Separation of time scales in one-dimensional directed nucleation-growth processes.

Phys Rev E Stat Nonlin Soft Matter Phys

Institut Curie, Centre de recherche, INSERM U932 Immunité et cancer, 12 rue Lhomond, 75005 Paris, France.

Published: December 2010

Proteins involved in homologous recombination such as RecA and hRad51 polymerize on single- and double-stranded DNA according to a nucleation-growth kinetics, which can be monitored by single-molecule in vitro assays. The basic models currently used to extract biochemical rates rely on ensemble averages and are typically based on an underlying process of bidirectional polymerization, in contrast with the often observed anisotropic polymerization of similar proteins. For these reasons, if one considers single-molecule experiments, the available models are useful to understand observations only in some regimes. In particular, recent experiments have highlighted a steplike polymerization kinetics. The classical model of one-dimensional nucleation growth, the Kolmogorov-Avrami-Mehl-Johnson (KAMJ) model, predicts the correct polymerization kinetics only in some regimes and fails to predict the steplike behavior. This work illustrates by simulations and analytical arguments the limitation of applicability of the KAMJ description and proposes a minimal model for the statistics of the steps based on the so-called stick-breaking stochastic process. We argue that this insight might be useful to extract information on the time and length scales involved in the polymerization kinetics.

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevE.82.061904DOI Listing

Publication Analysis

Top Keywords

polymerization kinetics
12
polymerization
5
separation time
4
time scales
4
scales one-dimensional
4
one-dimensional directed
4
directed nucleation-growth
4
nucleation-growth processes
4
processes proteins
4
proteins involved
4

Similar Publications

Synthetic organic dye such as methylene blue (MB) is non-biodegradable and highly toxic, released from textile wastewater. This work investigates the applicability of Ni@ZnO polymer nanocomposite for MB removal from the wastewater. To understand their differences before and after MB adsorption, composites' surface morphology was characterized by various techniques including scanning electron microscope (SEM), thermogravimetric analysis (TGA), X-ray diffraction (XRD), energy dispersive spectroscopy (EDS), Fourier transformation infrared (FT-IR) and UV-Vis spectrophotometer.

View Article and Find Full Text PDF

On-Demand Nitric Oxide Generation via Thermal Decomposition of N-Trityl Dihyrdo-1,2-Oxazines.

Angew Chem Int Ed Engl

January 2025

Wayne State University, Chemistry, 5101 Cass Avenue, RM 275, 48202, Detroit, UNITED STATES OF AMERICA.

Inhaled nitric oxide (iNO) is a promising therapy for a variety of pulmonary conditions but is limited by the cost, portability, and safety limitations of the compressed gas cylinders used in conventional iNO delivery systems. On-demand generation of iNO via thermally controlled decomposition of an NO-genic precursor is an attractive alternative to systems based on compressed gas cylinders. However, most NO-releasing materials, which would form the basis of such a system, are designed for in vivo applications, and not gas flow release at elevated temperatures.

View Article and Find Full Text PDF

Accelerating the Zn Transport Kinetics in the Pre-Solvated Artificial Protective Layer via Preferential Electrostatic Interactions for Stable Zinc Anode.

Small

January 2025

Key Lab for Spec ial Functional Materials of Ministry of Education, National & Local Joint Engineering Research Center for High Efficiency Display and Lighting Technology, School of Nano Science and Materials Engineering, Collaborative Innovation Center of Nano Functional Materials and Applications, Henan University, Kaifeng, 475 004, P. R. China.

The intrinsic safety and cost-effectiveness of the aqueous zinc ion batteries hold the potential for grid-scale energy storage. However, the uncontrolled dendrite growth, parasitic reactions, and electrochemical corrosion of the anode due to the random Zn transport near the anode hinder its practical applications. Herein, a pre-solvated artificial protective layer (ps-APL) with a nitrogen-containing functional group is constructed by an in situ polymerization strategy to stabilize the Zn anode via boosted Zn mass transport kinetics and oriented exposure of the Zn(002) facets.

View Article and Find Full Text PDF

Modeling time scale of integration in equilibrium passive sampling.

Environ Toxicol Chem

January 2025

Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, United States.

Passive samplers (PSs) deployed in the field for several months provide a time-averaged measurement of the freely dissolved concentration of pollutants, which is important for assessing ecological exposure and estimating pollutant loads. A comprehensive theoretical modeling assessment of the sampling time scale of integration (TSI) of an equilibrium PS is required to correctly interpret the results. We address this knowledge gap by modeling exchange kinetics of polychlorinated biphenyl congeners in low-density polyethylene (PE) PS based on diffusive transport and first-order kinetics.

View Article and Find Full Text PDF

Physical effects of crowdant size and concentration on collective microtubule polymerization.

Biophys J

January 2025

Div. of Biology, IISER Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India. Electronic address:

The polymerization of cytoskeletal filaments is regulated by both biochemical pathways, as well as physical factors such as crowding. The effect of crowding in vivo emerges from the density of intracellular components. Due to the complexity of the intracellular environment, most studies are based on either in vitro reconstitution or theory.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!