A novel program has been developed for the interpretation of 15N relaxation rates in terms of macromolecular anisotropic rotational diffusion. The program is based on a highly efficient simulated annealing/minimization algorithm, designed specifically to search the parametric space described by the isotropic, axially symmetric and fully anisotropic rotational diffusion tensor models. The high efficiency of this algorithm allows extensive noise-based Monte Carlo error analysis. Relevant statistical tests are systematically applied to provide confidence limits for the proposed tensorial models. The program is illustrated here using the example of the cytochrome c' from Rhodobacter capsulatus, a four-helix bundle heme protein, for which data at three different field strengths were independently analysed and compared.
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http://dx.doi.org/10.1023/a:1008305808620 | DOI Listing |
Materials (Basel)
January 2025
State Key Laboratory of Powder Metallurgy, Central South University, Changsha 410083, China.
To provide insight into the interface structure in Ti particle-reinforced Mg matrix composites, this study investigates the inherent Mg/Ti interface structure formed during the solidification of supercooled Mg melt on a (0001)Ti substrate using ab initio molecular dynamics (AIMD) simulations and density function theory (DFT) calculation. The resulting interface exhibits an orientation relationship of 0001Mg//0001Ti with a lattice mismatch of approximately 8%. Detailed characterizations reveal the occurrences of 0001Mg plane rotation and vacancy formation to overcome the lattice mismatch at the inherent Mg/Ti interface while allowing Mg atoms to occupy the energetically favorable hollow sites above the Ti atomic layer.
View Article and Find Full Text PDFBiomimetics (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 PDFEntropy (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 PDFLangmuir
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 PDFBiophys 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.
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