Collective Modes Of Motion Research Articles

Fourier coefficients of noninterdependent collective motions in heavy-ion collisions

We present a scenario in heavy-ion collisions where different modes of collective motions are noninterdependent, driven by factorized actions in the created nuclear medium. Such physics mechanisms could each dominate at a distinct evolution stage, or coexist simultaneously. If the probability of particle emission is modulated by each nondependent collective motion with a single-harmonic Fourier expansion, the particle azimuthal distribution should be the product of all these expansions. Consequently, nonleading cross terms between collectivity modes appear, and their contributions to experimental observables could be significant. In particular, we argue that the chiral magnetic effect (CME) and elliptic flow can develop separately, with their convolution affecting the observable that is sensitive to the shear-induced CME. We will use the event-by-event anomalous-viscous fluid dynamics model to illustrate the effects of this scenario. Besides giving insights into searches for the CME, we also propose feasible experimental tests based on conventional flow harmonics, and demonstrate the emergence of nonleading cross terms with a multiphase transport model.

Efficient numerical approach to high-fidelity phase-modulated gates in long chains of trapped ions.

Almost every quantum circuit is built with two-qubit gates in the current stage, which are crucial to the quantum computing in any platform. The entangling gates based on Mølmer-Sørensen schemes are widely exploited in the trapped-ion system, with the utilization of the collective motional modes of ions and two laser-controlled internal states, which are served as qubits. The key to realize high-fidelity and robust gates is the minimization of the entanglement between the qubits and the motional modes under various sources of errors after the gate operation. In this work, we propose an efficient numerical method to search high-quality solutions for phase-modulated pulses. Instead of directly optimizing a cost function, which contains the fidelity and the robustness of the gates, we convert the problem to the combination of linear algebra and the solution to quadratic equations. Once a solution with the gate fidelity of 1 is found, the laser power can be further reduced while searching on the manifold where the fidelity remains 1. Our method largely overcomes the problem of the convergence and is shown to be effective up to 60 ions, which suffices the need of the gate design in current trapped-ion experiments.

Experimental confirmation of the formation of a spin polariton in dilute solutions of paramagnetic particles.

Spin exchange during random bimolecular collisions of paramagnetic particles in dilute solutions leads to a surprising effect. Collective modes of motion of the average values of the transverse magnetization components (spin coherences) of subensembles of radicals with different resonant frequencies are formed. The elementary excitations of these modes can be considered as quasiparticles. As a result of interactions with the microwave field, these quasiparticles form spin polaritons. The theoretical prediction for the formation of spin polaritons was made on the basis that the resonance frequencies observed in the EPR experiment depend on the power of the microwave field. In this work, we present an experimental confirmation of the resonant frequency dependence of the spin ensemble on the microwave power for nitroxide radical [15N]-4-hydroxy-2,2,6,6-tetramethylpiperidine-1-oxyl in toluene.

Engineering an effective three-spin Hamiltonian in trapped-ion systems for applications in quantum simulation

Trapped-ion quantum simulators, in analog and digital modes, are considered a primary candidate to achieve quantum advantage in quantum simulation and quantum computation. The underlying controlled ion–laser interactions induce all-to-all two-spin interactions via the collective modes of motion through Cirac–Zoller or Mølmer–Sørensen schemes, leading to effective two-spin Hamiltonians, as well as two-qubit entangling gates. In this work, the Mølmer–Sørensen scheme is extended to induce three-spin interactions via tailored first- and second-order spin–motion couplings. The scheme enables engineering single-, two-, and three-spin interactions, and can be tuned via an enhanced protocol to simulate purely three-spin dynamics. Analytical results for the effective evolution are presented, along with detailed numerical simulations of the full dynamics to support the accuracy and feasibility of the proposed scheme for near-term applications. With a focus on quantum simulation, the advantage of a direct analog implementation of three-spin dynamics is demonstrated via the example of matter-gauge interactions in the U(1) lattice gauge theory within the quantum link model. The mapping of degrees of freedom and strategies for scaling the three-spin scheme to larger systems, are detailed, along with a discussion of the expected outcome of the simulation of the quantum link model given realistic fidelities in the upcoming experiments. The applications of the three-spin scheme go beyond the lattice gauge theory example studied here and include studies of static and dynamical phase diagrams of strongly interacting condensed-matter systems modeled by two- and three-spin Hamiltonians.

Collective motion of granular matter subjected to swirling excitation.

A two-dimensional granular packing under horizontally circular shaking exhibits various collective motion modes where nonuniform density distribution and correlated dynamics are present. For intermediate packing density and oscillation amplitude, a condensed phase travels around the container's side wall in the clockwise direction, while the oscillation itself is set anticlockwise. Further increasing the packing density towards that of hexagonal packing, the whole packing rotates collectively in the clockwise direction. The core of the packing rotates as a solid and is separated from the boundary by a fluid-like layer. Both motion modes are associated with the asymmetric motion of particles close to the side wall in one oscillation cycle, where the dependence of particle velocity on the local density plays a key role.

Articles of Significant Interest in This Issue.

Bacteria often display highly organized dynamic patterns at high cell densities. Nakane et al. (e00073-21) found a new mode of collective motion in nonflagellated bacteria; vortex patterns spontaneously appeared as a lattice and were integrated into a large-scale circular plate, which exhibited unidirectional rotation in a counterclockwise manner and expanded in size on agar. A series of collective motions was driven by gliding motility of the rod-shaped soil bacterium Flavobacterium johnsoniae. This collective motion might be an efficient strategy for cells of this species to find nutrients.

Large-Scale Vortices with Dynamic Rotation Emerged from Monolayer Collective Motion of Gliding Flavobacteria

A collective motion of self-driven particles has been a fascinating subject in physics and biology. Sophisticated macroscopic behavior emerges through a population in thousands or millions of bacterial cells, propelling itself by flagellar rotation and its chemotactic response. Here we found a series of collective motions accompanying successive phase-transitions in a non-flagellated rod-shaped soil bacterium, Flavobacterium johnsoniae, which was driven by a surface cell movement known as gliding motility. When we spot the cells on an agar plate with a low level of nutrients, the bacterial community exhibited vortex patterns that spontaneously appeared as lattice and integrated into a large-scale circular plate. All patterns exhibit with monolayer of bacteria, which enable to visualize an individual cell with a high resolution among a wide-range pattern two-dimensionally. The single cells moved at random orientation, but the cells connected with one another showed left-turn biased trajectories in starved environment. This feature is possibly due to the collision of cells inducing a nematic alignment of dense cells as self-propelled rods. Subsequently, each vortex oscillated independently, and then transformed to the rotating mode as an independent circular plate. Notably, the rotational direction of the circular plate was counterclockwise without exception. The plates developed accompanying rotation with constant angular velocity, suggesting that the mode is an efficient strategy for bacterial survival.ImportanceSelf-propelled bacteria propelled by flagella rotation often display highly organized dynamic patterns at high cell densities. Here we found a new mode of collective motion in non-flagellated bacteria: vortex patterns were spontaneously appeared as lattice and integrated into a large-scale circular plate comprising hundreds of thousands of cells, which exhibited unidirectional rotation in a counterclockwise manner and expanded in size on agar. A series of collective motions was driven by gliding motility of the rod-shaped soil bacterium Flavobacterium johnsoniae In a low nutrient environment, single cells moved at random orientation while cells at high density moved together as a unitary cluster. This might be an efficient strategy for cells of this species to find nutrients.

Investigations on Dynamical Stability in 3D Quadrupole Ion Traps

We firstly discuss classical stability for a dynamical system of two ions levitated in a 3D Radio-Frequency (RF) trap, assimilated with two coupled oscillators. We obtain the solutions of the coupled system of equations that characterizes the associated dynamics. In addition, we supply the modes of oscillation and demonstrate the weak coupling condition is inappropriate in practice, while for collective modes of motion (and strong coupling) only a peak of the mass can be detected. Phase portraits and power spectra are employed to illustrate how the trajectory executes quasiperiodic motion on the surface of torus, namely a Kolmogorov–Arnold–Moser (KAM) torus. In an attempt to better describe dynamical stability of the system, we introduce a model that characterizes dynamical stability and the critical points based on the Hessian matrix approach. The model is then applied to investigate quantum dynamics for many-body systems consisting of identical ions, levitated in 2D and 3D ion traps. Finally, the same model is applied to the case of a combined 3D Quadrupole Ion Trap (QIT) with axial symmetry, for which we obtain the associated Hamilton function. The ion distribution can be described by means of numerical modeling, based on the Hamilton function we assign to the system. The approach we introduce is effective to infer the parameters of distinct types of traps by applying a unitary and coherent method, and especially for identifying equilibrium configurations, of large interest for ion crystals or quantum logic.

Polarization-gradient cooling of 1D and 2D ion Coulomb crystals

We present experiments on polarization gradient cooling of Ca+ multi-ion Coulomb crystals in a linear Paul trap. Polarization gradient cooling of the collective modes of motion whose eigenvectors have overlap with the symmetry axis of the trap is achieved by two counter-propagating laser beams with mutually orthogonal linear polarizations that are blue-detuned from the S1/2 ↔ P1/2 transition. We demonstrate cooling of linear chains of up to 51 ions and 2D-crystals in zig-zag configuration with 22 ions. The cooling results are compared with numerical simulations and the predictions of a simple model of cooling in a moving polarization gradient.

Long-Range Multibody Interactions and Three-Body Antiblockade in a Trapped Rydberg Ion Chain.

Trapped Rydberg ions represent a flexible platform for quantum simulation and information processing that combines a high degree of control over electronic and vibrational degrees of freedom. The possibility to individually excite ions to high-lying Rydberg levels provides a system where strong interactions between pairs of excited ions can be engineered and tuned via external laser fields. We show that the coupling between Rydberg pair interactions and collective motional modes gives rise to effective long-range and multibody interactions consisting of two, three, and four-body terms. Their shape, strength, and range can be controlled via the ion trap parameters and strongly depends on both the equilibrium configuration and vibrational modes of the ion crystal. By focusing on an experimentally feasible quasi one-dimensional setup of ^{88}Sr^{+} Rydberg ions, we demonstrate that multibody interactions are enhanced by the emergence of soft modes associated with, e.g., a structural phase transition. This has a striking impact on many-body electronic states and results-for example-in a three-body antiblockade effect that can be employed as a sensitive probe to detect structural phase transitions in Rydberg ion chains. Our study unveils the possibilities offered by trapped Rydberg ions for studying exotic phases of matter and quantum dynamics driven by enhanced multibody interactions.

Conformational Changes Induced by S34Y and R98C Variants in the Death Domain of Myd88.

Myeloid differentiating factor 88 (Myd88) is a universal adaptor protein that plays a critical role in innate immunity by mediating TLR downstream signaling. Myd88 death domain (DD) forms an oligomeric complex by association with other DD-containing proteins such as IRAK4. Despite its universal role, polymorphisms in Myd88 can result in several diseases. Previous studies have suggested that, out of several non-synonymous single-nucleotide polymorphisms (nsSNPs), the variants S34Y and R98C in the DD of Myd88 disrupt the formation of the Myddosome complex. Therefore, we performed molecular dynamics (MD) simulations on wild-type (Myd88WT) and mutant (Myd88S34Y, Myd88R98C) DDs to evaluate the subtle conformational changes induced by these mutations. Our results suggest that the S34Y variant induces large structural transitions compared to the R98C variant as evidenced by residual flexibility at the variable loop regions, particularly in the H1–H2 loop, and variations in the collective modes of motion observed for wild-type and mutant Myd88 DDs. The residue interaction network strongly suggests a distortion in the interaction pattern at the location of the mutated residue between the wild type and mutants. Moreover, betweenness centrality values indicate that variations in the distribution of functionally important residues may be reflected by distinct residue signal transductions in both wild-type and mutant Myd88 DDs, which may influence the interaction with other DDs in TLR downstream signaling.

Stroboscopic approach to trapped-ion quantum information processing with squeezed phonons

In trapped-ion quantum information processing, interactions between spins (qubits) are mediated by collective modes of motion of an ion crystal. While there are many different experimental strategies to design such interactions, they all face both technical and fundamental limitations to the achievable coherent interaction strength. In general, obtaining strong interactions and fast gates is an ongoing challenge. Here, we extend previous work [W. Ge, B. C. Sawyer, J. W. Britton, K. Jacobs, J. J. Bollinger, and M. Foss-Feig, Phys. Rev. Lett. 122, 030501 (2019)] and present a general strategy for enhancing the interaction strengths in trapped-ion systems via parametric amplification of the ions' motion. Specifically, we propose a stroboscopic protocol using alternating applications of parametric amplification and spin-motion coupling. In comparison with the previous work, we show that the current protocol can lead to larger enhancements in the coherent interaction that increase exponentially with the gate time.

Two-qubit entangling gates within arbitrarily long chains of trapped ions

Ion trap systems are a leading platform for large scale quantum computers. Trapped ion qubit crystals are fully-connected and reconfigurable, owing to their long range Coulomb interaction that can be modulated with external optical forces. However, the spectral crowding of collective motional modes could pose a challenge to the control of such interactions for large numbers of qubits. Here, we show that high-fidelity quantum gate operations are still possible with very large trapped ion crystals, simplifying the scaling of ion trap quantum computers. To this end, we present analytical work that determines how parallel entangling gates produce a crosstalk error that falls off as the inverse cube of the distance between the pairs. We also show experimental work demonstrating entangling gates on a fully-connected chain of seventeen $^{171}{\rm{Yb}}^{+}$ ions with fidelities as high as $97(1)\%$.

Trapped Ion Quantum Information Processing with Squeezed Phonons

Trapped ions offer a pristine platform for quantum computation and simulation, but improving their coherence remains a crucial challenge. Here, we propose and analyze a new strategy to enhance the coherent interactions in trapped ion systems via parametric amplification of the ions' motion-by squeezing the collective motional modes (phonons), the spin-spin interactions they mediate can be significantly enhanced. We illustrate the power of this approach by showing how it can enhance collective spin states useful for quantum metrology, and how it can improve the speed and fidelity of two-qubit gates in multi-ion systems, important ingredients for scalable trapped ion quantum computation. Our results are also directly relevant to numerous other physical platforms in which spin interactions are mediated by bosons.

Pyrazinamide drug resistance in RpsA mutant (∆438A) of Mycobacterium tuberculosis: Dynamics of essential motions and free-energy landscape analysis.

Pyrazinamide is an essential first-line antitubercular drug which plays pivotal role in tuberculosis treatment. It is a prodrug that requires amide hydrolysis by mycobacterial pyrazinamidase enzyme for conversion into pyrazinoic acid (POA). POA is known to target ribosomal protein S1 (RpsA), aspartate decarboxylase (PanD), and some other mycobacterial proteins. Spontaneous chromosomal mutations in RpsA have been reported for phenotypic resistance against pyrazinamide. We have constructed and validated 3D models of the native and Δ438A mutant form of RpsA protein. RpsA protein variants were then docked to POA and long range molecular dynamics simulations were carried out. Per residue binding free-energy calculations, free-energy landscape analysis, and essential dynamics analysis were performed to outline the mechanism underlying the high-level PZA resistance conferred by the most frequently occurring deletion mutant of RpsA. Our study revealed the conformational modulation of POA binding site due to the disruptive collective modes of motions and increased conformational flexibility in the mutant than the native form. Residue wise MMPBSA decomposition and protein-drug interaction pattern revealed the difference of energetically favorable binding site in the wild-type (WT) protein in comparison with the mutant. Analysis of size and shape of minimal energy landscape area delineated higher stability of the WT complex than the mutant form. Our study provides mechanistic insights into pyrazinamide resistance in Δ438A RpsA mutant, and the results arising out of this study will pave way for design of novel and effective inhibitors targeting the resistant strains of Mycobacterium tuberculosis.

The physics of cooperative transport in groups of ants

Collective motion by animal groups is affected by internal interactions, external constraints and the influx of information. A quantitative understanding of how these different factors give rise to different modes of collective motion is, at present, lacking.} Here, we study how ants that cooperatively transport a large food item react to an obstacle blocking their path. Combining experiments with a statistical physics model of mechanically coupled active agents, we show that the constraint induces a deterministic collective oscillatory mode that facilitates obstacle circumvention. We provide direct experimental evidence, backed by theory, that this motion is an emergent group effect that does not require any behavioral changes at the individual level. We trace these relaxation oscillations to the interplay between two forces; informed ants pull the load towards the nest while uninformed ants contribute to the motion's persistence along the tangential direction. The model's predictions that oscillations appear above a critical system size, that the group can spontaneously transition into its ordered phase, and that the system can exhibit complete rotations are all verified experimentally. We expect that similar oscillatory modes emerge in collective motion scenarios where the structure of the environment imposes conflicts between individually held information and the group's tendency for cohesiveness.

Robust 2-Qubit Gates in a Linear Ion Crystal Using a Frequency-Modulated Driving Force.

In an ion trap quantum computer, collective motional modes are used to entangle two or more qubits in order to execute multiqubit logical gates. Any residual entanglement between the internal and motional states of the ions results in loss of fidelity, especially when there are many spectator ions in the crystal. We propose using a frequency-modulated driving force to minimize such errors. In simulation, we obtained an optimized frequency-modulated 2-qubit gate that can suppress errors to less than 0.01% and is robust against frequency drifts over ±1 kHz. Experimentally, we have obtained a 2-qubit gate fidelity of 98.3(4)%, a state-of-the-art result for 2-qubit gates with five ions.

Activity loss by H46A mutation in Mycobacterium tuberculosis isocitrate lyase is due to decrease in structural plasticity and collective motions of the active site

Mycobacterium tuberculosis isocitrate lyase (MtbICL) is a crucial enzyme of the glyoxylate cycle and is a validated anti-tuberculosis drug target. Structurally distant, non-active site mutation (H46A) in MtbICL has been found to cause loss of enzyme activity. The aim of the present work was to explore the structural alterations induced by H46A mutation that caused the loss of enzyme activity. The structural and dynamic consequences of H46A mutation were studied using multiple computational methods such as docking, molecular dynamics simulation and residue interaction network analysis (RIN). Principal component analysis and cross correlation analysis revealed the difference in conformational flexibility and collective modes of motions between the wild-type and mutant enzyme, particularly in the active site region. RIN analysis revealed that the active site geometry was disturbed in the mutant enzyme. Thus, the dynamic perturbation of the active site led to enzyme transition from its active form to inactive form upon mutation. The computational analyses elucidated the mutant-specific conformational alterations, differential dominant motions, and anomalous residue level interactions that contributed to the abrogated function of mutant MtbICL. An understanding of interactions of mutant enzymes may help in modifying the existing drugs and designing improved drugs for successful control of tuberculosis.

Mechanistic Principles Behind Molecular Mechanism of Rifampicin Resistance in Mutant RNA Polymerase Beta Subunit of Mycobacterium tuberculosis.

Evolution of drug-resistant Mycobacterium strains threatens the TB treatment and control programs globally. Rifampicin (RIF) is an important first line antitubercular drug. Resistance to Rifampicin is caused mainly by mutations in its target RNA polymerase beta subunit protein (RpoB). RpoB contains a Rifampicin resistance determining region (RRDR) and has several potent sites for mutations. In this study, we have investigated mutations of a single site (H451) to eight different amino acids, involved in RIF resistance. Long-term molecular dynamics simulations were performed on wild type (WT) and mutant protein structures and various structural analysis were carried out to elucidate the dynamic behavior of WT and mutant forms. Essential dynamics uncovered the difference in conformational flexibility and collective modes of motions between WT and mutants. MMPBSA calculations and interaction pattern analysis revealed the binding site relocation in some mutants. This study presents an exhaustive analysis of RIF binding to the WT and mutant RpoB and clearly highlights structural mechanism for differences in stable binding of Rifampicin with WT than the mutant targets. J. Cell. Biochem. 118: 4594-4606, 2017. © 2017 Wiley Periodicals, Inc.

Probing the Structural Dynamics of the NMDA Receptor Activation by Coarse-Grained Modeling

N-Methyl-D-aspartate (NMDA) receptors are glutamate-gated excitatory channels that play essential roles in brain functions. High-resolution structures have been solved for an allosterically inhibited and agonist-bound form of a functional NMDA receptor; however, other key functional states (particularly the active open-channel state) were only resolved at moderate resolutions by cryo-electron microscopy (cryo-EM). To decrypt the mechanism of the NMDA receptor activation, structural modeling is essential to provide presently missing information about structural dynamics. We performed systematic coarse-grained modeling using an elastic network model and related modeling/analysis tools (e.g., normal mode analysis, flexibility and hotspot analysis, cryo-EM flexible fitting, and transition pathway modeling) based on an active-state cryo-EM map. We observed extensive conformational changes that allosterically couple the extracellular regulatory and agonist-binding domains to the pore-forming trans-membrane domain (TMD), and validated these, to our knowledge, new observations against known mutational and functional studies. Our results predict two key modes of collective motions featuring shearing/twisting of the extracellular domains relative to the TMD, reveal subunit-specific flexibility profiles, and identify functional hotspot residues at key domain-domain interfaces. Finally, by examining the conformational transition pathway between the allosterically inhibited form and the active form, we predict a discrete sequence of domain motions, which propagate from the extracellular domains to the TMD. In summary, our results offer rich structural and dynamic information, which is consistent with the literature on structure-function relationships in NMDA receptors, and will guide in-depth studies on the activation dynamics of this important neurotransmitter receptor.