Article
Nanoscience & Nanotechnology
Sergei A. Egorov
Summary: In this study, we conducted a simulation to investigate hopping-based spin transport and examined the relationship between spin diffusion length and the strengths of spin-orbit coupling, hyperfine interactions, and exchange coupling.
PHYSICA E-LOW-DIMENSIONAL SYSTEMS & NANOSTRUCTURES
(2022)
Article
Chemistry, Physical
Md Iqbal Hossain, G. J. Blanchard
Summary: Room temperature ionic liquids (RTILs) have unique properties, including the ability to support induced free charge density gradient. When diluted, RTILs form micelle-like structures and show compositional non-uniformity. In this study, we investigated the dilution of two imidazolium RTILs with polar aprotic solvents and found that the properties depend on the RTIL anion. Evidence of aggregated domains in the non-affected regions of RTILs was observed, and the domain size increased with increasing dilution.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Physics, Fluids & Plasmas
Michael S. Rusanov, Vladimir S. Zverev, Ekaterina A. Elfimova
Summary: A simple theory of the dynamic response of a ferrofluid to an AC magnetic field has been obtained, taking into account interparticle dipole-dipole interactions and field amplitude dependence. The theory extends the applicability of existing theories for weak and strong AC field amplitudes, and analyzes the susceptibility spectra. The effects of interparticle interactions and field amplitude on the dynamic response of ferrofluids are opposite, leading to relaxation processes determined by the characteristic relaxation times for an ideal paramagnetic gas at certain field amplitudes.
Article
Physics, Multidisciplinary
Josep Ingla-Aynes, Franz Herling, Jaroslav Fabian, Luis E. Hueso, Felix Casanova
Summary: The ultimate goal of spintronics is to achieve electrically controlled coherent manipulation of electron spin at room temperature for devices such as spin field-effect transistors. The use of 2D materials with strong spin anisotropy and valley character provides unique control knobs for manipulating spin precession. Experimental results have shown successful coherent spin precession in the absence of an external magnetic field, even in the diffusive regime, by manipulating spin-orbit coupling in bilayer graphene.
PHYSICAL REVIEW LETTERS
(2021)
Article
Materials Science, Multidisciplinary
S. Titov, W. T. Coffey, Yu P. Kalmykov, M. Zarifakis
Summary: Analytic solutions for the longitudinal and transverse components of the magnetization of a single-domain ferromagnetic nanoparticle with simple uniaxial magnetocrystalline anisotropy and Zeeman energy are obtained through the undamped limit of the inertial Landau-Lifshitz-Gilbert equation. The nutation frequency is also determined in terms of the inverse period of a Jacobi elliptic function. Results originate from analogy of the ILLG equation to a symmetric top with an electric dipole, allowing for closed-form solutions for THz or ultrahigh-frequency magnetization observables as well as GHz ones associated with ferromagnetic resonance.
Article
Materials Science, Multidisciplinary
A. N. Afanasiev, P. S. Alekseev, A. A. Danilenko, A. A. Greshnov, M. A. Semina
Summary: In novel ultrapure materials, electron fluids exhibit unique dynamics compared to electron gases in ordinary conductors. By introducing a magnetic field, the rotational viscosity of the electron fluid can be measured, and visualization of the flow is possible through electrically detected spin resonance.
Article
Chemistry, Physical
Dustin T. T. Roberts, Seyed M. M. Sadeghi
Summary: We investigated the influence of photo-physical and photo-chemical properties on the lateral transport of excitons in quantum dot thin films. Our experiments revealed three distinct regimes of exciton diffusion, depending on the intensity mode profiles of the laser and the properties of the quantum dots. The formation of oxidation hole burning was found to significantly affect the transport of energy in the excited regions of the thin films, suppressing their emission and diffusion.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Materials Science, Multidisciplinary
Zahra Khatibi, Stephen R. Power
Summary: The intrinsic spin-orbit coupling in graphene can be enhanced by proximity effects in stacked heterostructures of graphene and transition metal dichalcogenides. We studied the evolution of this effect as the transition metal dichalcogenide layer was deliberately defected. Our findings suggest that the low-energy spin and electronic behavior can be described by a simplified effective medium model, depending only on the composition ratio of the metallic species in the transition metal dichalcogenide layer. Furthermore, we demonstrate the feasibility of tuning the topological state of these alloyed systems by controlling this ratio.
Article
Materials Science, Multidisciplinary
A. Ceferino, S. J. Magorrian, V Zolyomi, D. A. Bandurin, A. K. Geim, A. Patane, Z. D. Kovalyuk, Z. R. Kudrynskyi, I. Grigorieva, V. Fal'ko
Summary: The paper demonstrates the tunability of spin-orbit coupling strength in few-layer gamma-InSe films, potentially enabling electrically switchable spintronic devices. Theoretical calculations and experimental measurements show good agreement in terms of Dyakonov-Perel spin relaxation due to SOC.
Article
Optics
Ram Nandan Kumar, Yatish, Subhasish Dutta Gupta, Nirmalya Ghosh, Ayan Banerjee
Summary: This study reveals that the spin-orbit interaction can cause significant azimuthal rotation of the transverse intensity distribution in structured Gaussian beams without intrinsic orbital angular momentum, which is referred to as the rotational spin-Hall effect. The experimental results validate the theoretical findings, and it is observed that the refractive index contrast in the path of tightly focused light affects the rotational shift proportionally.
Article
Materials Science, Multidisciplinary
Xi Shen, Haoran Chen, Dong Shi, Hong Xia, Jia Xu, Fanlong Zeng, Yizheng Wu
Summary: The study investigates magnetization dynamics in disconnected kagome artificial spin ice (ASI) lattices using experimental and theoretical approaches. The research identifies the dynamical coupling effects and special magnon modes in different field orientations. This contributes to a better understanding of collective spin-dynamics behavior in nanomagnet systems.
Article
Chemistry, Physical
Nicolas Bolik-Coulon, Fabien Ferrage
Summary: Nuclear Magnetic Resonance (NMR) is a useful tool for studying molecular motions. The Model-Free (MF) approach has been widely used to analyze NMR relaxation rates, but complementing it with molecular dynamics (MD) simulations is necessary to obtain a mechanistic understanding of the motions. This paper demonstrates how to build explicit models of methyl-bearing protein side chain motions and compares them with the MF approach.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Rizwan Nabi, Jakob K. Staab, Andrea Mattioni, Jon G. C. Kragskow, Daniel Reta, Jonathan M. Skelton, Nicholas F. Chilton
Summary: Molecular materials are important for the development of optoelectronic and quantum technologies, and the study of spin-phonon coupling is crucial for understanding energy transfer processes and spin dynamics. Ab initio methods can accurately calculate spin-phonon coupling and spin dynamics in molecular solids, as demonstrated in this study.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Marta Bugaj-Zar, Jaroslaw Jazwinski
Summary: In this study, NMR parameters, shielding constants, and indirect spin-spin coupling constants (SSCC) were calculated in a large set of model compounds to determine the most appropriate methods for calculating these parameters. The calculated methods were then applied to (2E)- and (2Z)-3-fluoroprop-2-enoic acids. The results showed stable rotamers and the presence of noncovalent F...OH and F...HO bonds in certain rotamers.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Article
Biochemistry & Molecular Biology
Danuta Kruk, Elzbieta Masiewicz, Sylwia Lotarska, Roksana Markiewicz, Stefan Jurga
Summary: H-1 spin-lattice relaxation experiments were conducted on a series of ionic liquids containing different alkyl chain lengths of bis(trifluoromethanesulfonyl)imide anion and cations. The results provided insights into the rotational and translational dynamics of the cations in comparison to molecular liquids, indicating a temperature-dependent ratio between the correlation times of these motions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Correction
Biophysics
Andrew Hsu, Fabien Ferrage, Arthur G. Palmer
BIOPHYSICAL JOURNAL
(2020)
Article
Operations Research & Management Science
Jose F. S. Bravo-Ferreira, David Cowburn, Yuehaw Khoo, Amit Singer
Summary: Nuclear Magnetic Resonance (NMR) Spectroscopy is a key technique for protein structure determination, with a challenge being the assignment of resonance frequencies to atoms. The introduction of LIAN, a novel linear programming formulation, has led to state-of-the-art results in simulated and experimental datasets.
JOURNAL OF GLOBAL OPTIMIZATION
(2022)
Article
Biochemistry & Molecular Biology
Albert A. Smith, Nicolas Bolik-Coulon, Matthias Ernst, Beat H. Meier, Fabien Ferrage
Summary: This study demonstrates improvements in characterizing internal dynamics of methyl-bearing side chains by utilizing carbon-13 relaxometry in the small protein ubiquitin. The results show that relaxometry data provides better information about nanosecond motions compared to high-field relaxation data, especially with increasing correlation time of rotational diffusion.
JOURNAL OF BIOMOLECULAR NMR
(2021)
Article
Multidisciplinary Sciences
Updesh Dixit, Savita Bhutoria, Xuhong Wu, Liming Qiu, Menachem Spira, Sheeba Mathew, Richard Harris, Lucas J. Adams, Sean Cahill, Rajiv Pathak, P. Rajesh Kumar, Minh Nguyen, Seetharama A. Acharya, Michael Brenowitz, Steven C. Almo, Xiaoqin Zou, Alasdair C. Steven, David Cowburn, Mark Girvin, Ganjam Kalpana
Summary: INI1/SMARCB1 interacts with HIV-1 integrase (IN) through its Rpt1 domain and plays multiple roles in HIV-1 replication. Research shows that the residues at the interface of INI1-Rpt1/IN-CTD overlap with those required for IN/RNA interaction, indicating a common binding mechanism for INI1 and RNA. Additionally, computational modeling suggests structural mimicry between INI1-Rpt1 and TAR RNA in their interactions with IN-CTD.
NATURE COMMUNICATIONS
(2021)
Editorial Material
Biophysics
Fabien Ferrage, Damien Laage
BIOPHYSICAL JOURNAL
(2022)
Article
Chemistry, Physical
Nicolas Bolik-Coulon, Fabien Ferrage
Summary: Nuclear Magnetic Resonance (NMR) is a useful tool for studying molecular motions. The Model-Free (MF) approach has been widely used to analyze NMR relaxation rates, but complementing it with molecular dynamics (MD) simulations is necessary to obtain a mechanistic understanding of the motions. This paper demonstrates how to build explicit models of methyl-bearing protein side chain motions and compares them with the MF approach.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Microbiology
Ryan J. Malonis, George Georgiev, Denise Haslwanter, Laura A. VanBlargan, Georgia Fallon, Olivia Vergnolle, Sean M. Cahill, Richard Harris, David Cowburn, Kartik Chandran, Michael S. Diamond, Jonathan R. Lai
Summary: By creating a subunit-based nanoparticle immunogen, we were able to induce the production of neutralizing and protective antibodies against POWV infection in mice. Our study provides insights into the molecular determinants of antibody-mediated neutralization and protection against TBFVs.
Article
Chemistry, Multidisciplinary
Giridhar Sekar, Adam J. Stevens, Anahita Z. Mostafavi, Pulikallu Sashi, Tom W. Muir, David Cowburn
Summary: Split intein-mediated protein trans-splicing (PTS) is a widely used method in chemical biology and biotechnology for traceless and specific protein ligation. The efficiency of PTS can be limited by external residues flanking the intein. In this study, a recently developed atypically split intein (Cat) was further modified to enhance its PTS activity in the presence of unfavorable N-extein residues. The mechanism behind the enhanced activity was explored using nuclear magnetic resonance spectroscopy and molecular dynamics simulations, highlighting the contribution of a conserved histidine residue. This enhanced extein tolerance of Cat* expands the applicability of atypically split inteins and reveals common principles of extein dependence.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Olof Stenstroem, Candide Champion, Marc Lehner, Guillaume Bouvignies, Sereina Riniker, Fabien Ferrage
Summary: This mini-review describes recent developments in experimental techniques for studying protein dynamics, discusses different analysis approaches, and highlights the importance of combining NMR relaxation experiments with MD simulations.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Article
Physics, Multidisciplinary
Nicolas Bolik-Coulon, Olivier Languin-Cattoen, Diego Carnevale, Milan Zachrdla, Damien Laage, Fabio Sterpone, Guillaume Stirnemann, Fabien Ferrage
Summary: Nuclear magnetic relaxation is commonly used for studying protein dynamics, but the model-free approach falls short when it comes to describing large carbon-13 relaxation datasets in protein side chains. To overcome this limitation, molecular dynamics simulations are employed to design explicit models of motion and solve Fokker-Planck diffusion equations, resulting in improved agreement with relaxation data, mechanistic insight, and a direct linkage to configuration entropy.
PHYSICAL REVIEW LETTERS
(2022)
Review
Biochemistry & Molecular Biology
David Cowburn, Michael Rout
Summary: Nuclear pore complexes (NPCs) play a crucial role in material exchange between the nucleus and cytoplasm, with a specific focus on nucleic acids and proteins. While the static structure of NPCs has been well defined, the functional roles of certain dynamic components, such as phenylalanyl-glycyl (FG) repeat rich nucleoporins, remain unclear. However, advancements in technical approaches and modeling methods may soon provide a more accurate and detailed understanding of NPC transport, potentially at the atomic level. Such progress would be invaluable in comprehending the impact of malfunctioning NPCs in various diseases.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2023)
Article
Biochemical Research Methods
Nicolas Bolik-Coulon, Milan Zachrdla, Guillaume Bouvignies, Philippe Pelupessy, Fabien Ferrage
Summary: This article introduces a framework for the analysis of high-resolution relaxometry that uses intensity decays to calculate relaxation rates, allowing complex relaxation pathways to be taken into account. It eliminates the need for a correction of decay rates and for fitting multi-exponential decays with mono-exponential functions.
JOURNAL OF MAGNETIC RESONANCE
(2023)
Article
Chemistry, Multidisciplinary
Heng Lu, Alex Blokhuis, Rebecca Turk-MacLeod, Jayaprakash Karuppusamy, Andrea Franconi, Gabrielle Woronoff, Cyrille Jeancolas, Afshin Abrishamkar, Estelle Loire, Fabien Ferrage, Philippe Pelupessy, Ludovic Jullien, Eoers Szathmary, Philippe Nghe, Andrew D. Griffiths
Summary: Sustained autocatalysis coupled to compartment growth and division is shown in an artificial system, where autocatalytic reactions drive osmosis and diffusion leading to compartment growth. Variation in droplet growth rate is caused by competition for a common reactant, and these variations are transmitted after selective division, demonstrating the emergence of evolution by natural selection.
Article
Biochemistry & Molecular Biology
George Georgiev, Ryan J. Malonis, Ariel S. Wirchnianski, Alex W. Wessel, Helen S. Jung, Sean M. Cahill, Elisabeth K. Nyakatura, Olivia Vergnolle, Kimberly A. Dowd, David Cowburn, Theodore C. Pierson, Michael S. Diamond, Jonathan R. Lai
Summary: Researchers have developed a recombinant ZIKV immunogen using protein engineering techniques, which can elicit a protective immune response with reduced potential for producing enhancing antibodies.
CELL CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Physical
Alexey S. Kiryutin, Ivan V. Zhukov, Fabien Ferrage, Geoffrey Bodenhausen, Alexandra V. Yurkovskaya, Konstantin L. Ivanov
Summary: ZULF-TOCSY is a novel nuclear magnetic resonance method that achieves correlations between different nuclei by evenly distributing polarization, allowing for sequential assignments in peptides and other samples with natural isotopic abundance. This method provides a valuable alternative to traditional 2D experiments, such as HMBC, by offering more comprehensive spectral information.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
