Fickian yet non-Gaussian diffusion in two-dimensional Yukawa liquids

Ion-Ion Structural Correlation and Dynamics of Water in Aqueous NaCl Solutions with a Wide Range of Concentrations

The behavior of water in concentrated ionic solutions, including supersaturated conditions, is crucial for numerous material and energy conversion processes and fundamental research. All electrolytes whether they "structure-make" or "structure-break" the water structure lead to slower water motion. This study investigates the structure and dynamics of aqueous NaCl solutions across a wide range of concentrations. On the structural side, the primary focus is on ion-ion correlations. In terms of dynamics, we demonstrate that the slowing down of water dynamics continues even beyond the saturated state. We identify three distinct types of dynamics at large concentrations: ballistic, trapped, and diffusive. The van Hove correlation function exhibits no signs of relaxation within a time interval where particle motion is effectively halted. The system displays dynamical heterogeneities, confirmed by evaluating non-Gaussian parameters for the self-part of the van Hove function and identifying the mobile particles. These particles form clusters, with the largest sizes occurring when the non-Gaussian parameters are at their maximum. Additionally, we discuss the relaxation times associated with these systems using the incoherent intermediate scattering function and establish a connection with the mode-coupling theory.

Anomalous lateral diffusion of lipids during the fluid/gel phase transition of a lipid membrane

A lipid membrane undergoes a phase transition from fluid to gel phase upon changing external thermodynamic conditions, such as decreasing temperature and increasing pressure. Extremophilic organisms face the challenge of preventing this deleterious phase transition. The main focus of their adaptive strategy is to facilitate effective temperature sensing through sensor proteins, relying on the drastic changes in packing density and membrane fluidity during the phase transition. Although the changes in packing density parameters due to the fluid/gel phase transition are studied in detail, the impact on membrane fluidity is less explored in the literature. Understanding the lateral diffusive dynamics of lipids in response to temperature, particularly during the fluid/gel phase transition, is albeit crucial. Here we have simulated the phase transition of a single component lipid membrane composed of dipalmitoylphosphatidylcholine (DPPC) lipids using a coarse-grained (CG) model and studied the changes of the structural and dynamical properties. It is observed that near the phase transition point, both fluid and gel phase domains coexist together. The dynamics remains highly non-Gaussian for a long time even when the mean square displacement reaches the Fickian regime at a much earlier time. This Fickian yet non-Gaussian diffusion (FnGD) is a characteristic of a highly heterogeneous system, previously observed for the lateral diffusion of lipids in raft mimetic membranes having liquid-ordered and liquid-disordered phases co-existing together. We have analyzed the molecular trajectories and calculated the jump-diffusion of the lipids, stemming from sudden jump translations, using a translational jump-diffusion (TJD) approach. An overwhelming contribution of the jump-diffusion of the lipids is observed suggesting anomalous diffusion of lipids during fluid/gel phase transition of the membrane. These results are important in unravelling the intricate nature of lipid diffusion during the phase transition of the membrane and open up a new possibility of investigating the most significant change of membrane properties during phase transition, which can be effectively sensed by proteins.

SPEADI: Accelerated Analysis of IDP-Ion Interactions from MD-Trajectories

The disordered nature of Intrinsically Disordered Proteins (IDPs) makes their structural ensembles particularly susceptible to changes in chemical environmental conditions, often leading to an alteration of their normal functions. A Radial Distribution Function (RDF) is considered a standard method for characterizing the chemical environment surrounding particles during atomistic simulations, commonly averaged over an entire or part of a trajectory. Given their high structural variability, such averaged information might not be reliable for IDPs. We introduce the Time-Resolved Radial Distribution Function (TRRDF), implemented in our open-source Python package SPEADI, which is able to characterize dynamic environments around IDPs. We use SPEADI to characterize the dynamic distribution of ions around the IDPs Alpha-Synuclein (AS) and Humanin (HN) from Molecular Dynamics (MD) simulations, and some of their selected mutants, showing that local ion-residue interactions play an important role in the structures and behaviors of IDPs.

Structural relaxation dynamics of colloidal nanotrimers

By Molecular Dynamics simulation, we investigate the dynamics of isotropic fluids of colloidal nanotrimers whose interactions are described by varying the strength of attractive and repulsive terms of the Mie potential. To provide a consistent comparison between the systems described by different force fields, we determine the phase diagram and critical points of each system, characterize the morphology of high-density liquid phases at the same reduced temperature and density, and finally investigate their long-time relaxation dynamics. In particular, we detect an especially complex dynamics that reveals the existence of slow and fast nanotrimers and the resulting occurrence of non-Gaussianity, which develops at intermediate timescales. Deviations from Gaussianity are temporary and vanish within the timescales of the system's density fluctuations decay, when a Fickian-like diffusion regime is eventually observed.

Fickian Non-Gaussian Diffusion in Glass-Forming Liquids

Fickian yet non-Gaussian diffusion (FnGD), a most intriguing open issue in soft matter, is generically associated with some dynamical and/or structural heterogeneity of the environment. Here we investigate the features of FnGD in glass-forming liquids, the epitome of dynamical heterogeneity, drawing on experiments on hard-sphere colloidal suspensions and simulations of a simple model of molecular liquid. We demonstrate that FnGD strengthens on approaching the glass transition, by identifying distinct timescales for Fickianity, τ_{F}, and for restoring of Gaussianity, τ_{G}>τ_{F}, as well as their associated length scales, ξ_{F} and ξ_{G}. We find τ_{G}∝τ_{F}^{γ} with γ≃1.8 for both systems. In the deep FnGD regime, the displacement distributions display exponential tails. We show that, in simulations, the time-dependent decay lengths l(t) at different temperatures all collapse onto a power-law master curve [l(t)/(ξ_{G})]∝(t/τ_{G})^{α}, with α=0.33. A similar collapse, if less sharp, is also found in experiments, seemingly with the same exponent α. We further discuss the connections of the timescales and length scales characterizing FnGD with structural relaxation and dynamic heterogeneity.

Collective Dynamics of Model Pili-Based Twitcher-Mode Bacilliforms

Pseudomonas aeruginosa, like many bacilliforms, are not limited only to swimming motility but rather possess many motility strategies. In particular, twitching-mode motility employs hair-like pili to transverse moist surfaces with a jittery irregular crawl. Twitching motility plays a critical role in redistributing cells on surfaces prior to and during colony formation. We combine molecular dynamics and rule-based simulations to study twitching-mode motility of model bacilliforms and show that there is a critical surface coverage fraction at which collective effects arise. Our simulations demonstrate dynamic clustering of twitcher-type bacteria with polydomains of local alignment that exhibit spontaneous correlated motions, similar to rafts in many bacterial communities.