Pavel Fadeev, Sensitivity of 229Th nuclear clock transition to variation of the fine-structure constant, , 2020 pp. 1-5.
A nuclear clock has been proposed based on the isomeric transition between the ground state
and the first excited state of thorium-229. This transition was recognized as a potentially sensitive
probe of possible temporal variation of the fine-structure constant, α. The sensitivity to such a
variation can be determined from measurements of the mean-square charge radius and quadrupole
moment of the different isomers. However, current measurements of the quadrupole moment are yet
to achieve accuracy high enough to resolve non-zero sensitivity. Here we determine this sensitivity
using existing measurements of the change in mean-square charge radius, coupled with the ansatz of
4
The Coulomb energy EC depends on the shape of the nucleus. Unlike atomic systems, which are spherical due to the 1/r potential from pointlike nucleus (r is the dis- tance from the nucleus), nuclear systems can have de- formed shapes as the potential originates from the nucle- ons themselves. Ref. [20] showed that, by modeling the nucleus as a prolate spheroid [22], ∆EC can be deduced from measurements of the change in nuclear charge ra- dius and quadrupole moment between the isomeric and ground states. Using this model with measurements of nuclear parameters, the authors in [23] give a value of
∆EC =−0.29(43)MeV, (3)
where the dominant source of error is the uncertainty
in measured quadrupole moments of the ground and the
constant nuclear density. The enhancement factor for α-variation is K = −(0.9 ± 0.3) × 10 . For the current experimental limit δα/α 10−17 per year, the corresponding frequency shift is ∼200 Hz. This shift is six orders of magnitude larger than the projected accuracy of the nuclear clock, paving the way for increased accuracy for determination of δα and interaction strength with low mass scalar dark matter. We verify that the constant-nuclear-density ansatz is supported by nuclear theory and propose how to verify it experimentally. We also consider a possible effect of the octupole deformation on the sensitivity to α-variation.
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Anon. (2015), After 50 years, why are Protein X-ray Crystallographers still in business?, British Journal For The Philosophy Of Science, 2015 pp. 1-41.
It has long been held that the structure of a protein is determined solely by the interactions of the atoms in the sequence of amino acids of which it is composed, and thus the stable, biologically functional conformation should be predictable by ab initio or de novo methods. However, except for small proteins ab initio predictions have not been successful. We explain why this is the case and argue that the relationship among the different methods, models and representations of protein structure is one of integrative pluralism. Our defense appeals to specific features of the complexity of the functional protein structure and to the partial character of representation in general. We present examples of integrative strategies in protein science.
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Sai Chaitanya Chiliveri and Mandar V Deshmukh, Recent excitements in protein NMR: Large proteins and biologically relevant dynamics, Journal Of Biosciences, 41 (2016) 787-803.
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Charles J Divin et al., Whole spectrum fluorescence detection with ultrafast white light excitation, Optics Express, 15 (2007) 10439-10445.
We have developed a new detection mechanism for ultrabroadband multicolor fluorescence detection using an ultrafast supercontinuum white light source without spectral filtering to simultaneously excite different fluorophores. A nonlinear photonic crystal fiber was utilized in conjunction with a femtosecond laser to generate the supercontinuum. A time-resolved detector was tested to detect the whole spectrum fluorescence while gating out the excitation white light in the time domain.
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Jens Frahm, Biomedizinische NMR - The basic paper: Real-time MRI at a Resolution of 20 ms, Biomednmr.Mpg.De, 2019 pp. 1-3.
As I wrote e.g. here ten years ago , I consider Weinberg's "Asymptotic Safety" paradigm in quantum gravity to be a deep misunderstanding. ...
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Pamela N Gallo et al., Toward comprehensive measurement of protein hydration dynamics_ Facilitation of NMR-based methods by reverse micelle encapsulation, Methods, 148 (2018) 146-153.
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Eric Gloaguen et al., Spontaneous Formation of Hydrophobic Domains in Isolated Peptides, The Journal Of Physical Chemistry B, 117 (2013) 4945-4955.
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Samuel L Junod et al., Nucleocytoplasmic transport of intrinsically disordered proteins studied by high‐speed super‐resolution microscopy, Protein Science, 11 (2020) 161-14.
Both natively folded and intrinsically disordered proteins (IDPs) destined for the nucleus need to transport through the nuclear pore complexes (NPCs) in eukaryotic cells. NPCs allow for passive diffusion of small folded proteins while barricading large ones, unless they are facilitated by nuclear transport receptors. However, whether nucleocytoplasmic transport of IDPs would follow these rules remains unknown. By using a high-speed super-resolution fluorescence micros- copy, we have measured transport kinetics and 3D spatial locations of transport routes through native NPCs for various IDPs. Our data revealed that the rules executed for folded proteins are not well followed by the IDPs. Instead, both large and small IDPs can passively diffuse through the NPCs. Furthermore, their diffusion efficiencies and routes are differentiated by their content ratio of charged (Ch) and hydrophobic (Hy) amino acids. A Ch/Hy-ratio mechanism was finally suggested for nucleocytoplasmic transport of IDPs.
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Rainer Körber et al., SQUIDs in biomagnetism: a roadmap towards improved healthcare, Superconductor Science And Technology, 29 (2016) 113001-31.
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Jeff W Lichtman and José-Angel Conchello, Fluorescence microscopy, Nature Methods, 2 (2005) 910-919.
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Eugene Lin and Adam Alessio, What are the basic concepts of temporal, contrast, and spatial resolution in cardiac CT?, Journal Of Cardiovascular Computed Tomography, 3 (2009) 403-408.
An imaging instrument can be characterized by its spatial resolution, contrast resolution, and temporal resolution. The capabilities of computed tomography (CT) relative to other cardiac imaging modalities can be understood in these terms. The purpose of this review is to characterize the spatial, contrast, and temporal resolutions of cardiac CT in practical terms.
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Ripa Paul et al., Fluorescence Resonance Energy Transfer (FRET) as Biomarkers, Arxiv.Org, 2020 2005.01031v1, physics.bio-ph.
Applications of Fluorescence Resonance Energy Transfer (FRET) in biology have expanded tremendously in the last 25 years. This technique has become a staple technique in many biological and biophysical fields. FRET based chemical sensors and biosensors can play an important role as biomarkers. Development of new and effective FRET based assay for biological application is an emerging area of research needing multidisciplinary approach from biologists, chemists and physicists. Here we have discussed the use of FRET technique as biomarker.
Published in: Materials Today: Proceedings (2020)
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Steffen J Sahl and W E Moerner, Super-resolution fluorescence imaging with single molecules, Current Opinion In Structural Biology, 23 (2013) 778-787.
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Sviatlana Shashkova and Mark C Leake, Single-molecule fluorescence microscopy review: shedding new light on old problems, Bioscience Reports, 37 (2017) BSR20170031-19.
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P Shealy et al., Automated Assignment of Backbone Resonances Using Residual Dipolar Couplings Acquired from a Protein with Known Structure, Arxiv.Org, 2019.
Resonance assignment is a critical first step in the investigation of protein structures using NMR spectroscopy. The development of assignment methods that require less experimental data is possible with prior knowledge of the macromolecular structure. Automated methods of performing the task of resonance assignment can significantly reduce the financial cost and time requirement for protein structure determination. Such methods can also be beneficial in validating a protein's solution state structure. Here we present a new approach to the assignment problem. Our approach uses only RDC data to assign backbone resonances. It provides simultaneous order tensor estimation and assignment. Our approach compares independent order tensor estimates to determine when the correct order tensor has been found. We demonstrate the algorithm's viability using simulated data from the protein domain 1A1Z.
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Satoshi Takahashi et al., ScienceDirect Where the complex things are: single molecule and ensemble spectroscopic investigations of protein folding dynamics, Current Opinion In Structural Biology, 36 (2016) 1-9.
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B Verlhac et al., Atomic-scale spin sensing with a single molecule at the apex of a scanning tunneling microscope., Science, 366 (2019) 623-627.
Recent advances in scanning probe techniques rely on the chemical functionalization of the probe-tip termination by a single molecule. The success of this approach opens the prospect of introducing spin sensitivity through functionalization by a magnetic molecule. We used a nickelocene-terminated tip (Nc-tip), which offered the possibility of producing spin excitations on the tip apex of a scanning tunneling microscope (STM). When the Nc-tip was 100 picometers away from point contact with a surface-supported object, magnetic effects could be probed through changes in the spin excitation spectrum of nickelocene. We used this detection scheme to simultaneously determine the exchange field and the spin polarization of iron atoms and cobalt films on a copper surface with atomic-scale resolution.
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Anastasia Zhuravleva and Dmitry M Korzhnev, Progress in Nuclear Magnetic Resonance Spectroscopy, Progress In Nuclear Magnetic Resonance Spectroscopy, 100 (2017) 52-77.
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