1,516 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 The sole (domestic) supplier of PBNA has withdrawn this product from the market, primarily because of suspected health hazards.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
A Criterion That Determines Fast Folding of Proteins: A Model Study
We consider the statistical mechanics of a full set of two-dimensional
protein-like heteropolymers, whose thermodynamics is characterized by the
coil-to-globular () and the folding () transition temperatures.
For our model, the typical time scale for reaching the unique native
conformation is shown to scale as , where
, is the number of residues, and scales
algebraically with . We argue that scales linearly with the inverse of
entropy of low energy non-native states, whereas is almost
independent of it. As , non-productive intermediates
decrease, and the initial rapid collapse of the protein leads to structures
resembling the native state. Based solely on {\it accessible} information,
can be used to predict sequences that fold rapidly.Comment: 10 pages, latex, figures upon reques
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
Reply to Comment on "Criterion that Determines the Foldability of Proteins"
We point out that the correlation between folding times and in protein-like heteropolymer models where
and are the collapse and folding transition temperatures
was already established in 1993 before the other presumed equivalent criterion
(folding times correlating with alone) was suggested. We argue that the
folding times for these models show no useful correlation with the energy gap
even if restricted to the ensemble of compact structures as suggested by
Karplus and Shakhnovich (cond-mat/9606037).Comment: 6 pages, Latex, 2 Postscript figures. Plots explicitly showing the
lack of correlation between folding time and energy gap are adde
Experimental variables in the effects of postsession injections of strychnine sulphate on a classically conditioned response
Postsession strychnine injections have been shown to retard acquisition rates of the classically conditioned nictitating membrane response (CCNMR) of rabbits trained at a CS-US interval of 1000 msec. The particular interval value employed in CCNMR acquisition was found to be important in the magnitude of the postsession strychnine effect. Strychnine Ss trained at a CS-US interval=1250 msec (nonoptimal) were significantly depressed in acquisition rates relative to saline controls, while strychnine Ss trained at a CS-US interval=250 msec (optimal) were not. Interpretations are based upon the presumed effects of CNS excitants on memory consolidation and possible neurological correlates of the CS-US interval parameter.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46356/1/213_2004_Article_BF00402096.pd
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
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
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
Exploring the Levinthal limit in protein folding
According to the thermodynamic hypothesis, the native state of proteins is uniquely defined by their amino acid sequence. On the other hand, according to Levinthal, the native state is just a local minimum of the free energy and a given amino acid sequence, in the same thermodynamic conditions, can assume many, very different structures that are as thermodynamically stable as the native state. This is the Levinthal limit explored in this work. Using computer simulations, we compare the interactions that stabilize the native state of four different proteins with those that stabilize three non-native states of each protein and find that the nature of the interactions is very similar for all such 16 conformers. Furthermore, an enhancement of the degree of fluctuation of the non-native conformers can be explained by an insufficient relaxation to their local free energy minimum. These results favor Levinthal's hypothesis that protein folding is a kinetic non-equilibrium process.FCT - Foundation for Science and Technology, Portugal [UID/Multi/04326/2013]; Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP); Conselho Nacional de Desenvolvimento Cientia co e Tecnologico (CNPq
- …