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Pulsar.jl: A Unified Julia Framework for Pulse Design Across Magnetic Resonance and Quantum Technologies
David Joseph (Germany)
LinkedIn: David Joseph; X: @DaJo_1729; Bluesky: @dajo-1729.bsky.social
Abstract: Pulse shape design underpins modern magnetic resonance and, increasingly, other quantum technologies — yet its toolkits remain fragmented across sub-fields. We present Pulsar.jl (Pulse Design Library for Spin Control Algorithms and Rollout), an open-source Julia package that unifies pulse optimization across magnetic resonance (solution-state NMR, MAS solid-state NMR, EPR, MRI, and DNP) and quantum technology/computing platforms (transmon, trapped-ion, neutral-atom, and NV-center). A shared, layered core enables techniques to cross-pollinate between communities and lets users extend the framework to any application requiring pulse shaping. Pulsar.jl supports closed- and open-system (Lindblad) dynamics, automatic differentiation, and CPU/CUDA/Metal acceleration. Its algorithm layer comprises over 40 optimization methods, spanning quantum optimal control (GRAPE, Krotov, GOAT, CRAB, L-BFGS versions etc.) and metaheuristics (CMA-ES, particle swarm, basin hopping, Annealing, Monte Carlo etc.) and more. Optimized pulses can be exported directly to instrument-ready formats for magnetic resonance (Bruker, JEOL, EPR), quantum computing (Qiskit, Quil-T, QUA), and MRI. A driver-based benchmarking framework further enables matched, canonically re-evaluated comparisons against established packages including Spinach, SIMPSON, QuTiP, Krotov.jl, and Quandary, helping users identify the best tool for their application. By consolidating multi-regime physics, a comprehensive algorithm library, and reproducible cross-solver benchmarking, Pulsar.jl bridges pulse design for magnetic resonance and quantum technologies in a single framework.
Github: https://github.com/DaJo2025/Pulsar.jl and
documentation: https://dajo2025.github.io/Pulsar.jl/stable/8 responses to “Pulsar.jl: A Unified Julia Framework for Pulse Design Across Magnetic Resonance and Quantum Technologies”
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Hi David!
Nice work and presentation, thank you!
When I look at the benchmark table, I cannot help but notice that, time-wise, Pulsar confidently outperforms many packages at UR-90 and UR-180 and in some other cases too. Is this an intrinsic feature of Pulsar due to optimal algorithm implementation? Following up on this, does Pulsar offer a guided comparison of more or less standard methods by default? Or does the user need to try out several of those manually and decide afterwards?
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Hi Sergei,
Thanks!
Regarding the speedup: beyond the algorithmic implementation, a significant portion of the performance gain comes from Julia’s JIT compilation, which is one of the main reasons I chose to develop in Julia. In many common cases, Pulsar does outperform existing software. However, I am still working on a structured and fair comparison. I want to avoid misleading users, so I am actively identifying examples where different tools perform better than others. The goal is to ensure that personal bias does not influence the guidance. I expect this comparison to be publicly available soon (still in development stage). Ultimately, the benchmark tool is intended for new projects, helping users make informed decisions about which software or algorithmic implementation is best suited to their specific application.
Dav
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Very useful tool.
Have you compared the simulated B₀/B₁ robustness profiles with experimental profiles after exporting the pulse to a spectrometer, to assess how hardware-dependent waveform distortions affect the achieved fidelity?-
Hi Shubha,
Comparisons of simulated B₀/B₁ robustness profiles with experimental profiles has been extensively done for solution NMR. For example in one of my earlier work (https://www.science.org/doi/10.1126/sciadv.adj1133) contains extensive benchmarks of this sort from experiment and simulations for various optimal control pulses, check out the ~90 page long ESI.
Dav
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Dear David,
I saw all three of your presentations. Nice presentation.
I work primarily with quadrupolar nuclei, so I was wondering how well Pulsar.jl addresses the unique challenges of pulse design for these systems.
Does the software explicitly support pulse optimization for quadrupolar nuclei, or is its current focus mainly on spin-½ systems? Given the large quadrupolar couplings, can it design broadband, robust pulses that perform well over a distribution of quadrupolar interactions? Does it also support pulse optimization for multiple-quantum experiments, such as MQMAS?
Since quadrupolar nuclei often exhibit rapid relaxation, can relaxation mechanisms be incorporated directly into the optimization objective? In addition, is it possible to optimize pulses for selective excitation of the central transition while minimizing excitation of the satellite transitions?
More broadly, quadrupolar nuclei remain one of the most challenging areas for pulse optimization because of broad powder patterns, second-order quadrupolar effects, and fast relaxation. Do you see Pulsar.jl evolving into a platform for developing the next generation of robust quadrupolar NMR experiments? If so, are there any specific applications or directions that you are particularly excited about?
Thank you.
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Hi Madhusudan,
Thanks!
At the moment, Pulsar.jl provides partial support for pulse optimization of quadrupolar nuclei. Broadband excitation can equality be optimized, relaxation can be included in optimization, but additional development is likely needed to fully support other applications you mentioned. If there is enough interest in this direction, this could be included in a future release.
Pulsar.jl is an open-source project, so I encourage you to explore its development if you are interested in coding. It has the potential to contribute to the next generation of robust quadrupolar NMR experiments, given there would be an active community to support this objective. I would be glad to assist with this effort from my side.
Dav
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Dear David,
I saw all three of your presentations. Nice presentation.
I work primarily with quadrupolar nuclei, so I was wondering how well Pulsar.jl addresses the unique challenges of pulse design for these systems.
Does the software explicitly support pulse optimization for quadrupolar nuclei, or is its current focus mainly on spin-½ systems? Given the large quadrupolar couplings, can it design broadband, robust pulses that perform well over a distribution of quadrupolar interactions? Does it also support pulse optimization for multiple-quantum experiments, such as MQMAS?
Since quadrupolar nuclei often exhibit rapid relaxation, can relaxation mechanisms be incorporated directly into the optimization objective? In addition, is it possible to optimize pulses for selective excitation of the central transition while minimizing excitation of the satellite transitions?
More broadly, quadrupolar nuclei remain one of the most challenging areas for pulse optimization because of broad powder patterns, second-order quadrupolar effects, and fast relaxation. Do you see Pulsar.jl evolving into a platform for developing the next generation of robust quadrupolar NMR experiments? If so, are there any specific applications or directions that you are particularly excited about?
Thank you.
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Same as the above reply
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Quadrature-Symmetric PulsePol for Robust Quantum Control Beyond The Ideal Pulse Approximation
Author: Mayur Manoj Jhamnani (NYU Abu Dhabi, UAE)
LinkedIn: Mayur Jhamnani, X: @mayur_jhamnani
Abstract: PulsePol is an elegantly designed pulse-sequence-based quantum control scheme that enables polarization transfer between electron and nuclear spins. However, previous analyses of PulsePol assumed very strong, close to ideal, instantaneous microwave pulses, which is rarely achievable as one goes to higher magnetic fields. We revisit the PulsePol scheme under finite-pulse constraints and show that its performance significantly degrades because of finite-pulse effects. Using bimodal Floquet theory, we identify the symmetry-breaking mechanism responsible for this deteriorating fidelity. By phase adjustment, we reestablish the proper symmetry of the interaction-frame spin Hamiltonian—leading to a sequence called Q-PulsePol, where ‘Q’ reflects the restored quadrature symmetry. Our results demonstrate robustness to finite-pulse effects and improved polarization transfer efficiency, establishing Q-PulsePol as a practical and reliable scheme for bulk hyperpolarization of nuclear spins in solid-state using a single-mode (zero-quantum or double-quantum) transfer. This work bridges idealized quantum control with realistic pulse engineering, establishing design rules for spin-based quantum-control protocols.
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Real-time zero-field magnetometry using a single NV center coupled to a first-shell 13C nuclear spin in diamond
Pralekh Dubey (IISER Bhopal, India)
LinkedIn: Pralekh Dubey
Abstract: Nitrogen-vacancy (NV) centers in diamond are robust and versatile solid-state defects that serve as optically addressable spin qubits under ambient conditions. When coupled to nearby first-shell 13C nuclear spins, they form a hybrid electron-nuclear spin system with rich hyperfine structure, which can also serve as a quantum register for NMR, quantum information processing and sensing applications 1. Here, we explore this coupled system in the context of zero-field quantum sensing 2. We demonstrate real-time zero-field magnetometry using first-shell 13C-coupled single NV centers in diamond. The strong hyperfine interaction (~130MHz) 3 with the proximal 13C spin lifts the degeneracy of the NV spin transitions and provides an intrinsic bias in the absence of an external magnetic field 4,5. Selective addressing and tracking of individual transitions under zero-field conditions, allows time-varying magnetic fields (up to few Hz) to be monitored in real time. This work highlights how coupled NV-13C spin systems are valuable for real-time zero-field magnetometry, with possible extension to other solid-state systems.
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Reshaping an Epigenetic DNA Reader: Evolution Driven by Dynamics
Himanshu Singh (IIT Guwahati, India)
LinkedIn: Himanshu Singh
Abstract: The four canonical DNA bases are subject to a wide range of chemical modifications that play critical roles in genome regulation. In recent years, numerous modified DNA bases and the enzymes responsible for their processing have been discovered, highlighting their importance in human diseases such as cancer and neurological disorders. Epigenetic DNA modifications enable cells with identical genomes to acquire distinct functional identities. While cytosine methylation is relatively well characterized, the biological roles of many other DNA modifications remain poorly understood, largely due to challenges in their site-specific detection.
Engineered DNA reader proteins that selectively recognize individual epigenetic marks offer a promising strategy for interrogating the genome at single-base resolution. Understanding the structural and dynamic principles governing DNA recognition by both natural and designed readers is essential for developing molecular probes to study chromatin biology and disease-associated defects in target recognition.
Using a combination of mutagenesis, NMR relaxation experiments, structural analyses, and MD simulations, we demonstrated that the selectivity of the first engineered reader for an oxidized CpG epigenetic mark depends on finely tuned conformational plasticity acquired during the directed evolution of its natural progenitor. Our findings reveal that specific dynamic features are critical for achieving both high affinity and selectivity in DNA recognition.Leave a Reply
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Serum Metabolomic Profiling by ¹H-NMR Reveals Distinct Metabolic Signatures in Diabetic and Non-Diabetic Chronic Kidney Disease
Amrita Sahu (Centre of Biomedical research, India)
LinkedIn: Amrita Sahu
Abstract: Chronic kidney disease (CKD) and Type 2 diabetes mellitus (DM) are global health burdens, with diabetes being the leading cause of end-stage renal disease, both marked by systemic metabolic disruption. This study applied 1H NMR-based serum metabolomics to characterize metabolic alterations in CKD only (n = 31), DM (n = 33), and their comorbid state (CKD_DM; n = 45). A total of 45 polar metabolites and seven lipid signals were quantified, and statistical analysis was performed using MetaboAnalyst 6.0. The CKD_DM profile was not a linear combination of the CKD and DM profiles. Compared with DM, CKD_DM shows perturbation in pyruvate, glycerophospholipid, and butanoate metabolism, while tyrosine metabolism, TCA cycle, and cysteine–methionine were prominently altered in CKD only and CKD_DM group. CKD only and CKD_DM partially overlapped based on polar metabolites, and lipid-associated signals clearly separated all three groups. mROC analyses identified a significant six-metabolite panel (creatinine, glucose, urea, myo-inositol, glycine, choline) that robustly distinguished CKD_DM from DM(AUC>0.9). TMAO, isobutyrate, glycerol (AUC > 0.76), and a three-lipid-signal panel (AUC > 0.99) distinguished CKD only from CKD_DM, and the seven-metabolite panel separates CKD only from DM(AUC>0.9). Overall, CKD_DM emerges as a distinct metabolic phenotype with integrated metabolite and lipid signatures, enhanced disease stratification, and improved diagnostics.
Keywords: Chronic Kidney disease, Diabetes, NMR-based metabolomics, Metabolic biomarkersLeave a Reply
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Single-Scan Characterization of 14N Nuclei via 1H-Detected Rotating-Frame Relaxometry
Florin Teleanu (New York University, United States)
LinkedIn: Florin Teleanu, X: @teleanuflorin, BlueSky: @teleanuflorin.bsky.social
Abstract: 14N NMR is notoriously difficult to perform in liquids due to the very fast spin relaxation and the large quadrupolar couplings, which render many signals invisible. We show here how 14N nuclei of biomolecular constituents can be probed indirectly by reintroducing the scalar relaxation of the second kind contribution to the polarization lifetimes of J-coupled protons in double resonance spin-locking experiments. The enhanced 1H relaxation rates in the rotating-frame allow for direct evaluation of nitrogen chemical shift and polarization lifetimes, from which one- and even two-bond 1H-14N scalar couplings as well as 14N quadrupolar interactions can be determined. We demonstrate the versatility of this method by characterizing 1H-14N spin pairs in several molecules of biological importance, showing proton relaxation enhancements beyond one order of magnitude. We further observe a pronounced effect from intermolecular hydrogen bonding. Our approach can be readily integrated into existing biomolecular NMR methodologies, as demonstrated here for 1H-detected relaxation-editing experiments with water suppression. This method provides access to nitrogen’s picosecond-modulated quadrupolar interaction via single-scan proton detection in systems that would otherwise yield almost no detectable direct 14N signal even after averaging over thousands of transients.
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4 responses to “Single-Scan Characterization of 14N Nuclei via 1H-Detected Rotating-Frame Relaxometry”
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Hi Florin, very nice work. Could you comment on how long a 1H detected experiment is if reasonable resolution in the 14N dimension is desired ? You mention you are able to detect intermolecular H-bonding with this technique, how sensitive are you with this in terms of concentrations and would this be applicable in larger biomolecules ?
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I have few queries
1. Your method extracts information about an essentially “invisible”
14 N nucleus through its effect on proton rotating-frame relaxation. How can you rigorously distinguish relaxation enhancements arising from 14N scalar relaxation of the second kind from other proton relaxation mechanisms—such as chemical exchange, dipolar interactions, or cross-correlated relaxation that may also contribute under spin-lock conditions, especially in complex biomolecular systems?2. Since the method relies on the very fast quadrupolar relaxation of
14 N, is there an optimal relaxation regime? In other words, can the quadrupolar relaxation become so fast that the scalar relaxation pathway itself becomes inefficient, setting an upper limit on the sensitivity of your approach?3. Could the same relaxation mechanism be exploited to obtain dynamic information, such as local electric field fluctuations or hydrogen-bond lifetimes, rather than just static quadrupolar parameters?
4. Could this method distinguish transient hydrogen bonds from stable ones on biologically relevant timescales, or is the measured relaxation enhancement effectively averaged over all exchanging states?
5. You suggest that the method can be readily integrated into existing biomolecular NMR workflows. How does its sensitivity and information content compare quantitatively with established heteronuclear approaches using
15 N labeling, and in what situations would one genuinely prefer 14 N over simply isotopically enriching the sample?Sorry for such a long comment
But I would love to know more being a person interested in biomolecular NMR -
Your method relies on the presence of scalar coupling to a proton. Does this fundamentally restrict the approach to protonated nitrogens, or could it be extended to quaternary or non-protonated nitrogen sites through longer-range couplings?
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Hello Florin,
Nice presentation. I really enjoyed it.
I had one question regarding your observation of the pronounced effect of intermolecular hydrogen bonding. How did you arrive at this conclusion? Since DMSO is generally considered a strong hydrogen-bond-accepting solvent, is it an appropriate medium for probing intermolecular hydrogen-bonding effects? Did you also perform experiments in aprotic or less strongly interacting solvents to compare the results?
Thank you!
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Study of the palladium reduction step of the photo-catalyzed Heck reaction through NMR methods
João Pedro Brussolo da Silva (Universidade Estadual Campinas, Brazil)
LinkedIn: João Pedro Brussolo da Silva
Abstract: Palladium is one of the most extensively employed transition metals in organic catalysis, particularly in cross-coupling transformations. In many Heck reactions, phosphine ligands coordinate to palladium, while a Pd(II) precatalyst is reduced to Pd(0), generating the catalytically active species that enters the Heck catalytic cycle. More recently, the incorporation of photocatalysis has enabled a much faster reduction of palladium under light irradiation, leading to significant improvements in reaction rates. Nevertheless, the precise role of light throughout the catalytic cycle, as well as the identity of the active palladium species, remains incompletely understood. Because the performance of transition-metal-catalyzed cross-coupling reactions is highly dependent on the ligand environment, identifying the catalytic complex is essential for obtaining a deeper mechanistic understanding.
To address these questions, this work investigates the palladium reduction step using in situ NMR spectroscopy. Kinetic 31P NMR experiments were carried out to compare the reduction process under irradiated and dark conditions, allowing the influence of light on catalyst formation to be assessed. In addition, diffusion-ordered spectroscopy (DOSY) experiments were employed to estimate the molecular size of the species present in solution, providing complementary evidence for the identification of the catalytic complexes.
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6 responses to “Study of the palladium reduction step of the photo-catalyzed Heck reaction through NMR methods”
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Hi João, great talk, congratulations. I have a couple questions:
1) Your data suggest that the reaction in light conditions induces the formation of cis-Pd, and the reaction is faster. How the presence of cis-Pd influences the chemical shifts and line-broadening of the Pd0 equilibrium signal?
2) Your data also suggest the impact of temperature on the reaction. Is the cis-Pd formation faster in 0oC as it seems? If yes, why?Thanks!
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Nice work. Since the cis-Pd species is still evolving even at 0 °C, how did you rule out kinetic bias in the 31P DOSY coefficients from concentration changes during the gradient series?
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Nice work. Since the cis-Pd species is still evolving even at 0 °C, how did you rule out kinetic bias in the ^31P DOSY coefficients from concentration changes during the gradient series?
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Nice work. Since the 31P DOSY was performed at 0 °C to slow the consumption of the cis-Pd species, how did you verify that concentration changes during the gradient array did not bias the fitted diffusion coefficients?
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Hi, Karen!
Thank you for the comment!
1) The point is that the pre catalyst (Pd0(PPh3)n) has a faster formation from the cis-Pd complex in comparision to the trans-Pd one. So, once the light produces de cis isomer, the Pd0 equilibrium signal has a faster shift to 22 ppm region, and than, becomes sharper. This behaviour indicates that the equilibrium is shifted to pre catalyst formation. In fact, this shift can be seen on dark condition as well, without the presence of cis isomer, but in a much more slower way (more than 24h).
2) Nice question, but i think that is not a faster formation for cis in 0oC. The point is that probably, with the precatalyst faster formation in the higer temperature, the cis species are formed and faster consumed. In the case of 0oC, maybe we are seen the acumulation of cis isomer due to the it slower consuptiom.
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Hi Shubha,
To avoid the measurement error due to the consumption of the species, we monitored the signal in the kinetic experiment, and then, over a 15-minute interval, the variation was very small. So we performed an 11-minute DOSY measurement to avoid this problem.
Thank you for the question!
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Sustainability in NMR- Benchmarking A fully Cryogen-Free, High Field NMR System
Mathew Brevard (Superconducting Systems/ IMRIS, USA)
LinkedIn: @Mathew Brevard, Bluesky: @superconductingsys.bsky.social
Abstract: Helium has a high cost, massive supply volatility, can be stressful to manage and carries a HUGE carbon footprint. High Field NMR requires superconductivity, but cryogen-free (CF)high field magnets have been in production for 3 decades and are considerably smaller and more efficient. We applied the latest CF technology to a full NMR system to establish the viability of this approach.
NMR was performed on a shielded, superconducting and persistent 89mm clear bore (rampable 0.5 to 9.4T) CF magnet and put it up to a rigorous set of NMR experiments to test performance and stability.
Testing with a Bruker AV3 and RS2D Console connected to a 20 Channel Bruker BOSS1 Shim and a 2H/1H/X BB 5mmx 16mm L Bruker probe. We ran spectra on a slew of standardized samples including: 0.1% Ethylbenzene, 1% Chloroform, Cyclosporin, Gramacidin, Quinidine, Heptanone and Cholesterol.The system shimmed to superior levels with 0.1% Ethylbenzne producing full triplet and quadruplet splitting and an SNR of 495. Linewidth tests on 1% CHCL3 tests without spinning gave line widths of 0.26Hz @ 50%, 4 Hz @ 0.55% and 7Hz @ 0.11%. Spectra and 2D experiments for complex molecules have comparable performance to traditional NMR systems.
Results show that NMR in a fully cryogen-free magnet is fully viable. CF for routine high field NMR could substantially reduce the NMR communities reliance on non-renewable helium, reduce carbon emissions and also offer considerable space and energy savings over helium recapture systems.
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Helium independence for High-Field MRI
11 responses to “Sustainability in NMR- Benchmarking A fully Cryogen-Free, High Field NMR System”
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Does it need a helium compressor? How long can the magnet remain cold during a compressor failure?
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Yes, the magnet uses a pulse tube cryo-cooler to remove heat instead of using any liquid cryogenic.
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Thanks! The magnet uses a pulse tube cryocooler to cool the superconducting magnet coil instead of a liquid bath of cryogens.
If the power goes out, the magnet will loose field in about 15 minutes but there is no boiloff quench that occurs so the systems sits in vacuume at like 20-30K for many days. When the compressor is powered on, the magnet cools back down (usually 3-4 hours) and then it comes with a power supply so you just ramp it back up which takes about an hour. -
Thank you very much for your clear and informative presentation.
As someone who works with CF magnets, I have a question regarding the maintenance of the CF magnet you presented. How often does it require maintenance? Is there a risk of contamination? If so, could you provide an estimate of how frequently contamination occurs? -
Thanks for the question. A coldhead has a suggested rebuild interval of 30,000 hours. In the field we see longer service life actually though.
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As to risk, coldbhead swaps usually happen on site and so there have not been contamination issues in our several decades of building these magnets. The system has to be vacuum pumped after anyway.
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Thank you for your answers.
I have another question. Is it possible to adjust the probe temperature? For example, does the system allow temperature control in the same way as a Bruker system, where you can set and maintain a specific probe temperature during an experiment? -
Yes, probe temperature can be set on the console. The magnet and the control of its cooling and charging system is separate from the NMR console. Data presented from our work was made with a Bruker AV3 console and other data in an RS2D console. We offer the magnet as a stand alone replacement for tradition helium magnets where we interface all your existing coils, shims and console. We also offer a full system with an RS2D console and shim and probe.
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Okey thank you.
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Interesting talk,
I have one naive question, is the electricity consumption much higher compared to conventional magnets?
Thank you!
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Thanks, the cooling system uses 7kw peak power for cooling. That’s 1/3 the electricity an ultra low temperature freezer uses, so the power draw is not too substantial. You can also draw the field down anytime which reduces the power draw.
You can also turn the whole system off for any longer periods and then bring it back up anytime you wish.
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SYNTHESIS, CHARACTERIZATION AND BIOLOGICAL EVALUATION OF AROMATIC AMINES BASED THIADIAZINE THIONE ANALOGS
Fazal Habib (HEJ Research Institute of Chemistry, ICCBS, University of Karachi, Pakistan)
LinkedIn: Fazal Habib
Abstract: In organic chemistry, aromatic amines are compounds that contain an aromatic ring bonded to an amine group. They have a broad spectrum of applications across various industries, including pharmaceuticals, agrochemicals, and in the synthesis of diverse heterocyclic compounds. Heterocyclic compounds are characterized by rings that contain one or more heteroatoms, and they possess significant chemical and biological relevance. Among these, tetrahydro thiadiazine thiones (THTT) derivatives exhibit a wide spectrum of biological activities. They serve as precursor in drug delivery systems and demonstrate exceptional potential as structural units in the synthesis of novel drugs, agrochemicals, and functional materials owing to their combined lipophilic and hydrophilic properties. The synthesis of THTT derivatives was carried out by treating different alkyl/aryl amines with carbon disulfide in potassium hydroxide medium at room temperature. This was followed by the addition of
formaldehyde and a buffer solution containing 4-aminobenzoic acid, resulting in the formation of the corresponding THTT derivatives. These compounds were then refluxed in ethanol in the presence of sulfuric acid to obtain esterified THTT derivatives. The reaction progress was monitored by thin layer chromatography. Structural confirmation of the synthesized compounds was confirmed using proton nuclear magnetic resonance spectroscopy. The in vitro inhibition activities of the synthesized compounds were evaluated against α-amylase and urease enzymes. Among the tested compounds, F7 exhibited the lowest, F4 shows the highest, while the remaining six compounds demonstrated moderate αamylase and urease inhibitory activities.Leave a Reply
One response to “SYNTHESIS, CHARACTERIZATION AND BIOLOGICAL EVALUATION OF AROMATIC AMINES BASED THIADIAZINE THIONE ANALOGS”
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Hi Fazal
Could you explain what specific proton NMR experiments were conducted for the structural elucidation of products? Thank you.
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Systematic enumeration for describing the IDP and IDR conformations landscape
Therese Malliavin (CNRS, Université de Lorraine, France)
LinkedIn: @Therese Malliavin
Abstract: Intrinsically disordered proteins (IDP) and intrinsically disordered regions (IDR) are at the center of numerous regulation and control pathways in the cell, and attract consequently extreme interest nowadays in structural biology. Nevertheless, it is difficult to characterize the conformational landscape of IDP,
as they sample highly variable conformations of similar energy. Thus, the structural convergence criterion used in classical NMR structure determination does not apply here. Therefore, the analysis of IDP conformational spaces classically relies on the use of Monte Carlo and molecular dynamics simulations. We present here the use of the geometric Threading-Augmented interval Branch-and-Prune (TAiBP) approach which permits to enumerate systematically the possible conformations verifying a set of NMR chemical shifts. The combinatorial explosion due to the enumeration is alleviated by partitioning the input instances into consecutive peptide fragments and by systematic solutions clustering using self-organizing maps. The obtained sets of protein conformations can be further filtered using Small Angle X-ray Scattering (SAXS) curves or Residual Dipolar Coupling (RDC) values. Several applications will be presented.
References:
Huang, Shih, Jeng, Chang, Lin, Malliavin. pH Sensitivity of the SERF1a Conformational Ensemble. ACS Omega 2026 11:2614-2627. doi: 10.1021/acsomega.5c07620 Förster, Idier, Liberti, Mucherino, Lin, Malliavin. Low-resolution description of the conformational space for intrinsically disordered proteins. Sci Rep 2022 12:19057. doi: 10.1038/s41598-022-21648-9
Malliavin. Tandem domain structure determination based on a systematic enumeration of conformations. Sci Rep 2021 11:16925. doi: 10.1038/s41598-021-96370-z
Malliavin, Mucherino, Lavor, Liberti. Systematic Exploration of Protein Conformational Space Using a Distance Geometry Approach. J Chem Inf Model 2019 59:4486-4503
doi: 10.1021/acs.jcim.9b00215Leave a Reply
One response to “Systematic enumeration for describing the IDP and IDR conformations landscape”
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Thank you very much for your presentation!
I was wondering which resonances did you use as an input for your software? Were they only HN and N chemical shifts? Do you think that including larger sets of chemical shift data will improve the outcomes (such as including Ha, Ca, Cb etc..)? Does any other NMR observable might be useful for the scope as well (NOE, PREs)?
Is there any other experimental technique that might be used to refine or integrate the input data (such as smFRET)?
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T1 relaxation time in Ascorbic Acid: effect of concentration solution
Muhammad Roy Asrori (Universitas Negeri Malang, Indonesia)
X: @RoyAsrori; Bluesky: @muhammadroyasrori.bsky.social
Abstract: This study aims to determine the spin-lattice (T1) relaxation times of protons in ascorbic acid dissolved in deuterium oxide (D2O) to evaluate how molecular dynamics are influenced by varying solution concentrations. Nuclear Magnetic Resonance (NMR) T1 analyses were conducted on in-house prepared samples at a controlled temperature of 308.0 K. Data processing and fitting were performed using Bruker TopSpin and Dynamics Center software (version 2.8.4) , calculating relaxation times with the function f(t) = Io [1a*exp (-t/T1)]. Analysis of the first sample (1 mg in 1 mL D₂O) revealed T1 relaxation times of 1.09 s at 4.015 ppm and 0.958 s at 3.941 ppm. A second, more concentrated sample (10 mg in 1 mL D₂O) exhibited a broader range of proton signals, with downfield peaks showing longer relaxation times of 2.83 s at 5.184 ppm, 5.30 s at 4.311 ppm, and 2.86 s at 4.230 ppm. Conversely, other peaks in this higher-concentration sample demonstrated shorter T1 times, measuring 0.522 s at 4.074 ppm, 1.20 s at 4.022 ppm, and 1.03 s at 3.933 ppm. These results indicate that the T1 relaxation times of ascorbic acid in D2O at 308.0 K vary significantly, ranging from 0.522 s to 5.30 s depending on the specific proton environment, and suggest that an increase in concentration may influence intermolecular interactions—such as hydrogen bonding or molecular crowding—thereby altering the degrees of local mobility and relaxation mechanisms across the molecule.
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2 responses to “T1 relaxation time in Ascorbic Acid: effect of concentration solution”
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Dear Muhammad, thanks for your work. Could you elaborate on what you think the enviroments with dramatically reduced T1 time are and how they are specifically in ascorbic acid ?
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Dear Muhammad, thank you for presenting this work.
The 1 mg/mL sample shows two fitted resonances, whereas the 10 mg/mL sample shows six reported peak positions, and the proton assignments were not established. How did you determine which signals in the two samples correspond to the same ascorbic-acid proton sites? Without this assignment, what evidence supports attributing the different T1 values to concentration-dependent hydrogen bonding or molecular crowding rather than peak overlap, residual water, pD differences, or degradation?
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