Relative lifetimes of inherent double stranded DNA openings with lengths up to ten base pairs are presented for different gene promoters and corresponding mutants that either increase or decrease transcriptional activity in the framework of the Peyrard-Bishop-Dauxois model. Extensive microcanonical simulations are used with energies corresponding to physiological temperature. The bubble lifetime profiles along the DNA sequences demonstrate a significant reduction of the average lifetime at the mutation sites when the mutated promoter decreases transcription, while a corresponding enhancement of the bubble lifetime is observed in the case of mutations leading to increased transcription. The relative difference in bubble lifetimes between the mutated and wild type promoters at the position of mutation varies from 20% to more than 30% as the bubble length decreases.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1063/5.0060335 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
High-speed imaging of non-photochemical laser-induced nucleation in aqueous cesium chloride.
Phys Chem Chem Phys
March 2025
School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh, Scotland, EH9 3FJ, UK.
A study of non-photochemical laser-induced nucleation (NPLIN) of cesium chloride in aqueous supersaturated solutions is presented. Single, unfocused laser pulses (duration 5 ns, peak power density 180 MW cm) of 532 nm laser light were used to induce crystal nucleation, and the resulting dynamics were studied using imaging at frame rates up to 250 000 frames per second (4 μs per frame). Thermocavitation events were observed in a surrounding index-matching fluid, both in the bulk and at the exterior walls of vials.
View Article and Find Full Text PDFMulti-Microseconds Microbubbles Induced by Nanoseconds Pulsed-Laser Heating of Gold Nano-Particles.
ACS Omega
March 2025
Nuclear Professional School, The University of Tokyo, Hongo Campus, Bunkyo, Tokyo 113-8654, Japan.
This study examines the effect of gold-nanoparticles (GNPs) aggregation on the formation of multimicrosecond water-vapor (WV) microbubbles (MBs) generated by nanosecond pulsed-laser heating of GNPs in water. The MBs' dynamics reveal a "dual-nature" system involving both WV phase change and the release of dissolved gases (DGs). High-speed visualization (216 kfps) captures two distinct stages in the MB lifecycle: an initial fast growth-collapse of the WV phase (multimicrosecond duration), followed by a slow collapse driven by DG release (>milliseconds).
View Article and Find Full Text PDFHydrodynamic cavitation synthesis of water-soluble CdSe quantum dots: Effect of venturi tube parameters on size distribution and fluorescence properties, with application in Fe detection.
Anal Chim Acta
April 2025
College of Chemistry, Liaoning University, Shenyang, 110036, PR China; Institute of Dispersed Element Chemistry, Liaoning University, Shenyang, 110036, PR China. Electronic address:
Background: Fe is an important trace element in life metabolism and also the main component of industrial pollutant. How to improve the sensitivity of Fe detection is of great significance in biological and environmental analyses. Fluorescence probe for Fe detection has high sensitivity, but it is difficult to prepare a probe with high sensitivity.
View Article and Find Full Text PDFBubble coalescence principle in saline water.
Proc Natl Acad Sci U S A
February 2025
School of Chemical Engineering and Technology, China University of Mining and Technology, Xuzhou 221116, China.
Bubbles present in saline water typically exhibit a prolonged lifetime, making them attractive for various engineering processes. Herein, we unveil a transition from delayed bubble coalescence to rapid bursting within about one millisecond in salty solutions. The key aspect in understanding this transition lies in the combined influences of surface deformation and ion surface excess instead of characterizing the ions alone.
View Article and Find Full Text PDFDetecting a Long-Lived False Vacuum with Quantum Quenches.
Phys Rev Lett
December 2024
Center for Theoretical Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Distinguishing whether a system supports alternate low-energy (locally stable) states-stable (true vacuum) versus metastable (false vacuum)-by direct observation can be difficult when the lifetime of the state is very long but otherwise unknown. Here we demonstrate, in a tractable model system, that there are physical phenomena on much shorter timescales that can diagnose the difference. Specifically, we study the time evolution of the magnetization following a quench in the tilted quantum Ising model, and show that its magnitude spectrum is an effective diagnostic.
View Article and Find Full Text PDFWant 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!