2,912 research outputs found
Dynamical fluctuations in biochemical reactions and cycles
We develop theory for the dynamics and fluctuations in some cyclic and linear biochemical reactions. We use the approach of maximum caliber, which computes the ensemble of paths taken by the system, given a few experimental observables. This approach may be useful for interpreting single-molecule or few-particle experiments on molecular motors, enzyme reactions, ion-channels, and phosphorylation-driven biological clocks. We consider cycles where all biochemical states are observable. Our method shows how: (1) the noise in cycles increases with cycle size and decreases with the driving force that spins the cycle and (2) provides a recipe for estimating small-number features, such as probability of backward spin in small cycles, from experimental data. The back-spin probability diminishes exponentially with the deviation from equilibrium. We believe this method may also be useful for other few-particle nonequilibrium biochemical reaction systems
Geometrically Reduced Number of Protein Ground State Candidates
Geometrical properties of protein ground states are studied using an
algebraic approach. It is shown that independent from inter-monomer
interactions, the collection of ground state candidates for any folded protein
is unexpectedly small: For the case of a two-parameter Hydrophobic-Polar
lattice model for -mers, the number of these candidates grows only as .
Moreover, the space of the interaction parameters of the model breaks up into
well-defined domains, each corresponding to one ground state candidate, which
are separated by sharp boundaries. In addition, by exact enumeration, we show
there are some sequences which have one absolute unique native state. These
absolute ground states have perfect stability against change of inter-monomer
interaction potential.Comment: 9 page, 4 ps figures are include
Human dynamics revealed through Web analytics
When the World Wide Web was first conceived as a way to facilitate the
sharing of scientific information at the CERN (European Center for Nuclear
Research) few could have imagined the role it would come to play in the
following decades. Since then, the increasing ubiquity of Internet access and
the frequency with which people interact with it raise the possibility of using
the Web to better observe, understand, and monitor several aspects of human
social behavior. Web sites with large numbers of frequently returning users are
ideal for this task. If these sites belong to companies or universities, their
usage patterns can furnish information about the working habits of entire
populations. In this work, we analyze the properly anonymized logs detailing
the access history to Emory University's Web site. Emory is a medium size
university located in Atlanta, Georgia. We find interesting structure in the
activity patterns of the domain and study in a systematic way the main forces
behind the dynamics of the traffic. In particular, we show that both linear
preferential linking and priority based queuing are essential ingredients to
understand the way users navigate the Web.Comment: 7 pages, 8 figure
Three-body Interactions Improve the Prediction of Rate and Mechanism in Protein Folding Models
Here we study the effects of many-body interactions on rate and mechanism in
protein folding, using the results of molecular dynamics simulations on
numerous coarse-grained C-alpha-model single-domain proteins. After adding
three-body interactions explicitly as a perturbation to a Go-like Hamiltonian
with native pair-wise interactions only, we have found 1) a significantly
increased correlation with experimental phi-values and folding rates, 2) a
stronger correlation of folding rate with contact order, matching the
experimental range in rates when the fraction of three-body energy in the
native state is ~ 20%, and 3) a considerably larger amount of 3-body energy
present in Chymotripsin inhibitor than other proteins studied.Comment: 9 pages, 2 tables and 5 figure
A possible mechanism for cold denaturation of proteins at high pressure
We study cold denaturation of proteins at high pressures. Using
multicanonical Monte Carlo simulations of a model protein in a water bath, we
investigate the effect of water density fluctuations on protein stability. We
find that above the pressure where water freezes to the dense ice phase
( kbar), the mechanism for cold denaturation with decreasing
temperature is the loss of local low-density water structure. We find our
results in agreement with data of bovine pancreatic ribonuclease A.Comment: 4 pages for double column and single space. 3 figures Added
references Changed conten
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
Renovation of Seeded Warm-season Pastures with Atrazine
Numerous warm-season pastures have been established in the last 30 years in the central Great Plains. Some of these pastures are old enough to verify that they can be abused by overgrazing as easily as native tallgrass prairies. Overgrazed warm-season pastures are invaded and dominated by cool-season grasses such as smooth brome (Bromus inermis Leyss.) and Kentucky bluegrass (Poa pratensis L.), which diminishes the pasture productivity during the hot summer months. Since established warm-season grasses have greater tolerance to the herbicide atrazine than cool-season grasses, the effectiveness of atrazine applications in renovating invaded warm-season pastures was evaluated. A single, early spring application of atrazine (3.3 kg/ha) killed or sufficiently suppressed the cool-season grasses so that surviving warm-season remnants were able to effectively re-establish the warm-season pasture in a single growing season without any loss in total pasture forage production. Lower rates of atrazine were not as effective, particularly if smooth brome was the primary cool-season grass. The single atrazine application cost was approximately 25% of the seed cost associated with more conventional renovation. Pastures should not be grazed the treatment year but can be hayed rt the end of the growing season. The success of the practice is dependent on the presence of warm-season grass remnants. Spraying test strips in small fenced areas would be advisable before treating entire pastures
Comparative Cytogenetics Of Tree Frogs Of The Dendropsophus Marmoratus (laurenti, 1768) Group: Conserved Karyotypes And Interstitial Telomeric Sequences
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)The diploid number 2n = 30 is a presumed synapomorphy of Dendropsophus Fitzinger, 1843, although a noticeable variation in the number of biarmed/telocentric chromosomes is observed in this genus. Such a variation suggests that several chromosomal rearrangements took place after the evolutionary origin of the hypothetical ancestral 30-chromosome karyotype; however, the inferred rearrangements remain unknown. Distinct numbers of telocentric chromosomes are found in the two most cytogenetically studied species groups of Dendropsophus. In contrast, all three species of the Dendropsophus marmoratus (Laurenti, 1768) group that are already karyotyped presented five pairs of telocentric chromosomes. In this study, we analyzed cytogenetically three additional species of this group to investigate if the number of telocentric chromosomes in this group is not as variable as in other Dendropsophus groups. We described the karyotypes of Dendropsophus seniculus (Cope, 1868), D. soaresi (Caramaschi & Jim, 1983) and D. novaisi (Bokermann, 1968) based on Giemsa staining, C-banding, silver impregnation and in situ hybridization with telomeric probes. Dendropsophus seniculus, D. soaresi and D. novaisi presented five pairs of telocentric chromosomes, as did the remaining species of the group previously karyotyped. Though the species of this group show a high degree of karyotypic similarity, D. soaresi was unique in presenting large blocks of het-ITSs (heterochromatic internal telomeric sequences) in the majority of the centromeres. Although the ITSs have been interpreted as evidence of ancestral chromosomal fusions and inversions, the het- ITSs detected in the karyotype of D. soaresi could not be explained as direct remnants of ancestral chromosomal rearrangements because no evidence of chromosomal changes emerged from the comparison of the karyotypes of all of the species of the D. marmoratus group.104753767Brazilian agency Sao Paulo Research Foundation (FAPESP)Brazilian agency Fundo de Apoio ao Ensino, a Pesquisa e Extensao (FAEPEX) da Universidade Estadual de CampinasFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP
Two State Behavior in a Solvable Model of -hairpin folding
Understanding the mechanism of protein secondary structure formation is an
essential part of protein-folding puzzle. Here we describe a simple model for
the formation of the -hairpin, motivated by the fact that folding of a
-hairpin captures much of the basic physics of protein folding. We argue
that the coupling of ``primary'' backbone stiffness and ``secondary'' contact
formation (similar to the coupling between the ``secondary'' and ``tertiary''
structure in globular proteins), caused for example by side-chain packing
regularities, is responsible for producing an all-or-none 2-state
-hairpin formation. We also develop a recursive relation to compute the
phase diagram and single exponential folding/unfolding rate arising via a
dominant transition state.Comment: Revised versio
The Origin of the Designability of Protein Structures
We examined what determines the designability of 2-letter codes (H and P)
lattice proteins from three points of view. First, whether the native structure
is searched within all possible structures or within maximally compact
structures. Second, whether the structure of the used lattice is bipartite or
not. Third, the effect of the length of the chain, namely, the number of
monomers on the chain. We found that the bipartiteness of the lattice structure
is not a main factor which determines the designability. Our results suggest
that highly designable structures will be found when the length of the chain is
sufficiently long to make the hydrophobic core consisting of enough number of
monomers.Comment: 17 pages, 2 figure
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