Dynamics of polymer chain collapse into compact states

Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional interactions. Different native-state packing arrangements and chain lengths are explored; the organization of the native state is found to affect both the ability of the chain to fold successfully and the nature of the folding pathway as the system is gradually cooled. An order parameter based on contact counts is used to provide information about the folding process, with contacts additionally classified according to criteria such as core and surface sites or local and distant site pairs. Fully detailed contact maps and their evolution are also examined.Comment: 11 pages, 11 figures (some low resolution

Proteinlike behavior of a spin system near the transition between ferromagnet and spin glass

A simple spin system is studied as an analog for proteins. We investigate how the introduction of randomness and frustration into the system effects the designability and stability of ground state configurations. We observe that the spin system exhibits protein-like behavior in the vicinity of the transition between ferromagnet and spin glass. Our results illuminate some guiding principles in protein evolution.Comment: 12 pages, 4 figure

Compact phases of polymers with hydrogen bonding

We propose an off-lattice model for a self-avoiding homopolymer chain with two different competing attractive interactions, mimicking the hydrophobic effect and the hydrogen bond formation respectively. By means of Monte Carlo simulations, we are able to trace out the complete phase diagram for different values of the relative strength of the two competing interactions. For strong enough hydrogen bonding, the ground state is a helical conformation, whereas with decreasing hydrogen bonding strength, helices get eventually destabilized at low temperature in favor of more compact conformations resembling $\beta$-sheets appearing in native structures of proteins. For weaker hydrogen bonding helices are not thermodynamically relevant anymore.Comment: 5 pages, 3 figures; revised version published in PR

Protein sequence and structure: Is one more fundamental than the other?

We argue that protein native state structures reside in a novel "phase" of matter which confers on proteins their many amazing characteristics. This phase arises from the common features of all globular proteins and is characterized by a sequence-independent free energy landscape with relatively few low energy minima with funnel-like character. The choice of a sequence that fits well into one of these predetermined structures facilitates rapid and cooperative folding. Our model calculations show that this novel phase facilitates the formation of an efficient route for sequence design starting from random peptides.Comment: 7 pages, 4 figures, to appear in J. Stat. Phy

What is "system": the information-theoretic arguments

The problem of "what is 'system'?" is in the very foundations of modern quantum mechanics. Here, we point out the interest in this topic in the information-theoretic context. E.g., we point out the possibility to manipulate a pair of mutually non-interacting, non-entangled systems to employ entanglement of the newly defined '(sub)systems' consisting the one and the same composite system. Given the different divisions of a composite system into "subsystems", the Hamiltonian of the system may perform in general non-equivalent quantum computations. Redefinition of "subsystems" of a composite system may be regarded as a method for avoiding decoherence in the quantum hardware. In principle, all the notions refer to a composite system as simple as the hydrogen atom.Comment: 13 pages, no figure

Reversible stretching of homopolymers and random heteropolymers

We have analyzed the equilibrium response of chain molecules to stretching. For a homogeneous sequence of monomers, the induced transition from compact globule to extended coil below the $\theta$-temperature is predicted to be sharp. For random sequences, however, the transition may be smoothed by a prevalence of necklace-like structures, in which globular regions and coil regions coexist in a single chain. As we show in the context of a random copolymer, preferential solvation of one monomer type lends stability to such structures. The range of stretching forces over which necklaces are stable is sensitive to chain length as well as sequence statistics.Comment: 14 pages, 4 figure

Model for the hydration of non-polar compounds and polymers

We introduce an exactly solvable statistical-mechanical model of the hydration of non-polar compounds, based on grouping water molecules in clusters where hydrogen bonds and isotropic interactions occur; interactions between clusters are neglected. Analytical results show that an effective strengthening of hydrogen bonds in the presence of the solute, together with a geometric reorganization of water molecules, are enough to yield hydrophobic behavior. We extend our model to describe a non-polar homopolymer in aqueous solution, obtaining a clear evidence of both ``cold'' and ``warm'' swelling transitions. This suggests that our model could be relevant to describe some features of protein folding.Comment: REVTeX, 6 pages, 3 figure

Synthesis, characterization and thermochemistry of synthetic Pb–As, Pb–Cu and Pb–Zn jarosites

The enthalpy of formation from the elements of well characterized Pb-As, Pb-Cu, and Pb-Zn synthetic jarosites, corresponding to chemical formulas (H3O)0.68±0.03Pb0.32±0.002Fe2.86±0.14(SO4)1.69±0.08(AsO4)0.31±0.02(OH)5.59±0.28(H2O)0.41±0.02, (H3O)0.67±0.03Pb0.33±0.02Fe2.71±0.14Cu0.25±0.01(SO4)2±0.00(OH)5.96±0.30(H2O)0.04±0.002 and (H3O)0.57±0.03Pb0.43±0.02Fe2.70±0.14Zn0.21±0.01(SO4)2±0.00(OH)5.95±0.30(H2O)0.05±0.002, was measured by high temperature oxide melt solution calorimetry and gave ΔH°f = -3691.2 ± 8.6 kJ/mol, ΔH°f = -3653.6 ± 8.2 kJ/mol, and ΔH°f = -3669.4 ± 8.4 kJ/mol, respectively. Using estimated entropies, the standard Gibbs free energy of formation from elements at 298 K ΔG°f of the three compounds were calculated to be -3164.8 ± 9.1 kJ/mol, -3131.4 ± 8.7 kJ/mol, and -3153.6 ± 8.9 kJ/mol, respectively. Based on these free energies, their logKsp values are -13.94 ± 1.89, -4.38 ± 1.81 and -3.75 ± 1.80, respectively. For this compounds, a log10{Pb2+} - pH diagram is presented. The diagram shows that the formation of Pb-As jarosite may decrease aqueous arsenic and lead concentrations to meet drinking water standards. The new thermodynamic data confirm that transformation of Pb-As jarosite to plumbojarosite is thermodynamically possible

Universal behavior of localization of residue fluctuations in globular proteins

Localization properties of residue fluctuations in globular proteins are studied theoretically by using the Gaussian network model. Participation ratio for each residue fluctuation mode is calculated. It is found that the relationship between participation ratio and frequency is similar for all globular proteins, indicating a universal behavior in spite of their different size, shape, and architecture.Comment: 4 pages, 3 figures. To appear in Phys. Rev.

Flat histogram simulation of lattice polymer systems

We demonstrate the use of a new algorithm called the Flat Histogram sampling algorithm for the simulation of lattice polymer systems. Thermodynamics properties, such as average energy or entropy and other physical quantities such as end-to-end distance or radius of gyration can be easily calculated using this method. Ground-state energy can also be determined. We also explore the accuracy and limitations of this method. Key words: Monte Carlo algorithms, flat histogram sampling, HP model, lattice polymer systemsComment: 7 RevTeX two-column page