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At least 1,081 records · Page 60

A quantitative analysis of weak intermolecular interactions & quantum chemical calculations (DFT) of novel chalcone derivatives

The novel chalcone derivatives have widespread applications in material science and medicinal industries. The density functional theory (DFT) is used to optimized the molecular structure of the three chalcone derivatives (M-I, II, III). The observed discrepancies between the theoretical and experimental (X-ray data) results attributed to different environments of the molecules, the experimental values are of the molecule in solid state there by subjected to the intermolecular forces, like non-bonded hydrogen bond interactions, where as isolated state in gas phase for theoretical studies. The lattice energy of all the molecules have been calculated using PIXELC module in Coulomb –London –Pauli (CLP) package and is partitioned into corresponding coulombic, polarization, dispersion and repulsion contributions. Lattice energy data confirm and strengthen the finding of the X-ray results that the weak but significant intermolecular interactions like C-H…O, Π- Π and C-H… Π plays an important role in the stabilization of crystal packing.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Fluorophilic Sigma(σ)‐Lock Self‐Healable Copolymers

Although F-Containing molecules and macromolecules are often used in molecular biology to increase the binding with Lewis acidic groups by introducing favorable C−F dipoles, there is virtually no experimental evidence and limited understanding of the nature of these interactions, especially their role in synthetic polymeric materials. These studies elucidate the molecular origin of inter- and intra-Chain interactions responsible for self-healing of F-Containing copolymers composed of pentafluorostyrene and n-butyl acrylate units (p(PFS/nBA). Guided by dynamic surface oscillating force (SOF) and spectroscopic measurements supported by molecular dynamics (MD) simulations, these studies show that the reformation of σ-σ orbitals in −C−F of PFS and CH 3 CH 2 − of nBA units enables the recovery of entropic energy via fluorophilic-σ-lock van der Waals forces when PFS/nBA molar ratios are ~50/50. The strength of these interactions determined experimentally for self-healable PFS/nBA compositions is in the order ~0.3 kcal/mol which primarily comes from fluorophilic-σ-lock (~70 %) contributions. These interactions are significantly diminished for non-self-healable counterparts. Strongly polarized −C−F σ orbitals create lateral dipolar forces enhancing the affinity towards −C−H orbitals, facilitating energetically favorable interactions. Entropic recovery driven by non-Covalent bonding offers a valuable tool in designing materials with unique functionalities, particularly self-healable batteries and energy storage devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Conformational change due to intramolecular hydrophobic interaction leads to large blue-shifted emission from single molecular cage solutions

In this communication, we demonstrate a unique negative solvatochromic emission (NSE) process from a conformational change of a coordination cage in response to solvent composition. The cationic cage contains two tetra-(4-pyridylphenyl)ethylene (TPPE) luminogens on two opposite faces, linked by Pt(PEt 3 ) 2 and isophthalate. When the solvent changes from acetone/acetonitrile/methanol to water, the emission of single cages gradually shifts to short wavelength (NSE) with a drastic value of ~60 nm. Small angle X-ray scattering (SAXS) measurements indicate a molecular conformational change during the process and intramolecular $\pi–\pi$ stacking and hydrophobic interaction between the TPPE planes could be the driving forces. As a comparison, a cage with a longer inter-fluorophore distance does not have such strong intramolecular interactions and only shows regular positive solvatochromic emission (PSE) under the same conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Fluid and gas dynamics

A clearer understanding of the interactions of the hot gas flow with the structure in the duct system, the flow passages of the rotating machinery, and the thrust chamber nozzle is sought for the purpose of finding ways and means to increase the life and performance of the systems. The objective of the transient nozzle test is to understand the shock-boundary layer interactions during transient flow and the resulting large side forces acting on the nozzle skirt. The Fluctuating Pressures in Ducts study deals mainly with the fluid-structural interactions of the lox post tube banks in the injector. The Ablative Nozzle Insert Study (H4) has as its goal the performance improvement of the space shuttle main engine.

Povinelli, L.↗

Characterizing Dynamics of Anion/Pi Interactions through Molecular Dynamics Simulations

Proteins are not static structures, but undergo dynamical variations at room temperature that can lead to changes in the number and strength of different non-covalent interactions. The negatively charged (Asp/Glu) and aromatic (Phe/Trp/Tyr) amino acid groups in proteins can form anion/pi interactions, that have been shown to have a distance and angle dependency. This study characterizes the dynamic stability of these interactions in RmlC (PDB-1EP0), a homodimeric epimerase showing a cluster of six anion/pi pairs in crystal structure, as a function of time using Molecular Dynamics (MD) simulations. The dynamic variations found in these interactions correspond to a potential of mean force (PMF) that exhibits a relatively wide range of distances (~4.5 to~8.5Å) and angles (0 to~45deg) sampled by these anion/pi pairs. The corresponding PMF indicates an associated free energy change that can be more stabilizing (up to -5kcal/mol) than the ab initio-calculated interaction energy for the pairs in the crystal structure (-2.2kcal/mol). Possible anion/pi pairs and triplets (anion/anion/pi or anion/pi/pi) not seen in the crystal structure are also observed in other conformations sampled by the protein- both at the dimer interface and active site of the protein, forming an extensive network of anion/pi interactions covering most of the protein structure. Initial site-directed mutagenesis (SDM) experiments targeting one of these pairs, Asp84-Phe112, show that the single Phe/Met mutation decreases the stability of the protein compared to the wild type. Together these results suggest that anion-pi interactions can play an important role in maintaining both the structural stability and function of the proteins.

Kapoor, Karan↗

Forward doubly-virtual Compton scattering off an unpolarized deuteron in pionless effective field theory

In this work, we calculate the forward unpolarised doubly-virtual Compton scattering (VVCS) off the deuteron in the framework of pionless effective field theory, up to next-to-next-to-next-to-leading order (N3LO) for the longitudinal and next-to-leading order (NLO) for the transverse amplitude. The charge elastic form factor of the deuteron, obtained from the residue of the longitudinal VVCS amplitude, is used to extract the value of the single unknown two-nucleon one-photon contact coupling that enters the longitudinal amplitude at N3LO. We also study the lowest spin-independent generalised polarisabilities of the deuteron. The calculated unpolarised VVCS amplitude provides a high-precision model-independent input for a future calculation of the two-photon-exchange correction to the Lamb shift of muonic deuterium.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Instabilities in the Early Solar System Due to a Self-gravitating Disk

Modern studies of the early solar system routinely invoke the possibility of an orbital instability among the giant planets triggered by gravitational interactions between the planets and a massive exterior disk of planetesimals. Previous works have suggested that this instability can be substantially delayed (about hundreds of megayears) after the formation of the giant planets. Bodies in the disk are typically treated in a semi-active manner, wherein their gravitational force on the planets is included, but interactions between the planetesimals are ignored. We perform N-body numerical simulations using GENGA, which makes use of GPUs to allow for the inclusion of all gravitational interactions between bodies. Although our simulated Kuiper Belt particles are more massive than the probable masses of real primordial Kuiper Belt objects, our simulations indicate that the self-stirring of the primordial Kuiper Belt is very important to the dynamics of the giant planet instability. We find that interactions between planetesimals dynamically heat the disk and typically prevent the outer solar system’s instability from being delayed by more than a few tens of megayears after giant planet formation. Longer delays occur in a small fraction of systems that have at least 3.5 au gaps between the planets and planetesimal disk. Our final planetary configurations match the solar system at a rate consistent with other previous works in most regards. Pre-instability heating of the disk typically yields final Jovian eccentricities comparable to the modern solar system’s value, which has been a difficult constraint to match in past works.

79 ASTRONOMY AND ASTROPHYSICS↗

All-Atom Modeling and Simulation of Biopolymer Interface: Dual Role of Antifouling Polymer Brushes

Antifouling polymer brushes are well-known for their exceptional resistance to unwanted protein adsorption. While experimental studies have extensively characterized protein–polymer brush interactions, computational investigations remain limited, largely due to the challenges in accurately modeling and integrating these complex, multicomponent systems without resorting to oversimplification. To address this challenge, this study presents one of the most comprehensive and realistic model systems to date, comprising the substrate, grafted polymers, and proteins. Our work interprets the interactions between polymer brush and protein based on realistic modeling without simplification. In particular, this study utilizes molecular modeling and simulation of polycationic and polyzwitterionic brushes─poly(dimethylaminoethyl methacrylate) (PDMAEMA), poly(2-(N-oxide-N,N-dimethylamino)ethyl methacrylate) (PNOMA), and poly(2-(N-3-sulfopropyl-N,N-dimethylammonium)ethyl methacrylate) (PSBMA)─grafted onto α-quartz substrates via polymerization initiator linkers. The brush models were developed to closely replicate experimentally synthesized samples and to provide detailed insights into structural and dynamical changes at the molecular level during protein adsorption. Using steered molecular dynamics simulations, we show that the PSBMA brush, due to its high local density, exhibits the greatest resistance to protein insertion. Cα root-mean-square deviation and interaction pattern analyses further reveal that the PSBMA brush also induces the most significant destabilization of lysozyme, while the PDMAEMA brush enhances protein stability through ion-mediated interactions. The PNOMA brush, while requiring the lowest force for protein adsorption, induces greater protein destabilization than the PDMAEMA brush, primarily due to electrostatic repulsion caused by a short carbon spacer length. Hydration analysis reveals that both the PSBMA brush and the lysozyme interacting with it exhibit the most rapid dehydration, attributed to the brush’s high local chain density, which results in the greatest lysozyme destabilization and the highest adsorption force. These findings highlight the dual role of antifouling polymer brushes: resisting protein adsorption and modulating protein structural dynamics. In conclusion, this study provides valuable insights for the rational design of next-generation antifouling materials and offers a framework for realistic model development in complex multicomponent systems.

Adsorption↗

Pore elimination mechanisms during 3D printing of metals

Laser powder bed fusion (LPBF) is a 3D printing technology that can print metal parts with complex geometries without the design constraints of traditional manufacturing routes. However, the parts printed by LPBF normally contain many more pores than those made by conventional methods, which severely deteriorates their properties. Here, by combining in-situ high-speed high-resolution synchrotron x-ray imaging experiments and multi-physics modeling, we unveil the dynamics and mechanisms of pore motion and elimination in the LPBF process. We find that the high thermocapillary force, induced by the high temperature gradient in the laser interaction region, can rapidly eliminate pores from the melt pool during the LPBF process. The thermocapillary force driven pore elimination mechanism revealed here may guide the development of 3D printing approaches to achieve pore-free 3D printing of metals.

36 MATERIALS SCIENCE↗

Driven assembly with multiaxial fields: Creating a soft mode in assemblies of anisometric induced dipoles

We show that multiaxial fields can induce time-averaged, noncentrosymmetric interactions between particles having polarization anisotropy, yet the multiaxial field itself does not exert either a force or a torque on an isolated particle. These induced interactions lead to particle assemblies whose energy is strongly dependent on both the translational and orientational degrees of freedom of the system. The situation is similar to a collection of permanent dipoles, but the symmetry of the time-averaged interaction is quite distinct, and the scale of the system energy can be dynamically controlled by the magnitude of the applied multiaxial field. In our paper, the case of polarizable rods is considered in detail, and it is suggested that collections of rods embedded in spheres can be used to create a material with a dynamically tunable magnetic permeability or dielectric permittivity. We report on Monte Carlo simulations performed to investigate the behavior of assemblies of both multiaxial-field induced dipoles and permanent dipoles arranged onto two-dimensional lattices. Lastly, the ground state of the induced dipoles is an orientational soft mode of aligned dipoles, whereas that of the permanent dipoles is a vortex state.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Recent advances in chiral EFT based nuclear forces and their applications

During the past two decades, chiral effective field theory has evolved into a powerful tool to derive nuclear forces from first principles. Nearly all two-nucleon interactions have been worked out up to sixth order of chiral perturbation theory, while, with few exceptions, three-nucleon forces, which play a subtle, but crucial role in microscopic nuclear structure calculations, have been derived up to fifth order. We review the current status of these forces as well as their applications in nuclear many-body systems. While the ab initio description of light nuclei is generally very successful, we point out and analyze problems encountered with medium-mass nuclei. We also survey the construction of equations of state for symmetric nuclear matter and neutron-rich matter based on chiral forces. A focal point is the symmetry energy and its impact on neutron skins and systems of astrophysical relevance. The physics of neutron-rich systems, from nuclei to compact stars, is essentially determined by the density dependence of the symmetry energy. Here, we review the status of predictions in comparison with latest empirical constraints, with particular attention to those extracted from parity-violating electron scattering.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Deuteron-α scattering: Separable versus nonseparable Faddeev approach

Deuteron-induced reactions are widely used to probe nuclear structure and astrophysical information. Those (d,p) reactions may be viewed as three-body reactions and described with Faddeev techniques. Faddeev-AGS equations in momentum space have a long tradition of utilizing separable interactions in order to arrive at sets of coupled integral equations in one variable. However, it needs to be demonstrated that observables calculated based on separable interactions agree exactly with those based on nonseparable forces. Momentum space AGS equations are solved with separable and nonseparable forces as coupled integral equations. Deuteron-α scattering is calculated via momentum space AGS equations using the CD-Bonn neutron-proton force and a Woods-Saxon type neutron(proton)- 4 He force, for which the Pauli-forbidden S-wave bound state is projected out. Elastic as well as breakup observables are calculated and compared to results in which the interactions in the two-body sub-systems are represented by separable interactions derived in the Ernst-Shakin-Thaler (EST) framework. We find that the calculations based on the separable representation of the interactions and the original interactions give results that are in excellent agreement. Specifically, integrated cross sections and angular distributions for elastic scattering agree within ≈ 1 %, which is well below typical experimental errors. In addition, the fivefold differential cross sections corresponding to breakup of the deuteron agree extremely well.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

p62 regulates CD40-mediated NFκB activation in macrophages through interaction with TRAF6

CD40 is a member of the tumor necrosis factor (TNF) receptor family. Activation-induced recruitment of adapter proteins, so-called TNF-receptor-associated factors (TRAFs) to the cytoplasmic tail of CD40 triggers signaling cascades important in the immune system, but has also been associated with excessive inflammation in diseases such as atherosclerosis and rheumatoid arthritis. Especially, pro-inflammatory nuclear factor κB (NFκB) signaling emanating from CD40-associated TRAF6 appears to be a key pathogenic driving force. Consequently, targeting the CD40-TRAF6 interaction is emerging as a promising therapeutic strategy, but the underlying molecular machinery of this signaling axis is to date poorly understood. Here, we identified the multifunctional adaptor protein p62 as a critical regulator in CD40-mediated NFκB signaling via TRAF6. CD40 activation triggered formation of a TRAF6-p62 complex. Disturbing this interaction tremendously reduced CD40-mediated NFκB signaling in macrophages, while TRAF6-independent signaling pathways remained unaffected. This highlights p62 as a potential target in hyper-inflammatory, CD40-associated pathologies. - Highlights: • CD40 activation triggers interaction of the adapter protein TRAF6 with p62. • TRAF6-p62 interaction regulates CD40-mediated NFκB signaling in macrophages. • Defective TRAF6-p62 interaction reduces CD40-mediated NFκB activation in macrophages.

60 APPLIED LIFE SCIENCES↗

Formation of a memristor matrix based on titanium oxide and investigation by probe-nanotechnology methods

The results of investigation of a memristor-matrix model on the basis of titanium-oxide nanoscale structures (ONSs) fabricated by methods of focused ion beams and atomic-force microscopy (AFM) are presented. The effect of the intensity of interaction between the AFM probe and the sample surface on the memristor effect in the titanium ONS is shown. The memristor effect in the titanium ONS is investigated by an AFM in the mode of spreading-resistance map. The possibility of the recording and erasure of information in the submicron cells is shown on the basis of using the memristor effect in the titanium ONS, which is most promising for developing the technological processes of the formation of resistive operation memory cells.

36 MATERIALS SCIENCE↗

Optimization of the Reax force field for the lithium–oxygen system using a high fidelity charge model

Studies using molecular dynamics (MD) have long struggled to simulate the failure modes of materials, predicting unrealistically high ductility and failing to capture brittle fracture. The primary cause of this shortcoming is an inadequate description of bond breaking. While reactive force fields such as ReaxFF show improvements compared to traditional force fields, the charge models used yield unphysical partial charges, especially during dissociation of ionic bonds. This flaw may be remedied by using the atom-condensed Kohn–Sham density functional theory (DFT) approximated to a second order (ACKS2) charge model for determining partial charges. In this work, we present a new ACKS2-enabled Reax force field for fracture simulations of lithium oxide systems, which was obtained by training against an extensive set of DFT, multireference configuration interaction (MRCI), and MRCI+Q reference data using genetic optimization techniques. This new force field significantly improves the bond breaking behavior, but still cannot fully capture the brittle fracture in MD simulations, suggesting more research is needed to improve simulation of brittle fracture.

36 MATERIALS SCIENCE↗

Comment on “Isolating the non-polar contributions to the intermolecular potential for water-alkane interactions” [J. Chem. Phys. 141, 064905 (2014)]

The manuscript by Ballal et al.(Ref 1) presents an interesting study demonstrating the inability of popular force fields with standard combination rules to accurately describe water/alkane interactions. The authors find that the Lorentz-Berthelot combination rules on the SPC/E water and TraPPE alkane potentials give a cross interaction that fails to predict the (low-water content) water solubility in various alkanes. Realizing that both explicit polarization as well as the static octupole moment of methane are missing in these potentials, the authors examine the effect of these terms, but are still unable to resolve the discrepancy. They conclude with the statement that “the research community lacks a complete picture of water-alkane interactions at the molecular level.

36 MATERIALS SCIENCE↗

Microgravity-Enhanced Stem Cell Selection

Stem cells, both embryonic and adult, promise to revolutionize the practice of medicine in the future. In order to realize this potential, a number of hurdles must be overcome. Most importantly, the signaling mechanisms necessary to control the differentiation of stem cells into tissues of interest remain to be elucidated, and much of the present research on stem cells is focused on this goal. Nevertheless, it will also be essential to achieve large-scale expansion and, in many cases, assemble cells in 3D as transplantable tissues. To this end, microgravity analog bioreactors can play a significant role. Microgravity bioreactors were originally conceived as a tool to study the cellular responses to microgravity. However, the technology can address some of the shortcomings of conventional cell culture systems; namely, the deficiency of mass transport in static culture and high mechanical shear forces in stirred systems. Unexpectedly, the conditions created in the vessel were ideal for 3D cell culture. Recently, investigators have demonstrated the capability of the microgravity bioreactors to expand hematopoietic stem cells compared to static culture, and facilitate the differentiation of umbilical cord stem cells into 3D liver aggregates. Stem cells are capable of differentiating into functional cells. However, there are no reliable methods to induce the stem cells to form specific cells or to gain enough cells for transplantation, which limits their application in clinical therapy. The aim of this study is to select the best experimental setup to reach high proliferation levels by culturing these cells in a microgravity-based bioreactor. In typical cell culture, the cells sediment to the bottom surface of their container and propagate as a one-cell-layer sheet. Prevention of such sedimentation affords the freedom for self-assembly and the propagation of 3D tissue arrays. Suspension of cells is easily achievable using stirred technologies. Unfortunately, in conventional bioreactors, stirring invokes deleterious forces that disrupt cell aggregation and results in cell death. First-generation rotating bioreactors provided rotation on the horizontal axis, which resulted in the suspension of cells without stirring, thus providing a suitable environment to propagate cells without sedimentation to a surface. The rotating wall bioreactors did not provide a way to remove air bubbles that were causing shear and disrupting 3D cultures. Johnson Space Center successfully engineered the hydrofocusing bioreactor (HFB) that resolved the problem of removing the air bubbles from the fluid medium of NASA's rotating-wall space bioreactors. The HFB uses the principle of hydrodynamic focusing that simultaneously produces a low-shear fluid culture environment and a variable hydrofocusing force that can control the movement, location, and removal of suspended cells, tissues, and air bubbles from the bioreactor. The HFB is a rotating, domeshaped cell culture vessel with a centrally located sampling port and an internal viscous spinner. The vessel and spinner can rotate at different speeds either in the same or opposite directions. Rotation of the vessel and viscous interaction at the spinner generate a hydrofocusing force. Adjusting the differential rotation rate between vessel and spinner controls the magnitude of the force.

Claudio, Pier Paolo↗

A Solar System Survey of Forced Librations in Longitude

Forced librations are periodic rotational rate variations due to gravitational interactions with an orbital partner. We have developed an analytic theory capable of calculating expected amplitudes of forced librations for nonresonant rotators as well as for bodies existing in a spin-orbit resonance. The theory has been applied to 34 solar system bodies, including terrestrial planets, planetary satellites, and the asteroid Eros. Parameters governing libration amplitude are the body s orbital eccentricity, moment difference, and the ratio of its spin rate to its orbital rate. In each case the largest libration amplitude is associated with the forcing frequency 2 (p - 1) n, where n is the orbital mean motion and p is the spin/orbit rate ratio. This dominant frequency is simply semidiurnal as seen from the position of the torquing body. The maximum libration angular amplitude is 1.3 x 10(exp -2) radians for Thebe, and the maximum mean equatorial displacement is 1.4 km for Mimas.

Cornstock, Robert L.↗