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At least 919 records · Page 51

InteraChem: Virtual Reality Visualizer for Reactive Interactive Molecular Dynamics

Interactive molecular dynamics in virtual reality (IMD-VR) simulations provide a digital molecular playground for students as an alternative or complement to traditional molecular modeling kits or 2D illustrations. Previous IMD-VR studies have used molecular mechanics to enable simulations of macromolecules such as proteins and nanostructures for the classroom setting with considerable success. Here, we present the InteraChem molecular visualizer, intended for reactive IMD-VR simulation using semiempirical and ab initio methods. InteraChem visualizes not only the molecular geometry but also (1) isosurfaces such as molecular orbitals and electrostatic potentials and (2) two-dimensional graphs of time-varying simulation quantities such as kinetic/potential energy, internal coordinates, and user-applied force. Additionally, InteraChem employs speech recognition to facilitate user interaction and introduces a novel “atom happiness” visualization using emojis to indicate the energetic feasibility of a particular bonding arrangement. Furthermore, we include a set of accompanying exercises that we have used to teach chemical reactivity in small molecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Pendellösung interferometry probes the neutron charge radius, lattice dynamics, and fifth forces

Setting bounds on a fifth force Some extensions to the Standard Model of particle physics posit the existence of a fifth force to complement the existing four fundamental forces. To set bounds on the strength of such an interaction, experiments on vastly different length scales have been performed. Heacock et al . used an unusual method called Pendellösung interferometry to measure the neutron structure factors of silicon. The momentum dependence of the structure factors enabled the researchers to put more stringent bounds on the strength of a type of fifth force called the Yukawa force, as well as measure the charge radius of the neutron. —JS

Science & Technology - Other Topics↗

Kaon–proton strong interaction at low relative momentum via femtoscopy in Pb–Pb collisions at the LHC

In quantum scattering processes between two particles, aspects characterizing the strong and Coulomb forces can be observed in kinematic distributions of the particle pairs. The sensitivity to the interaction potential reaches a maximum at low relative momentum and vanishing distance between the two particles. Ultrarelativistic heavy-ion collisions at the LHC provide an abundant source of many hadron species and can be employed as a measurement method of scattering parameters that is complementary to scattering experiments. This study confirms that momentum correlations of particles produced in Pb–Pb collisions at the LHC provide an accurate measurement of kaon–proton scattering parameters at low relative momentum, allowing precise access to the K – p $\rightarrow$ K – p process. This work also validates the femtoscopic measurement in ultrarelativistic heavy-ion collisions as an alternative to scattering experiments and a complementary tool to the study of exotic atoms with comparable precision. In this work, the first femtoscopic measurement of momentum correlations of K – p (K + $\bar{p}$) and K + p (K – $\bar{p}$) pairs in Pb–Pb collisions at centre-of-mass energy per nucleon pair of $\sqrt{s_{NN}}$ =5.02 TeV registered by the ALICE experiment is reported. The components of the K – p complex scattering length are extracted and found to be $\mathfrak{R}$f 0 = -0.91±0.03(stat)$^{+0.17}_{-0.03}$(syst) and $\mathfrak{T}$f 0 =0.92±0.05(stat)$^{+0.12}_{-0.33}$(syst). The results are compared with chiral effective field theory predictions as well as with existing data from dedicated scattering and exotic kaonic atom experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Solution Structure and Hydration Forces between Mica and Hydrophilic Versus Hydrophobic Surfaces

Solid-liquid interfaces are central to a range of interesting phenomena including catalysis, heterogeneous nucleation, water desalination, and biomolecular assembly. While three-dimensional Fast Force Mapping (3D FFM) has emerged as a technique for resolving interfacial solution structure at the molecular scale, key challenges for data interpretation persist, most notably regarding the influence of the probe on the measured structure. Using the mica-water system as a case study, we investigate the effect of hydrophilic and hydrophobic probes on interfacial solution structure measured by 3D FFM. Data from hydrophilic silicon-based probes are in good agreement with molecular dynamics simulations, wherein the innermost water molecules adsorb preferentially at the surface ditrigonal cavity sites followed by two subsequent hydration layers. In contrast, the hydrophobic carbon-based probes detect vertical oscillatory features, but do not show lateral patterning that matches the underlying mica lattice. At high ionic strength, up to six of these oscillatory features are observed extending 2 nm into the solution phase with an average spacing of 0.29 ± (0.04) nm. Further, we also determine that the repulsive hydration force between mica and the hydrophilic probe depends on the nature and concentration of ions in solution. Specifically, solutions with stronger ion-water and ion-ion interactions increase the interfacial viscosity, which results in a stronger repulsive hydration force as the probe approaches the surface. Based on these observations, we present a scheme for controlling the outcomes of particle attachment and aggregation by varying the solution conditions to tune the hydration force.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ion-dependent protein–surface interactions from intrinsic solvent response

Significance Hard–soft interfaces between inorganic surfaces and biomolecules promote self-assembly processes with broad implications in biogeochemistry, energy sciences, nanomedicine, and origins of life. Yet, detailed molecular-scale understanding of inorganic–biomolecule interactions and their dependence on solution conditions is missing. We present a theory for the initial stages of inorganic–biomolecule assembly based on the far-field response of water, using experimentally characterized interactions between muscovite surfaces and mica-binding proteins as model systems. Our work connects molecular details of the solution to assembly outcomes and suggests the initial driving forces for assembly are dominated by long-range, ion-specific interactions. The connections made between interfacial structure and long-range surface–biomolecule interactions provide insights toward a predictive understanding of biomolecular self-assembly on mineral surfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Analysis of the Diurnal Cycle of Precipitation and its Relation to Cloud Radiative Forcing Using TRMM Products

In order to improve our understanding of the interactions between clouds, radiation, and the hydrological cycle simulated in the Colorado State University General Circulation Model (CSU GCM), we focused our research on the analysis of the diurnal cycle of precipitation, top-of-the-atmosphere and surface radiation budgets, and cloudiness using 10-year long Atmospheric Model Intercomparison Project (AMIP) simulations. Comparisons the simulated diurnal cycle were made against the diurnal cycle of Earth Radiation Budget Experiment (ERBE) radiation budget and International Satellite Cloud Climatology Project (ISCCP) cloud products. This report summarizes our major findings over the Amazon Basin.

Randall, David A.↗

Dark magnetohydrodynamics: Black hole accretion in superradiant dark photon clouds

Black holes threaded by massive vector fields can be subject to a superradiant instability, growing a cloud of massive vector particles around it. In this work, we consider what happens if such a dark matter candidate field mimicking a dark photon interacts with an accretion flow onto the black hole. By including a kinetic mixing term with the standard model photon, we extend the commonly used equations of general-relativistic magnetohydrodynamics to a dark photon constituent. The coupling to the dark photon then appears as an effective dynamo term together with a dark Lorentz force acting on the accreting matter. We numerically study the interactions between the superradiant dark photon cloud and the inner accretion flow by solving the coupled system in full numerical relativity. By parameterically varying the mixing parameter between the dark and standard model sector, we provide a first investigation of how the accretion flow could be modified. In conclusion, depending on the coupling strength, our solutions exhibit increased wind launching, as well as oscillation modes in the disk.

79 ASTRONOMY AND ASTROPHYSICS↗

INTEGRATION OF FLEX EQUIPMENT AND OPERATOR ACTIONS IN PLANT FORCE-ON-FORCE MODELS WITH DYNAMIC RISK ASSESSMENT

The overall operation and maintenance cost to protect nuclear power plants accounts for approximately 7% of the total cost of power generation, with labor accounting for half of this cost. In the current research, from interaction with utilities and other stakeholders, it was determined that physical security forces account for nearly 20% of the entire workforce at several nuclear power plants. Labor costs continue to rise in the U.S., so any measures to reduce the cost of operating a nuclear power plant will need to include a reduction in labor. The physical security pathway within the DOE’s Light Water Reactor Sustainability program aims to lower the cost of physical security through directed research into modeling and simulation, application of advanced sensors or deployment of advanced weapons. This report presents a modeling and simulation framework for integrating Diverse and Flexible Mitigation Capability (FLEX) portable equipment performance with Force on Force models of a plant’s physical security posture. The generic framework is described in detail, followed by a case study of modeling an adversarial attack aimed at causing a radiological release by sabotaging the plant’s power supply and its ultimate heat sink capabilities at a hypothetical nuclear power plant. Two different FLEX deployment strategies, series and parallel, are modeled with distinct timelines. The results of the adversarial attack modeled in a commercial Force on Force tool are integrated with the FLEX deployment model in INL’s dynamic modeling tool EMRALD. Monte Carlo simulation is used to model the distribution of the timeline in FLEX deployment strategies. The results demonstrate that, even in the extreme case of a successful adversarial attack, deployment of FLEX equipment can result in a significantly high likelihood of preventing radiological release. The modeling and simulation framework integrating FLEX equipment with Force on Force models enables the nuclear power plants to credit FLEX portable equipment in the plant security posture, resulting in an efficient and optimized physical security.

97 MATHEMATICS AND COMPUTING↗

Numerical simulation of stratospheric sudden warmings with a primitive equation spectral model

A 26-level primitive equation spherical harmonic spectral model allowing for wave-wave and wave-zonal flow interactions is presented for the study of stratospheric sudden warmings. The warmings are simulated by the forcing of a single planetary wave at the tropopause. Four numerical experiments were performed. Nonlinear wave-wave interactions appear to play an important role in the evolution of the flow and temperature fields in the middle to upper stratosphere. In the case involving both wave-wave and wave-zonal flow interactions, this was manifested by the split in the initial polar vortex into a quasi-wave number 2 pattern. In the cases at 60 deg N, easterlies develop first in the upper mesosphere and descend gradually. About the same time or a little later, easterlies also develop in the mid-stratosphere. The linear cases exhibit warmings which are more shallow and more intense at 30 km than the nonlinear cases.

Lordi, N. J.↗

Acoustic force spectroscopy reveals subtle differences in cellulose unbinding behavior of carbohydrate-binding modules

Protein adsorption to solid carbohydrate interfaces is critical to many biological processes, particularly in biomass deconstruction. To engineer more-efficient enzymes for biomass deconstruction into sugars, it is necessary to characterize the complex protein–carbohydrate interfacial interactions. A carbohydrate-binding module (CBM) is often associated with microbial surface-tethered cellulosomes or secreted cellulase enzymes to enhance substrate accessibility. However, it is not well known how CBMs recognize, bind, and dissociate from polysaccharides to facilitate efficient cellulolytic activity, due to the lack of mechanistic understanding and a suitable toolkit to study CBM–substrate interactions. Our work outlines a general approach to study the unbinding behavior of CBMs from polysaccharide surfaces using a highly multiplexed single-molecule force spectroscopy assay. Here, we apply acoustic force spectroscopy (AFS) to probe a Clostridium thermocellum cellulosomal scaffoldin protein (CBM3a) and measure its dissociation from nanocellulose surfaces at physiologically relevant, low force loading rates. An automated microfluidic setup and method for uniform deposition of insoluble polysaccharides on the AFS chip surfaces are demonstrated. The rupture forces of wild-type CBM3a, and its Y67A mutant, unbinding from nanocellulose surfaces suggests distinct multimodal CBM binding conformations, with structural mechanisms further explored using molecular dynamics simulations. Applying classical dynamic force spectroscopy theory, the single-molecule unbinding rate at zero force is extrapolated and found to agree with bulk equilibrium unbinding rates estimated independently using quartz crystal microbalance with dissipation monitoring. However, our results also highlight critical limitations of applying classical theory to explain the highly multivalent binding interactions for cellulose–CBM bond rupture forces exceeding 15 pN.

09 BIOMASS FUELS↗

Life cycles of transient planetary waves

In recent years there has been an increasing effort devoted to understanding the physical and dynamical processes that govern the global-scale circulation of the atmosphere. This effort has been motivated, in part, from: (1) a wealth of new satellite data; (2) an urgent need to assess the potential impact of chlorofluorocarbons on our climate; (3) an inadequate understanding of the interactions between the troposphere and stratosphere and the role that such interactions play in short and long-term climate variability; and (4) the realization that addressing changes in our global climate requires understanding the interactions among various components of the earth system. The research currently being carried out represents an effort to address some of these issues by carrying out studies that combine radiation, ozone, seasonal thermal forcing and dynamics. Satellite and ground-based data that is already available is being used to construct basic states for our analytical and numerical models. Significant accomplishments from 1991-1992 are presented and include the following: ozone-dynamics interaction; (2) periodic local forcing and low frequency variability; and (3) steady forcing and low frequency variability.

Nathan, Terrence↗

Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

Jaffe, Richard↗

Long-Term Aging in Miscible Polymer Nanocomposites

Here we find that the initial, solvent-cast state of nanoparticles (NPs) in a polymer matrix temporally evolves during thermal annealing such that, at steady state, NPs maximize their distance from each other subject to mass balance constraints. The observed timescales for this unexpected structural reorganization, as probed by small-angle X-ray scattering, are temperature-dependent and can be prohibitively large, especially at temperatures around and below 1.2Tg. X-ray photon correlation spectroscopy measurements during reorganization reveal that the collective NP dynamics slow down with annealing at constant temperature; this is accompanied by changes in the low-frequency regime in macroscopic viscoelastic measurements in equilibrated materials. By ruling out other potential sources for these effects (i.e., electrostatic interactions, adsorbed layers), we attribute these results to a long-ranged repulsive force between the NPs caused by fluctuations in the polymer phase, i.e., the "anti-Casimir" effect proposed by Obhukhov and Semenov [Long-range interactions in polymer melts: The anti-Casimir effect. Phys Rev Lett 2005, 95 (3), 038305]. Thus, our results highlight the important role of long-term, slow NP reorganization on the structure and, subsequently, the properties of polymer nanocomposites (PNCs), even in the case of nominally miscible polymer nanoparticle hybrids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computational study of TATB

We have performed a computational study of TATB. The study is composed of two parts, one where we perform static T = 0 K calculations with several different DFT functionals, to investigate structural properties and obtain a cold curve. Even though the functionals used in this study give poor results at ambient pressure, they perform much better at compression, when the dominance of the van der Waals’ forces in the binding is replaced by more normal interactions. In particular AM05 gives good results, mainly because it doesn’t include any “faulty” van der Waals’. Indeed the van der Waals’ corrected functional (PBE+D2) results shows the worst performance on structural properties. For the cold curve the PBE+D2 functional gives the best results compared to experiments (room temperature) but since the structural properties were bad with this functional we cannot for sure say that this is in any way a validation. It is shown that scaling the AM05 results with a common factor reproduces the experimental data. We leave the question on why to a follow up study but speculate that maybe the experiment and our calculations do not represent the same system set-up. From the structural properties we identify a site in the TATB lattice that contains a high concentration of oxygen and hydrogen. The consequences of this finding, if any, are left to a future project. In the second part of the study we perform extensive high-quality DFT-MD (molecular dynamics with DFT forces) calculations to obtain points on the Hugoniot. This part of the study did not get finished within this project and a more extensive summary of this part will be given in a follow up report at a future date. However, we show that obtaining calculated data is essential for equations of state development since the existing experimental Hugoniot data barely deviates from room temperature isotherm data and thus give no information of the high temperature dependency of materials properties. Our conclusion so far in the project is that being able to calculate materials properties is essential for high explosives since experiments are unable to give information in the high temperature part of phase space. While blind use of DFT cannot (yet) give unambiguous answers, we can still explore qualitatively and use such information to guide us in EOS development. However, the main conclusion is that we need better functionals in DFT to easily extract needed properties from calculations.

36 MATERIALS SCIENCE↗

Exploring entanglement and spectral split correlations in three-flavor collective neutrino oscillations

In environments with prodigious numbers of neutrinos, such as core-collapse supernovae, neutron star mergers, or the early Universe, neutrino-neutrino interactions are dynamically significant. They can dominate neutrino flavor evolution and force it to be nonlinear, causing collective neutrino oscillations. Such collective oscillations have been studied numerically, for systems with up to millions of neutrinos, using mean-field or one-particle effective approximations. However, such a system of interacting neutrinos is a quantum many-body system, wherein quantum correlations could play a significant role in the flavor evolution—thereby motivating the exploration of many-body treatments that follow the time evolution of these correlations. In many-body flavor evolution calculations with two neutrino flavors, the emergence of spectral splits in the neutrino energy distributions has been found to be correlated with the degree of quantum entanglement across the spectrum. In this work, for the first time, we investigate the emergence of spectral splits in the three-flavor many-body collective neutrino oscillations. We find that the emergence of spectral splits resembles the number and location found in the mean-field approximation but not in the width. Moreover, unlike in the two-flavor many-body calculations, we find that additional degrees of freedom make it more difficult to establish a correlation between the location of the spectral splits and the degree of quantum entanglement across the neutrino energy spectrum. The observation from the two-flavor case, that neutrinos nearest to the spectral split frequency exhibit the highest level of entanglement, is more difficult to ascertain in the three-flavor case because of the presence of multiple spectral splits across different pairwise combinations of flavor and/or mass states. Published by the American Physical Society 2025

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Impact of aeroelasticity on propulsion and longitudinal flight dynamics of an air-breathing hypersonic vehicle

Many air-breathing hypersonic aerospacecraft design concepts incorporate an elongated fuselage forebody acting as the aerodynamic compression surface for a hypersonic combustion module, or scram jet. This highly integrated design approach creates the potential for an unprecedented form of aero-propulsive-elastic interaction in which deflections of the vehicle fuselage give rise to propulsion transients, producing force and moment variations that may adversely impact the rigid body flight dynamics and/or further excite the fuselage bending modes. To investigate the potential for such interactions, a math model was developed which included the longitudinal flight dynamics, propulsion system, and first seven elastic modes of a hypersonic air-breathing vehicle. Perturbation time histories from a simulation incorporating this math model are presented that quantify the propulsive force and moment variations resulting from aeroelastic vehicle deflections. Root locus plots are presented to illustrate the effect of feeding the propulsive perturbations back into the aeroelastic model. A concluding section summarizes the implications of the observed effects for highly integrated hypersonic air-breathing vehicle concepts.

Raney, David L.↗

Atomic Force Microscopy to Characterize Antimicrobial Peptide-Induced Defects in Model Supported Lipid Bilayers

Antimicrobial peptides (AMPs) interact with bacterial cell membranes through a variety of mechanisms, causing changes extending from nanopore formation to microscale membrane lysis, eventually leading to cell death. Several AMPs also disrupt mammalian cell membranes, despite their significantly different lipid composition and such collateral hemolytic damage hinders the potential therapeutic applicability of the AMP as an anti-microbial. Elucidating the mechanisms underlying the AMP–membrane interactions is challenging due to the variations in the chemical and structural features of the AMPs, the complex compositional variations of cell membranes and the inadequacy of any single experimental technique to comprehensively probe them. (1) Background: Atomic Force Microscopy (AFM) imaging can be used in combination with other techniques to help understand how AMPs alter the orientation and structural organization of the molecules within cell membranes exposed to AMPs. The structure, size, net charge, hydrophobicity and amphipathicity of the AMPs affect how they interact with cell membranes of differing lipid compositions. (2) Methods: Our study examined two different types of AMPs, a 20-amino acid, neutral, α-helical (amphipathic) peptide, alamethicin, and a 13-amino acid, non-α-helical cationic peptide, indolicidin (which intramolecularly folds, creating a hydrophobic core), for their interactions with supported lipid bilayers (SLBs). Robust SLB model membranes on quartz supports, incorporating predominantly anionic lipids representative of bacterial cells, are currently not available and remain to be developed. Therefore, the SLBs of zwitterionic egg phosphatidylcholine (PC), which represents the composition of a mammalian cell membrane, was utilized as the model membrane. This also allows for a comparison with the results obtained from the Quartz Crystal Microbalance with Dissipation (QCM-D) experiments conducted for these peptides interacting with the same zwitterionic SLBs. Further, in the case of alamethicin, because of its neutrality, the lipid charge may be less relevant for understanding its membrane interactions. (3) Results: Using AFM imaging and roughness analysis, we found that alamethicin produced large, unstable defects in the membrane at 5 µM concentrations, and completely removed the bilayer at 10 µM. Indolicidin produced smaller holes in the bilayer at 5 and 10 µM, although they were able to fill in over time. The root-mean-square (RMS) roughness values for the images showed that the surface roughness caused by visible defects peaked after peptide injection and gradually decreased over time. (4) Conclusions: AFM is useful for helping to uncover the dynamic interactions between different AMPs and cell membranes, which can facilitate the selection and design of more efficient AMPs for use in therapeutics and antimicrobial applications.

Swana, Kathleen W.↗

New Class of Three-Nucleon Forces and Their Implications

Here, we identify a new class of three-nucleon forces that arises in the low-energy effective theory of nuclear interactions including pions. We estimate their contribution to the energy of neutron and nuclear matter and find that it can be as important as the leading-order three-nucleon forces previously considered in the literature. The magnitude of this force is set by the strength of the coupling of pions to two nucleons and is presently not well constrained by experiments. The implications for nuclei, nuclear matter, and the equation of state of neutron matter are briefly discussed.

chiral perturbation theory↗