Vacancy localization in the square dimer model.

Phys Rev E Stat Nonlin Soft Matter Phys

Service de Physique Théorique, CEA/DSM/SPhT, Unité de recherche associée au CNRS, CEA/Saclay, 91191 Gif sur Yvette Cedex, France.

Published: October 2007

We study the classical dimer model on a square lattice with a single vacancy by developing a graph-theoretic classification of the set of all configurations which extends the spanning tree formulation of close-packed dimers. With this formalism, we can address the question of the possible motion of the vacancy induced by dimer slidings. We find a probability 57/4-10[sqrt2] for the vacancy to be strictly jammed in an infinite system. More generally, the size distribution of the domain accessible to the vacancy is characterized by a power law decay with exponent 9/8. On a finite system, the probability that a vacancy in the bulk can reach the boundary falls off as a power law of the system size with exponent 1/4. The resultant weak localization of vacancies still allows for unbounded diffusion, characterized by a diffusion exponent that we relate to that of diffusion on spanning trees. We also implement numerical simulations of the model with both free and periodic boundary conditions.

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevE.76.041140DOI Listing

Publication Analysis

Top Keywords

dimer model
8
power law
8
vacancy
6
vacancy localization
4
localization square
4
square dimer
4
model study
4
study classical
4
classical dimer
4
model square
4

Similar Publications

Crystalline pentacene is a model solid-state light-harvesting material because its quantum efficiencies exceed 100% via ultrafast singlet fission. The singlet fission mechanism in pentacene crystals is disputed due to insufficient electronic information in time-resolved experiments and intractable quantum mechanical calculations for simulating realistic crystal dynamics. Here we combine a multiscale multiconfigurational approach and machine learning photodynamics to understand competing singlet fission mechanisms in crystalline pentacene.

View Article and Find Full Text PDF

Microtubule plus-end tracking proteins (+TIPs) participate in nearly all microtubule-based cellular processes and have recently been proposed to function as liquid condensates. However, their formation and internal organization remain poorly understood. Here, we have study the phase separation of Bik1, a CLIP-170 family member and key +TIP involved in budding yeast cell division.

View Article and Find Full Text PDF

I'm Not Dead Yet (INDY) functions as a transporter for citrate, a key metabolite in the citric acid cycle, across the plasma membrane. Partial deficiency of INDY extends lifespan, akin to the effects of caloric restriction. In this work, we use cryo-electron microscopy to determine structures of INDY in the presence and absence of citrate and in complex with the well-known inhibitor 4,4'-diisothiocyano-2,2'-disulfonic acid stilbene (DIDS) at resolutions ranging from 2.

View Article and Find Full Text PDF

Design of a light and Ca switchable organic-peptide hybrid.

Proc Natl Acad Sci U S A

February 2025

SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic of Korea.

The design of organic-peptide hybrids has the potential to combine our vast knowledge of protein design with small molecule engineering to create hybrid structures with complex functions. Here, we describe the computational design of a photoswitchable Ca-binding organic-peptide hybrid. The designed molecule, designated Ca-binding switch (CaBS), combines an EF-hand motif from classical Ca-binding proteins such as calmodulin with a photoswitchable group that can be reversibly isomerized between a spiropyran (SP) and merocyanine (MC) state in response to different wavelengths of light.

View Article and Find Full Text PDF

Cryo-EM structure of AAV2 Rep68 bound to integration site AAVS1: insights into the mechanism of DNA melting.

Nucleic Acids Res

January 2025

Department of Physiology and Biophysics, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298, United States.

The Rep68 protein from Adeno-Associated Virus (AAV) is a multifunctional SF3 helicase that performs most of the DNA transactions necessary for the viral life cycle. During AAV DNA replication, Rep68 assembles at the origin of replication, catalyzing the DNA melting and nicking reactions during the hairpin rolling replication process to complete the second-strand synthesis of the AAV genome. We report the cryo-electron microscopy structures of Rep68 bound to the adeno-associated virus integration site 1 in different nucleotide-bound states.

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!