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At least 379 records · Page 21

Global Phase Diagram of a Spin-Orbital Kondo Impurity Model and the Suppression of Fermi-Liquid Scale

Many correlated metallic materials are described by Landau Fermi-liquid theory at low energies, but for Hund metals the Fermi-liquid coherence scale $T_{FL}$ is found to be surprisingly small. In this Letter, we study the simplest impurity model relevant for Hund metals, the three-channel spin-orbital Kondo model, using the numerical renormalization group (NRG) method and compute its global phase diagram. In this framework, $T_{FL}$ becomes arbitrarily small close to two new quantum critical points that we identify by tuning the spin or spin-orbital Kondo couplings into the ferromagnetic regimes. We find quantum phase transitions to a singular Fermi-liquid or a novel non-Fermi-liquid phase. The new non-Fermi-liquid phase shows frustrated behavior involving alternating overscreenings in spin and orbital sectors, with universal power laws in the spin (ω -1/5 ), orbital (ω 1/ 5 ) and spin-orbital (ω 1 ) dynamical susceptibilities. These power laws, and the NRG eigenlevel spectra, can be fully understood using conformal field theory arguments, which also clarify the nature of the non-Fermi-liquid phase.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Assembly of polyelectrolyte star block copolymers at the oil–water interface

To understand and resolve adsorption, reconfiguration, and equilibrium conformations of charged star copolymers, we carried out an integrated experimental and coarse-grained molecular dynamics simulation study of the assembly process at the oil–water interface. This is important to guide development of novel surfactants or amphiphiles for chemical transformations and separations. The star block copolymer consisted of arms that are comprised of hydrophilic–hydrophobic block copolymers that are covalently tethered via the hydrophobic blocks to one point. The hydrophobic core represents polystyrene (PS) chains, while the hydrophilic corona represents quaternized poly(2-vinylpyridine) (P2VP) chains. The P2VP is modeled to become protonated when in contact with an acidic aqueous phase, thereby massively increasing the hydrophilicity of this block, and changing the nature of the star at the oil–water interface. This results in a configurational change whereby the chains comprising the hydrophilic corona are significantly stretched into the aqueous phase, while the hydrophobic core remains solubilized in the oil phase. In the simulations, we followed the kinetics of the anchoring and assembly of the star block copolymer at the interface, monitoring the lateral assembly, and the subsequent reconfiguration of the star via changes in the interfacial tension that varies as the degree-of-protonation increases. At low fractions of protonation, the arm cannot fully partition into the aqueous side of the interface and instead interacts with other arms in the oil phase forming a network near the interface. These insights were used to interpret the non-monotonic dependence of pH with the asymptotic interfacial tension from pendant drop tensiometry experiments and spectral signatures of aromatic stretches seen in vibrational sum frequency generation (SFG) spectroscopy. We describe the relationship of interfacial tension to the star assembly via the Frumkin isotherm, which phenomenologically describes anti-cooperativity in adsorbing stars to the interface due to crowding. Although our model explicitly considers long-range electrostatics, the contribution of electrostatics to interfacial tension is small and brought about by strong counterion condensation at the interface. Finally, these results provide key insights into resolving the adsorption, reconfiguration, and equilibrium conformations of charged star block copolymers as surfactants.

36 MATERIALS SCIENCE↗

Simulation studies of polypeptoids using replica exchange with dynamical scaling and dihedral biasing

Polypeptoids differ from polypeptides in that the amide bond can more frequently adopt both cis and trans conformations. The transition between the two conformations requires overcoming a large energy barrier, making it difficult for conventional molecular simulations to adequately visit the cis and trans structures. A replica-exchange method is presented that allows for easy rotations of the amide bond and also an efficient linking to a high temperature replica. The method allows for just three replicas (one at the temperature and Hamiltonian of interest, a second high temperature replica with a biased dihedral potential, and a third connecting them) to overcome the amide bond sampling problem and also enhance sampling for other coordinates. Here our results indicate that for short peptoid oligomers, the conformations can range from all cis to all trans with an average cis/trans ratio that depends on side chain and potential model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural basis of RNA conformational switching in the transcriptional regulator 7SK RNP

7SK non-coding RNA (7SK) negatively regulates RNA polymerase II (RNA Pol II) elongation by inhibiting positive transcription elongation factor b (P-TEFb), and its ribonucleoprotein complex (RNP) is hijacked by HIV-1 for viral transcription and replication. Methylphosphate capping enzyme (MePCE) and La-related protein 7 (Larp7) constitutively associate with 7SK to form a core RNP, while P-TEFb and other proteins dynamically assemble to form different complexes. Here, we present the cryo-EM structures of 7SK core RNP formed with two 7SK conformations, circular and linear, and uncover a common RNA-dependent MePCE-Larp7 complex. Further, together with NMR, biochemical, and cellular data, these structures reveal the mechanism of MePCE catalytic inactivation in the core RNP, unexpected interactions between Larp7 and RNA that facilitate a role as an RNP chaperone, and that MePCE-7SK-Larp7 core RNP serves as a scaffold for switching between different 7SK conformations essential for RNP assembly and regulation of P-TEFb sequestration and release.

59 BASIC BIOLOGICAL SCIENCES↗

Frank–Kasper Phases of Diblock Copolymer Melts: Self-Consistent Field Results of Two Commonly Used Models

We constructed phase diagrams of conformationally asymmetric diblock copolymer A-B melts using the polymer self-consistent field (SCF) calculations of both the dissipative particle dynamics chain (DPDC) model (i.e., compressible melts of discrete Gaussian chains with the DPD non-bonded potential) and the “standard” model (i.e., incompressible melts of continuous Gaussian chains with the Dirac δ-function non-bonded potential) in the χN-ε plane, where χN and ε characterize, respectively, the repulsion and conformational asymmetry between the A and B blocks, at the A-block volume fraction f = 0.2 and 0.3. Consistent with previous SCF calculations of the “standard” model, σ and A15 are the only stable Frank–Kasper (FK) phases among the five FK (i.e., σ, A15, C14, C15 and Z) phases considered. The stability of σ and A15 is due to their delicate balance between the energetic and entropic contributions to the Helmholtz free energy per chain of the system, which, within our parameter range, increases in the order of σ/A15, Z, and C14/C15. While in general the SCF phase diagrams of these two models are qualitatively consistent, A15 is not stable for the DPDC model at the copolymer chain length N = 10 and f = 0.3; any differences in the SCF phase diagrams are solely due to the differences between these two models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Control over Conformational Landscapes of Polypeptoids by Monomer Sequence Patterning

The ability to program chain conformation and structure through control over the monomer sequence of synthetic polymers has broad implications for next-generation material design. While related problems of protein-folding and de novo design have generated accurate predictions of 3D folded chain structures, generalization to synthetic polymers remains intractable due to the requirement of large structural databases and the intrinsically disordered nature of polymer building blocks. In this work, polypeptoids, a class of peptidomimetic synthetic polymers, are utilized to build a general workflow for the study of relationships between monomer sequence and dynamic 3D chain structure in solution. Furthermore, this work demonstrates how control over the monomer sequence can alter the conformational landscape of synthetic polymers to deviate dramatically from classical chain statistics. Specifically, the distribution of end-to-end distances, as measured by double electron-electron resonance spectroscopy in dilute solvent, is systematically skewed towards shorter distances with an increasing number of hydrophobes and further refined by hydrophobe arrangement in amphiphilic polypeptoid chains.

36 MATERIALS SCIENCE↗

The Role of Ligand–Ligand Interactions in Multimodal Ligand Conformational Equilibria and Surface Pattern Formation

Multimodal chromatography uses multiple modes of interaction such as charge, hydrophobic, or hydrogen bonding to separate proteins. Recently, we used molecular dynamics (MD) simulations to show that ligands immobilized on surfaces can interact and associate with neighboring ligands to form hydrophobic and charge patches, which may have important implications for the nature of protein–surface interactions. Here, we study interfacial systems of increasing complexity—from a single immobilized multimodal ligand to high density surfaces—to better understand how ligand behavior is affected by the presence of a surface and the presence of other ligands in the vicinity, and how this behavior scales to larger systems. Furthermore, we find that tethering a ligand to a surface restricts its conformations to a subset of those observed in free solution, yet the ligand maintains flexibility in the plane of the surface and can form contacts with neighboring ligands. We find that although the formation of a contact between two neighboring ligands is slightly unfavorable, three neighboring ligands exhibit a preference for the formation of a fully connected cluster. To explore how these trends in ligand association extend to a larger surface with high density of ligands, we performed coarse-grained Monte Carlo (MC) simulations of a 132-ligand surface using ligand interactions parametrized based on free energies obtained from the three-ligand MD simulations. Despite their simplicity, the coarse-grained simulations qualitatively capture the cluster size distribution of ligands observed in detailed MD simulations. Quantitative differences between the two suggest opportunities for improvements in the coarse-grained energy function for efficient predictions of cluster and pattern formations. Our approach presents a promising route to the engineering of multimodal patterns for future chromatographic resin design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural and dynamic changes in P-Rex1 upon activation by PIP 3 and inhibition by IP 4

PIP 3 -dependent Rac exchanger 1 (P-Rex1) is abundantly expressed in neutrophils and plays central roles in chemotaxis and cancer metastasis by serving as a guanine-nucleotide exchange factor (GEF) for Rac. The enzyme is synergistically activated by PIP 3 and heterotrimeric Gβγ subunits, but mechanistic details remain poorly understood. While investigating the regulation of P-Rex1 by PIP 3 , we discovered that Ins(1,3,4,5)P 4 (IP 4 ) inhibits P-Rex1 activity and induces large decreases in backbone dynamics in diverse regions of the protein. Cryo-electron microscopy analysis of the P-Rex1·IP 4 complex revealed a conformation wherein the pleckstrin homology (PH) domain occludes the active site of the Dbl homology (DH) domain. This configuration is stabilized by interactions between the first DEP domain (DEP1) and the DH domain and between the PH domain and a 4-helix bundle (4HB) subdomain that extends from the C-terminal domain of P-Rex1. Disruption of the DH–DEP1 interface in a DH/PH-DEP1 fragment enhanced activity and led to a more extended conformation in solution, whereas mutations that constrain the occluded conformation led to decreased GEF activity. Variants of full-length P-Rex1 in which the DH–DEP1 and PH–4HB interfaces were disturbed exhibited enhanced activity during chemokineinduced cell migration, confirming that the observed structure represents the autoinhibited state in living cells. Interactions with PIP 3 -containing liposomes led to disruption of these interfaces and increased dynamics protein-wide. Our results further suggest that inositol phosphates such as IP 4 help to inhibit basal P-Rex1 activity in neutrophils, similar to their inhibitory effects on phosphatidylinositol-3-kinase.

59 BASIC BIOLOGICAL SCIENCES↗

Crystalline Peptoid Nanofibers with a Single-Unit Cell Cross Section

Ultranarrow crystalline one-dimensional nanostructures formed from soft materials facilitate precise structural control in nanomaterial design, which is essential for biomedicine and nanotechnology applications. Systematic control of their hierarchical structure is challenging due to the complexities of simultaneously manipulating multiple noncovalent interactions at such small scales. We employed a polypeptoid crystal motif as a supramolecular synthon to engineer ultranarrow crystalline nanofibers constrained to a single lattice axis by incorporating a single ionizable side chain into the hydrophobic core of a nanosheet-forming peptoid. Cryogenic transmission electron microscopy of the nanofibers revealed detailed molecular arrangements of a unit-cell cross-section and the presence of distinct pH-dependent lattice isoforms that resulted in morphological transformations. Molecular dynamics simulations demonstrated that the ionizable side chain plays a critical role in changing the local conformation of the unit cell, which further impacts the dimensionality of hierarchical structures. Moreover, these fibers were readily functionalized with biological ligands to afford one-dimensional (1D) protein arrays. This approach for the high-precision bottom-up assembly of ultranarrow 1D nanostructures offers significant potential for developing novel biomimetic nanostructures.

Lee, Yen Jea↗

Mechanisms of activation and desensitization of full-length glycine receptor in lipid nanodiscs

Glycinergic synapses play a central role in motor control and pain processing in the central nervous system. Glycine receptors (GlyRs) are key players in mediating fast inhibitory neurotransmission at these synapses. While previous high-resolution structures have provided insights into the molecular architecture of GlyR, several mechanistic questions pertaining to channel function are still unanswered. Here, we present Cryo-EM structures of the full-length GlyR protein complex reconstituted into lipid nanodiscs that are captured in the unliganded (closed), glycine-bound (open and desensitized), and allosteric modulator-bound conformations. A comparison of these states reveals global conformational changes underlying GlyR channel gating and modulation. The functional state assignments were validated by molecular dynamics simulations, and the observed permeation events are in agreement with the anion selectivity and conductance of GlyR. These studies provide the structural basis for gating, ion selectivity, and single-channel conductance properties of GlyR in a lipid environment.

59 BASIC BIOLOGICAL SCIENCES↗

Self-assembly and regulation of protein cages from pre-organised coiled-coil modules

Coiled-coil protein origami (CCPO) is a modular strategy for the de novo design of polypeptide nanostructures. CCPO folds are defined by the sequential order of concatenated orthogonal coiled-coil (CC) dimer-forming peptides, where a single-chain protein is programmed to fold into a polyhedral cage. Self-assembly of CC-based nanostructures from several chains, similarly as in DNA nanotechnology, could facilitate the design of more complex assemblies and the introduction of functionalities. Here, we show the design of a de novo triangular bipyramid fold comprising 18 CC-forming segments and define the strategy for the two-chain self-assembly of the bipyramidal cage from asymmetric and pseudo-symmetric pre-organised structural modules. In addition, by introducing a protease cleavage site and masking the interfacial CC-forming segments in the two-chain bipyramidal cage, we devise a proteolysis-mediated conformational switch. This strategy could be extended to other modular protein folds, facilitating the construction of dynamic multi-chain CC-based complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Association of Cl with C 2 H 2 by unified variable-reaction-coordinate and reaction-path variational transition-state theory

Significance A key issue in chemical kinetics is advancing the theoretical framework to handle reactions beyond the domain of textbook transition-state theory by including––for example––anharmonicity, barrierless transition states, transition states in series, and the effect of conformational flexibility on equilibrium constants. Other key issues are validating affordable electronic structure methods for direct dynamics and the direct calculation of high-pressure limiting rate constants, which are often obtainable experimentally only by extrapolation. The present article addresses all these issues for a prototype radical–molecule association reaction and thereby demonstrates how to combine improved theoretical methods to provide rate constants in cases where experimental data are uncertain or missing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

RNA structures and dynamics with Å resolution revealed by x-ray free-electron lasers

RNA macromolecules, like proteins, fold to assume shapes that are intimately connected to their broadly recognized biological functions; however, because of their high charge and dynamic nature, RNA structures are far more challenging to determine. We introduce an approach that exploits the high brilliance of x-ray free-electron laser sources to reveal the formation and ready identification of angstrom-scale features in structured and unstructured RNAs. Previously unrecognized structural signatures of RNA secondary and tertiary structures are identified through wide-angle solution scattering experiments. With millisecond time resolution, we observe an RNA fold from a dynamically varying single strand through a base-paired intermediate to assume a triple-helix conformation. While the backbone orchestrates the folding, the final structure is locked in by base stacking. This method may help to rapidly characterize and identify structural elements in nucleic acids in both equilibrium and time-resolved experiments.

59 BASIC BIOLOGICAL SCIENCES↗

Quantum phase transition dynamics in the two-dimensional transverse-field Ising model

The quantum Kibble-Zurek mechanism (QKZM) predicts universal dynamical behavior near the quantum phase transitions (QPTs). It is now well understood for the one-dimensional quantum matter. Higher-dimensional systems, however, remain a challenge, complicated by the fundamentally different character of the associated QPTs and their underlying conformal field theories. In this work, we take the first steps toward theoretical exploration of the QKZM in two dimensions for interacting quantum matter. We study the dynamical crossing of the QPT in the paradigmatic Ising model by a joint effort of modern state-of-the-art numerical methods, including artificial neural networks and tensor networks. As a central result, we quantify universal QKZM behavior close to the QPT. We also note that, upon traversing further into the ferromagnetic regime, deviations from the QKZM prediction appear. We explain the observed behavior by proposing an extended QKZM taking into account spectral information as well as phase ordering. Our work provides a testing platform for higher-dimensional quantum simulators.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Exact reaction coordinates for flap opening in HIV-1 protease

The primary goal of protein science is to understand how proteins function, which requires understanding the functional dynamics responsible for transitions between different functional structures of a protein. A central concept is the exact reaction coordinates that can determine the value of committor for any protein configuration, which provide the optimal description of functional dynamics. Despite intensive efforts, identifying the exact reaction coordinates (RCs) in complex molecules remains a formidable challenge. Using the recently developed generalized work functional, we report the discovery of the exact RCs for an important functional process—the flap opening of HIV-1 protease. Our results show that this process has six RCs, each one is a linear combination of ~240 backbone dihedrals, providing the precise definition of collectivity and cooperativity in the functional dynamics of a protein. Applying bias potentials along each RC can accelerate flap opening by 10 3 to 10 4 folds. The success in identifying the RCs of a protein with 198 residues represents a significant progress beyond that of the alanine dipeptide, currently the only other complex molecule for which the exact RCs for its conformational changes are known. Our results suggest that the generalized work functional (GWF) might be the fundamental operator of mechanics that controls protein dynamics.

Science & Technology - Other Topics↗

Insights into distorted lamellar phases with small-angle scattering and machine learning

Lamellar phases are essential in various soft matter systems, with topological defects significantly influencing their mechanical properties. In this report, we present a machine-learning approach for quantitatively analyzing the structure and dynamics of distorted lamellar phases using scattering techniques. By leveraging the mathematical framework of Kolmogorov–Arnold networks, we demonstrate that the conformations of these distorted phases – expressed as superpositions of complex waves – can be reconstructed from small-angle scattering intensities. Through the contour analysis of wave field phase singularities, we obtain the statistics of the spatial distribution of topological defects. Furthermore, we establish that the temporal evolution of these defects can be derived from the time-dependent traveling wave field, informed by the dispersion relation of spectral components. This method opens new avenues for investigating the dynamics of distorted lamellar phases using various dynamic scattering techniques such as neutron spin echo and X-ray photon correlation spectroscopy. These findings enhance our microscopic understanding of how defects influence the physical properties of lamellar materials, with implications for both equilibrium and non-equilibrium states in general lamellar systems.

36 MATERIALS SCIENCE↗

Self-inhibited State of Venezuelan Equine Encephalitis Virus (VEEV) nsP2 Cysteine Protease: A Crystallographic and Molecular Dynamics Analysis

The Venezuelan equine encephalitis virus (VEEV) belongs to the Togaviridae family and is pathogenic to both humans and equines. The VEEV non-structural protein 2 (nsP2) is a cysteine protease (nsP2pro) that processes the polyprotein and thus it is a drug target for inhibitor discovery. The atomic structure of the VEEV nsP2 catalytic domain was previously characterized by both X-ray crystallography and computational studies. A modified nsP2pro harboring a N475A mutation in the N terminus was observed to exhibit an unexpected conformation: the N-terminal residues bind to the active site, mimicking binding of a substrate. The large conformational change of the N terminus was assumed to be induced by the N475A mutation, as N475 has an important role in stabilization of the N terminus and the active site. This conformation was first observed in the N475A mutant, but we also found it while determining a crystal structure of the catalytically active nsP2pro containing the wild-type N475 active site residue and K741A/K767A surface entropy reduction mutations. This suggests that the N475A mutation is not a prerequisite for self-inhibition. Here, we describe a high resolution (1.46 Å) crystal structure of a truncated nsP2pro (residues 463–785, K741A/K767A) and analyze the structure further by molecular dynamics to study the active and self-inhibited conformations of nsP2pro and its N475A mutant. A comparison of the different conformations of the N-terminal residues sheds a light on the interactions that play an important role in the stabilization of the enzyme.

59 BASIC BIOLOGICAL SCIENCES↗

Advances for QCD and the standard model: color-confining light-front holography and the principle of maximum conformality

Here, I review how the application of superconformal quantum mechanics and light-front holography leads to new insights into the physics of color confinement, the spectroscopy and dynamics of hadrons, as well as surprising supersymmetric relations between the masses of mesons, baryons, and tetraquarks. Spontaneous chiral symmetry breaking is automatically fulfilled by supersymmetric Light-Front QCD. The light-front holographic approach (HLFQCD) also predicts the behavior of the QCD running coupling and other observables from the nonperturbative color-confining domain to the perturbative domain. One can determine the QCD running coupling to high precision from the data of just a single experiment over the entire perturbative regime by using the Principle of Maximum Conformality (PMC). The PMC, which generalizes the conventional Gell-Mann-Low method for scale-setting in perturbative QED to non-Abelian QCD, provides a rigorous method for achieving unambiguous scheme-independent, fixed-order Standard Model predictions, consistent with the principles of the renormalization group. I also briefly review a novel feature of hadronic physics predicted by QCD: intrinsic heavy quarks.

Brodsky, Stanley J. [SLAC National Accelerator Lab↗