1,636 research outputs found
Replacement of PBNA in HB and HC polymers used in SRM propellant and liner
The antioxidant phenyl-beta-naphthylamine (PBNA) was used in both HB and HC polymers. The sole (domestic) supplier of PBNA has withdrawn this product from the market, primarily because of suspected health hazards. Commercially available substitute(s) were selected and qualified for use in the two polymers
Pathways to folding, nucleation events and native geometry
We perform extensive Monte Carlo simulations of a lattice model and the Go
potential to investigate the existence of folding pathways at the level of
contact cluster formation for two native structures with markedly different
geometries. Our analysis of folding pathways revealed a common underlying
folding mechanism, based on nucleation phenomena, for both protein models.
However, folding to the more complex geometry (i.e. that with more non-local
contacts) is driven by a folding nucleus whose geometric traits more closely
resemble those of the native fold. For this geometry folding is clearly a more
cooperative process.Comment: Accepted in J. Chem. Phy
A Multicanonical Molecular Dynamics Study on a Simple Bead-Spring Model for Protein Folding
We have performed a multicanonical molecular dynamics simulation on a simple
model protein.We have studied a model protein composed of charged, hydrophobic,
and neutral spherical bead monomers.Since the hydrophobic interaction is
considered to significantly affect protein folding, we particularly focus on
the competition between effects of the Coulomb interaction and the hydrophobic
interaction. We found that the transition which occurs upon decreasing the
temperature is markedly affected by the change in both parameters and forms of
the hydrophobic potential function, and the transition changes from first order
to second order, when the Coulomb interaction becomes weaker.Comment: 7 pages, 6 postscript figures, To appear in J.Phys.Soc.Jpn. Vol.70
No.
Protein Folding and Spin Glass
We explicitly show the connection between the protein folding problem and
spin glass transition. This is then used to identify appropriate quantities
that are required to describe the transition. A possible way of observing the
spin glass transition is proposed.Comment: Revtex3+epsf, 8 pages and one postscript figure tarred, compressed
and uuencoded--appended at the end of the file. Minor TeX change
The effect of local thermal fluctuations on the folding kinetics: a study from the perspective of the nonextensive statistical mechanics
Protein folding is a universal process, very fast and accurate, which works
consistently (as it should be) in a wide range of physiological conditions. The
present work is based on three premises, namely: () folding reaction is a
process with two consecutive and independent stages, namely the search
mechanism and the overall productive stabilization; () the folding kinetics
results from a mechanism as fast as can be; and () at nanoscale
dimensions, local thermal fluctuations may have important role on the folding
kinetics. Here the first stage of folding process (search mechanism) is focused
exclusively. The effects and consequences of local thermal fluctuations on the
configurational kinetics, treated here in the context of non extensive
statistical mechanics, is analyzed in detail through the dependence of the
characteristic time of folding () on the temperature and on the
nonextensive parameter .The model used consists of effective residues
forming a chain of 27 beads, which occupy different sites of a D infinite
lattice, representing a single protein chain in solution. The configurational
evolution, treated by Monte Carlo simulation, is driven mainly by the change in
free energy of transfer between consecutive configurations. ...Comment: 19 pages, 3 figures, 1 tabl
TRANSFORMATION INDUCED BY SIMIAN VIRUS 40 IN NEWBORN SYRIAN HAMSTER RENAL CELL CULTURES
Sequence Dependence of Self-Interacting Random Chains
We study the thermodynamic behavior of the random chain model proposed by
Iori, Marinari and Parisi, and how this depends on the actual sequence of
interactions along the chain. The properties of randomly chosen sequences are
compared to those of designed ones, obtained through a simulated annealing
procedure in sequence space. We show that the transition to the folded phase
takes place at a smaller strength of the quenched disorder for designed
sequences. As a result, folding can be relatively fast for these sequences.Comment: 14 pages, uuencoded compressed postscript fil
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
Twist and writhe dynamics of stiff filaments
This letter considers the dynamics of a stiff filament, in particular the
coupling of twist and bend via writhe. The time dependence of the writhe of a
filament is for a linear filament and for a curved filament. Simulations are used to study the relative
importance of crankshaft motion and tube like motion in twist dynamics.
Fuller's theorem, and its relation with the Berry phase, is reconsidered for
open filamentsComment: 7 Pages with 2 figure
Highly Designable Protein Structures and Inter Monomer Interactions
By exact computer enumeration and combinatorial methods, we have calculated
the designability of proteins in a simple lattice H-P model for the protein
folding problem.
We show that if the strength of the non-additive part of the interaction
potential becomes larger than a critical value, the degree of designability of
structures will depend on the parameters of potential. We also show that the
existence of a unique ground state is highly sensitive to mutation in certain
sites.Comment: 14 pages, Latex file, 3 latex and 6 eps figures are include
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