HP models

A related study was the exhaustive enumeration of the global minimum energy structure for all iP possible sequences of the HP model described in Section 10.3.1 [Li et al. 1996 Ihis showed that 4 75% of these sequences have a unique ground state (i.e. just on... 

For the purpose of comparison all spectra taken from the literature were digitized by means of a Hewlett-Packard Digitizer (model 9864 A) on-line with a small computer (HP, model 9820) and replotted on a common scale (HP, model 9862 A). 

Pyrolysis-Gas Chromatography-Mass Spectrometry. In the experiments, about 2 mg of sample was pyrolyzed at 900°C in flowing helium using a Chemical Data System (CDS) Platinum Coil Pyrolysis Probe controlled by a CDS Model 122 Pyroprobe in normal mode. Products were separated on a 12 meter fused capillary column with a cross-linked poly (dimethylsilicone) stationary phase. The GC column was temperature programmed from -50 to 300°C. Individual compounds were identified with a Hewlett Packard (HP) Model 5995C low resolution quadruple GC/MS System. Data acquisition and reduction were performed on the HP 100 E-series computer running revision E RTE-6/VM software. 

Wiist, T., Landau, D.P. The HP model of protein folding a challenging testing ground for Wang-Landau sampling. Comput. Phys. Commun. 2008, 179, 124-7. 

Aqueous-phase concentrations of PCE were determined by GC using a Hewlett-Packard (HP) Model 6890 gas chromatograph equipped with an autosampler, a precolumn surfactant trap, an HP-5 crosslinked 5% PH Siloxane column, and a flame ionization detector (FID). The precolumn trap was installed to prevent surfactant fouling of GC inlets, column and detector. Samples were prepared by adding approximately 0.4 mL of aqueous sample to 1.2 mL of isopropanol in glass autosampler vials. The GC vials were sealed with Teflon backed aluminum caps to minimize volatilization. Triplicate injections of each sample were performed. 

There are many kinds of polymerizing monomers used to make up copolymers. These differ in physical and chemical properties. One of the most important differences (essential features) is their solubility, that is, how much they like or dislike a solvent, e.g., water. Hence the chemical and atomistic details of different monomeric units may not be necessary to understand the properties of many two-letter copolymers. In what follows, we will mainly use the so-called HP model [31]. This two-letter model of a linear hydrophobic/hydrophilic macromolecule reflects the spirit of minimalist models, in that it is simple yet based on a physical principle. 

The HP model is a coarse-grained (lattice or off-lattice) polymer model that abstracts from real polymers in two important ways (i) Instead of modeling the positions of all atoms of the polymer, it models only the backbone structure of the polymer, i.e., one position for each monomeric unit, (ii) Usually, only the hydrophobic interaction between the monomeric units is modeled, therefore the model distinguishes only two kinds of monomeric units, namely hydrophobic (H) and hydrophilic (or polar, P). 

One of the possible extensions of the HP model is the HA side chain model introduced in [212]. This is a more realistic coarse-grained model of amphiphilic polymers where the dualistic character of each monomeric unit is explicitly represented. 

As we will see in Sect. 3.4, such a relatively trivial modification of the standard HP model can lead to some nontrivial consequences when studying the collapse for the single-chain amphiphilic polymers and their aggregation in solution. 

Another method leading to nonaggregating copolymers may be connected with the molecular design of their monomeric units. We have discussed an extended variant of the HP model, the HA side-chain model [97], that explicitly takes into account the amphiphilic nature of hydrophilic segments. 

Fig. 2 Schematic representation of a the HP model and b the dumbbell HA model of an amphiphilic copolymer. P-units are hydrophilic (polar), H-units are hydrophobic, and A-units are amphiphilic. (Adapted from Ref. [25])...

Some attention should be also paid to the fact that some copolymers with special sequence distribution do not assume cylindrical shape within the HA model. For example, this is the case for protein-like sequences. Protein-like sequences correspond to a copolymer which forms globules with a hydrophobic core and a hydrophilic shell showing no tendency to aggregation. Proteinlike copolymers have been previously studied within the HP model [32-34], Application of the more realistic HA model showed that the globules formed by protein-like copolymers under worsening solvent quality assume conventional spherical shape and show no tendency to aggregate [23]. The stability for HA model protein-like copolymers is much higher than for those within the HP model. 

The forward and reflected electric power is measured in continuous wave (CW) mode before the exposures using a digital power meter (HP Model) and a dual directional coupler (Werlatone Model C1373). 

We have studied [38] the use of GAs to fold proteins on a two-dimensional square lattice in the HP model [19] where proteins consist of only two types of... 

Chemical Analysis. Gas chromatography-mass spectrometry (GC-MS) and high-performance liquid chromatography (HPLC) techniques were used to analyze 4-chlorophenol and its oxidation intermediates. For GC-MS analysis, the samples were acetylated in pyridine. The samples were first evaporated to dryness. Then 200 xL of pyridine and 200 (xL of acetic anhydride were added to the dry residue. The samples were heated at 65 °C for 2-3 h to ensure the complete acetylation reaction, and then gently evaporated to dryness in a nitrogen stream. Finally, the residue was redissolved in 0.1 mL of hexane for GC analysis. A GC (HP model 5890) equipped with mass selective detector (HP model 5971) and SPB-5 capillary column (Supelco Co., PA., 25- X 0.2-mm i.d. X 0.33-p.m film thickness) was used. To separate different intermediate products, various oven-temperature programs were performed. The GC-MS interface line was maintained at 300 °C. The mass-... 

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