OrganL: Dynamic triangulation of biomembranes using curved elements.

We describe a method for simulating biomembranes of arbitrary shape. In contrast to other dynamically triangulated surface (DTS) algorithms, our method provides a rich, quasi-tangent-continuous, yet local description of the surface. We use curved Nagata triangles, which we generalize to cubic order to achieve the requisite flexibility. The resulting interpolation can be constructed locally without iterations, at the cost of having only approximate tangent continuity away from the vertices. This allows us to provide a parallelized and fine-tuned Monte Carlo implementation. As a first example of the potential benefits of the enhanced description, our method supports inhomogeneous lipid distributions as well as lipid mixing. It also supports restraints and constraints of various types and is constructed to be as easily extensible as possible. We validate the approach by testing its numerical accuracy, followed by reproducing the known Helfrich solutions for shapes with rotational symmetry. Finally, we present some example applications, including curvature-driven demixing and stylized effects of proteins. Input files for these examples, as well as the implementation itself, are freely available for researchers under the name OrganL (https://zenodo.org/doi/10.5281/zenodo.11204709).

Hydration of biologically relevant tetramethylammonium cation by neutron scattering and molecular dynamics.

Neutron scattering and molecular dynamics studies were performed on a concentrated aqueous tetramethylammonium (TMA) chloride solution to gain insight into the hydration shell structure of TMA, which is relevant for understanding its behavior in biological contexts of, e.g., properties of phospholipid membrane headgroups or interactions between DNA and histones. Specifically, neutron diffraction with isotopic substitution experiments were performed on TMA and water hydrogens to extract the specific correlation between hydrogens in TMA (HTMA) and hydrogens in water (HW). Classical molecular dynamics simulations were performed to help interpret the experimental neutron scattering data. Comparison of the hydration structure and simulated neutron signals obtained with various force field flavors (e.g. overall charge, charge distribution, polarity of the CH bonds and geometry) allowed us to gain insight into how sensitive the TMA hydration structure is to such changes and how much the neutron signal can capture them. We show that certain aspects of the hydration, such as the correlation of the hydrogen on TMA to hydrogen on water, showed little dependence on the force field. In contrast, other correlations, such as the ion-ion interactions, showed more marked changes. Strikingly, the neutron scattering signal cannot discriminate between different hydration patterns. Finally, ab initio molecular dynamics was used to examine the three-dimensional hydration structure and thus to benchmark force field simulations. Overall, while neutron scattering has been previously successfully used to improve force fields, in the particular case of TMA we show that it has only limited value to fully determine the hydration structure, with other techniques such as ab initio MD being of a significant help.

Nanoscale membrane curvature sorts lipid phases and alters lipid diffusion.

The precise spatiotemporal control of nanoscale membrane shape and composition is the result of a complex interplay of individual and collective molecular behaviors. Here, we employed single-molecule localization microscopy and computational simulations to observe single-lipid diffusion and sorting in model membranes with varying compositions, phases, temperatures, and curvatures. Supported lipid bilayers were created over 50-nm-radius nanoparticles to mimic the size of naturally occurring membrane buds, such as endocytic pits and the formation of viral envelopes. The curved membranes recruited liquid-disordered lipid phases while altering the diffusion and sorting of tracer lipids. Disorder-preferring fluorescent lipids sorted to and experienced faster diffusion on the nanoscale curvature only when embedded in a membrane capable of sustaining lipid phase separation at low temperatures. The curvature-induced sorting and faster diffusion even occurred when the sample temperature was above the miscibility temperature of the planar membrane, implying that the nanoscale curvature could induce phase separation in otherwise homogeneous membranes. Further confirmation and understanding of these results are provided by continuum and coarse-grained molecular dynamics simulations with explicit and spontaneous curvature-phase coupling, respectively. The curvature-induced membrane compositional heterogeneity and altered dynamics were achieved only with a coupling of the curvature with a lipid phase separation. These cross-validating results demonstrate the complex interplay of lipid phases, molecular diffusion, and nanoscale membrane curvature that are critical for membrane functionality.

Small ionic radii limit time step in Martini 3 molecular dynamics simulations.

Among other improvements, the Martini 3 coarse-grained force field provides a more accurate description of the solvation of protein pockets and channels through the consistent use of various bead types and sizes. Here, we show that the representation of Na+ and Cl- ions as "tiny" (TQ5) beads limits the accessible time step to 25 fs. By contrast, with Martini 2, time steps of 30-40 fs were possible for lipid bilayer systems without proteins. This limitation is relevant for systems that require long equilibration times. We derive a quantitative kinetic model of time-integration instabilities in molecular dynamics (MD) as a function of the time step, ion concentration and mass, system size, and simulation time. We demonstrate that ion-water interactions are the main source of instability at physiological conditions, followed closely by ion-ion interactions. We show that increasing the ionic masses makes it possible to use time steps up to 40 fs with minimal impact on static equilibrium properties and dynamical quantities, such as lipid and solvent diffusion coefficients. Increasing the size of the bead representing the ions (and thus changing their hydration) also permits longer time steps. For a soluble protein, we find that increasing the mass of tiny beads also on the protein permits simulations with 30-fs time steps. The use of larger time steps in Martini 3 results in a more efficient exploration of configuration space. The kinetic model of MD simulation crashes can be used to determine the maximum allowed time step upfront for an efficient use of resources and whenever sampling efficiency is critical.

Anisotropic diffusion of membrane proteins at experimental timescales.

Single-particle tracking (SPT) experiments of lipids and membrane proteins provide a wealth of information about the properties of biomembranes. Careful analysis of SPT trajectories can reveal deviations from ideal Brownian behavior. Among others, this includes confinement effects and anomalous diffusion, which are manifestations of both the nanoscale structure of the underlying membrane and the structure of the diffuser. With the rapid increase in temporal and spatial resolution of experimental methods, a new aspect of the motion of the particle, namely, anisotropic diffusion, might become relevant. This aspect that so far received only little attention is the anisotropy of the diffusive motion and may soon provide an additional proxy to the structure and topology of biomembranes. Unfortunately, the theoretical framework for detecting and interpreting anisotropy effects is currently scattered and incomplete. Here, we provide a computational method to evaluate the degree of anisotropy directly from molecular dynamics simulations and also point out a way to compare the obtained results with those available from SPT experiments. In order to probe the effects of anisotropic diffusion, we performed coarse-grained molecular dynamics simulations of peripheral and integral membrane proteins in flat and curved bilayers. In agreement with the theoretical basis, our computational results indicate that anisotropy can persist up to the rotational relaxation time [τ=(2Dr)-1], after which isotropic diffusion is observed. Moreover, the underlying topology of the membrane bilayer can couple with the geometry of the particle, thus extending the spatiotemporal domain over which this type of motion can be detected.

Alexithymia and emotion regulation in patients with Raynaud's disease.

OBJECTIVES: Besides cold, emotional distress is the most important trigger of Raynaud's disease (RD) attacks, although little is known about the factors that contribute to the effectiveness of coping with emotional distress. The aim of the present study was to explore alexithymia and emotion regulation and their relationship with depression and quality of life among patients with RD. METHODS: Total of 110 patients (mean age 53.65; 96 women) with RD completed self-report measures. RESULTS: Alexithymia was associated with adverse emotional regulation skills, depression, and quality of life impairment. Detailed analysis revealed that there are significant differences between alexithymic and nonalexithymic patients in emotion regulation. CONCLUSION: Alexithymia is a significant factor affecting health status in RD since it plays a significant role in emotion regulation. A multidisciplinary approach is essential to improve treatment outcome by identifying patients with high alexithymia, and to improve their emotional regulation skills.

Pytim: A python package for the interfacial analysis of molecular simulations.

Pytim is a versatile python framework for the analysis of interfacial properties in molecular simulations. The code implements several algorithms for the identification of instantaneous interfaces of arbitrary shape, and analysis tools written specifically for the study of interfacial properties, such as intrinsic profiles. The code is written in the python language, and makes use of the numpy and scipy packages to deliver high computational performances. Pytim relies on the MDAnalysis library to analyze the trajectory file formats of popular simulation packages such as gromacs, charmm, namd, lammps or Amber, and can be used to steer OpenMM simulations. Pytim can write information about surfaces and surface atomic layers to vtk, cube, and pdb files for easy visualization. The classes of Pytim can be easily customized and extended to include new interfacial algorithms or analysis tools. The code is available as open source and is free of charge. © 2018 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.

[Quality of life of patients with Raynaud's disease]. / Raynaud-szindrómás betegek életminoségének jellemzoi.

INTRODUCTION: Raynaud's disease is characterized by episodic vasospastic attacks and digital ischemia usually followed by pain, numbness and cold. Despite the severity of the symptoms, the investigation of the quality of life in this disease received less attention yet. AIM: The aim of the study was to examine how the disease affects the patients' quality of life. METHOD: Semi-structured interviews were made with 28 patients diagnosed with Raynaud's disease. RESULTS: Almost every domain of quality of life is negatively affected. The somatic symptoms cause significant suffering, they are accompanied by loss of functionality; frequent preventive actions are needed; furthermore they affect job performance, commuting and sleep quality. Emotional and cognitive burdens and negative changes in interpersonal relationships were found. CONCLUSION: The findings of this study show that the disease is present as significant hardship in every aspect of daily life. Because of the decrease in the quality of life and the psychological burdens caused by this chronic disease, not only the basic medical care, but psychological treatment is also indicated. Orv Hetil. 2018; 159(16): 636-641.

[Investigation of sleep and fatigue in patients with cancer]. / Az alvás és a kimerültség vizsgálata daganatos betegek körében.

INTRODUCTION: The diagnosis of cancer elicits greater distress than any other diagnosis. The prevalence of psychological difficulties is high in cancer, and resources of the medical staff are limited. The development of efficient screening measures is therefore of utmost importance. Sleep is vital to all psychological functioning and poor sleep is a known problem in cancer. AIM: The main goal of the present study was testing of visual analogue scales assessing sleep quality and fatigue. METHOD: Sleep quality and fatigue were assessed with visual analogue scales. The Sleep Condition Indicator, the Athens Insomnia Scale and the Cancer Fatigue Scale were also included. Psychological distress was assessed with the Generalized Anxiety Disorder Scale, the Beck Depression Inventory and the Brief Difficulties in Emotion Regulation Scale. Pain and well-being was measured with the Faces of Pain Scale and the WHO Well-being Scale, respectively. A total of 71 patients with cancer were enrolled in this study. RESULTS: Insomnia and fatigue - measuring them with visual and several-item scales - showed high correlation with the measures of distress (anxiety, depression, emotion regulation difficulties) and pain. Distress and pain showed significant negative correlation with well-being. CONCLUSIONS: It has been affirmed that sleep quality is crucial in the changes of distress, pain and general well-being in cancer patients. It affirms that the visual analogue scales assessing sleep quality and fatigue - besides sleep quality and fatigue - are acceptable screening tools of distress and decreased well-being. Their use in clinical practice is recommended for screening in cancer patients and providing indications for onco-psychological treatment. Orv Hetil. 2018; 159(42): 1720-1726.

[Medically Unexplained Symptoms].

The term "medically unexplained symptoms" (MUS) refers to the manifestation of multiple somatic complaints not explained satisfactorily by organic changes, where the origin of the symptoms is not psychoactive drug use or simulation. Even though the beginnings of the investigations of this topic are dated back to the mid-18th century, still no adequate conceptual consensus has been reached. In the treatment of MUS we face the challenges of the need for multidisciplinarity and the issue of not putting enough emphasis in the medical training on the evaluation of the possible psychological background of somatic symptoms and on the teaching of communication skills. This study outlines the main characteristics of MUS, the related epidemiological results and - together with the effect of MUS on the healthcare system and economy - highlights the attitudes of patients and medical doctors. We make practical and theoretical points, which may contribute to the efficient treatment of MUS.