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## Adaptable Lipid Matrix Promotes Protein-Protein Association in Membranes

The cell membrane is "stuffed" with proteins, whose transmembrane (TM) helical domains spontaneously associate to form functionally active complexes. For a number of membrane receptors, a modulation of TM domains' oligomerization has been shown to contribute to the development of severe pathological states, thus calling for detailed studies of the atomistic aspects of the process. Despite considerable progress achieved so far, several crucial questions still remain: How do the helices recognize each other in the membrane? What is the driving force of their association? Here, we assess the dimerization free energy of TM helices along with a careful consideration of the interplay between the structure and dynamics of protein and lipids using atomistic molecular dynamics simulations in the hydrated lipid bilayer for three different model systems - TM fragments of glycophorin A, polyalanine and polyleucine peptides. We observe that the membrane driven association of TM helices exhibits a prominent entropic character, which depends on the peptide sequence. Thus, a single TM peptide of a given composition induces strong and characteristic perturbations in the hydrophobic core of the bilayer, which may facilitate the initial "communication" between TM helices even at the distances of 20-30 Å. Upon tight helix-helix association, the immobilized lipids accommodate near the peripheral surfaces of the dimer, thus disturbing the packing of the surrounding. The dimerization free energy of the modeled peptides corresponds to the strength of their interactions with lipids inside the membrane being the lowest for glycophorin A and similarly higher for both homopolymers. We propose that the ability to accommodate lipid tails determines the dimerization strength of TM peptides and that the lipid matrix directly governs their association. © 2015 American Chemical Society.

Natural polycationic membrane-active peptides typically lack disulfide bonds and exhibit fusion, cell-penetrating, antimicrobial activities. They are mostly unordered in solution, but adopt a helical structure, when bound to phospholipid membranes. Structurally different are cardiotoxins (or cytotoxins, СTs) from cobra venom. They are fully b-structured molecules, characterized by the three-finger fold (TFF). Affinity of CTs to lipid bilayer was shown to depend on amino acid sequence in the tips of the three loops. In the present review, CT-membrane interactions are analyzed through the prism of data on binding of the toxins to phospholipid liposomes and detergent micelles, as well as their structural and computational studies in membrane mimicking environments. We assess different hydrophobicity scales to compare membrane partitioning of various CTs and their membrane effects. A comparison of hydrophobic/hydrophilic properties of CTs and linear polycationic peptides provides a key to their biological activity and reveal rationality for design of new membrane-interacting compounds. Finally, since the viewpoint of the data obtained on model lipid membranes, cytotoxic activity of CTs against cancer cells is discussed.

The quantum nuclear effects are studied in water using centroid molecular dynamics (CMD) method. The aim is the calibration of CMD implementation in LAMMPS. The calculated intramolecular energy, atoms gyration radii and radial distribution functions are shown in comparison with previous works. The work is assumed to be the step toward to solution of the discrepancy between the simulation results and the experimental data of liquid n-alkane properties in our previous works.

It is well recognized that excessive ice accumulation at low-temperature conditions can cause significant damage to civil infrastructure. The passive anti-icing surfaces provide a promising solution to suppress ice nucleation and enhance ice removal. However, despite extensive efforts, it remains a challenge to design anti-icing surfaces with low ice adhesion. Using all-atom molecular dynamics (MD) simulations, we show that surfaces with single-walled carbon nanotube array (CNTA) significantly reduce ice adhesion due to the extremely low solid areal fraction. It was found that the CNTA surface exhibits up to a 45% decrease in the ice adhesion strength in comparison with the atomically smooth graphene surface. The details of the ice detachment from the CNTA surface were examined for different water-carbon interaction energies and temperatures of the ice cube. Remarkably, the results of MD simulations demonstrate that the ice detaching strength depends linearly on the ratio of the ice-surface interaction energy and the ice temperature. These results open the possibility for designing novel robust surfaces with low ice adhesion for passive anti-icing applications.

Molecular-level knowledge of the thermodynamic, structural, and transport properties of water confined by interfaces and nanopores of various materials is crucial for quantitative understanding and prediction of many natural and technological processes, including carbon sequestration, water desalination, nuclear waste storage, cement chemistry, fuel cell technology, etc. Computational molecular modeling is capable to significantly complement the experimental investigations of such systems by providing invaluable atomic-scale information leading to improved understanding of the specific effects of the substrate structure and composition on the structure, dynamics and reactivity of interfacial and nano-confined aqueous solutions. This paper offers a brief overview of recent efforts to quantify some of these effects for individual H2O molecules and hydrated ions confined at the interfaces and in nanopores of several typical hydrophilic and hydrophobic materials. The first molecular layer of aqueous solution at all substrates is often highly ordered, indicating reduced translational and orientational mobility of the H2O molecules. This ordering cannot be simply described as “ice-like”, but rather resembles the behavior of supercooled water or amorphous ice, although with very significant substrate-specific variations.

In this work, we perform coexistence simulations of methane hydrates for pressures up to 5000 bar for different water models. We calculate the kinetic stability boundary of the superheated metastable sI structure and analyze the effects of the heating rate, system size and cage occupancy. We also report molecular dynamics simulation of several possible structuresfor the new hydrogen hydrate clathrate. We show the strength of molecular simulation as a supplement tool for the analysis of experimental data. © 2015 by Nova Science Publishers, Inc. All rights reserved.

Cooling of tokamak boundary plasma owing to radiation of non-fully stripped lithium ions is considered as a promising way for protection of plasma facing elements (PFE) in tokamak. It may be effectively realized when the main part of lithium ions are involved in the closed circuit of migration between plasma and PFE surface. Such an approach may be implemented with the use of lithium device whose hot (500-600 °C) area to be effected by plasma serves as a Li-emitter and the cold part (∼180 °C) as a Li-collector in the shadow. Capillary-pore system (CPS) provides the returning of collected and condensed lithium to emitting zone by capillary forces. The main goals of the last T-11M lithium experiments were investigating Li ions transport in the tokamak scrape of layer (SOL) and their collecting by different kinds of limiters. The design of devices based on lithium CPS with different ratio of emitting/collecting area is the main subject of this paper. © 2015 The Authors.

The dynamics of a two-component Davydov-Scott (DS) soliton with a small mismatch of the initial location or velocity of the high-frequency (HF) component was investigated within the framework of the Zakharov-type system of two coupled equations for the HF and low-frequency (LF) fields. In this system, the HF field is described by the linear Schrödinger equation with the potential generated by the LF component varying in time and space. The LF component in this system is described by the Korteweg-de Vries equation with a term of quadratic influence of the HF field on the LF field. The frequency of the DS soliton`s component oscillation was found analytically using the balance equation. The perturbed DS soliton was shown to be stable. The analytical results were confirmed by numerical simulations.

Radiation conditions are described for various space regions, radiation-induced effects in spacecraft materials and equipment components are considered and information on theoretical, computational, and experimental methods for studying radiation effects are presented. The peculiarities of radiation effects on nanostructures and some problems related to modeling and radiation testing of such structures are considered.

Let k be a field of characteristic zero, let G be a connected reductive algebraic group over k and let g be its Lie algebra. Let k(G), respectively, k(g), be the field of k- rational functions on G, respectively, g. The conjugation action of G on itself induces the adjoint action of G on g. We investigate the question whether or not the field extensions k(G)/k(G)^G and k(g)/k(g)^G are purely transcendental. We show that the answer is the same for k(G)/k(G)^G and k(g)/k(g)^G, and reduce the problem to the case where G is simple. For simple groups we show that the answer is positive if G is split of type A_n or C_n, and negative for groups of other types, except possibly G_2. A key ingredient in the proof of the negative result is a recent formula for the unramified Brauer group of a homogeneous space with connected stabilizers. As a byproduct of our investigation we give an affirmative answer to a question of Grothendieck about the existence of a rational section of the categorical quotient morphism for the conjugating action of G on itself.

This proceedings publication is a compilation of selected contributions from the “Third International Conference on the Dynamics of Information Systems” which took place at the University of Florida, Gainesville, February 16–18, 2011. The purpose of this conference was to bring together scientists and engineers from industry, government, and academia in order to exchange new discoveries and results in a broad range of topics relevant to the theory and practice of dynamics of information systems. Dynamics of Information Systems: Mathematical Foundation presents state-of-the art research and is intended for graduate students and researchers interested in some of the most recent discoveries in information theory and dynamical systems. Scientists in other disciplines may also benefit from the applications of new developments to their own area of study.

Let G be a connected semisimple algebraic group over an algebraically closed field k. In 1965 Steinberg proved that if G is simply connected, then in G there exists a closed irreducible cross-section of the set of closures of regular conjugacy classes. We prove that in arbitrary G such a cross-section exists if and only if the universal covering isogeny Ĝ → G is bijective; this answers Grothendieck's question cited in the epigraph. In particular, for char k = 0, the converse to Steinberg's theorem holds. The existence of a cross-section in G implies, at least for char k = 0, that the algebra k[G]G of class functions on G is generated by rk G elements. We describe, for arbitrary G, a minimal generating set of k[G]G and that of the representation ring of G and answer two Grothendieck's questions on constructing generating sets of k[G]G. We prove the existence of a rational (i.e., local) section of the quotient morphism for arbitrary G and the existence of a rational cross-section in G (for char k = 0, this has been proved earlier); this answers the other question cited in the epigraph. We also prove that the existence of a rational section is equivalent to the existence of a rational W-equivariant map T- - - >G/T where T is a maximal torus of G and W the Weyl group.