A simple atomistic model for the simulation of the gel phase of lipid bilayers

In this paper we present the results of a large-scale numerical investigation of structural properties of a model of cell membrane, simulated as a bilayer of flexible molecules in vacuum. The study was performed by carrying out extensive Molecular Dynamics simulations, in the (NVE) micro-canonical ensemble, of two systems of different sizes (2x32 and 2x256 molecules), over a fairly large set of temperatures and densities, using parallel platforms and more standard serial computers. Depending on the dimension of the system, the dynamics was followed for physical times that go from few hundred of picoseconds for the largest system to 5--10 nanoseconds for the smallest one. We find that the bilayer remains stable even in the absence of water and neglecting Coulomb interactions in the whole range of temperatures and densities we have investigated. The extension of the region of physical parameters that we have explored has allowed us to study significant points in the phase diagram of the bilayer and to expose marked structural changes as density and temperature are varied, which are interpreted as the system passing from a crystal to a gel phase.Comment: 41 pages, 13 figure

The Thermodynamic Evaluation of the Interphase Distribution of Elements in the Chromium and Nickel-containing System

The results of thermodynamic modeling of the process of element reducing from a chrome-containing ore-lime melt by silicon ferronickel depending on temperature are presented in this article. The consumption of reducing agent is equal to 105% of the required stoichiometric amount of reducing agent for complete reduction of iron and chromium in the temperature range of 1300–2200∘С. The chemical composition of the ore-lime melt is, wt. %: 24 Cr2O3; 13 FeO; 42 CaO; 3 SiO2; 9 MgO; 9 Al2O3 and of silicon ferronickel is, wt. %: 65 Si; 28 Fe; 7 Ni. The HSC Chemistry 6.12 software package developed by Outokumpu Research Oy (Finland) is used. The composition of oxide Cr2O3-FeO-CaO-SiO2-MgO-Al2O3 and metallic Fe-Si-Ni-Cr systems are calculated using the module «Equilibrium Compositions». A gas phase pressure is 1 atm. The gas phase of the system contains 2,24 m3 N2. It is established that the increase in the process temperature from 1300 to 2200∘С contributes to reducing of the degree of chromium reduction from 98,9 to 69,8%. The degree of reduction of aluminum and magnesium increases from 0,2 to 8,7% and from 0,007 to 2,5% respectively, and the degree of reduction of iron doesn’t change over the entire temperature range and is equal to 100%. The chromium content in the metallic phase decreases with increasing temperature from 51,7 to 41% and the residual CrO content in the slag increases. The chemical composition of the alloy is, wt. %: 50,41 Cr; 44,06 Fe; 1,97 Si; 3,3 Ni; 0,035 Mg; 0,21 Al; 0,005 P at the temperature of 1700∘С. The results of thermodynamic modeling can be used for laboratory experiments and technological calculations for obtaining chromium and nickel-containing complex ferroalloys suitable for smelting stainless steel grades. Keywords: thermodynamics, system, interphase distribution, reducing agent consumption, degree of recovery, temperature, chromium, nicke

Parallel computing and molecular dynamics of biological membranes

In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does not seem to affect the numerical accuracy of the simulations, while the absence of integer addressing from CPU to individual nodes puts strong constraints on the possible programming strategies. Liquids can be very satisfactorily simulated using the "systolic" method. For more complex systems, like the biological ones at which we are ultimately interested in, the "domain decomposition" approach is best suited to beat the quadratic growth of the inter-molecular computational time with the number of elementary components of the system. The promising perspectives of using this strategy for extensive simulations of lipid bilayers are briefly reviewed.Comment: 4 pages LaTeX, 2 figures included, espcrc2.sty require

The Reduction of Boron By Silicothermal Method

Thermodynamic modeling (TM) of the boron reduction process from the CaO–SiO2– MgO–B2O3 oxide system by silicon of ferrosilicon of FeSi65 and FeSi75 grades has been carried out. TM is made using the HSC 6.12 Chemistry software package developed by Outokumpu Research Oy (Finland). The equilibrium composition of oxide CaO-SiO2-MgO-B2O3 and metallic Si-Al-Fe systems was determined using the Equilibrium Compositions module in a given temperature range of 1400–1700∘C and a gas phase pressure of 1 atm. The effect of silicon of ferrosilicon grades (FeSi65 and FeSi75) on the degree of boron reduction (

Determination of technological parameters for continiuous casting of a hollow pipe billet

This article presents a method for calculating the speed of a hollow steel billet continuous casting for the seamless hot-rolled pipes production. As the initial data, used the values of the technological parameters of a round pipe billet production at the Pavlodar branch of LLP “KSP Steel” and physical modeling data of a hollow aluminum billet continuous casting at the laboratory facility of Toraighyrov University. The recalculation of the modeling results into the actual volumes of industrial production was carried out according to the condition of the similarity criterion of Fourier numbers. The casting speed of a steel hollow billet are determined, the increase of which, compared with a solid billet, amounted to 16 %

RESULTS FOR THE B-MESON DECAY CONSTANT FROM THE APE COLLABORATION

The decay constant for the B-meson in the static limit is calculated using the Wilson and clover actions at various lattice spacings. We show that both the contamination of our results by excited states and the effects finite lattice spacing are at most the order of the statistical uncertainties. A comparison is made of our results and those obtained in other studies. Values for $f^{stat}_{B_S}/f^{stat}_B$ and $M_{B_S} - M_B$ are also given.Comment: Contribution to Lattice'94, 3 pages PostScript, uuencoded compresse

Dormant non-culturable Mycobacterium tuberculosis retains stable low-abundant mRNA

BACKGROUND: Dormant Mycobacterium tuberculosis bacilli are believed to play an important role in latent tuberculosis infection. Previously, we have demonstrated that cultivation of M. tuberculosis in K(+)-deficient medium resulted in generation of dormant cells. These bacilli were non-culturable on solid media (a key feature of dormant M. tuberculosis in vivo) and characterized by low metabolism and tolerance to anti-tuberculosis drugs. The dormant bacteria demonstrated a high potential to reactivation after K(+) reintroduction even after prolonged persistence under rifampicin. In this work, we studied the transcriptome and stability of transcripts in persisting dormant bacilli under arrest of mRNA de novo synthesis. RESULTS: RNA-seq-based analysis of the dormant non-culturable population obtained under rifampicin exposure revealed a 30–50-fold decrease of the total mRNA level, indicating global transcriptional repression. However, the analysis of persisting transcripts displayed a cohort of mRNA molecules coding for biosynthetic enzymes, proteins involved in adaptation and repair processes, detoxification, and control of transcription initiation. This ‘dormant transcriptome’ demonstrated considerable stability during M. tuberculosis persistence and mRNA de novo synthesis arrest. On the contrary, several small non-coding RNAs showed increased abundance on dormancy. Interestingly, M. tuberculosis entry into dormancy was accompanied by the cleavage of 23S ribosomal RNA at a specific point located outside the ribosome catalytic center. CONCLUSIONS: Dormant non-culturable M. tuberculosis bacilli are characterized by a global transcriptional repression. At the same time, the dormant bacilli retain low-abundant mRNAs, which are considerably stable during in vitro persistence, reflecting their readiness for translation upon early resuscitation steps. Increased abundance of non-coding RNAs on dormancy may indicate their role in the entry into and maintenance of M. tuberculosis dormant non-culturable state. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-2197-6) contains supplementary material, which is available to authorized users

Tetranuclear Group 7/8 Mixed-Metal and Open Trinuclear Group 7 Metal Carbonyl Clusters Bearing Bridging 2-mercapto-1-methylimidazole Ligands

The reactivity of group 7 metal dinuclear carbonyl complexes [M2(CO)6(μ-SN2C4H5)2] (1, M = Re; 2, M = Mn) toward group 8 metal trinuclear carbonyl clusters were examined. Reactions of 1 and 2 with [Os3(CO)10(NCMe)2] in refluxing benzene furnished the tetranuclear mixed-metal clusters [Os3Re(CO)13(μ3-SN2C4H5)] (3) and [Os3Mn(CO)13(μ3-SN2C4H5)] (4), respectively. Similar treatment of 1 and 2 with Ru3(CO)12 yielded the ruthenium analogs [Ru3Re(CO)13(μ3-SN2C4H5)] (5), and [Ru3Mn(CO)13(μ3-SN2C4H5)] (6), but in the case of 2 a secondary product [Mn3(CO)10(μ-Cl)(μ3-SN2C4H5)2] (7) was also formed. Compounds 3–6 have a butterfly core of four metal atoms with the M (Mn or Re) at a wingtip of the butterfly and containing a noncrystallographic mirror plane of symmetry. This result provides a potential method for the synthesis of a series of new group 7/8 mixed metal complexes containing a bifunctional heterocyclic ligand. Compound 7 is a unique example of a 54-electron trimanganese complex having bridging 2-mercapto-1-methylimidazolate and chloride ligands. Interestingly, the reaction of 1 with Fe3(CO)12 at 70–75 °C furnished the tri- and dirhenium complexes [Re3(CO)10(μ-H)(μ3-SN2C4H5)2] (8) and [Re2(CO)6(N2C4H5)(μ-SN2C4H5)2] (9), respectively instead of the expected formation of the mixed-metal clusters. The former is an interesting example of a 52-electron trirhenium-hydridic complex containing bridging 2-mercapto-1-methylimidazolate ligand, while the latter can be viewed as a 1-methylimidazole adduct of 1. No mixed Fe–Re complexes were produced in this reaction. The molecular structures of the new compounds 3–5 and 7–9 were established by single-crystal X-ray diffraction analyses and the DFT studies of compounds 5, 7 and 8 are reported