Computational methods and theory for ion channel research.

Ion channels are fundamental biological devices that act as gates in order to ensure selective ion transport across cellular membranes; their operation constitutes the molecular mechanism through which basic biological functions, such as nerve signal transmission and muscle contraction, are carried out. Here, we review recent results in the field of computational research on ion channels, covering theoretical advances, state-of-the-art simulation approaches, and frontline modeling techniques. We also report on few selected applications of continuum and atomistic methods to characterize the mechanisms of permeation, selectivity, and gating in biological and model channels.

Characterization of hydration water in supercooled water-trehalose solutions: The role of the hydrogen bonds network.

The structural and dynamical properties of hydration water in aqueous solutions of trehalose are studied with molecular dynamics simulation. We simulate the systems in the supercooled region to investigate how the interaction with the trehalose molecules modifies the hydrogen bond network, the structural relaxation, and the diffusion properties of hydration water. The analysis is performed by considering the radial distribution functions, the residence time of water molecules in the hydration shell, the two body excess entropy, and the hydrogen bond water-water and water-trehalose correlations of the hydration water. The study of the two body excess entropy shows the presence of a fragile to strong crossover in supercooled hydration water also found in the relaxation time of the water-water hydrogen bond correlation function, and this is in agreement with predictions of the mode coupling theory and of previous studies of the oxygen-oxygen density correlators [A. Iorio et al., J. Mol. Liq. 282, 617 (2019); Sci. China: Phys., Mech. Astron. 62, 107011 (2019)]. The water-trehalose hydrogen bond correlation function instead evidences a strong to strong crossover in the relaxation time, and this crossover is related to a trehalose dynamical transition. This signals the role that the strong interplay between the soluted molecules and the surrounding solvent has in determining the dynamical transition common to both components of the system that happens upon cooling and that is similar to the well known protein dynamical transition. We connect our results with the cryoprotecting role of trehalose molecules.

High density liquid structure enhancement in glass forming aqueous solution of LiCl.

We investigate using molecular dynamics simulations the dynamical and structural properties of LiCl:6H2O aqueous solution upon supercooling. This ionic solution is a glass forming liquid of relevant interest in connection with the study of the anomalies of supercooled water. The LiCl:6H2O solution is easily supercooled and the liquid state can be maintained over a large decreasing temperature range. We performed simulations from ambient to 200 K in order to investigate how the presence of the salt modifies the behavior of supercooled water. The study of the relaxation time of the self-density correlation function shows that the system follows the prediction of the mode coupling theory and behaves like a fragile liquid in all the range explored. The analysis of the changes in the water structure induced by the salt shows that while the salt preserves the water hydrogen bonds in the system, it strongly affects the tetrahedral hydrogen bond network. Following the interpretation of the anomalies of water in terms of a two-state model, the modifications of the oxygen radial distribution function and the angular distribution function of the hydrogen bonds in water indicate that LiCl has the role of enhancing the high density liquid component of water with respect to the low density component. This is in agreement with recent experiments on aqueous ionic solutions.

Structural properties and fragile to strong transition in confined water.

We derive by computer simulation the radial distribution functions of water confined in a silica pore modeled to reproduce MCM-41. We perform the calculations in a range of temperatures from ambient to deep supercooling for the subset of water molecules that reside in the inner shell (free water) by applying the excluded volume corrections. By comparing with bulk water we find that the first shell of the oxygen-oxygen and hydrogen-hydrogen radial distribution functions is less sharp and the first minimum fills in while the oxygen-hydrogen structure does not significantly change, indicating that the free water keeps the hydrogen bond short range order. The two body excess entropy of supercooled water is calculated from the radial distribution functions. We connect the behavior of this function to the relaxation time of the same system already studied in previous simulations. We show that the two body entropy changes its behavior in coincidence with the crossover of the relaxation time from the mode coupling fragile to the strong Arrhenius regime. As for bulk water also in confinement, the two body entropy has a strict connection with the dynamical relaxation.

Microscopic origin of the fragile to strong crossover in supercooled water: The role of activated processes.

We perform an accurate analysis of the density self-correlation functions of TIP4P/2005 supercooled water on approaching the region of the liquid-liquid critical point. In a previous work on this model, we provided evidence of a fragile to strong crossover of the dynamical behavior in the deep supercooled region. The structural relaxation follows the Mode Coupling theory in the fragile region and then deviates from Mode Coupling regime to a strong Arrhenius behavior. This crossover is particularly important in water because it is connected to the thermodynamics of the supercooled region. To better understand the origin of this crossover, we compute now the Van Hove self-correlation functions. In particular we aim at investigating the presence and the role of the hopping phenomena that are the cause of the fragile to strong crossover in simple liquids. In TIP4P/2005 water, we find hopping processes too and we analyze how they depend on temperature and density upon approaching the fragile to strong crossover and the Mode Coupling ideal crossover temperature. Our results show that water behaves like a simple glass former. After an initial ballistic regime, the cage effect dominates the mild supercooled region, with diffusion taking place at long time. At the fragile to strong crossover, we find that hopping (activated) processes start to play a role. This is evidenced by the appearance of peaks in the Van Hove correlation functions. In the deep supercooled regime, our analysis clearly indicates that activated processes dominate the dynamics. The comparison between the Van Hove functions and the radial distribution functions allows to better understand the mechanism of hopping phenomena in supercooled water and to connect their onset directly with the crossing of the Widom Line.

Two structural relaxations in protein hydration water and their dynamic crossovers.

We study the translational single particle dynamics of hydration water of lysozyme upon cooling by means of molecular dynamics simulations. We find that water close to the protein exhibits two distinct relaxations. By characterizing their behavior upon cooling, we are able to assign the first relaxation to the structural α-relaxation also present in bulk water and in other glass-forming liquids. The second, slower, relaxation can be ascribed to a dynamic coupling of hydration water motions to the fluctuations of the protein structure. Both relaxation times exhibit crossovers in the behavior upon cooling. For the α-process, we find upon cooling a crossover from a fragile behavior to a strong behavior at a temperature which is about five degrees higher than that of bulk water. The long-relaxation time appears strictly connected to the protein motion as it shows upon cooling a temperature crossover from a strong behavior with a lower activation energy to a strong behavior with a higher activation energy. The crossover temperature coincides with the temperature of the protein dynamical transition. These findings can help experimentalists to disentangle the different information coming from total correlators and to better characterize hydration water relaxations in different biomolecules.

Mode coupling theory and fragile to strong transition in supercooled TIP4P/2005 water.

We study by molecular dynamics simulations supercooled water with the TIP4P/2005 potential. This model is able to predict many properties of water in a large range of the thermodynamic space in agreement with experiments. We explore the dynamical behavior and, in particular, the self intermediate scattering function of the oxygen atoms. We find that the structural relaxation in the range of mild supercooling is in agreement with the Mode Coupling Theory (MCT). The ideal MCT crossover takes place at decreasing temperature with increasing density. Deviations from the MCT behavior are found upon further supercooling. A crossover from the MCT, fragile, regime to a strong, Arrhenius, regime is found and it is connected to the presence of a liquid-liquid phase transition and the Widom line emanating from the liquid-liquid critical point.

An Italian national multicenter study for the definition of reference ranges for normal values of peripheral blood lymphocyte subsets in healthy adults.

BACKGROUND AND OBJECTIVE: Reference ranges are necessary in clinical chemistry and hematology to compare an observed value and to provide meaningful information. The aim of this multicenter study was the definition of reference ranges of the relative and absolute numbers of lymphocyte subsets by evaluating a large cohort of healthy adults and by using a standard protocol to reduce the variability in both sample preparation methodology and flow cytometer operation. Other aims of this study were the evaluation of the influence of sex, age, obesity, smoking, sport and some methodological variables on lymphocyte subsets and the comparison of differential white blood cell values obtained by flow cytometry and those obtained by hematology counters. DESIGN AND METHODS: Blood samples from 1311 healthy adults (blood donors and volunteers chosen according to the Italian law for donor selection) were analyzed to study, by flow cytometry, the immunophenotype of lymphocyte subsets and their distribution in terms of percentages and absolute values. Pre-analytical and analytical phases were performed according to the guidelines of the International Federation of Clinical Chemistry (IFCC) and the Italian Group of Cytometry (GIC). T cells were defined by the expression of CD3; T subpopulations by the coexpression of CD4 or CD8 or HLA-DR; B-lymphocytes were identified by the expression of CD19 while natural killer lymphocytes were identified by positivity of CD16 and/or CD56 without CD3. We calculated, for each laboratory and for all data collected, the frequency distribution percent values and absolute values of each lymphocyte subset. The influence of age, sex, smoking, obesity and sport was calculated by the t-test. The influence of some methodological variables was calculated by the t-test and multiple regression test. RESULTS: Fifty-three flow cytometry laboratories at different institutions in Italy participated in this study. Data was obtained from 1311 healthy adults aged from 18 to 70; 968 phenotype analyses (74%) were considered eligible for statistical analysis. Significant results were found as regards sex, smoking and some methodological variables (quantity of sample, washing procedures, brand of monoclonal antibodies and kind of instruments used). The comparison between hematology counters and cytometers showed no difference for any of the parameters considered. INTERPRETATION AND CONCLUSIONS: The large number of cases, the different kinds of laboratories and their distribution throughout the country make our sample representative of the Italian adult population. The standardization criteria of pre-analytical and analytical phases (the most important issues in evaluating reference values for an indicator) assured good reproducibility among laboratories so that the obtained reference ranges may be useful for interlaboratory comparison of results. Instruments and the brand of monoclonal antibodies may represent an inevitable cause of variability.