Finite-size effects and optimal system sizes in simulations of surfactant micelle self-assembly

Jonathan J. Harris; George A. Pantelopulos; John E. Straub

Home/Archive/arXiv

arXiv · 2012.00315

Finite-size effects and optimal system sizes in simulations of surfactant micelle self-assembly

Jonathan J. Harris·George A. Pantelopulos·John E. Straub

View original source ↗Read source document ↗Export metadata ↓

Abstract

The spontaneous formation of micelles in aqueous solutions is governed by the amphipathic nature of surfactants and is practically interesting due to the regular use of micelles as membrane mimics, for the characterization of protein structure, and for drug design and delivery. We performed a systematic characterization of the finite-size effect observed in single-component dodecylphosphocholine (DPC) micelles with the coarse-grained MARTINI model. Of multiple coarse-grained solvent models investigated using large system sizes, the non-polarizable solvent model was found to most-accurately reproduce SANS spectra of 100 mM DPC in aqueous solution. We systematically investigated the finite-size effect at constant 100 mM concentration in 23 systems of sizes 40 to 150 DPC, confirming the finite-size effect to manifest as an oscillation in the mean micelle aggregation number about the thermodynamic aggregation number as the system size increases, mostly diminishing once the system supports formation of three micelles. The accuracy of employing a multiscale simulation approach to avoid finite-size effects in the micelle size distribution and SANS spectra using MARTINI and CHARMM36 was explored using multiple long timescale 500-DPC coarse-grained simulations which were back-mapped to CHARMM36 all-atom systems. It was found that the MARTINI model generally occupies more volume than the all-atom model, leading to the formation of micelles that are of a reasonable radius of gyration, but are smaller in aggregation number. The systematic characterization of the finite-size effect and exploration of multiscale modeling presented in this work provides guidance for the accurate modeling of micelles in simulations.

Explore related subjects

physics.chem-ph

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Jonathan J. Harris, George A. Pantelopulos, John E. Straub. 2020-12-01. Finite-size effects and optimal system sizes in simulations of surfactant micelle self-assembly. https://arxiv.org/abs/2012.00315

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

KEEP EXPLORING

Related papers

arXiv2026

Charge Transfer with a Spin. I: A Variational Constrained-CASSCF Framework for Investigating Charge Transfer in the Presence of Spin-Orbit Coupling

Charge transfer in open-shell molecular systems can involve a delicate interplay between charge localization, orbital relaxation, and spin-orbit coupling (SOC), particularly near ground-excited state crossings. Here, we introduce a very inexpensive variational framework for treating these effects in odd-electron systems by extending the electron/hole-transfer Dynamically-weighted State-Averaged Constrained CASSCF (eDSC/hDSC) method to include SOC. Our method incorporates the SOC Hamiltonian directly into the variational orbital optimization through complex-valued spinor orbitals, allowing orbital and spin degrees of freedom to relax self-consistently while preserving the time-reversal symmetry of doublet states. The method achieves smooth potential energy surfaces and rapid self-consistent field (SCF) convergence; moreover, from physically small to artificially large SOC strengths, the calculation can be converged to very tight thresholds across the whole potential energy surface. While the results presented here are for systems with two charge centers, as shown in the appendix, the theory is quite general and can be adapted to either a system of $N$ charge centers or a metal-molecule surface with a continuum of states, so that charge transport (and not just charge transfer) can also be studied. The approach therefore provides a route towards ab initio studies of spin-dependent charge transfer and charge transport in molecular systems with nontrivial spin degrees of freedom.

physics.chem-ph↗

arXiv2026

Charge Transfer with a Spin. II: A Framework for Diabatization which Localizes Charge and Spin

We investigate a diabatization procedure that localizes charges (in real space) and localizes spins (in spin space) for open-shell systems that exhibit charge transfer in the presence of spin-orbit coupling. The procedure is applied to a two-state crossing between pairs of Kramers-restricted doublet states (which can also be considered effectively a four-state crossing). To generate the relevant diabatic states, we employ a two-step optimization over complex-unitary rotations that sequentially maximizes dipole and spin moments through iterative Jacobi sweeps; the resulting update rules are effectively equivalent to those of approximate joint diagonalization (AJD) applied to charge and spin. The method converges rapidly and yields smooth diabatic potential energy surfaces that preserve dipole and spin properties (e.g., a smoothly varying spin quantization axis) along the reaction coordinate while maintaining time-reversal symmetry.

physics.chem-ph↗

arXiv2026

Fixed-Dimensional Latent Flow for Generating Variable-Size 3D Molecules

Molecular size is coupled to composition, structure, and function, yet most 3D molecular generators require a predefined atom count. We introduce Equivariant-Free Transformer-Autoencoded Latent Flow Matching, a two-stage framework that samples a fixed-dimensional latent vector using flow matching and uses an autoregressive Transformer to determine molecular size, atom types, coordinates, and chemical attributes. Canonical atom ordering and rigid-pose alignment enable Transformers without equivariant layers, while decoded attributes guide bond reconstruction. On PCQM4Mv2, unconditional generation yields 87.9\% unique, novel molecules passing sanitization and PoseBusters checks, exceeding baselines with lower end-to-end training and sampling time and higher end-to-end throughput. Across ten target HOMO-LUMO gaps, internal ranking retains 30\% of screened candidates and increases the density functional theory-verified hit rate within 0.1 eV from 25.0\% to 52.4\%, while largely preserving novelty and diversity. These results demonstrate fixed-dimensional latent generation with autoregressive decoding as a practical approach to molecular design without prespecifying size.

physics.chem-ph↗