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Category: chemistry – Page 86

Cassini proves complex chemistry in Enceladus ocean

Scientists digging through data collected by the Cassini spacecraft have found new complex organic molecules spewing from Saturn’s moon Enceladus. This is a clear sign that complex chemical reactions are taking place within its underground ocean. Some of these reactions could be part of chains that lead to even more complex, potentially biologically relevant molecules.

Published in Nature Astronomy, this discovery further strengthens the case for a dedicated European Space Agency (ESA) mission to orbit and land on Enceladus.

In 2005, Cassini found the first evidence that Enceladus has a hidden ocean beneath its icy surface. Jets of water burst from cracks close to the moon’s south pole, shooting ice grains into space. Smaller than grains of sand, some of the tiny pieces of ice fall back onto the moon’s surface, while others escape and form a ring around Saturn that traces Enceladus’s orbit.

Physicists detect water’s ultraviolet fingerprint in interstellar comet 3I/ATLAS

For millions of years, a fragment of ice and dust drifted between the stars—like a sealed bottle cast into the cosmic ocean. This summer, that bottle finally washed ashore in our solar system and was designated 3I/ATLAS, only the third known interstellar comet. When Auburn University scientists pointed NASA’s Neil Gehrels Swift Observatory toward it, they made a remarkable find: the first detection of hydroxyl (OH) gas from this object, a chemical fingerprint of water.

Swift’s space-based telescope could spot the faint ultraviolet glow that ground observatories can’t see—because, high above Earth’s atmosphere, it captures light that never reaches Earth’s surface.

Detecting water—through its ultraviolet by-product, hydroxyl—is a major breakthrough for understanding how interstellar comets evolve. In solar-system comets, water is the yardstick by which scientists measure their overall activity and track how sunlight drives the release of other gases. It’s the chemical benchmark that anchors every comparison of volatile ices in a ’s nucleus.

Flash Joule heating lights up lithium extraction from ores

A new one‑step, water‑, acid‑, and alkali‑free method for extracting high‑purity lithium from spodumene ore has the potential to transform critical metal processing and enhance renewable energy supply chains. The study is published in Science Advances.

As the demand for lithium continues to rise, particularly for use in , smartphones and power storage, current extraction methods are struggling to keep pace. Extracting lithium from is a lengthy process, and traditional methods that use heat and chemicals to extract lithium from rock produce significant amounts of harmful waste.

Researchers led by James Tour, the T.T. and W.F. Chao Professor of Chemistry and professor of materials science and nanoengineering at Rice University, have developed a faster and cleaner method using flash Joule heating (FJH). This technique rapidly heats materials to thousands of degrees within milliseconds and works in conjunction with chlorine gas, exposing the rock to intense heat and chlorine gas, they can quickly convert spodumene ore into usable lithium.

Eco-friendly technology removes toxic PFAS from water

Rice University researchers, in collaboration with international partners, have developed the first eco-friendly technology to rapidly capture and destroy toxic “forever chemicals” (PFAS) in water. The findings, recently published in Advanced Materials, mark a major step toward addressing one of the world’s most persistent environmental threats.

The study was led by Youngkun Chung, a postdoctoral fellow under the mentorship of Michael S. Wong, a professor at Rice’s George R. Brown School of Engineering and Computing, and conducted in collaboration with Seoktae Kang, professor at the Korea Advanced Institute of Science and Technology (KAIST), and Keon-Ham Kim, professor at Pukyung National University in South Korea.

PFAS, short for per-and polyfluoroalkyl substances, are synthetic chemicals first manufactured in the 1940s and used in products ranging from Teflon pans to waterproof clothing and food packaging. Their ability to resist heat, grease and water has made them valuable for industry and consumers. But that same resistance means they do not easily degrade, earning them the nickname “forever chemicals.”

How order and disorder direct chemical reactivity

In nature, the behavior of systems—whether large or small—is always governed by a few fundamental principles. For instance, objects fall downward because it minimizes their energy. At the same time, order and disorder are key variables that also shape physical processes. Systems—especially our homes—tend to become increasingly disordered over time. Even at the microscopic level, systems tend to favor increased disorder, a phenomenon known as an increase in so-called entropy.

These two variables—energy and entropy—play an important role in . Processes occur automatically when energy can be reduced or entropy (disorder) increases.

Under standard conditions—such as in a glass of water—water autodissociation is hindered by both factors, making it a highly unlikely event. However, when strong electric fields are applied, the process can be dramatically accelerated.

Two-step excitation unlocks and steers exotic nanolight

An international team of researchers has developed a novel technique to efficiently excite and control highly-confined light-matter waves, known as higher-order hyperbolic phonon polaritons. Their method not only sets new records for the quality and propagation distance of these waves but also uses a sharp boundary to create a form of pseudo-birefringence, sorting and steering the waves by mode into different directions.

This advance, published in Nature Photonics, opens new avenues for developing nanoscale optical devices for high-speed signal processing and ultra-sensitive chemical detection.

In the quest for ultra-compact, light-based circuits, scientists are turning to polaritons—hybrid modes formed from the coupling of light with optically active material excitations such as plasmons or phonons. These remarkable quasiparticles can squeeze light into spaces far smaller than its natural wavelength, overcoming the conventional limits of far-field optics. However, exciting most confined variants—higher-order polaritons—has been a major challenge, as they demand a much larger momentum boost than single-step excitation methods can deliver.

Topsicle: a method for estimating telomere length from whole genome long-read sequencing data

Long read sequencing technology (advanced by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (Nanopore)) is revolutionizing the genomics field [43] and it has major potential to be a powerful computational tool for investigating the telomere length variation within populations and between species. Read length from long read sequencing platforms is orders of magnitude longer than short read sequencing platforms (tens of kilobase pairs versus 100–300 bp). These long reads have greatly aided in resolving the complex and highly repetitive regions of the genome [44], and near gapless genome assemblies (also known as telomere-to-telomere assembly) are generated for multiple organisms [45, 46]. The long read sequences can also be used for estimating telomere length, since whole genome sequencing using a long read sequencing platform would contain reads that span the entire telomere and subtelomere region. Computational methods can then be developed to determine the telomere–subtelomere boundary and use it to estimate the telomere length. As an example, telomere-to-telomere assemblies have been used for estimating telomere length by analyzing the sequences at the start and end of the gapless chromosome assembly [47,48,49,50]. But generating gapless genome assemblies is resource intensive and cannot be used for estimating the telomeres of multiple individuals. Alternatively, methods such as TLD [51], Telogator [52], and TeloNum [53] analyze raw long read sequences to estimate telomere lengths. These methods require a known telomere repeat sequence but this can be determined through k-mer based analysis [54]. Specialized methods have also been developed to concentrate long reads originating from chromosome ends. These methods involve attaching sequencing adapters that are complementary to the single-stranded 3′ G-overhang of the telomere, which can subsequently be used for selectively amplifying the chromosome ends for long read sequencing [55,56,57,58]. While these methods can enrich telomeric long reads, they require optimization of the protocol (e.g., designing the adapter sequence to target the G-overhang) and organisms with naturally blunt-ended telomeres [59, 60] would have difficulty implementing the methods.

An explosion of long read sequencing data has been generated for many organisms across the animal and plant kingdom [61, 62]. A computational method that can use this abundant long read sequencing data and estimate telomere length with minimal requirements can be a powerful toolkit for investigating the biology of telomere length variation. But so far, such a method is not available, and implementing one would require addressing two major algorithmic considerations before it can be widely used across many different organisms. The first algorithmic consideration is the ability to analyze the diverse telomere sequence variation across the tree of life. All vertebrates have an identical telomere repeat motif TTAGGG [63] and most previous long read sequencing based computational methods were largely designed for analyzing human genomic datasets where the algorithms are optimized on the TTAGGG telomere motif. But the telomere repeat motif is highly diverse across the animal and plant kingdom [64,65,66,67], and there are even species in fungi and plants that utilize a mix of repeat motifs, resulting in a sequence complex telomere structure [64, 68, 69]. A new computational method would need to accommodate the diverse telomere repeat motifs, especially across the inherently noisy and error-prone long read sequencing data [70]. With recent improvements in sequencing chemistry and technology (HiFi sequencing for PacBio and Q20 + Chemistry kit for Nanopore) error rates have been substantially reduced to 1% [71, 72]. But even with this low error rate, a telomeric region that is several kilobase pairs long can harbor substantial erroneous sequences across the read [73] and hinder the identification of the correct telomere–subtelomere boundary. In addition, long read sequencers are especially error-prone to repetitive homopolymer sequences [74,75,76], and the GT-rich microsatellite telomere sequences are predicted to be an especially erroneous region for long read sequencing. A second algorithmic consideration relates to identifying the telomere–subtelomere boundary. Prior long read sequencing based methods [51, 52] have used sliding windows to calculate summary statistics and a threshold to determine the boundary between the telomere and subtelomere. Sliding window and threshold based analyses are commonly used in genome analysis, but they place the burden on the user to determine the appropriate cutoff, which for telomere length measuring computational methods may differ depending on the sequenced organism. In addition, threshold based sliding window scans can inflate both false positive and false negative results [77,78,79,80,81,82] if the cutoff is improperly determined.

Here, we introduce Topsicle, a computational method that uses a novel strategy to estimate telomere lengths from raw long read sequences from the entire whole genome sequencing library. Methodologically, Topsicle iterates through different substring sizes of the telomere repeat sequence (i.e., telomere k-mer) and different phases of the telomere k-mer are used to summarize the telomere repeat content of each sequencing read. The k-mer based summary statistics of telomere repeats are then used for selecting long reads originating from telomeric regions. Topsicle uses those putative reads from the telomere region to estimate the telomere length by determining the telomere–subtelomere boundary through a binary segmentation change point detection analysis [83]. We demonstrate the high accuracy of Topsicle through simulations and apply our new method on long read sequencing datasets from three evolutionarily diverse plant species (A. thaliana, maize, and Mimulus) and human cancer cell lines. We believe using Topsicle will enable high-resolution explorations of telomere length for more species and achieve a broad understanding of the genetics and evolution underlying telomere length variation.

How a Molecular Motor Minimizes Energy Waste

Turning a biologically important molecular motor at a constant rate saves energy, according to experiments.

Within every biological cell is an enzyme, called adenosine triphosphate (ATP) synthase, that churns out energy-rich molecules for fueling the cell’s activity. New experiments investigate the functioning of this “energy factory” by artificially cranking one of the enzyme’s molecular motors [1]. The results suggest that maintaining a fixed rotation rate minimizes energy waste caused by microscopic fluctuations. Future work could confirm the role of efficiency in the evolutionary design of biological motors.

ATP synthase consists of two rotating molecular motors, Fo and F1, that are oriented along a common rotation axis and locked together so that the rotation of Fo exerts a torque on the shaft in the middle of F1. The resulting motion within F1 helps bring together the chemical ingredients of the molecule ATP, which stores energy that can later be used in cellular processes.

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