Vibrational Analysis of Hydration-Layer Water around Ubiquitin, Unpeeled Layer by Layer: Molecular-Dynamics Perceptions.

Classical molecular-dynamics simulations have been performed to examine the interplay between ubiquitin and its hydration-water sub-layers, chiefly from a vibrational-mode and IR viewpoint-where we analyse individual sub-layers characteristics. The vibrational Density of States (VDOS) revealed that the first solvation sub-shell indicates a confined character therein. For layers of increasing distance from the surface, the adoption of greater bulk-like spectral behaviour was evident, suggesting that vibrational harmonisation to bulk occurs within 6-7 Å of the surface.

Double Life of Methanol: Experimental Studies and Nonequilibrium Molecular-Dynamics Simulation of Methanol Effects on Methane-Hydrate Nucleation.

We have investigated systematically and statistically methanol-concentration effects on methane-hydrate nucleation using both experiment and restrained molecular-dynamics simulation, employing simple observables to achieve an initially homogeneous methane-supersaturated solution particularly favorable for nucleation realization in reasonable simulation times. We observe the pronounced "bifurcated" character of the nucleation rate upon methanol concentration in both experiments and simulation, with promotion at low concentrations and switching to industrially familiar inhibition at higher concentrations. Higher methanol concentrations suppress hydrate growth by in-lattice methanol incorporation, resulting in the formation of "defects", increasing the energy of the nucleus. At low concentrations, on the contrary, the detrimental effect of defects is more than compensated for by the beneficial contribution of CH3 in easing methane incorporation in the cages or replacing it altogether.

Investigation of Dipolar Response of the Hydrated Hen-Egg White Lysozyme Complex under Externally Applied Electric Fields: Insights from Non-equilibrium Molecular Dynamics.

Given its ubiquitous presence in the environment of bio-macromolecules, water is well known to play a fundamental part in biological activity, often as a regulating agent. In parallel, with increasing attention focused on the potential damage of microwave-frequency radiation exposure to human health, the effects of extraneous electric and electromagnetic (e/m) fields on water shells surrounding proteins, and, indeed, biomolecules themselves, are becoming a particularly pertinent issue. In this study, non-equilibrium molecular dynamics simulations of hydrated hen-egg white lysozyme have been performed in both the absence and presence of external electric fields of varying intensity (0.005-0.02 V/Å) and frequency (static, i.e., zero-frequency, together with oscillating fields of 2.45-100 GHz). By comparing the effect of different electric-field conditions on both the protein's and surrounding hydration layer's dipole moments and their underlying relaxation dynamics, clear and evident non-thermal field effects were observed on the dipolar response of both the protein and hydration layer. This occurred primarily as a consequence of the protein's dipolar alignment with the external field and increased with the growth of field intensity. In addition, it was found that the lag time of dipolar response to the applied field itself, for both the protein and the first hydration sub-shell (i.e., directly adsorbed layer), under oscillating fields is longer than that in both the second hydration sub-layer and bulk water, owing to strong direct protein-water adsorption. In that respect, we also probe and discuss the effect of protein-water hydrogen bonds, dissecting the subtleties of "bio-water" dipolar response.

Pressure-Induced Densification of Ice Ih under Triaxial Mechanical Compression: Dissociation versus Retention of Crystallinity for Intermediate States in Atomistic and Coarse-Grained Water Models.

Molecular-dynamics (MD) simulation of triaxially pressurized ice Ih up to 30 kbar at 240 K (with sudden mechanical pressurization from its ambient-pressure structure) has been carried out with both the single-particle mW and atomistic TIP4P-Ice water potentials on systems of up to ∼1 million molecules, for times of the order of 100 ns. It was found that the TIP4P-Ice systems adopted a high-density liquid state above ∼7 kbar, while densification of the mW systems retained essentially crystalline order, owing to a failure for the tetrahedral network to break down appreciably from its ice Ih lattice structure. Both are intermediate states adopted along the path toward respective thermodynamically stable states (and with pressure removal show reversion to Ih for mW and to supercooled liquid for TIP4P-Ice), similar to recent ice electro-freezing simulations in "No Man's Land". Densification kinetics showed faster mW-system adaptation.

Electro-nucleation of water nano-droplets in No Man's Land to fault-free ice Ic.

Elucidating water-to-ice freezing, especially in "No Man's Land" (150 K < T < 235 K), is fundamentally important (e.g., predicting upper-troposphere cirrus-cloud formation) - and elusive. An oft-neglected aspect of tropospheric ice-crystallite formation lies in inevitably-present electric fields' role. Exploring nucleation in No Man's Land is technically demanding, owing to rapid nucleation rates, to mention nothing of difficulties of applying relevant electric fields thereto. Here, we tackle these intriguing open questions, via non-equilibrium molecular-dynamics simulations of sub-microsecond formation of rhombus-shaped ice Ic nano-crystallites from aggressively-quenched supercooled water nano-droplets in the gas phase, in external static electric fields. We explore droplets' nano-confined geometries and the entropic-ordering agent of external electric fields as a means of realising cubic-ice formation, especially with very few stacking faults and defects.

Electro-suppression of water nano-droplets' solidification in no man's land: Electromagnetic fields' entropic trapping of supercooled water.

Understanding water solidification, especially in "No Man's Land" (NML) (150 K < T < 235 K) is crucially important (e.g., upper-troposphere cloud processes) and challenging. A rather neglected aspect of tropospheric ice-crystallite formation is inevitably present electromagnetic fields' role. Here, we employ non-equilibrium molecular dynamics of aggressively quenched supercooled water nano-droplets in the gas phase under NML conditions, in externally applied electromagnetic (e/m) fields, elucidating significant differences between effects of static and oscillating fields: although static fields induce "electro-freezing," e/m fields exhibit the contrary - solidification inhibition. This anti-freeze action extends not only to crystal-ice formation but also restricts amorphisation, i.e., suppression of low-density amorphous ice which forms otherwise in zero-field NML environments. E/m-field applications maintain water in the deeply supercooled state in an "entropic trap," which is ripe for industrial impacts in cryo-freezing, etc.

Hydrogen-bond dynamics at the bio-water interface in hydrated proteins: a molecular-dynamics study.

Water is fundamental to the biochemistry of enzymes. It is well known that without a minimum amount of water, enzymes are not biologically active. Bare minimal solvation for biological function corresponds to about a single layer of water covering enzymes' surfaces. Many contradictory studies on protein-hydration-water-coupled dynamics have been published in recent decades. Following prevailing wisdom, a dynamical crossover in hydration water (at around 220 K for hydrated lysozymes) can trigger larger-amplitude motions of the protein, activating, in turn, biological functions. Here, we present a molecular-dynamics-simulation study on a solvated model protein (hen egg-white lysozyme), in which we determine, inter alia, the relaxation dynamics of the hydrogen-bond network between the protein and its hydration water molecules on a residue-per-residue basis. Hydrogen-bond breakage/formation kinetics is rather heterogeneous in temperature dependence (due to the heterogeneity of the free-energy surface), and is driven by the magnitude of thermal motions of various different protein residues which provide enough thermal energy to overcome energy barriers to rupture their respective hydrogen bonds with water. In particular, arginine residues exhibit the highest number of such hydrogen bonds at low temperatures, losing almost completely such bonding above 230 K. This suggests that hydration water's dynamical crossover, observed experimentally for hydrated lysozymes at ∼220 K, lies not at the origin of the protein residues' larger-amplitude motions, but rather arises as a consequence thereof. This highlights the need for new experimental investigations, and new interpretations to link protein dynamics to functions, in the context of key interrelationships with the solvation layer.

Perturbation of hydration layer in solvated proteins by external electric and electromagnetic fields: Insights from non-equilibrium molecular dynamics.

Given the fundamental role of water in governing the biochemistry of enzymes, and in regulating their wider biological activity (e.g., by local water concentration surrounding biomolecules), the influence of extraneous electric and electromagnetic (e/m) fields thereon is of central relevance to biophysics and, more widely, biology. With the increase in levels of local and atmospheric microwave-frequency radiation present in modern life, as well as other electric-field exposure, the impact upon hydration-water layers surrounding proteins, and biomolecules generally, becomes a particularly pertinent issue. Here, we present a (non-equilibrium) molecular-dynamics-simulation study on a model protein (hen egg-white lysozyme) hydrated in water, in which we determine, inter alia, translational self-diffusivities for both hen egg-white lysozyme and its hydration layer together with relaxation dynamics of the hydrogen-bond network between the protein and its hydration-layer water molecules on a residue-per-residue basis. Crucially, we perform this analysis both above and below the dynamical-transition temperature (at ∼220 K), at 300 and 200 K, respectively, and we compare the effects of external static-electric and e/m fields with linear-response-régime (r.m.s.) intensities of 0.02 V/Å. It was found that the translational self-diffusivity of hen egg-white lysozyme and its hydration-water layer are increased substantially in static fields, primarily due to the induced electrophoretic motion, whilst the water-protein hydrogen-bond-network-rearrangement kinetics can also undergo rather striking accelerations, primarily due to the enhancement of a larger-amplitude local translational and rotational motion by charged and dipolar residues, which serves to promote hydrogen-bond breakage and re-formation kinetics. These external-field effects are particularly evident at 200 K, where they serve to induce the protein- and solvation-layer-response effects redolent of dynamical transition at a lower temperature (∼200 K) vis-à-vis the zero-field case (∼220 K).

Role of Hydration Layer in Dynamical Transition in Proteins: Insights from Translational Self-Diffusivity.

Elucidation of the role of hydration water underpinning dynamical crossover in proteins has proven challenging. Indeed, many contradictory findings in the literature seek to establish either causal or correlative links between water and protein behavior. Here, via molecular dynamics, we compute the temperature dependence of mean-square displacement and translational self-diffusivities for both hen egg white lysozyme and its hydration layer from 190 to 300 K. We find that the protein's mobility increases sharply at ∼230 K, indicating dynamical onset; concerted motion with hydration-water molecules is evident up to ∼285 K, confirming dynamical correlation between them. Exploring underlying mechanisms of such concerted motion, we scrutinize the water-protein hydrogen-bonding network as a function of temperature, noting sharp deviation from linearity of the hydrogen bond number's profile with temperature originating near the protein dynamical transition. Our studies reveal a common temperature profile/dependence of self-diffusivity values of the protein, hydration water, and the bulk solvent, originating from a common dependence on the bulk solvent viscosity, ηS. The key mechanistic role adopted by the protein-water hydrogen bond network in relation to the onset of proteins' dynamical transition is also discussed.

Waxing and waning of dynamical heterogeneity in the superionic state.

Using molecular dynamics simulations of UO2-a type II superionic conductor-we identify a well-defined onset of dynamic disorder (Tα), which is remarkably correlated to a nontrivial advance of dynamical heterogeneity (DH). Quantified by the correlations in the dynamic propensity and van Hove self-correlation function, the DH is shown to grow with increasing temperature from Tα, peak at an intermediate temperature between Tα and Tλ-the superionic transition temperature-and then recede. Surprisingly, the DH attributes are not uniform across the temperatures-our investigation shows a low temperature (αT) stage DH, which is characterized by weak correlations and a plateaulike period in the correlations of the propensity, and a high temperature (λT) stage DH with strong correlations that are analogous to those in typical supercooled liquids. Our work, which has rigorously identified the onset of superionicity, gives a different direction for interpreting scattering experiments on the basis of statistical, correlated dynamics.