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At least 19 records

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DOE OSTI2017

Molecular Spring Enabled High-Performance Anode for Lithium Ion Batteries

Flexible butyl interconnection segments are synthetically incorporated into an electronically conductive poly(pyrene methacrylate) homopolymer and its copolymer. The insertion of butyl segment makes the pyrene polymer more flexible, and can better accommodate deformation. This new class of flexible and conductive polymers can be used as a polymer binder and adhesive to facilitate the electrochemical performance of a silicon/graphene composite anode material for lithium ion battery application. They act like a “spring” to maintain the electrode mechanical and electrical integrity. High mass loading and high areal capacity, which are critical design requirements of high energy batteries, have been achieved in the electrodes composed of the novel binders and silicon/graphene composite material. A remarkable area capacity of over 5 mAh/cm 2 and volumetric capacity of over 1700 Ah/L have been reached at a high current rate of 333 mA/g.

25 ENERGY STORAGE↗

DOE OSTI2020

Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules

Due to the central role of DNA, its interactions with inorganic salts and small organic molecules are important. For example, such interactions play important roles in various fundamental cellular processes in living systems and are involved in many DNA-damage related diseases. Strategies to improve the sensitivity of existing techniques for studying DNA interactions with other molecules would be appreciated in situations where the interactions are too weak. Here we report our development and demonstration of bent DNA bows for amplifying, sensing, and detecting the interactions of 14 inorganic salts and small organic molecules with DNA. With the bent DNA bows, these interactions were easily visualized and quantified in gel electrophoresis, which were difficult to measure without bending. In addition, the strength of the interactions of DNA with the various salts/molecules were quantified using the modified Hill equation. This work highlights the amplification effects of the bending elastic energy stored in the DNA bows and the potential use of the DNA bows for quantitatively measuring DNA interactions with small molecules as simple economic methods; it may also pave the way for exploiting the bent DNA bows for other applications such as screening DNA-interacting molecules and drugs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Force Sensing in Nanoscale: Integration of Virtual Spring for Sensing the Interactions of β-Amyloid Grabbed by Prefoldin

Analysis of atomic forces in molecular scale including the reciprocal internal force directions, quantity, and Young’s modulus, and more detailed analysis via diagrams, is one of the most current research topics. This research aims to analyze the bilateral forces applied between a nano-actuator and a cargo from a new perspective. While virtual springs have been used as a tool to convey forces in the previous steered molecular dynamics simulations, this study uses the spring as a sensor for measuring the internal forces. This study introduces atomic sensing via the steered molecular dynamics method. Following the previous studies, the protein employed in this study is the mutated Archetype Prefoldin being used to control the pathogenic cargo beta-amyloid (Alzheimer’s). The powerful Gromacs software carries out the simulations for the calculation of the total force and force for each branch. The simulation results illustrate the total force between the cargo and nano-actuator is ~ 2.8 nN, while each branch needs a force of ~ 1.2–1.5 nN to release the cargo. The results demonstrate the validity of the method and applicability of the virtual sensor for assessing the microscopic forces. This investigation is a pioneer study for the advent of the sensor as an assessment tool for the mechanical analysis and precise atomic force studies.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Impact of salinity origin on microbial communities in saline springs within the Illinois Basin, USA

Abstract Saline springs within the Illinois Basin result from the discharge of deep‐seated evaporated seawater (brine) and likely contain diverse and complex microbial communities that are poorly understood. In this study, seven saline/mineral springs with different geochemical characteristics and salinity origins were investigated using geochemical and molecular microbiological analyses to reveal the composition of microbial communities inhabiting springs and their key controlling factors. The 16S rRNA sequencing results demonstrated that each spring harbours a unique microbial community influenced by its geochemical properties and subsurface conditions. The microbial communities in springs that originated from Cambrian/Ordovician strata, which are deep confined units that have limited recharge from overlying formations, share a greater similarity in community composition and have a higher species richness and more overlapped taxa than those that originated from shallower Pennsylvanian strata, which are subject to extensive regional surface and groundwater recharge. The microbial distribution along the spring flow paths at the surface indicates that 59.8%–94.2% of total sequences in sedimentary samples originated from spring water, highlighting the role of springs in influencing microbiota in the immediate terrestrial environment. The results indicate that the springs introduce microbiota with a high biodiversity into surface terrestrial or aquatic ecosystems, potentially affecting microbial reservoirs in downstream ecosystems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Nonlinear Shear Rheology of Entangled Polymer Rings

Steady-state shear viscosity η($\bar{γ}$) of unconcatenated ring polymer melts as a function of the shear rate $\bar{γ}$ is studied by a combination of experiments, simulations, and theory. Experiments using polystyrenes with Z ≈ 5 and Z ≈ 11 entanglements indicate weaker shear thinning for rings compared to linear polymers exhibiting power law scaling of shear viscosity η ~ $\bar{γ}$ –0.56 ± 0.02 , independent of chain length, for Weissenberg numbers up to about 10 2 . Nonequilibrium molecular dynamics simulations using the bead-spring model reveal a similar behavior with η ~ $\bar{γ}$ -0.57 ± 0.08 for 4 ≤ Z ≤ 57. Viscosity decreases with chain length for high $\bar{γ}$. In our experiments, we see the onset of this regime, and in simulations, which we extended to Wi ~ 10 4 , the nonuniversality is fully developed. In addition to a naive scaling theory yielding for the universal regime η ~ $\bar{γ}$ –0.57 , we developed a novel shear slit model explaining many details of observed conformations and dynamics as well as the chain length-dependent behavior of viscosity at large $\bar{γ}$. The signature feature of the model is the presence of two distinct length scales: the size of tension blobs and much larger thickness of a shear slit in which rings are self-consistently confined in the velocity gradient direction and which is dictated by the size of a chain section with relaxation time 1/$\bar{γ}$. These two length scales control the two normal stress differences. In this model, the chain length-dependent onset of nonuniversal behavior is set by tension blobs becoming as small as about one Kuhn segment. This model explains the approximate applicability of the Cox–Merz rule for ring polymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Bead–Spring Simulation of Ionomer Melts—Studying the Effects of Chain-Length and Associating Group Fraction on Equilibrium Structure and Extensional Flow Behavior

Ionomers are associative polymers with diverse applications ranging from selective membranes and high-performance adhesives to abrasion- and chemical-resistant coatings, insulation layers, vacuum packaging, and foamed sheets. Within equilibrium melt, the ionic or associating groups are known to form thermally reversible, associative clusters whose presence can significantly affect the system’s mechanical, viscoelastic, and transport properties. It is, thus, of great interest to understand how to control such clusters’ size distribution, shape, and stability through the designed choice of polymer architecture and the ionic groups’ fraction, arrangement, and interaction strength. In this work, we represent linear associating polymers using a Kremer–Grest type bead–spring model and perform large-scale MD simulations to explore the effect of polymer chain-length (l) and fraction (f s ) of randomly placed associating groups on the size distribution and stability of formed clusters. We consider different chain-lengths (below and above entanglement), varying fractions of associating groups (represented by ‘sticky’ beads) between 5 and 20%, and a fixed sticky–sticky nonbond interaction strength of four times that between regular non-associating beads. For all melts containing associating groups the equilibrium structure factor S(q) displays a signature ionomer peak at low wave vector q whose intensity increases with increasing f s and l. The average cluster size Nc increases with f s . However, the effect of chain-length on Nc appears to be pronounced only at higher values of f s . Under extensional flows, the computed stress (and viscosity) is higher at higher f s and l regardless of strain rate. Beyond a critical strain rate, we observe fragmentation of the associative clusters, which has interesting effects on the stress/viscous response.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Overlap Concentration in Salt-Free Polyelectrolyte Solutions

For strongly charged polyelectrolytes in salt-free solutions, we use molecular dynamics simulations of a coarse-grained bead-spring model to calculate overlap concentrations c* and chain structure for polymers containing N = 10 to 1600 monomers. Over much of this range, we find that the end-to-end distance R* at c* increases faster than linearly with increasing N, as chains at the overlap concentration approach strongly extended conformations. This trend results in the overlap concentration c* decreasing as a stronger function of N than the classical prediction c* ~ N –2 . Finally, this stronger dependence can be fit either by a logarithmic correction to scaling or by an apparent scaling c* ~ N –m , with m > 2.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Effects of spherical confinement and backbone stiffness on flexible polymer jamming

We use molecular simulations to study jamming of a crumpled bead-spring model polymer in a finite container and compare to jamming of repulsive spheres. After proper constraint counting, the onset of rigidity is seen to occur isostatically as in the case of repulsive spheres. Despite this commonality, the presence of the curved container wall and polymer backbone bonds introduce new mechanical properties. Notably, these include additional bands in the vibrational density of states that reflect the material structure as well as oscillations in local contact number and density near the wall but with lower amplitude for polymers. Polymers have fewer boundary contacts, and this low-density surface layer strongly reduces the global bulk modulus. Here, we further show that bulk-modulus dependence on backbone stiffness can be described by a model of stiffnesses in series and discuss potential experimental and biological applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2019

Improved Upper Limit on the Neutrino Mass from a Direct Kinematic Method by KATRIN

We report on the neutrino mass measurement result from the first four-week science run of the Karlsruhe Tritium Neutrino experiment KATRIN in spring 2019. Beta-decay electrons from a high-purity gaseous molecular tritium source are energy analyzed by a high-resolution MAC-E filter. A fit of the integrated electron spectrum over a narrow interval around the kinematic end point at 18.57 keV gives an effective neutrino mass square value of (-1.0 +0.9 -1.1 eV 2 . From this, we derive an upper limit of 1.1 eV (90% confidence level) on the absolute mass scale of neutrinos. This value coincides with the KATRIN sensitivity. It improves upon previous mass limits from kinematic measurements by almost a factor of 2 and provides model-independent input to cosmological studies of structure formation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

ToPolyAgent: AI agents for coarse-grained bead-spring topological polymer simulations

We introduce ToPolyAgent, a multi-agent AI framework for performing coarse-grained molecular dynamics (MD) simulations of topological polymers through natural language instructions. By integrating large language models (LLMs) with domain-specific computational tools, ToPolyAgent supports both interactive and autonomous simulation workflows across diverse polymer architectures, including linear, ring, brush, and star polymers, as well as dendrimers. The system consists of four LLM-powered agents: a Config Agent for generating initial polymer–solvent configurations, a Simulation Agent for executing LAMMPS-based MD simulations and conformational analyses, a Report Agent for compiling markdown reports, and a Workflow Agent for streamlined autonomous operations. Interactive mode incorporates user feedback loops for iterative refinements, while autonomous mode enables end-to-end task execution from detailed prompts. We demonstrate ToPolyAgent's versatility through case studies involving diverse polymer architectures under varying solvent conditions, thermostats, and simulation lengths. Furthermore, we highlight its potential as a research assistant by directing it to investigate the effect of interaction parameters on the linear polymer conformation, and the influence of grafting density on the persistence length of the brush polymer. By coupling natural language interfaces with rigorous simulation tools, ToPolyAgent lowers barriers to complex computational workflows and advances AI-driven materials discovery in polymer science. It lays the foundation for autonomous and extensible multi-agent scientific research ecosystems.

Ding, Lijie [Oak Ridge National Laboratory (ORNL),↗

DOE OSTI2021

Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution

With advances in DNA sequencing and miniaturized molecular biology workflows, rapid and affordable sequencing of single-cell genomes has become a reality. Compared to 16S rRNA gene surveys and shotgun metagenomics, large-scale application of single-cell genomics to whole microbial communities provides an integrated snapshot of community composition and function, directly links mobile elements to their hosts, and enables analysis of population heterogeneity of the dominant community members. To that end, we sequenced nearly 500 single-cell genomes from a low diversity hot spring sediment sample from Dewar Creek, British Columbia, and compared this approach to 16S rRNA gene amplicon and shotgun metagenomics applied to the same sample. We found that the broad taxonomic profiles were similar across the three sequencing approaches, though several lineages were missing from the 16S rRNA gene amplicon dataset, likely the result of primer mismatches. At the functional level, we detected a large array of mobile genetic elements present in the single-cell genomes but absent from the corresponding same species metagenome-assembled genomes. Moreover, we performed a single-cell population genomic analysis of the three most abundant community members, revealing differences in population structure based on mutation and recombination profiles. While the average pairwise nucleotide identities were similar across the dominant species-level lineages, we observed differences in the extent of recombination between these dominant populations. Most intriguingly, the creek's Hydrogenobacter sp. population appeared to be so recombinogenic that it more closely resembled a sexual species than a clonally evolving microbe. Together, this work demonstrates that a randomized single-cell approach can be useful for the exploration of previously uncultivated microbes from community composition to population structure.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Effects of interaction strength of associating groups on linear and star polymer dynamics

A small number of associating groups incorporated onto a polymer backbone have dramatic effects on the mobility and viscoelastic response of the macromolecules in melts. These associating groups assemble, driving the formation of clusters, whose lifetime affects the properties of the polymers. In this study, we probe the effects of the interaction strength on the structure and dynamics of two topologies, linear and star polymer melts, and further investigate blends of associative and non-associating polymers using molecular dynamics simulations. Polymer chains of approximately one entanglement length are described by a bead–spring model, and the associating groups are incorporated in the form of interacting beads with an interaction strength between them that is varied from 1 to 20 k B T. We find that, for all melts and blends, interaction of a few k B T between the associating groups drives cluster formation, where the size of the clusters increases with increasing interaction strength. These clusters act as physical crosslinkers, which slow the chain mobility. Blends of chains with and without associating groups macroscopically phase separate for interaction strength between the associating groups of a few k B T and above. For weakly interacting associating groups, the static structure function S(q) is well fit by functional form predicted by the random phase approximation where a clear deviation occurs as phase segregation takes place, providing a quantitative assessment of phase segregation.

36 MATERIALS SCIENCE↗

DOE OSTI2024