We present one effective multicanonical molecular dynamics (MCMD) algorithm accelerating the convergence of rough energy landscapes simulations via an adaptive force-biased iteration scheme. Our method utilizes several short MCMD simulations with dynamically updated weights and combines them to estimate the density of states via multiple histogram technique. The key step of our algorithm is the adaptive refinement for the derivative of multicanonical weight, which allows the system to enlarge the sampling energy range maintaining the statistical accuracy. The performance of our method has been validated for atomic Lennard-Jones clusters.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1103/PhysRevE.70.057103 | DOI Listing |
Plant Physiol Biochem
January 2025
Department of Agriculture, Food and Environment, University of Pisa, Italy; Centre of Agro-Ecological Research "Enrico Avanzi" (CiRAA), Pisa, Italy.
Tomato (Solanum lycopersicum L.) is a major crop in the Mediterranean basin, vulnerable to drought at any crop stage. Landraces are traditional, locally adapted varieties with greater resilience to water scarcity than modern cultivars.
View Article and Find Full Text PDFPLoS One
November 2024
Cybermedia Center, Osaka University, Toyonaka, Japan.
The mutation-selection mechanism of Darwinian evolution gives rise not only to adaptation to environmental conditions but also to the enhancement of robustness against mutations. When two or more phenotypes have the same fitness value, the robustness distribution for different phenotypes can vary. Thus, we expect that some phenotypes are favored in evolution and that some are hardly selected because of a selection bias for mutational robustness.
View Article and Find Full Text PDFInt J Biol Macromol
November 2024
Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan. Electronic address:
We previously revealed the structural basis of Ca dependent regulation of a polyethylene terephthalate (PET)-degrading enzyme, Cut190, and proposed a unique reaction cycle in which the enzyme repeatedly binds and releases Ca. Here, we report crystal structures of Cut190 mutants with high thermal stability complexed with PET-like ligands that contain aromatic rings. The structural information has allowed us to perform further computational analyses using a PET-trimer bound model.
View Article and Find Full Text PDFJ Chem Inf Model
May 2024
Graduate School of Information Science, University of Hyogo, 7-1-28 minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
The cyclic peptide OS1 (amino acid sequence: CTERMALHNLC), which has a disulfide bond between both termini cysteine residues, inhibits complex formation between the platelet glycoprotein Ibα (GPIbα) and the von Willebrand factor (vWF) by forming a complex with GPIbα. To study the binding mechanism between GPIbα and OS1 and, therefore, the inhibition mechanism of the protein-protein GPIbα-vWF complex, we have applied our multicanonical molecular dynamics (McMD)-based dynamic docking protocol starting from the unbound state of the peptide. Our simulations have reproduced the experimental complex structure, although the top-ranking structure was an intermediary one, where the peptide was bound in the same location as in the experimental structure; however, the β-switch of GPIbα attained a different conformation.
View Article and Find Full Text PDFACS Omega
January 2024
Graduate School of Information Science, University of Hyogo, 7-1-28 minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
Flavin mononucleotide riboswitches are common among many pathogenic bacteria and are therefore considered to be an attractive target for antibiotics development. The riboswitch binds riboflavin (RBF, also known as vitamin B), and although an experimental structure of their complex has been solved with the ligand bound deep inside the RNA molecule in a seemingly unreachable state, the binding mechanism between these molecules is not yet known. We have therefore used our Multicanonical Molecular Dynamics (McMD)-based dynamic docking protocol to analyze their binding mechanism by simulating the binding process between the riboswitch aptamer domain and the RBF, starting from the apo state of the riboswitch.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!