scholarly journals Utilizing pre-polarization to enhance SNMR signals—effect of imperfect switch-off

2020 ◽  
Vol 222 (2) ◽  
pp. 815-826 ◽  
Author(s):  
Thomas Hiller ◽  
Raphael Dlugosch ◽  
Mike Müller-Petke
Keyword(s):  
Spin Dynamics ◽  
Subsurface Water ◽  
Spin Excitation ◽  
Forward Modelling ◽  
Response Signal ◽  
Small Surface ◽  
Dynamics Simulations ◽  
Measured Response ◽  
Established Technique

SUMMARY Surface nuclear magnetic resonance (SNMR) is a well-established technique for the hydrogeological characterization of the subsurface up to depths of about 150 m. Recently, SNMR has been adapted to investigate also the shallow unsaturated zone with small surface loop setups. Due to the decreased volume, a pre-polarization (PP) field prior to the classical spin excitation is applied to enhance the measured response signal. Depending on the strength and orientation of the applied PP-field, the enhancement can often reach several orders of magnitude in the vicinity of the PP-loop. The theoretically achievable enhancement depends on the assumption of an adiabatic, that is perfect, switch-off of the corresponding PP-field. To study the effect of imperfect switch-off, we incorporate full spin dynamics simulations into the SNMR forward modelling. The affected subsurface volume strongly depends on the chosen PP switch-off ramp and the geometry of the loop setup. Due to the imperfect switch-off, the resulting SNMR sounding curves can have significantly decreased signal amplitudes. For comparison, the signal amplitudes of either a 1 ms exponential or linear switch-off ramp are reduced by 17 and 65 per cent, respectively. Disregarding this effect would therefore yield an underestimation of the corresponding subsurface water content of similar magnitude.

scholarly journals Characterization of design grammar of peptides for regulating liquid droplets and aggregates of FUS

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kiyoto Kamagata ◽  
Rika Chiba ◽  
Ichiro Kawahata ◽  
Nanako Iwaki ◽  
Saori Kanbayashi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Electrostatic Interactions ◽  
Amyloid Fibrils ◽  
Droplet Formation ◽  
Liquid Droplets ◽  
Proof Of Concept ◽  
Aggregate Formation ◽  
Fused In Sarcoma ◽  
Dynamics Simulations

AbstractLiquid droplets of aggregation-prone proteins, which become hydrogels or form amyloid fibrils, are a potential target for drug discovery. In this study, we proposed an experiment-guided protocol for characterizing the design grammar of peptides that can regulate droplet formation and aggregation. The protocol essentially involves investigation of 19 amino acid additives and polymerization of the identified amino acids. As a proof of concept, we applied this protocol to fused in sarcoma (FUS). First, we evaluated 19 amino acid additives for an FUS solution and identified Arg and Tyr as suppressors of droplet formation. Molecular dynamics simulations suggested that the Arg additive interacts with specific residues of FUS, thereby inhibiting the cation–π and electrostatic interactions between the FUS molecules. Second, we observed that Arg polymers promote FUS droplet formation, unlike Arg monomers, by bridging the FUS molecules. Third, we found that the Arg additive suppressed solid aggregate formation of FUS, while Arg polymer enhanced it. Finally, we observed that amyloid-forming peptides induced the conversion of FUS droplets to solid aggregates of FUS. The developed protocol could be used for the primary design of peptides controlling liquid droplets and aggregates of proteins.

scholarly journals A simple interferometric method to measure the calibration factor and displacement amplification in piezoelectric flextensional actuators

2010 ◽  
Vol 21 (6) ◽  
pp. 577-587 ◽  
Author(s):  
Francisco de Assis Andrade Barbosa ◽  
Gilder Nader ◽  
Ricardo Tokio Higuti ◽  
Cláudio Kitano ◽  
Emílio Carlos Nelli Silva
Keyword(s):  
Modulation Depth ◽  
Low Cost ◽  
Michelson Interferometer ◽  
Laser Interferometry ◽  
Optimization Method ◽  
Calibration Factor ◽  
Simple Method ◽  
Interferometric Method ◽  
Established Technique

Laser interferometry is a well-established technique for the characterization of piezoelectric actuators. In this work, by using a low cost Michelson interferometer, the measurement of the calibration factor and the displacement amplification of a novel piezoelectric flextensional actuator (PFA), designed by using the topology optimization method, is performed. A simple method, based on small phase modulation depth when the PFA is driven by a triangular waveform, allows the absolute interferometer calibration. The free-displacement of the PFA for various drive voltages is measured and the displacement amplification is determined. The linearity and frequencyresponse of the PFA are evaluated up to 20 kHz

scholarly journals HT-SuMD: Making Molecular Dynamics Simulations Suitable for Fragment-Based Screening. a Comparative Study with NMR

2020 ◽  
Author(s):  
Francesca Ferrari ◽  
Maicol Bissaro ◽  
Simone Fabbian ◽  
Jessica de Almeida Roger ◽  
Stefano Mammi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Solution Nmr ◽  
Protein Recognition ◽  
Fragment Screening ◽  
Fragment Library ◽  
Dynamics Simulations ◽  
A Prospective Study ◽  
First Time ◽  
Established Technique ◽  
State Of Art

<p>In this manuscript, for the first time, we presented a fragment library and we validated its performance by comparison with a well-established technique for fragment screening as solution NMR. We were able to screen 400 different fragments producing a total of 1200 independent fragment-protein recognition pathways. As far as we know, this represents the largest screening based on Molecular dynamics ever reported. Our simulations successfully detected the true binders in the library in a prospective study, showing a notable agreement with a state-of-art screening we performed by NMR on the same dataset.</p>

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