum membrane model, enabling systematic investigation of how lattice geometry and rigidity influence dynamic membrane remodeling. We validate the coupled model by comparing simulation results with theoretical predictions for membranes under increasing tension. Using buckling-based deformations of pre-assembled clathrin lattices, we quantify the lattice flexural rigidity and establish a direct relationship between the force constants in the coarse-grained energy and the emergent mechanical properties of the lattice. We then compare this flexural rigidity to an effective rigidity commonly used in continuum descriptions of sphere-forming protein assemblies. Although the flexural rigidity is set solely by the energy function, the effective rigidity depends on lattice size and connectivity, with the two measures converging only for weakly connected lattices. As a result, the effective rigidity relevant for spherical bud formation increases as the lattice grows. This size-dependent stiffening highlights the importance of structural details in interpreting lattice mechanics and cautions against assuming a single constant stiffness throughout assembly. We demonstrate the generality of the method by applying it to pre-assembled viral lattices generated with NERDSS. This work provides a validated framework for simulating how deformable, stable protein assemblies of diverse geometry couple to membrane dynamics and remodeling.

cond-mat.soft↗

arXiv2026

Membrane-Associated Self-Assembly for Cellular Decision Making

Cellular decision-making based on information received from the external environment is frequently initiated by transmembrane receptors. These receptors are known to propagate such information by triggering a series of irreversible, energy-consuming reactions. While this active mechanism ensures switch-like responses, here we show how spontaneous self-assembly of native 3D subunits on a two-dimensional substrate can similarly act as a tunable and robust switch for detecting receptors at physiological concentrations. This mechanism is much more sensitive than other passive mechanisms for receptor detection. We derive analytical expressions for the critical receptor density driving stable subunit assembly, in close agreement with stochastic reaction-diffusion simulations. The theory provides testable predictions for how lipids, subunits, and receptors each can control decision boundaries and magnitude of response.

physics.bio-ph↗

arXiv2025

A simulation that recapitulates the dynamics of PER-directed colloidal assembly

The self-assembly of DNA-coated colloids controlled by enzymatic reactions has the potential to enable the formation of materials with hierarchical organization and switchable configurations. However, the problem of designing such self-assembly is complex, and an effective simulation is necessary to assist in searching for appropriate design protocols. Typical computational methodologies such as molecular dynamics and Brownian dynamics have limited ability to access the long time scales required for these hierarchical self-assembly processes. Here we adopt a particle-based reaction-diffusion algorithm to model the spatial-temporal evolution of hundreds to thousands of micron-scale DNA-coated colloid self-assembly process over hours. In order to demonstrate the capability of this digital twin, we compared its predicted core-shell assembly process to results from experiments. The model can qualitatively reproduce the core-shell structures observed in experiment by recapitulating the emergence of compositional heterogeneity when delays between distinct assembly times are introduced. These results support the idea that this approach can successfully capture dynamics over long time scales and the appropriate scale of structure formation. We then use the model to explore different protocols for structure evolution, suggesting how this tool can aid in the design of complex self-organization processes.

math.DS↗

arXiv2007

Representability problems for coarse-grained water potentials

The use of an effective intermolecular potential often involves a compromise between more accurate, complex functional forms and more tractable simple representations. To study this choice in detail, we systematically derive coarse-grained isotropic pair potentials that accurately reproduce the oxygen-oxygen radial distribution function of the TIP4P-Ew water model at state points over density ranges from 0.88-1.30g/cc and temperature ranges from 235K-310K. Although by construction these effective potentials correctly represent the isothermal compressibility of TIP4P-Ew water, they do not accurately resolve other thermodynamic properties such as the virial pressure, the internal energy or thermodynamic anomalies. Because at a given state point the pair potential that reproduces the pair structure is unique, we have therefore explicitly demonstrated that it is impossible to simultaneously represent the pair-structure and several key equilibrium thermodynamic properties of water with state-point dependent radially symmetric pair potentials. We argue that such representability problems are related to, but different from, more widely acknowledged transferability problems, and discuss in detail the implications this has for the modeling of water and other liquids by coarse-grained potentials. Nevertheless, regardless of thermodynamic inconsistencies, the state-point dependent effective potentials for water do generate structural and dynamical anomalies.

cond-mat.stat-mech↗