The structure of the enigmatic ripple phase in saturated bilayers resolved: Machine learning reveals four lipid populations

A new mixed radial-angular, three-particle correlation function method in combination with unsupervised machine learning (ML) was applied to examine the emergence of the ripple phase in dipalmitoyphosphatidylcholine (DPPC) lipid bilayers using data from atomistic molecular dynamics (MD) simulations of system sizes ranging from 128 to 4,096 lipids. Based on the acyl tail conformations, the analysis revealed the presence of four distinct conformational populations of lipids in the ripple phases of the DPPC lipid bilayers. The expected gel- (ordered;Lo) and fluid-like (disordered;Ld) lipids are found along with their splayed tail equivalents (Lo,s and Ld,s). These lipids differ based on their gauche distribution and tail packing. The disordered (Ld)and disordered splayed (Ld,s) lipids spatially cluster in the ripple in the groove side,that is, in an asymmetric manner across the bilayer leaflets. The ripple phase does not contain large numbers of Ld lipids, instead they only exist on the interface of the groove side of the undulation. The bulk of the groove side is a complex coexistence of Lo,Lo,s and Ld,s lipids. The convex side of the undulation contains predominantly Lo lipids. Thus, the structure of the ripple phase is neither a simple coexistence of ordered and disordered lipids nor a coexistence of ordered interdigitating gel-like (Lo) and ordered splayed (Lo,s) lipids, but instead a coexistence of an ordered phase and a complex mixed phase. Principal component analysis (PCA) further confirmed the existence of the four lipid groups.

Ripple Band Phase Precession of Place Cell Firing during Replay

Phase coding offers several theoretical advantages for information transmission compared to an equivalent rate code. Phase coding is shown by place cells in the rodent hippocampal formation, which fire at progressively earlier phases of the movement related 6-12Hz theta rhythm as their spatial receptive fields are traversed. Importantly, however, phase coding is independent of carrier frequency, and so we asked whether it might also be exhibited by place cells during 150-250Hz ripple band activity, when they are thought to replay information to neocortex. We demonstrate that place cells which fire multiple spikes during candidate replay events do so at progressively earlier ripple phases, and that spikes fired across all replay events exhibit a negative relationship between decoded location within the firing field and ripple phase. These results provide insights into the mechanisms underlying phase coding and place cell replay, as well as the neural code propagated to downstream neurons.

Evaluating coarse-grained MARTINI force-fields for capturing the ripple phase of lipid membranes

Phospholipids, which are an integral component of cell membranes, exhibit a rich variety of lamellar phases modulated by temperature and composition. Molecular dynamics (MD) simulations have greatly enhanced our understanding of phospholipid membranes by capturing experimentally observed phases and phase transitions at molecular resolution. However, the ripple (Pβ′) membrane phase, observed as an intermediate phase below the main gel-to-liquid crystalline transition with some lipids, has been challenging to capture with MD simulations, both at all-atom and coarse-grained resolution. Here, we systematically assess the ability of five coarse-grained MARTINI 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipid force-field (FF) variants, parametrized to reproduce the DPPC gel and fluid phases, for their ability to capture the Pβ′ phase. Upon cooling from the fluid phase to below the phase transition temperature with smaller (380-lipid) and larger (> 2200-lipid) MARTINI and all-atom (CHARMM36 FF) DPPC lipid bilayers, we observed that smaller bilayers with both all-atom and MARTINI FFs sampled interdigitated Pβ′ and ripple-like states, respectively. However, while all-atom simulations of the larger DPPC membranes exhibited the formation of the Pβ′ phase, similar to previous studies, MARTINI membranes did not sample interdigitated ripple-like states at larger system sizes. We then demonstrated that the ripple-like states in smaller MARTINI membranes were kinetically-trapped structures caused by finite size effects rather than being representative of true Pβ′ phases. We showed that even a MARTINI FF variant that could capture the tilted Lβ′ gel phase, a prerequisite for stabilizing the Pβ′ phase, could not capture the rippled phase upon cooling. Our study reveals that the current MARTINI FFs may require specific re-parametrization of the interaction potentials to stabilize lipid interdigitation, a characteristic of the ripple phase.

Unveiling the Uniqueness of Crystal Structure and Crystalline Phase Behavior of Anhydrous Octyl β-D-Glucoside Using Aligned Assembly on a Surface

Although the anomalous low crystallinity of octyl β-D-glucoside (β-OGlu) was first proposed more than 30 years ago, many fundamental aspects of its crystal structure and of the crystalline phase behavior of the pure substance have remained uncertain. In this paper, we employ grazing-incidence wide-angle X-ray-diffraction measurements using a two-dimensional detector (2D-GI-WAXD) and perpendicularly aligned crystalline films to demonstrate that β-OGlu forms crystal structures consisting of an intermediate phase—like a ripple phase with two large crystal-lattice constants, a and c, comparable to the lengths of its bilayer structures. Furthermore, solid-to-solid phase transitions accompanied by latent heat confirm the existence of a solid-solution-like phase consisting of a crystalline and a liquid-crystal (LC) phase, which persists over a 20 °C temperature range, in a single-component system. In addition, the system forms a superlattice, accompanied by a change in packing of the component sugars in the partial-melting state; this shift is different from the gel-crystal transition observed for a typical lipid system. These facts indicate that even in the crystalline phase formed from a single component, each individual β-OGlu molecule in a single-component phase plays a versatile role in the crystallisation and melting processes. These findings must somewhat explain the specific co-assembling features with proteins of β-OGlu, which has long been used empirically in biochemistry.

Flaws in Spectral Ripple Stimuli for Listeners with Cochlear Implants

ObjectivesSpectral resolution is an important aspect of hearing speech accurately, and a known limiting factor in cochlear implants (CIs). The spectral ripple discrimination task is a psychophysical measure that has been found to correlate with word recognition, music perception, and various aspects of CI processing. It was hypothesized that the limited spectral sampling of CI processors would distort the output of spectral ripple stimuli in ways that could be problematic for their use in CI research. DesignIdealized acoustic ripple spectra were analyzed through synthetic filters matched to CI processor channels, and the output was examined for spectral density and modulation depth cross a wide range of inputs. Existing data showing correlations between ripple discrimination and speech recognition were re-analyzed with special consideration of scores above the spectral aliasing limit. ResultsThe analysis revealed numerous complicating factors in the transmission of spectral ripples through CIs, including spectral aliasing and modulation depth neutralization. These unintended distortions are nonlinear in nature, with the consequence that spectral ripple thresholds above a certain number cannot be ordered monotonically along a single parametric axis/dimension. For the Cochlear device, the critical limit for spectral aliasing is around 2.1 RPO, and the critical limit for modulation saturation is about 3.5 RPO. Neither limitation is remediated by changing stimulus phase. Changes in modulation depth are limited by the single channel with the narrowest input filter octave-scaled bandwidth (channel 9 in the Cochlear device). Correlations between ripple discrimination and various measures of speech recognition are improved when high ripple scores are dismissed or winsorized. An additional difficulty with interpreting discrimination thresholds is that ripple stimuli often do not match the spectral characteristics of modulations found in actual speech sounds.ConclusionsThe authors conclude that the practice of identifying the highest spectral density at which ripple phase inversion can be detected should be abandoned because (1) it lacks the well-behaved mathematical properties a psychophysical experimenter requires, and (2) high spectral densities are a poor representation of ecologically-relevant cues. Alternative testing strategies (ripple depth detection, ripple phase shift, acoustic-phonetic cue perception) should be taken, with the specific consideration of real speech acoustics in their development.

Estimates of Ripple-Density Resolution Based on the Discrimination From Rippled and Nonrippled Reference Signals

Rippled-spectrum stimuli are used to evaluate the resolution of the spectro-temporal structure of sounds. Measurements of spectrum-pattern resolution imply the discrimination between the test and reference stimuli. Therefore, estimates of rippled-pattern resolution could depend on both the test stimulus and the reference stimulus type. In this study, the ripple-density resolution was measured using combinations of two test stimuli and two reference stimuli. The test stimuli were rippled-spectrum signals with constant phase or rippled-spectrum signals with ripple-phase reversals. The reference stimuli were rippled-spectrum signals with opposite ripple phase to the test or nonrippled signals. The spectra were centered at 2 kHz and had an equivalent rectangular bandwidth of 1 oct and a level of 70 dB sound pressure level. A three-alternative forced-choice procedure was combined with an adaptive procedure. With rippled reference stimuli, the mean ripple-density resolution limits were 8.9 ripples/oct (phase-reversals test stimulus) or 7.7 ripples/oct (constant-phase test stimulus). With nonrippled reference stimuli, the mean resolution limits were 26.1 ripples/oct (phase-reversals test stimulus) or 22.2 ripples/oct (constant-phase test stimulus). Different contributions of excitation-pattern and temporal-processing mechanisms are assumed for measurements with rippled and nonrippled reference stimuli: The excitation-pattern mechanism is more effective for the discrimination of rippled stimuli that differ in their ripple-phase patterns, whereas the temporal-processing mechanism is more effective for the discrimination of rippled and nonrippled stimuli.