The influence of the bead-bead interaction on the rotational dynamics of macromolecules which are immersed into a solution has been investigated by starting from the microscopic theory of the macromolecular motion, i.e., from a Fokker-Planck equation for the phase-space distribution function. From this equation, we then derived an explicit expression for the configuration-space distribution function of a nonrigid molecule which is immobilized on a surface. This function contains all the information about the interaction among the beads as well as the effects from the surrounding solvent particles and from the surface. For the restricted rotational motion, the dynamics of the macromolecules can now be characterized in terms of a rotational diffusion coefficient as well as a radial distribution functions. Detailed computations for the rotational diffusion coefficient and the distribution functions have been carried out for HOOKEAN, finitely extensible nonlinear elastic, and a DNA type bead-bead interaction.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1063/1.1787831 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Theoretical and Experimental Study of an Electrokinetic Micromanipulator for Biological Applications.
Biomimetics (Basel)
January 2025
College of Engineering, Design, and Physical Sciences, Brunel University London, Uxbridge UB8 3PH, UK.
The ability to control and manipulate biological fluids within microchannels is a fundamental challenge in biological diagnosis and pharmaceutical analyses, particularly when buffers with very high ionic strength are used. In this study, we investigate the numerical and experimental study of fluidic biochips driven by ac electrothermal flow for controlling and manipulating biological samples inside a microchannel, e.g.
View Article and Find Full Text PDFLattice Boltzmann Modeling of Additive Manufacturing of Functionally Graded Materials.
Entropy (Basel)
December 2024
AGH University of Krakow, Faculty of Metals Engineering and Industrial Computer Science, al. Mickiewicza 30, 30-059 Kraków, Poland.
Functionally graded materials (FGMs) show continuous variations in properties and offer unique multifunctional capabilities. This study presents a simulation of the powder bed fusion (PBF) process for FGM fabrication using a combination of Unity-based deposition and lattice Boltzmann method (LBM)-based process models. The study introduces a diffusion model that allows for the simulation of material mixtures, in particular AISI 316L austenitic steel and 18Ni maraging 300 martensitic steel.
View Article and Find Full Text PDFInvestigating Cell-Induced Mixing Dynamics in Microfluidic Droplets Using the Lattice Boltzmann Method.
Langmuir
January 2025
CNNFM Lab, School of Mechanical Engineering, College of Engineering, University of Tehran, P.O. Box 11155-4563 Tehran, Iran.
This study investigates the impact of cell dynamics on mixing efficiency within a microfluidic droplet, emphasizing the relationship between cell motion, deformability, and resultant asymmetry in velocity and concentration fields. Simulations were conducted for droplets containing encapsulated cells at varying Peclet numbers ( = 100-800) and coupling constants ( = 0.0025, 0.
View Article and Find Full Text PDFProtein Target Search Diffusion-association/dissociation Free Energy Landscape around DNA Binding Site with Flanking Sequences.
Biophys J
January 2025
Department of Physics and Astronomy, Department of Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California, USA. Electronic address:
In this work we present a minimal structure-based model of protein diffusional search along local DNA amid protein binding and unbinding events on the DNA, taking into account protein-DNA electrostatic interactions and hydrogen-bonding (HB) interactions or contacts at the interface. We accordingly constructed the protein diffusion-association/dissociation free energy surface and mapped it to 1D as the protein slides along DNA, maintaining the protein-DNA interfacial HB contacts that presumably dictate the DNA sequence information detection. Upon DNA helical path correction, the protein 1D diffusion rates along local DNA can be physically derived to be consistent with experimental measurements.
View Article and Find Full Text PDFA Combined Approach to Extract Rotational Dynamics of Globular Proteins Undergoing Liquid-Liquid Phase Separation.
J Phys Chem B
January 2025
Department of Physical Chemistry, Sciences II, University of Geneva, 30 Quai Ernest Ansermet, Geneva 1211, Switzerland.
The formation of protein condensates (droplets) via liquid-liquid phase separation (LLPS) is a commonly observed phenomenon in vitro. Changing the environmental properties with cosolutes, molecular crowders, protein partners, temperature, pressure, etc. has been shown to favor or disfavor the formation of protein droplets by fine-tuning the water-water, water-protein, and protein-protein interactions.
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!