Renaissance of Bernal's random close packing and hypercritical line in the theory of liquids

We review the scientific history of random close packing (RCP) of equal spheres, advocated by J D Bernal as a more plausible alternative to the non-ideal gas or imperfect crystal as a structural model of simple liquids. After decades of neglect, computer experiments are revealing a central role for RCP in the theory of liquids. These demonstrate that the RCP amorphous state of hard spheres can be well defined, is reproducible, and has the thermodynamic status of a metastable ground state. Further evidence from simulations of square-well model liquids indicates an extended role of RCP as an amorphous ground state that terminates a supercooled liquid coexistence line, suggesting likewise for real liquids. A phase diagram involving percolation boundaries has been proposed in which there is no merging of liquid and gas phases, and no critical singularity as assumed by van der Waals. Rather, the liquid phase continuously spans all temperatures, but above a critical dividing line on the Gibbs density surface, it is bounded by a percolation transition and separated from the gas phase by a colloidal supercritical mesophase. The colloidal-like inversion in the mesophase as it changes from gas-in-liquid to liquid-in-gas can be identified with the hypercritical line of Bernal. We therefore argue that the statistical theory of simple liquids should start from the RCP reference state rather than the ideal gas. Future experimental priorities are to (i) find evidence for an amorphous ground state in real supercooled liquids, (ii) explore the microscopic structures of the supercritical mesophase, and (iii) determine how these change from gas to liquid, especially across Bernal's hypercritical line. The theoretical priority is a statistical geometrical theory of RCP. Only then might we explain the coincident values of the RCP packing fraction with Buffon's constant, and the RCP residual entropy with Boltzmann's ideal gas constant.info:eu-repo/semantics/publishedVersio

Enzyme activity below the dynamical transition at 220 K

Enzyme activity requires the activation of anharmonic motions, such as jumps between potential energy wells. However, in general, the forms and time scales of the functionally important anharmonic dynamics coupled to motion along the reaction coordinate remain to be determined. In particular, the question arises whether the temperature-dependent dynamical transition from harmonic to anharmonic motion in proteins, which has been observed experimentally and using molecular dynamics simulation, involves the activation of motions required for enzyme function. Here we present parallel measurements of the activity and dynamics of a cryosolution of glutamate dehydrogenase as a function of temperature. The dynamical atomic fluctuations faster than ~100 ps were determined using neutron scattering. The results show that the enzyme remains active below the dynamical transition observed at ~220 K, i.e., at temperatures where no anharmonic motion is detected. Furthermore, the activity shows no significant deviation from Arrhenius behavior down to 190 K. The results indicate that the observed transition in the enzyme's dynamics is decoupled from the rate-limiting step along the reaction coordinate

Direct determination of vibrational density of states change on ligand binding to a protein

The change in the vibrational density of states of a protein (dihydrofolate reductase) on binding a ligand (methotrexate) is determined using inelastic neutron scattering. The vibrations of the complex soften significantly relative to the unbound protein. The resulting free-energy change, which is directly determined by the density of states change, is found to contribute significantly to the binding equilibrium

Ice XV: a new thermodynamically stable phase of ice

A new phase of ice, named ice XV, has been identified and its structure determined by neutron diffraction. Ice XV is the hydrogen-ordered counterpart of ice VI and is thermodynamically stable at temperatures below ~130 K in the 0.8 to 1.5 GPa pressure range. The regions of stability in the medium pressure range of the phase diagram have thus been finally mapped, with only hydrogen-ordered phases stable at 0 K. The ordered ice XV structure is antiferroelectric, in clear disagreement with recent theoretical calculations predicting ferroelectric ordering

‘Eastern African paradox’ rainfall decline due to shorter not less intense long rains

An observed decline in the Eastern African Long Rains from the 1980s to late 2000s appears contrary to the projected increase under future climate change. This “Eastern African climate paradox” confounds use of climate projections for adaptation planning across Eastern Africa. Here we show the decline corresponds to a later onset and earlier cessation of the long rains, with a similar seasonal maximum in area-averaged daily rainfall. Previous studies have explored the role of remote teleconnections, but those mechanisms do not sufficiently explain the decline or the newly identified change in seasonality. Using a large ensemble of observations, reanalyses and atmospheric simulations, we propose a regional mechanism that explains both the observed decline and the recent partial recovery. A decrease in surface pressure over Arabia and warmer north Arabian Sea is associated with enhanced southerlies and an earlier cessation of the long rains. This is supported by a similar signal in surface pressure in many atmosphere-only models giving lower May rainfall and an earlier cessation. Anomalously warm seas south of Eastern Africa delay the northward movement of the tropical rain-band, giving a later onset. These results are key in understanding the paradox. It is now a priority to establish the balance of mechanisms that have led to these trends, which are partially captured in atmosphere-only simulations

Future changes in seasonality in Eastern Africa from regional simulations with explicit and parametrised convection

The Eastern Africa precipitation seasonal cycle is of significant societal importance, and yet the current generation of coupled global climate models fails to correctly capture this seasonality. The use of convective parametrisation schemes is a known source of precipitation bias in such models. Recently, a high-resolution regional model was used to produce the first pan-African climate change simulation that explicitly models convection. Here, this is compared with a corresponding parametrised-convection simulation, to explore the effect of the parametrisation on representation of Eastern Africa precipitation seasonality. Both models capture current seasonality, although an overestimate in September-October in the parametrised simulation leads to an early bias in the onset of the boreal autumn short rains, associated with higher convective instability and near-surface moist static energy. This bias is removed in the explicit model. Under future climate change both models show the short rains getting later and wetter. For the boreal spring long rains, the explicit convection simulation shows the onset advancing but the parametrised simulation shows little change. Over Uganda and western Kenya both simulations show rainfall increases in the January-February dry season, and large increases in boreal summer and autumn rainfall, particularly in the explicit convection model, changing the shape of the seasonal cycle, with potential for pronounced socio-economic impacts. Interannual variability is similar in both models. Results imply that parameterisation of convection may be a source of uncertainty for projections of changes in seasonal timing from global models, and that potentially impactful changes in seasonality should be highlighted to users

Extreme rainfall in East Africa October 2019 – January 2020 and context under future climate change

The 2019 October-December rains over East Africa were one of the wettest seasons on record, with many locations receiving more than double the climatological rainfall, leading to floods and landslides across the region. Above average rainfall continued into January 2020. The persistently high rainfall also contributed to the locust plagues that affected much of East Africa in January 2020. Wet conditions in East Africa are typically associated with El Nino and/or positive Indian Ocean Dipole events. In October-December 2019 a warm anomaly was present in the western Indian Ocean while a cool anomaly was present in the eastern Indian Ocean (a positive Indian Ocean Dipole); conditions known to give above average rainfall over East Africa. The warm anomaly in the western Indian Ocean persisted into January 2020. Seasonal and monthly forecasts correctly predicted above average rainfall during the October-December season. January rainfall is found to be correlated with sea surface temperatures over the western Indian Ocean. Climate model projections suggest that strong positive Indian Ocean Dipole events and wet October-December seasons may become more frequent under future climate change, with associated increased risks of floods

Chemotaxis: a feedback-based computational model robustly predicts multiple aspects of real cell behaviour

The mechanism of eukaryotic chemotaxis remains unclear despite intensive study. The most frequently described mechanism acts through attractants causing actin polymerization, in turn leading to pseudopod formation and cell movement. We recently proposed an alternative mechanism, supported by several lines of data, in which pseudopods are made by a self-generated cycle. If chemoattractants are present, they modulate the cycle rather than directly causing actin polymerization. The aim of this work is to test the explanatory and predictive powers of such pseudopod-based models to predict the complex behaviour of cells in chemotaxis. We have now tested the effectiveness of this mechanism using a computational model of cell movement and chemotaxis based on pseudopod autocatalysis. The model reproduces a surprisingly wide range of existing data about cell movement and chemotaxis. It simulates cell polarization and persistence without stimuli and selection of accurate pseudopods when chemoattractant gradients are present. It predicts both bias of pseudopod position in low chemoattractant gradients and-unexpectedly-lateral pseudopod initiation in high gradients. To test the predictive ability of the model, we looked for untested and novel predictions. One prediction from the model is that the angle between successive pseudopods at the front of the cell will increase in proportion to the difference between the cell's direction and the direction of the gradient. We measured the angles between pseudopods in chemotaxing Dictyostelium cells under different conditions and found the results agreed with the model extremely well. Our model and data together suggest that in rapidly moving cells like Dictyostelium and neutrophils an intrinsic pseudopod cycle lies at the heart of cell motility. This implies that the mechanism behind chemotaxis relies on modification of intrinsic pseudopod behaviour, more than generation of new pseudopods or actin polymerization by chemoattractant