rotational diffusion
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Shivaraj A. Patil ◽  
Nagachandra K.H. ◽  
James R. Mannekutla ◽  
Shrikrupa K. Chavan ◽  
Sanjeev R. Inamdar

2022 ◽  
Vol 130 (1) ◽  
pp. 138
В.П. Дресвянский ◽  
С.А. Зилов ◽  
Е.Ф. Мартынович

Single F2 and F3+- color centers in the LiF crystal were studied by confocal fluorescence microscopy. The time dependences of their fluorescence intensity were analyzed and statistically processed. Our studies show that, the F3+- color center, being photoexcited, is able enter the triplet state, while in ground (singlet) state it changes orientation with a frequency of 1.5 – 2 Hz at room temperature, due to reorientational diffusion, unlike the F2- center, which is reoriented only being in the triplet state. This subtype of rotational diffusion of the center does not lead to its translational diffusion.

2021 ◽  
Vol 11 (1) ◽  
Szu-Ning Lin ◽  
Remus T. Dame ◽  
Gijs J. L. Wuite

AbstractArchitectural DNA–binding proteins are involved in many important DNA transactions by virtue of their ability to change DNA conformation. Histone-like protein from E. coli strain U93, HU, is one of the most studied bacterial architectural DNA–binding proteins. Nevertheless, there is still a limited understanding of how the interactions between HU and DNA are affected by ionic conditions and the structure of DNA. Here, using optical tweezers in combination with fluorescent confocal imaging, we investigated how ionic conditions affect the interaction between HU and DNA. We directly visualized the binding and the diffusion of fluorescently labelled HU dimers on DNA. HU binds with high affinity and exhibits low mobility on the DNA in the absence of Mg2+; it moves 30-times faster and stays shorter on the DNA with 8 mM Mg2+ in solution. Additionally, we investigated the effect of DNA tension on HU–DNA complexes. On the one hand, our studies show that binding of HU enhances DNA helix stability. On the other hand, we note that the binding affinity of HU for DNA in the presence of Mg2+ increases at tensions above 50 pN, which we attribute to force-induced structural changes in the DNA. The observation that HU diffuses faster along DNA in presence of Mg2+ compared to without Mg2+ suggests that the free energy barrier for rotational diffusion along DNA is reduced, which can be interpreted in terms of reduced electrostatic interaction between HU and DNA, possibly coinciding with reduced DNA bending.

2021 ◽  
Tianben Ding ◽  
Matthew D. Lew

AbstractWithin condensed matter, single fluorophores are sensitive probes of their chemical environments, but it is difficult to use their limited photon budget to image precisely their positions, 3D orientations, and rotational diffusion simultaneously. We demonstrate the polarized vortex point spread function (PSF) for measuring these parameters, including characterizing the anisotropy of a molecule’s wobble, simultaneously from a single image. Even when imaging dim emitters (∼500 photons detected), the polarized vortex PSF is able to obtain 12 nm localization precision, 4-8° orientation precision, and 26° wobble precision. We use the vortex PSF to measure the emission anisotropy of fluorescent beads, the wobble dynamics of Nile red (NR) within supported lipid bilayers, and the distinct orientation signatures of NR in contact with amyloid-beta fibrils, oligomers, and tangles. The unparalleled sensitivity of the vortex PSF transforms single-molecule microscopes into nanoscale orientation imaging spectrometers, where the orientations and wobbles of individual probes reveal structures and organization of soft matter that are nearly impossible to perceive using molecular positions alone.

Crystals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1053
Vladimir G. Chigrinov ◽  
Aleksey A. Kudreyko ◽  
Fedor V. Podgornov

Recent achievements in the photoalignment technique for fabrication of optically rewritable electronic paper with high performance characteristics are surveyed with emphasis on temporal constraints on the exposure process. The possibility of creating electrode-free electronic paper has very important practical aspects. However, many existing studies do not include sufficient analysis on how to achieve acceptable reflective characteristics within short exposure time. In order to achieve this goal, we have applied the rotational diffusion model. We find that the parameters of the diffusion model can be adjusted to get acceptable light-reflecting characteristics within 10 s of exposure. In comparison with the long-time exposure, the reflectance coefficient reduces by 24%. The route to material improvements for optimized e-paper device is discussed.

2021 ◽  
Vol 118 (34) ◽  
pp. e2105826118
Zixi Hu ◽  
Jeffrey J. Donatelli ◽  
James A. Sethian

Coefficients for translational and rotational diffusion characterize the Brownian motion of particles. Emerging X-ray photon correlation spectroscopy (XPCS) experiments probe a broad range of length scales and time scales and are well-suited for investigation of Brownian motion. While methods for estimating the translational diffusion coefficients from XPCS are well-developed, there are no algorithms for measuring the rotational diffusion coefficients based on XPCS, even though the required raw data are accessible from such experiments. In this paper, we propose angular-temporal cross-correlation analysis of XPCS data and show that this information can be used to design a numerical algorithm (Multi-Tiered Estimation for Correlation Spectroscopy [MTECS]) for predicting the rotational diffusion coefficient utilizing the cross-correlation: This approach is applicable to other wavelengths beyond this regime. We verify the accuracy of this algorithmic approach across a range of simulated data.

Santhosh K. Matam ◽  
C. Richard A. Catlow ◽  
Ian P. Silverwood ◽  
Alexander J. O’Malley

AbstractMethanol dynamics in zeolite H-ZSM-5 (Si/Al of 25) with a methanol loading of ~ 30 molecules per unit cell has been studied at 298, 323, 348 and 373 K by incoherent quasi-elastic neutron scattering (QENS). The elastic incoherent structure factor (EISF) reveals that the majority of methanol is immobile, in the range between 70 and 80%, depending on the measurement temperature. At 298 K, ≈ 20% methanol is mobile on the instrumental timescale, exhibiting isotropic rotational dynamics with a rotational diffusion coefficient (DR) of 4.75 × 1010 s−1. Upon increasing the measurement temperature from 298 to 323 K, the nature of the methanol dynamics changes from rotational to translational diffusion dynamics. Similar translational diffusion rates are measured at 348 and 373 K, though with a larger mobile fraction as temperature increases. The translational diffusion is characterised as jump diffusion confined to a sphere with a radius close to that of a ZSM-5 channel. The diffusion coefficients may be calculated using either the Volino–Dianoux (VD) model of diffusion confined to a sphere, or the Chudley–Elliot (CE) jump diffusion model. The VD model gives rise to a self-diffusion co-efficient (Ds) of methanol in the range of 7.8–8.4 × 10–10 m2 s−1. The CE model gives a Ds of around 1.2 (± 0.1) × 10–9 m2 s−1 with a jump distance of 2.8 (either + 0.15 or − 0.1) Å and a residence time (τ) of ~ 10.8 (either + 0.1 or − 0.2) ps. A correlation between the present and earlier studies that report methanol dynamics in H-ZSM-5 with Si/Al of 36 is made, suggesting that with increasing Si/Al ratio, the mobile fraction of methanol increases while DR decreases.

2021 ◽  
Alan Hicks ◽  
Matthew MacAinsh ◽  
Huan-Xiang Zhou

Molecular dynamics simulations are widely used to determine equilibrium and dynamic properties of proteins. Nearly all simulations nowadays are carried out at constant temperature, with a Langevin thermostat among the most widely used. Thermostats distort protein dynamics, but whether or how such distortions can be corrected has long been an open question. Here we show that constant-temperature simulations with a Langevin thermostat dilate protein dynamics and present a correction scheme to remove the dynamic distortions. Specifically, ns- scale time constants for overall rotation are dilated significantly but sub-ns time constants for internal motions are dilated modestly, while all motional amplitudes are unaffected. The correction scheme involves contraction of the time constants, with the contraction factor a linear function of the time constant to be corrected. The corrected dynamics of eight proteins are validated by NMR data for rotational diffusion and for backbone amide and side-chain methyl relaxation. The present work demonstrates that, even for complex systems like proteins with dynamics spanning multiple timescales, one can predict how thermostats distort protein dynamics and remove such distortions. The correction scheme will have wide applications, facilitating force-field parameterization and propelling simulations to be on par with NMR and other experimental techniques in determining dynamic properties of proteins.

2021 ◽  
Vol 44 (6) ◽  
Sebastian Rode ◽  
Jens Elgeti ◽  
Gerhard Gompper

Abstract The dynamics and motion of multi-ciliated microswimmers with a spherical body and a small number N (with $$5< N < 60$$ 5 < N < 60 ) of cilia with length comparable to the body radius, is investigated by mesoscale hydrodynamics simulations. A metachronal wave is imposed for the cilia beat, for which the wave vector has both a longitudinal and a latitudinal component. The dynamics and motion is characterized by the swimming velocity, its variation over the beat cycle, the spinning velocity around the main body axis, as well as the parameters of the helical trajectory. Our simulation results show that the microswimmer motion strongly depends on the latitudinal wave number and the longitudinal phase lag. The microswimmers are found to swim smoothly and usually spin around their own axis. Chirality of the metachronal beat pattern generically generates helical trajectories. In most cases, the helices are thin and stretched, i.e., the helix radius is about an order of magnitude smaller than the pitch. The rotational diffusion of the microswimmer is significantly smaller than the passive rotational diffusion of the body alone, which indicates that the extended cilia contribute strongly to the hydrodynamic radius. The swimming velocity is found to increase with the cilia number N with a slightly sublinear power law, consistent with the behavior expected from the dependence of the transport velocity of planar cilia arrays on the cilia separation. Graphic abstract

2021 ◽  
Vol 103 (5) ◽  
S. V. Titov ◽  
W. T. Coffey ◽  
Yu. P. Kalmykov ◽  
M. Zarifakis ◽  
A. S. Titov

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