arXiv subjects

Amit K. Samanta

Publications and source records attributed to Amit K. Samanta.

16 recordsLinked to original sources

arXiv2026

Controlled beams of cryo-cooled protein-like nanoparticles

We report a cryogenic buffer-gas-cell-aerodynamic-lens-stack setup that enables the generation of shock-frozen, dense, and controllable beams of various nanoparticles in the gas phase, including small and low-density species such as isolated proteins. We demonstrate characterization of the setup using strong-field ionization combined with velocity-map imaging, allowing the unambiguous detection of nanoparticles in the protein-size range and full reconstruction of the particle beams including determination of particle flux and number density. The generation and characterization workflow presented here provides a valuable approach for protein-like sample preparation and delivery in single-particle diffractive imaging, microscopy, and low-temperature nanoscience.

physics.ins-det↗

arXiv2025

Single-Particle X-ray Scattering Reveals a High Local Supersaturation of Precursors as the Origin of CoO Assembly Formation

Single-particle small-angle X-ray scattering (SP-SAXS) enables quantitative morphological analysis by recording diffraction snapshots from isolated particles using X-ray free-electron laser (XFEL) pulses. Unlike conventional X-ray techniques, which average over the entire illuminated sample volume, SP-SAXS resolves low-contrast, less abundant, or transient species within heterogeneous particle populations that would otherwise remain hidden. Here, we apply SP-SAXS to investigate the solvothermal formation of CoO nanocrystal assemblies from a Co(acac)$_3$ precursor in benzyl alcohol. The single-particle data reveal amorphous, uniform-density Co(acac)$_2$ spheres as transient intermediates that directly crystallize into cavernous CoO nanocrystal assemblies, which explains why CoO forms as hierarchical aggregates rather than as isolated nanocrystals. These results demonstrate that SP-SAXS provides a powerful framework for disentangling morphological heterogeneity in nanoparticle formation processes.

cond-mat.mes-hall↗

arXiv2025

An improved numerical simulation methodology for nanoparticle injection through aerodynamic lens systems

Aerosol injectors applied in single-particle diffractive imaging experiments demonstrated their potential in efficiently delivering nanoparticles with high density. Continuous optimization of injector design is crucial for achieving high-density particle streams, minimizing background gas, enhancing X-ray interactions, and generating high-quality diffraction patterns. We present an updated simulation framework designed for the fast and effective exploration of the experimental parameter space to enhance the optimization process. The framework includes both the simulation of the carrier gas and the particle trajectories within injectors and their expansion into the experimental vacuum chamber. A hybrid molecular-continuum-simulation method (DSMC/CFD) is utilized to accurately capture the multi-scale nature of the flow. The simulation setup, initial benchmark results of the coupled approach, and the validation of the entire methodology against experimental data are presented.

physics.flu-dyn↗

arXiv2024

Observation of Aerosolization-induced Morphological Changes in Viral Capsids

Single-stranded RNA viruses co-assemble their capsid with the genome and variations in capsid structures can have significant functional relevance. In particular, viruses need to respond to a dehydrating environment to prevent genomic degradation and remain active upon rehydration. Theoretical work has predicted low-energy buckling transitions in icosahedral capsids which could protect the virus from further dehydration. However, there has been no direct experimental evidence, nor molecular mechanism, for such behaviour. Here we observe this transition using X-ray single particle imaging of MS2 bacteriophages after aerosolization. Using a combination of machine learning tools, we classify hundreds of thousands of single particle diffraction patterns to learn the structural landscape of the capsid morphology as a function of time spent in the aerosol phase. We found a previously unreported compact conformation as well as intermediate structures which suggest an incoherent buckling transition which does not preserve icosahedral symmetry. Finally, we propose a mechanism of this buckling, where a single 19-residue loop is destabilised, leading to the large observed morphology change. Our results provide experimental evidence for a mechanism by which viral capsids protect themselves from dehydration. In the process, these findings also demonstrate the power of single particle X-ray imaging and machine learning methods in studying biomolecular structural dynamics.

q-bio.BM↗

arXiv2024

Accuracy and Performance Evaluation of Low Density Internal and External Flow Predictions using CFD and DSMC

The Direct Simulation Monte Carlo (DSMC) method was widely used to simulate low density gas flows with large Knudsen numbers. However, DSMC encounters limitations in the regime of lower Knudsen numbers (Kn<0.1). In such cases, approaches from classical computational fluid dynamics (CFD) relying on the continuum assumption are preferred, offering accurate solutions at acceptable computational costs. In experiments aimed at imaging aerosolized nanoparticles in vacuo a wide range of Knudsen numbers occur, which motivated the present study on the analysis of the advantages and drawbacks of DSMC and CFD simulations of rarefied flows in terms of accuracy and computational effort. Furthermore, the potential of hybrid methods is evaluated. For this purpose, DSMC and CFD simulations of the flow inside a convergent-divergent nozzle (internal expanding flow) and the flow around a conical body (external shock generating flow) were carried out. CFD simulations utilize the software OpenFOAM and the DSMC solution is obtained using the software SPARTA. The results of these simulation techniques are evaluated by comparing them with experimental data (1), evaluating the time-to-solution (2) and the energy consumption (3), and assessing the feasibility of hybrid CFD-DSMC approaches (4). Keywords: DSMC; SPARTA; Continuum assumption; Transition regime; Rarefied flow; high-performance computing

physics.flu-dyn↗

arXiv2024

Resolving non-equilibrium shape variations amongst millions of gold nanoparticles

Nanoparticles, exhibiting functionally relevant structural heterogeneity, are at the forefront of cutting-edge research. Now, high-throughput single-particle imaging (SPI) with x-ray free-electron lasers (XFELs) creates unprecedented opportunities for recovering the shape distributions of millions of particles that exhibit functionally relevant structural heterogeneity. To realize this potential, three challenges have to be overcome: (1) simultaneous parametrization of structural variability in real and reciprocal spaces; (2) efficiently inferring the latent parameters of each SPI measurement; (3) scaling up comparisons between $10^5$ structural models and $10^6$ XFEL-SPI measurements. Here, we describe how we overcame these three challenges to resolve the non-equilibrium shape distributions within millions of gold nanoparticles imaged at the European XFEL. These shape distributions allowed us to quantify the degree of asymmetry in these particles, discover a relatively stable `shape envelope' amongst nanoparticles, discern finite-size effects related to shape-controlling surfactants, and extrapolate nanoparticles' shapes to their idealized thermodynamic limit. Ultimately, these demonstrations show that XFEL SPI can help transform nanoparticle shape characterization from anecdotally interesting to statistically meaningful.

cond-mat.mes-hall↗

arXiv2023

Laser-induced alignment of nanoparticles and macromolecules for single-particle-imaging applications

Laser-induced alignment of particles and molecules was long envisioned to support three-dimensional structure determination using "single-molecule diffraction" with x-ray free-electron lasers [PRL 92, 198102 (2004)]. However, the alignment of isolated macromolecules has not yet been demonstrated, also because quantitative modeling is very expensive. We computationally demonstrated that the alignment of nanorods and proteins is possible with standard laser technology. We performed a comprehensive analysis on the dependence of the degree of alignment on molecular properties and experimental details, e.g., particle temperature and laser-pulse energy. Considering the polarizability anisotropy of about 150,000 proteins, our analysis revealed that most of these proteins can be aligned using realistic experimental parameters.

physics.comp-ph↗

arXiv2021

Unsupervised learning approaches to characterize heterogeneous samples using X-ray single particle imaging

One of the outstanding analytical problems in X-ray single particle imaging (SPI) is the classification of structural heterogeneity, which is especially difficult given the low signal-to-noise ratios of individual patterns and that even identical objects can yield patterns that vary greatly when orientation is taken into consideration. We propose two methods which explicitly account for this orientation-induced variation and can robustly determine the structural landscape of a sample ensemble. The first, termed common-line principal component analysis (PCA) provides a rough classification which is essentially parameter-free and can be run automatically on any SPI dataset. The second method, utilizing variation auto-encoders (VAEs) can generate 3D structures of the objects at any point in the structural landscape. We implement both these methods in combination with the noise-tolerant expand-maximize-compress (EMC) algorithm and demonstrate its utility by applying it to an experimental dataset from gold nanoparticles with only a few thousand photons per pattern and recover both discrete structural classes as well as continuous deformations. These developments diverge from previous approaches of extracting reproducible subsets of patterns from a dataset and open up the possibility to move beyond studying homogeneous sample sets and study open questions on topics such as nanocrystal growth and dynamics as well as phase transitions which have not been externally triggered.

eess.IV↗

arXiv2021

Charge-state distribution of aerosolized nanoparticles

In single particle imaging experiments, beams of individual nanoparticles are exposed to intense pulses of x-rays from free-electron lasers to record diffraction patterns of single, isolated molecules. The reconstruction for structure determination relies on signal from many identical particles. Therefore, well-defined-sample delivery conditions are desired in order to achieve sample uniformity, including avoidance of charge polydispersity. We have observed charging of 220 nm polystyrene particles in an aerosol beam created by a gas-dynamic virtual nozzle focusing technique, without intentional charging of the nanoparticles. Here, we present a deflection method for detecting and characterizing the charge states of a beam of aerosolized nanoparticles. Our analysis of the observed charge-state distribution using optical light-sheet localization microscopy and quantitative particle trajectory simulations is consistent with previous descriptions of skewed charging probabilities of triboelectrically charged nanoparticles.

physics.chem-ph↗

arXiv2021

Optimizing the geometry of aerodynamic lens injectors for single-particle coherent diffractive imaging of gold nanoparticles

Single-particle x-ray diffractive imaging (SPI) of small (bio-)nanoparticles (NPs) requires optimized injectors to collect sufficient diffraction patterns to reconstruct the NP structure with high resolution. Typically, aerodynamic-lens-stack injectors are used for single NP injection. However, current injectors were developed for larger NPs ($\gg\!100$ nm) and their ability to generate high-density NP beams suffers with decreasing NP size. Here, an aerodynamic-lens-stack injector with variable geometry and the geometry-optimization procedure are presented. The optimization for 50 nm gold NP (AuNP) injection using a numerical simulation infrastructure capable of calculating the carrier gas flow and the particle trajectories through the injector is introduced. The simulations are experimentally validated using spherical AuNPs and sucrose NPs. In addition, the optimized injector is compared to the standard-installation "Uppsala-injector" for AuNPs and results for these heavy particles show a shift in the particle-beam focus position rather than a change in beam size, which results in a lower gas background for the optimized injector. Optimized aerodynamic-lens stack injectors will allow to increase NP beam density, reduce the gas background, discover the limits of current injectors, and contribute to structure determination of small NPs using SPI.

physics.ins-det↗

arXiv2020

New aerodynamic lens injector for single particle diffractive imaging

An aerodynamic lens injector was developed specifically for the needs of single-particle diffractive imaging experiments at free-electron lasers. Its design allows for quick changes of injector geometries and focusing properties in order to optimize injection for specific individual samples. Here, we present results of its first use at the FLASH free-electron-laser facility. Recorded diffraction patterns of polystyrene spheres are modeled using Mie scattering, which allowed for the characterization of the particle beam under diffractive-imaging conditions and yield good agreement with particle-trajectory simulations.

physics.ins-det↗

arXiv2020

3D diffractive imaging of nanoparticle ensembles using an X-ray laser

We report the 3D structure determination of gold nanoparticles (AuNPs) by X-ray single particle imaging (SPI). Around 10 million diffraction patterns from gold nanoparticles were measured in less than 100 hours of beam time, more than 100 times the amount of data in any single prior SPI experiment, using the new capabilities of the European X-ray free electron laser which allow measurements of 1500 frames per second. A classification and structural sorting method was developed to disentangle the heterogeneity of the particles and to obtain a resolution of better than 3 nm. With these new experimental and analytical developments, we have entered a new era for the SPI method and the path towards close-to-atomic resolution imaging of biomolecules is apparent.

physics.app-ph↗

arXiv2020

Microscopic force for aerosol transport

A key ingredient for single particle diffractive imaging experiments is the successful and efficient delivery of sample. Current sample-delivery methods are based on aerosol injectors in which the samples are driven by fluid-dynamic forces. These are typically simulated using Stokes' drag forces and for micrometer-size or smaller particles, the Cunningham correction factor is applied. This is not only unsatisfactory, but even using a temperature dependent formulation it fails at cryogenic temperatures. Here we propose the use of a direct computation of the force, based on Epstein's formulation, that allows for high relative velocities of the particles to the gas and also for internal particle temperatures that differ from the gas temperature. The new force reproduces Stokes' drag force for conditions known to be well described by Stokes' drag. Furthermore, it shows excellent agreement to experiments at 4 K, confirming the improved descriptive power of simulations over a wide temperature range.

physics.flu-dyn↗

arXiv2020

Controlled beams of shockfrozen, isolated, biological and artificial nanoparticles

X-ray free-electron lasers (XFELs) promise the diffractive imaging of single molecules and nanoparticles with atomic spatial resolution. This relies on the averaging of millions of diffraction patterns of identical particles, which should ideally be isolated in the gas phase and preserved in their native structure. Here, we demonstrated that polystyrene nanospheres and Cydia pomonella granulovirus can be transferred into the gas phase, isolated, and very quickly shockfrozen, i.e. cooled to 4~K within microseconds in a helium-buffer-gas cell, much faster than state-of-the-art approaches. Nanoparticle beams emerging from the cell were characterized using particle-localization microscopy with light-sheet illumination, which allowed for the full reconstruction of the particle beams, focused to $<100\:μ\text{m}$, as well as for the determination of particle flux and number density. The experimental results were quantitatively reproduced and rationalized through particle-trajectory simulations. We propose an optimized setup with cooling rates for few-nanometers particles on nanoseconds timescales. The produced beams of shockfrozen isolated nanoparticles provide a breakthrough in sample delivery, e.g. for diffractive imaging and microscopy or low-temperature nanoscience.

physics.bio-ph↗

arXiv2019

Light-sheet imaging for the recording of transverse absolute density distributions of gas-phase particle-beams from nanoparticle injectors

Imaging biological molecules in the gas-phase requires novel sample delivery methods, which generally have to be characterized and optimized to produce high-density particle beams. A non-destructive characterization method of the transverse particle beam profile is presented. It enables the characterization of the particle beam in parallel to the collection of, for instance, x-ray-diffraction patterns. As a rather simple experimental method, it requires the generation of a small laser-light sheet using a cylindrical telescope and a microscope. The working principle of this technique was demonstrated for the characterization of the fluid-dynamic-focusing behavior of 220 nm polystyrene beads as prototypical nanoparticles. The particle flux was determined and the velocity distribution was calibrated using Mie-scattering calculations.

physics.optics↗

arXiv2018

Optimized cell geometry for buffer-gas-cooled molecular-beam sources

We have designed, constructed, and commissioned a cryogenic helium buffer-gas source for producing a cryogenially-cooled molecular beam and evaluated the effect of different cell geometries on the intensity of the produced molecular beam, using ammonia as a test molecule. Planar and conical entrance and exit geometries are tested. We observe a three fold enhancement in the NH$_3$ signal for a cell with planar-entrance and conical-exit geometry, compared to that for a typically used `box'-like geometry with planar entrance and exit. These observations are rationalized by flow-field simulations for the different buffer-gas cell geometries. The full thermalization of molecules with the helium buffer-gas is confirmed through rotationally-resolved REMPI spectra yielding a rotational temperature of 5 K.

physics.chem-ph↗