Search results for "Method"
showing 10 items of 13253 documents
Structure-based statistical analysis of transmembrane helices
2012
Recent advances in determination of the high-resolution structure of membrane proteins now enable analysis of the main features of amino acids in transmembrane (TM) segments in comparison with amino acids in water-soluble helices. In this work, we conducted a large-scale analysis of the prevalent locations of amino acids by using a data set of 170 structures of integral membrane proteins obtained from the MPtopo database and 930 structures of water-soluble helical proteins obtained from the protein data bank. Large hydrophobic amino acids (Leu, Val, Ile, and Phe) plus Gly were clearly prevalent in TM helices whereas polar amino acids (Glu, Lys, Asp, Arg, and Gln) were less frequent in this …
Computer Simulation of Polymers: Physics and Methods from Specific to Universal
2004
We will discuss in this contribution several aspects of the physics of polymers on different length and time scales and the simulation methods suited for their study. A Molecular Dynamics (MD) simulation of a chemically realistic model is needed to get quantitative insight into local relaxation processes. This study will also reveal the importance of four-particle correlations in polymer dynamics resulting from the presence of dihedral potentials along the chain. Universal largescale chain relaxation can be studied by realistic models as well, but in far better statistical accuracy by Monte Carlo (MC) simulations of a coarse-grained lattice model. Finally we will present considerations for …
Improved Preparations of Molybdenum Coordination Compounds from Tetrachlorobis(diethyl ether)molybdenum(IV)
2001
International audience; The reduction of MoCl5 with metallic tin in diethyl ether provides a rapid and convenient entry to [MoCl4(OEt2)2] This compound can be transformed easily and in high yields into a variety of other useful synthons. The loss of ether in the solid state affords a new and reactive form of MoCl4. Treatment with THF, PMe3 or LiOtBu affords [MoCl4(THF)2], [MoCl4(PMe3)3] or [Mo(OtBu)4] in high isolated yields. Treatment with metallic tin in THF affords [MoCl3(THF)3] All of these reactions can be carried out under simple experimental conditions and represent significant improvements relative to previously reported syntheses of the same compounds.
Phase transitions in polymeric systems: A challenge for Monte Carlo simulation
1995
Polymers are more difficult to simulate than small molecule systems, due to the large size of random polymer coils (and their slow relaxation, that is observed when dynamic simulation algorithms are used). However, variation of the chain length N of a flexible polymer chain provides a very useful additional control parameter, allowing stringent tests of theories, and new physical phenomena may emerge. As an example of these concepts, critical phenomena in polymer mixtures are described. It is shown that unmixing of symmetrical mixtures ( N A = N B = N ) is described by an equation for the critical temperature T c ( N ) = aN + b rather than T c ∝ N as claimed by some theories. While for fini…
Green extraction approach for the recovery of polyphenols from Croatian olive leaves (Olea europea)
2017
Abstract Pressurized liquid extraction (PLE) is shown as an innovative green technology for the effective extraction of the various phytochemicals from food by-products, therefore the aims of this study were to evaluate the application of PLE to engineer green extracts of Croatian olive leaves ( Olea europaea , cv. Oblica) for potential industrial production (functional foods/pharmaceuticals). PLE was conducted under various cycle numbers (1, 2), temperature (60, 80, 100 °C) and static times (5, 10, 15 min). Obtained extracts were characterized in terms of: (i) total polyphenols (TP); (ii) total flavonoids (TF); hydroxycinnamic acids (HCA); and (iv) flavonols (FLA). Response surface methodo…
Capillary electroendoosmotic chromatography of peptides
2000
This review focuses on the current state of peptide separation by capillary electroendoosmotic chromatography (CEC). When carried out under optimised conditions, peptide separation by CEC methods represents an orthogonal and complementary technique to micro-HPLC (micro-HPLC) and high-performance capillary zone electrophoresis (HPCZE). The origin of the selectivity differences that can be achieved with these three separation techniques (CEC, micro-HPLC and HPCZE), respectively are discussed, and the current limits of performance with CEC methods documented. Peptide separations by CEC methods with n-alkyl bonded silicas or mixed-mode phases are also illustrated. The development of different v…
Standard Definitions of Persistence Length Do Not Describe the Local “Intrinsic” Stiffness of Real Polymer Chains
2010
On the basis of extensive Monte Carlo simulations of lattice models for linear chains under good and Θ solvents conditions, and for bottle-brush polymers under good solvent conditions, different me...
Structure of bottle brush polymers on surfaces: weak versus strong adsorption.
2011
Large-scale Monte Carlo simulations are presented for a coarse-grained model of cylindrical molecular brushes adsorbed on a flat structureless substrate, varying both the chain length N of the side chains and the backbone chain length N(b). For the case of good solvent conditions, both the cases of weak adsorption (only 10 to 15% of the monomers being bound to the surface) and strong adsorption (~40% of the monomers being bound to the surface, forcing the bottle brush into an almost 2D conformation) are studied. We focus on the scaling of the total linear dimensions of the cylindrical brush with both chain lengths N and N(b), demonstrating a crossover from rod-like behavior (for not very la…
Phase Separation of Colloid Polymer Mixtures Under Confinement
2013
Colloid polymer mixtures exhibit vapor-liquid like and liquid-solid like phase transitions in bulk suspensions, and are well-suited model systems to explore confinement effects on these phase transitions. Static aspects of these phenomena are studied by large-scale Monte Carlo simulations, including novel “ensemble switch” methods to estimate excess free energies due to confining walls. The kinetics of phase separation is investigated by a Molecular Dynamics method, where hydrodynamic effects due to the solvent are included via the multiparticle collision dynamics method.
Coil-bridge transition in a single polymer chain as an unconventional phase transition: theory and simulation.
2014
The coil-bridge transition in a self-avoiding lattice chain with one end fixed at height H above the attractive planar surface is investigated by theory and Monte Carlo simulation. We focus on the details of the first-order phase transition between the coil state at large height H ⩾ Htr and a bridge state at H ⩽ Htr, where Htr corresponds to the coil-bridge transition point. The equilibrium properties of the chain were calculated using the Monte Carlo pruned-enriched Rosenbluth method in the moderate adsorption regime at (H/Na)tr ⩽ 0.27 where N is the number of monomer units of linear size a. An analytical theory of the coil-bridge transition for lattice chains with excluded volume interact…