145 research outputs found
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
-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 -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 PbâAs, PbâCu and PbâZn 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 ÎH°f = -3691.2 ± 8.6 kJ/mol, ÎH°f = -3653.6 ± 8.2 kJ/mol, and ÎH°f = -3669.4 ± 8.4 kJ/mol, respectively. Using estimated entropies, the standard Gibbs free energy of formation from elements at 298 K ÎG°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.
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