Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · physics/9810035

The Scaling Behaviour of Stochastic Minimization Algorithms in a Perfect Funnel Landscape

K. Hamacher·W. Wenzel
View original source ↗Read source document ↗Export metadata ↓

Abstract

We determined scaling laws for the numerical effort to find the optimal configurations of a simple model potential energy surface (PES) with a perfect funnel structure that reflects key characteristics of the protein interactions. Generalized Monte-Carlo methods(MCM, STUN) avoid an enumerative search of the PES and thus provide a natural resolution of the Levinthal paradox. We find that the computational effort grows with approximately the eighth power of the system size for MCM and STUN, while a genetic algorithm was found to scale exponentially. The scaling behaviour of a derived lattice model is also rationalized.

Explore related subjects

physics.bio-ph

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

K. Hamacher, W. Wenzel. 1998-10-19. The Scaling Behaviour of Stochastic Minimization Algorithms in a Perfect Funnel Landscape. https://doi.org/10.1103/physreve.59.938

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

KEEP EXPLORING

Related papers

arXiv2026

Spontaneous polarization for protrusion-driven cell crawling

We propose a minimal one-dimensional continuum model for the spontaneous initiation of protrusion-driven cell crawling on a rigid substrate. The cell cytoskeleton is represented as a viscous actin meshwork that turns over in the bulk and polymerizes at two moving cell edges. Symmetry breaking arises from the feedback between cell motion, an external chemical regulator of actin nucleation, and actin polymerization at the cell fronts. When the cell moves, the regulator becomes polarized around the moving boundaries, thereby imposing different actin nucleation densities at the two edges. This generates unequal protrusive rates, which in turn reinforce motion and sustain the chemical polarization. Above a critical protrusive activity, the static symmetric state loses stability and the system undergoes a bifurcation toward a motile polarized state. Depending on how the external cue controls actin nucleation, the transition can be either supercritical or subcritical, leading in the latter case to coexistence between static and motile states. Using parameter values appropriate for keratocyte cells, the model predicts crawling speeds of the correct order of magnitude and actin-density profiles that are qualitatively similar to experimental observations, including asymmetric edge-localized density peaks. These results identify a generic mechanism by which external biochemical regulation of actin nucleation can trigger spontaneous motility along a one-dimensional track without requiring molecular motors, specific adhesion dynamics, deformable substrates, or pre-existing polarity.

physics.bio-ph↗
arXiv2026

A Transient-Network Model of Condensate Aging and Morphology Transition in Phase Separation

Biomolecular condensates can undergo striking changes, such as transitioning from a liquid-like to a gel- or a solid-like aggregate due to changes in molecular interactions in response to changes in the biochemical environment. The question of how modified molecular interactions lead to such a transition in the material properties and spatial organization of condensates has not yet been elucidated. To address this question, we represent the biochemical environment as a triphasic mixture comprising a liquid-like protein-rich phase, a network-like protein-rich phase, and solvent. Owing to a change in the biochemical environment, protein molecules can reversibly switch between two conformational states. In a switched conformational state, the cross-linking domains of molecules are exposed which promote transient network formation in phase separated states. We develop a transient-network model and a continuum framework that couples phase separation, molecular switching, and dynamic cross-linking to predict condensate morphology and mechanics. The transient-network model predicts that a non-aging network behaves like a Maxwell fluid. When a network slowly ages via stabilization of cross-links, it shows Maxwell-like behavior and waiting time-dependent relaxation. However, a strongly aged network shows elastic recoil like characteristic of a Kelvin-Voigt solid. Our coupled continuum model demonstrates that the interplay of molecular switching and dynamic cross-linking in network formation shapes the spatial organization of condensate phases. In summary, this work demonstrates a mechanistic route explaining how conformational switching and molecular cross-linking regulate material properties and morphology of condensates.

physics.bio-ph↗
arXiv2026

Unraveling Primary Energy Conversion Dynamics in Intact Cells of Gemmatimonas groenlandica

Photosynthetic bacteria have evolved specialized light-harvesting structures to efficiently capture sunlight. Here, we investigate the ultrafast dynamics in intact cells of Gemmatimonas groenlandica, featuring unique double-ring LHh-LH1 photosynthetic complexes containing bacteriochlorophyll a. Two-dimensional electronic spectroscopy with lock-in detection allows us to directly observe primary energy-conversion processes, from excitation-energy transfer within the antenna system to the formation of a charge-separated state in the reaction center, taking place on 50 ps time scale. Through comparison with Rhodospirillum rubrum, which lacks the outer antenna ring, we use a combination of global analysis and nodal/center line slope analyses to resolve LHh-LH1 excitation energy transfer which occurs on a ~1-2 ps timescale in Gemmatimonas groenlandica.

physics.bio-ph↗