We present a theoretical analysis that associates the resonances of extraordinary acoustic Raman (EAR) spectroscopy [Wheaton et al., Nat. Photonics 9, 68 (2015)] with the collective modes of proteins. The theory uses the anisotropic elastic network model to find the protein acoustic modes, and calculates Raman intensity by treating the protein as a polarizable ellipsoid. Reasonable agreement is found between EAR spectra and our theory. Protein acoustic modes have been extensively studied theoretically to assess the role they play in protein function; this result suggests EAR spectroscopy as a new experimental tool for studies of protein acoustic modes.

Membrane tubes and tubular networks are ubiquitous in living cells. Inclusions like proteins are vital for both the stability and the dynamics of such networks. These inclusions interact via the curvature deformations they impose on the membrane. We analytically study the resulting membrane mediated interactions in strongly curved tubular membranes. We model inclusions as constraints coupled to the curvature tensor of the membrane tube. First, as special test cases, we analyze the interaction between ring- and rod-shaped inclusions. Using Monte Carlo simulations, we further show how pointlike inclusions interact to form linear aggregates. To minimize the curvature energy of the membrane, inclusions self-assemble into either line- or ringlike patterns. Our results show that the global curvature of the membrane strongly affects the interactions between proteins embedded in it, and can lead to the spontaneous formation of biologically relevant structures.

In recent experiments [T. Basta et al., Proc. Natl. Acad. Sci. U.S.A. 111, 670 (2014)] lipids and membrane proteins were observed to self-assemble into membrane protein polyhedral nanoparticles (MPPNs) with a well-defined polyhedral protein arrangement and characteristic size. We develop a model of MPPN self-assembly in which the preferred symmetry and size of MPPNs emerge from the interplay of protein-induced lipid bilayer deformations, topological defects in protein packing, and thermal effects. With all model parameters determined directly from experiments, our model correctly predicts the observed symmetry and size of MPPNs. Our model suggests how key lipid and protein properties can be modified to produce a range of MPPN symmetries and sizes in experiments.

A Bose-Einstein condensate is used as an atomic source for a high precision sensor. A $5\times 10^6\mathrm{atom}$ $F=1$ spinor condensate of ${}^{87}\mathrm{Rb}$ is released into free fall for up to 750 ms and probed with a $T=130\mathrm{ms}$ Mach-Zehnder atom interferometer based on Bragg transitions. The Bragg interferometer simultaneously addresses the three magnetic states $|m_f=1,0,-1⟩$, facilitating a simultaneous measurement of the acceleration due to gravity with a 1000 run precision of $\mathrm{\Delta }g/g=1.45\times {10}^{-9}$ and the magnetic field gradient to a precision of $120\mathrm{pT}/\mathrm{m}$.

We demonstrate through Brownian dynamics simulations a phase transition in plastic crystalline assemblies of Janus spheres through controlled pressure anisotropy. When the pressure in plane with hexagonally ordered layers is increased relative to that normal to the layers, a rapid first-order rotator-to-lamellar transition of Janus sphere orientation occurs at constant temperature. We show that the underlying mechanism closely follows the Maier-Saupe theory, originally developed for isotropic-to-nematic transition in positionally disordered materials but here applied to positionally ordered ones. Since the transition involves almost no translational diffusion or volume change, and occurs rapidly by particle rotation, the results should help guide the design of rapidly switchable colloidal crystals.

Delay-coupled electro-optical systems have received much attention for their dynamical properties and their potential use in signal processing. In particular, it has recently been demonstrated, using the artificial intelligence algorithm known as reservoir computing, that photonic implementations of such systems solve complex tasks such as speech recognition. Here, we show how the backpropagation algorithm can be physically implemented on the same electro-optical delay-coupled architecture used for computation with only minor changes to the original design. We find that, compared to when the backpropagation algorithm is not used, the error rate of the resulting computing device, evaluated on three benchmark tasks, decreases considerably. This demonstrates that electro-optical analog computers can embody a large part of their own training process, allowing them to be applied to new, more difficult tasks.

The stochastic kinetics of transcription is typically inferred from the distribution of RNA numbers in individual cells. However, cellular RNA reflects additional processes downstream of transcription, hampering this analysis. In contrast, nascent (actively transcribed) RNA closely reflects the kinetics of transcription. We present a theoretical model for the stochastic kinetics of nascent RNA, which we solve to obtain the probability distribution of nascent RNA per gene. The model allows us to evaluate the kinetic parameters of transcription from single-cell measurements of nascent RNA. The model also predicts surprising discontinuities in the distribution of nascent RNA, a feature which we verify experimentally.

We demonstrate a technique for IR action spectroscopy that enables measuring IR spectra in a background-free fashion for low-temperature neutral gas-phase molecules of arbitrary structure. The method is exemplified experimentally for $N$-methylacetamide molecules in the mid-IR spectral range of $1000–1800{\mathrm{cm}}^{-1}$, utilizing the free electron laser FELIX. The technique involves the resonant absorption of multiple mid-IR photons, which induces molecular dissociation. The dissociation products are probed with 10.49 eV vacuum ultraviolet photons and analyzed with a mass spectrometer. We also demonstrate the capability of this method to record, with unprecedented ease, mid-IR spectra for the molecular associates, such as clusters and oligomers, present in a molecular beam. In this way the mass-selected spectra of low-temperature gas-phase dimers and trimers of $N$-methylacetamide are measured in the full amide I–III range.

We study the collective motion of a suspension of rodlike microswimmers in a two-dimensional film of viscoelastic fluids. We find that the fluid elasticity has a small effect on a suspension of pullers, while it significantly affects the pushers. The attraction and orientational ordering of the pushers are enhanced in viscoelastic fluids. The induced polymer stresses break down the large-scale flow structures and suppress velocity fluctuations. In addition, the energy spectra and induced mixing in the suspension of pushers are greatly modified by fluid elasticity.

Self-assembly into target structures is an efficient material design strategy. Combining analytical calculations and computational techniques of evolutionary and Monte Carlo types, we report about a remarkable structural variability of Wigner bilayer ground states, when charges are confined between parallel charged plates. Changing the interlayer separation, or the plate charge asymmetry, a cascade of ordered patterns emerges. At variance with the symmetric case phenomenology, the competition between commensurability features and charge neutralization leads to long range attraction, appearance of macroscopic charges, exotic phases, and nonconventional phase transitions with distinct critical indices, offering the possibility of a subtle, but precise and convenient control over patterns.

Shear thinning—a reduction in suspension viscosity with increasing shear rates—is understood to arise in colloidal systems from a decrease in the relative contribution of entropic forces. The shear-thinning phenomenon has also been often reported in experiments with noncolloidal systems at high volume fractions. However its origin is an open theoretical question and the behavior is difficult to reproduce in numerical simulations where shear thickening is typically observed instead. In this letter we propose a non-Newtonian model of interparticle lubrication forces to explain shear thinning in noncolloidal suspensions. We show that hidden shear-thinning effects of the suspending medium, which occur at shear rates orders of magnitude larger than the range investigated experimentally, lead to significant shear thinning of the overall suspension at much smaller shear rates. At high particle volume fractions the local shear rates experienced by the fluid situated in the narrow gaps between particles are much larger than the averaged shear rate of the whole suspension. This allows the suspending medium to probe its high-shear non-Newtonian regime and it means that the matrix fluid rheology must be considered over a wide range of shear rates.

We consider a granular gas under the action of gravity, fluidized by a vibrating base. We show that a horizontal temperature gradient, here induced by limiting dissipative lateral walls (DLW), leads always to a granular thermal convection (DLW TC) that is essentially different from ordinary bulk-buoyancy-driven convection (BBD TC). In an experiment where BBD TC is inhibited, by reducing gravity with an inclined plane, we always observe a DLW TC cell next to each lateral wall. Such a cell squeezes towards the nearest wall as the gravity and/or the number of grains increase. Molecular dynamics simulations reproduce the experimental results and indicate that at large gravity or number of grains the DLW TC is barely detectable.

We study dynamically crowded solutions of stiff fibers deep in the semidilute regime, where the motion of a single constituent becomes increasingly confined to a narrow tube. The spatiotemporal dynamics for wave numbers resolving the motion in the confining tube becomes accessible in Brownian dynamics simulations upon employing a geometry-adapted neighbor list. We demonstrate that in such crowded environments the intermediate scattering function, characterizing the motion in space and time, can be predicted quantitatively by simulating a single freely diffusing phantom needle only, yet with very unusual diffusion coefficients.

We experimentally study the crystallization of a monolayer of vibrated discs with a built-in polar asymmetry, a model system of active liquids, and contrast it with that of vibrated isotropic discs. Increasing the packing fraction $\varphi$, the quasicontinuous crystallization reported for isotropic discs is replaced by a transition, or a crossover, towards a “self-melting” crystal. Starting from the liquid phase and increasing the packing fraction, clusters of dense hexagonal-ordered packed discs spontaneously form, melt, split, and merge, leading to a highly intermittent and heterogeneous dynamics. For a packing fraction larger than ${\varphi }^{*}$, a few large clusters span the system size. The cluster size distribution is monotonically decreasing for $\varphi <{\varphi }^{*}$, nonmonotonic for $\varphi >{\varphi }^{*}$, and is a power law at the transition. The system is, however, never dynamically arrested. The clusters permanently melt from place to place, forming droplets of an active liquid which rapidly propagate across the system. This self-melting crystalline state subsists up to the highest possible packing fraction, questioning the stability of the crystal for active discs unless it is at ordered close packing.

We show that the interaction of an oil-dispersed colloidal particle with an oil-water interface is highly tunable from attractive to repulsive, either by varying the sign of the colloidal charge via charge regulation or by varying the difference in hydrophilicity between the dissolved cations and anions. In addition, we investigate the yet unexplored interplay between the self-regulated colloidal surface charge distribution with the planar double layer across the oil-water interface and the spherical one around the colloid. Our findings explain recent experiments and have direct relevance for tunable Pickering emulsions.

A sharp transition between liquefaction and transient solidification is observed during impact on a granular suspension depending on the initial packing fraction. We demonstrate, via high-speed pressure measurements and a two-phase modeling, that this transition is controlled by a coupling between the granular pile dilatancy and the interstitial fluid pressure generated by the impact. Our results provide a generic mechanism for explaining the wide variety of impact responses in particulate media, from dry quicksand in powders to impact hardening in shear-thickening suspensions like cornstarch.