Information encoding and encryption in acoustic analogues of qubits.

Cryptography is crucial in protecting sensitive information and ensuring secure transactions in a time when data security and privacy are major concerns. Traditional cryptography techniques, which depend on mathematical algorithms and secret keys, have historically protected against data breaches and illegal access. With the advent of quantum computers, traditional cryptography techniques are at risk. In this work, we present a cryptography idea using logical phi-bits, which are classical analogues of quantum bits (qubits) and are supported by driven acoustic metamaterials. The state of phi-bits displays superpositions similar to quantum bits, with complex amplitudes and phases. We present a representation of the state vector of single and multi-phi-bit systems. The state vector of multiple phi-bits system lies in a complex exponentially scaling Hilbert space and is used to encode information or messages. By changing the driving conditions of the metamaterial, the information can be encrypted with exceptional security and efficiency. We illustrate experimentally the practicality and effectiveness of encoding and encryption of a message using a 5 phi-bits system and emphasize the scalability of this approach to an N phi-bits system with the same processing time.

Monitoring damage growth and topographical changes in plate structures using sideband peak count-index and topological acoustic sensing techniques.

Some topographies in plate structures can hide cracks and make it difficult to monitor damage growth. This is because topographical features convert homogeneous structures to heterogeneous one and complicate the wave propagation through such structures. At certain points destructive interference between incident, reflected and transmitted elastic waves can make those points insensitive to the damage growth when adopting acoustics based structural health monitoring (SHM) techniques. A newly developed nonlinear ultrasonic (NLU) technique called sideband peak count - index (or SPC-I) has shown its effectiveness and superiority compared to other techniques for nondestructive testing (NDT) and SHM applications and is adopted in this work for monitoring damage growth in plate structures with topographical features. The performance of SPC-I technique in heterogeneous specimens having different topographies is investigated using nonlocal peridynamics based peri-ultrasound modeling. Three types of topographies - "X" topography, "Y" topography and "XY" topography are investigated. It is observed that "X" and "XY" topographies can help to hide the crack growth, thus making cracks undetectable when the SPC-I based monitoring technique is adopted. In addition to the SPC-I technique, we also investigate the effectiveness of an emerging sensing technique based on topological acoustic sensing. This method monitors the changes in the geometric phase; a measure of the changes in the acoustic wave's spatial behavior. The computed results show that changes in the geometric phase can be exploited to monitor the damage growth in plate structures for all three topographies considered here. The significant changes in geometric phase can be related to the crack growth even when these cracks remain hidden for some topographies during the SPC-I based single point inspection. Sensitivities of both the SPC-I and the topological acoustic sensing techniques are also investigated for sensing the topographical changes in the plate structures.

Underwater acoustic sensing using the geometric phase.

We present a sensing modality using the geometric phase of acoustic waves propagating in an underwater environment. We experimentally investigate the effect of scattering by a small subwavelength perturbation on a flat submerged surface. We represent the state of an acoustic field in the unperturbed and perturbed cases as multidimensional vectors. The change in geometric phase is obtained by calculating the angle between those vectors. This angle represents a rotation of the state vector of the wave due to scattering by the perturbation. We perform statistical analysis to define a signal-to-noise ratio to quantify the sensitivity of the geometric phase measurement and compare it to magnitude based measurements. This geometric phase sensing modality is shown to have higher sensitivity than the magnitude based sensing approach.

Effect of stress on the dissolution/crystallization of apatite in aqueous solution: a thermochemical equilibrium study.

Bone mineralization is critical to maintaining tissue mechanical function. The application of mechanical stress via exercise promotes bone mineralization via cellular mechanotransduction and increased fluid transport through the collagen matrix. However, due to its complex composition and ability to exchange ions with the surrounding body fluids, bone mineral composition and crystallization is also expected to respond to stress. Here, a combination of data from materials simulations, namely density functional theory and molecular dynamics, and experimental studies were input into an equilibrium thermodynamic model of bone apatite under stress in an aqueous solution based on the theory of thermochemical equilibrium of stressed solids. The model indicated that increasing uniaxial stress induced mineral crystallization. This was accompanied by a decrease in calcium and carbonate integration into the apatite solid. These results suggest that weight-bearing exercises can increase tissue mineralization via interactions between bone mineral and body fluid independent of cell and matrix behaviours, thus providing another mechanism by which exercise can improve bone health. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.

Demonstration of a two-bit controlled-NOT quantum-like gate using classical acoustic qubit-analogues.

The Controlled-NOT (CNOT) gate is the key to unlock the power of quantum computing as it is a fundamental component of a universal set of gates. We demonstrate the operation of a two-bit C-NOT quantum-like gate using classical qubit acoustic analogues, called herein logical phi-bits. The logical phi-bits are supported by an externally driven nonlinear acoustic metamaterial composed of a parallel array of three elastically coupled waveguides. A logical phi-bit has a two-state degree of freedom associated with the two independent relative phases of the acoustic wave in the three waveguides. A simple physical manipulation involving the detuning of the frequency of one of the external drivers is shown to operate on the complex vectors in the Hilbert space of pairs of logical phi-bits. This operation achieves a systematic and predictable C-NOT gate with unambiguously measurable input and output. The possibility of scaling the approach to more phi-bits is promising.

Experimental classical entanglement in a 16 acoustic qubit-analogue.

The possibility of achieving and controlling scalable classically entangled, i.e., inseparable, multipartite states, would fundamentally challenge the advantages of quantum systems in harnessing the power of complexity in information science. Here, we investigate experimentally the extent of classical entanglement in a [Formula: see text] acoustic qubit-analogue platform. The acoustic qubit-analogue, a.k.a., logical phi-bit, results from the spectral partitioning of the nonlinear acoustic field of externally driven coupled waveguides. Each logical phi-bit is a two-level subsystem characterized by two independently measurable phases. The phi-bits are co-located within the same physical space enabling distance independent interactions. We chose a vector state representation of the [Formula: see text]-phi-bit system which lies in a [Formula: see text]-dimensional Hilbert space. The calculation of the entropy of entanglement demonstrates the possibility of achieving inseparability of the vector state and of navigating the corresponding Hilbert space. This work suggests a new direction in harnessing the complexity of classical inseparability in information science.

Experimental demonstration of coherent superpositions in an ultrasonic pseudospin.

We experimentally demonstrate the existence and control of coherent superpositions of elastic states in the direction of propagation of an ultrasonic pseudospin i.e., a φ-bit. The experimental realization of this mechanical pseudospin consists of an elastic aluminum rod serving as a waveguide sandwiched between two heavy steel plates. The Hertzian contact between the rod and the plates leads to restoring forces which couple the directions of propagation (forward and backward). This coupling generates the coherence of the superposition of elastic states. We also demonstrate φ-bit gate operations on the coherent superposition analogous to those used in quantum computing. In the case of a φ-bit, the coherent superposition of states in the direction of propagation are immune to wave function collapse upon measurement as they result from classical waves.

Spectral analysis of amplitudes and phases of elastic waves: Application to topological elasticity.

The topological characteristics of waves in elastic structures are determined by the geometric phase of waves and, more specifically, by the Berry phase, as a characterization of the global vibrational behavior of the system. A computational procedure for the numerical determination of the geometrical phase characteristics of a general elastic structure is introduced: the spectral analysis of amplitudes and phases method. Molecular dynamics simulation is employed to computationally generate the band structure, traveling modes' amplitudes and phases, and subsequently the Berry phase associated with each band of periodic superlattices. In an innovative procedure, the phase information is used to selectively excite a particular mode in the band structure. It is shown analytically and numerically, in the case of one-dimensional elastic superlattices composed of various numbers of masses and spring stiffness, how the Berry phase varies as a function of the spatial arrangement of the springs. A symmetry condition on the arrangement of springs is established, which leads to bands with Berry phase taking the values of 0 or π. Finally, it is shown how the Berry phase may vary upon application of unitary operations that mathematically describe transformations of the structural arrangement of masses and springs within the unit cells.

Structure of ZnCl2 Melt. Part II: Fragile-to-Strong Transition in a Tetrahedral Liquid.

The fraction of edge- and corner-sharing tetrahedra in liquid ZnCl2 is quantified as a function of temperature using Raman spectroscopy and ab initio molecular dynamic simulations. Two distinct regimes are found in the temperature dependence of the change in these structural units. This behavior is consistent with the existence of a fragile-to-strong transition in liquid ZnCl2 as suggested by calorimetric and viscosity measurements. The structural origin of this transition is rationalized in terms of a constraint counting formalism. It is suggested that the ratio of edge- to corner-sharing tetrahedra controls the configurational entropy and in turn the viscosity of the melt. The temperature dependence of this ratio above the melting point is also found to be qualitatively consistent with neutron diffraction data. The observation of a similar fragile-to-strong transition in the isostructural GeSe2 melt indicates that it may be a common feature of tetrahedral liquids.

Cellular Architecture Regulates Collective Calcium Signaling and Cell Contractility.

A key feature of multicellular systems is the ability of cells to function collectively in response to external stimuli. However, the mechanisms of intercellular cell signaling and their functional implications in diverse vascular structures are poorly understood. Using a combination of computational modeling and plasma lithography micropatterning, we investigate the roles of structural arrangement of endothelial cells in collective calcium signaling and cell contractility. Under histamine stimulation, endothelial cells in self-assembled and microengineered networks, but not individual cells and monolayers, exhibit calcium oscillations. Micropatterning, pharmacological inhibition, and computational modeling reveal that the calcium oscillation depends on the number of neighboring cells coupled via gap junctional intercellular communication, providing a mechanistic basis of the architecture-dependent calcium signaling. Furthermore, the calcium oscillation attenuates the histamine-induced cytoskeletal reorganization and cell contraction, resulting in differential cell responses in an architecture-dependent manner. Taken together, our results suggest that endothelial cells can sense and respond to chemical stimuli according to the vascular architecture via collective calcium signaling.

Structure of ZnCl2 Melt. Part I: Raman Spectroscopy Analysis Driven by Ab Initio Methods.

The structure of molten ZnCl2 is investigated using a combination of computer simulation and experimental methods. Ab initio molecular dynamics (AIMD) is used to model the structure of ZnCl2 at 600 K. The structure factors and pair distribution functions derived from AIMD show a good match with those previously measured by neutron diffraction (ND). In addition, Raman spectroscopy is used to investigate the structure of liquid ZnCl2 and identify the relative fractions of constituent structural units. To ascertain the assignment of each Raman mode, a series of ZnCl2 crystalline prototypes are modeled and the corresponding Raman modes are derived by first-principles calculations. Curve fitting of experimental Raman spectra using these mode assignments shows excellent agreement with both AIMD and ND. These results confirm the presence of significant fractions of edge-sharing tetrahedra in liquid ZnCl2. The presence of these structural motifs has significant impact on the fragility of this tetrahedral glass-forming liquid. The assignment of Raman bands present in molten ZnCl2 is revised and discussed in view of these results.

Graphene mediated self-assembly of fullerene nanorods.

A simple procedure for solution-based self-assembly of C60 fullerene nanorods on graphene substrates is presented. Using a combination of electron microscopy, X-ray diffraction and Raman spectroscopy, it is shown that the size, shape and morphology of the nanorods can be suitably modified by controlling the kinetics of self-assembly.

Multi-phonon scattering processes in one-dimensional anharmonic biological superlattices: understanding the dissipation of mechanical waves in mineralized tissues.

The scattering of elastic waves in a one dimensional phononic (PnC) crystal composed of alternate collagen and hydroxy-apatite constituent layers is studied. These superlattices are metaphors for mineralized tissues present in bones and teeth. The collagen is treated as an open system elastic medium with water content which can vary depending on the level of stress applied. The open system nature of the collagen-water system leads to a non-linear stress-strain response. The finite difference time domain method is employed to investigate the propagation of non-linear mechanical waves through the superlattice. The spectral energy density method enables the calculation of the non-linear vibrational wave band structure. The non-linearity in the mechanical response of the collagen-water system enables a variety of multi-phonon scattering processes resulting in an increase in the number of channels for the dissipation of elastic waves and therefore for the dissipation of mechanical energy. These results provide an explanation for the relationship between bone fragility and decreased hydration.

Mechanically induced intercellular calcium communication in confined endothelial structures.

Calcium signaling in the diverse vascular structures is regulated by a wide range of mechanical and biochemical factors to maintain essential physiological functions of the vasculature. To properly transmit information, the intercellular calcium communication mechanism must be robust against various conditions in the cellular microenvironment. Using plasma lithography geometric confinement, we investigate mechanically induced calcium wave propagation in networks of human umbilical vein endothelial cells organized. Endothelial cell networks with confined architectures were stimulated at the single cell level, including using capacitive force probes. Calcium wave propagation in the network was observed using fluorescence calcium imaging. We show that mechanically induced calcium signaling in the endothelial networks is dynamically regulated against a wide range of probing forces and repeated stimulations. The calcium wave is able to propagate consistently in various dimensions from monolayers to individual cell chains, and in different topologies from linear patterns to cell junctions. Our results reveal that calcium signaling provides a robust mechanism for cell-cell communication in networks of endothelial cells despite the diversity of the microenvironmental inputs and complexity of vascular structures.

Architecture-dependent signal conduction in model networks of endothelial cells.

Signal conduction between endothelial cells along the walls of vessels appears to play an important role in circulatory function. A recently developed approach to calculate analytically the spectrum of propagating compositional waves in models of multicellular architectures is extended to study putative signal conduction dynamics across networks of endothelial cells. Here, compositional waves originate from negative feedback loops, such as between Ca2+ and inositol triphosphate (IP3) in endothelial cells, and are shaped by their connection topologies. We consider models of networks constituted of a main chain of endothelial cells and multiple side chains. The resulting transmission spectra encode information concerning the position and size of the side branches in the form of gaps. This observation suggests that endothelial cell networks may be able to "communicate" information regarding long-range order in their architecture.

Calcium wave propagation in chains of endothelial cells with nonlinear reaction dynamics: Green's function approach.

We present a Green's function-based perturbative approach to solving nonlinear reaction-diffusion problems in networks of endothelial cells. We focus on a single component (Ca2+), piecewise nonlinear model of endoplasmic calcium dynamics and trans-membrane diffusion. The decoupling between nonlinear reaction dynamics and the linear diffusion enables the calculation of the diffusion part of the Green's function for network of cells with nontrivial topologies. We verify analytically and then numerically that our approach leads to the known transition from propagation of calcium front to failure of propagation when the diffusion rate is varied relative to the reaction rates. We then derive the Green's function for a semi-infinite chain of cells with various boundary conditions. We show that the calcium dynamics of cells in the vicinity of the end of the semi-infinite chain is strongly dependent on the boundary conditions. The behavior of the semi-infinite chain with absorbing boundary conditions, a simple model of a multicellular structure with an end in contact with the extracellular matrix, suggests behavioral differentiation between cells at the end and cells embedded within the chain.

Heterogeneous and homogeneous nucleation of Taxol crystals in aqueous solutions and gels: effect of tubulin proteins.

In this study we report crystallization of Taxol in pure water, aqueous solutions containing tubulin proteins and tubulin-containing agarose gels. We show that crystallization of Taxol in tubulin-free aqueous solutions occurs by the formation of sheaf-like crystals, while in the presence of tubulin Taxol crystallizes in the form of spherulites. Whereas sheaves are characteristic for crystals formed by homogeneous nucleation, the spherical symmetry of the Taxol crystal formed in the presence of tubulin suggests they result from heterogeneous nucleation. To explain the formation of tubulin-Taxol nuclei we suggest a new, secondary Taxol-binding site within the tubulin heterodimer. Contrary to the known binding site, where the Taxol molecule is almost completely buried in the protein, the Taxol molecule in the secondary binding site is partially exposed to the solution and may serve as a bridge, connecting other Taxol molecules. Results presented in this work are important for in vivo and in vitro microtubule studies due to the possibility of mistaking these Taxol spherulites for microtubule asters, moreover a novel variable is proposed in the study of cells treated with Taxol for cancer treatment via sequestration of tubulin.

A theoretical study of zinc(II) interactions with amino acid models and peptide fragments.

Density functional theory calculations have been employed to study the interaction between the Zn2+ ion and some standard amino acid models. The highest affinities towards the Zn2+ ion are predicted for serine, cysteine, and histidine. Relatively high affinities are reported also for proline and glutamate/aspartate residues. It was found that the zinc complexes with cysteine adopt a tetrahedral conformation. Conversely, complexes with one or two histidine moieties remain in an octahedral geometry, while those with three or more histidine groups adopt a square-planar geometry.

Nucleation and growth of microtubules from gamma-tubulin-functionalized gold surfaces.

Microtubules are protein filaments that are emerging as potential building blocks in manufacturing nanoscale structures and systems such as interconnecting nanowires. Future development in using microtubules necessitates a control of their nucleation and growth. We report the controlled nucleation and growth of microtubules from functionalized gold on a hydrophilic oxidized silicon wafer. The gold substrate is functionalized with gamma-tubulin, a natural nucleating agent for microtubule growth. We show that the attached gamma-tubulin retains its biological functionality and leads to nucleation and assembly of microtubules from the functionalized gold surface. We also analyze the interplay between the geometry of the nucleating substrates and the morphology of microtubules arrays and networks grown from them. We consider two geometrical arrangements of the substrates: (a) a square lattice of small gold pads on a hydrophilic oxidized silicon wafer and (b) a large flat surface. Fluorescence microscopy and scanning electron microscopy are employed to provide a detailed characterization of the length and morphology of the nucleated and grown microtubules. The observed microtubule morphologies are modeled, analyzed and discussed within the context of reaction-diffusion and nucleation controlled processes.

Two-dimensional Monte Carlo simulations of ionic and nonionic silane self-assembly on hydrophilic surfaces.

Aqueous chemistries have recently been shown to be useful for the deposition of hydrophobic films of nonionic and cationic silanes on hydrophilic substrates for the prevention of stiction in MEMS. The Monte Carlo method is used to simulate in two dimensions the self-assembly of silane films on a hydrophilic surface. We investigate the impact of charged group in cationic silane on the overall structure of the films. We characterize the film structure with spatial pair correlations at each molecular layer of the deposited films. The simulations reveal long-range correlations for the film of cationic silanes. Based on our two-dimensional simulations, we report an average "most probable" structure for the films of nonionic and cationic silanes.