853,039 research outputs found
On how good DFT exchange-correlation functionals are for H bonds in small water clusters: Benchmarks approaching the complete basis set limit
The ability of several density-functional theory (DFT) exchange-correlation
functionals to describe hydrogen bonds in small water clusters (dimer to
pentamer) in their global minimum energy structures is evaluated with reference
to second order Moeller Plesset perturbation theory (MP2). Errors from basis
set incompleteness have been minimized in both the MP2 reference data and the
DFT calculations, thus enabling a consistent systematic evaluation of the true
performance of the tested functionals. Among all the functionals considered,
the hybrid X3LYP and PBE0 functionals offer the best performance and among the
non-hybrid GGA functionals mPWLYP and PBE1W perform the best. The popular BLYP
and B3LYP functionals consistently underbind and PBE and PW91 display rather
variable performance with cluster size.Comment: 9 pages including 4 figures; related publications can be found at
http://www.fhi-berlin.mpg.de/th/th.htm
Optimality of the genetic code with respect to protein stability and amino acid frequencies
How robust is the natural genetic code with respect to mistranslation errors?
It has long been known that the genetic code is very efficient in limiting the
effect of point mutation. A misread codon will commonly code either for the
same amino acid or for a similar one in terms of its biochemical properties, so
the structure and function of the coded protein remain relatively unaltered.
Previous studies have attempted to address this question more quantitatively,
namely by statistically estimating the fraction of randomly generated codes
that do better than the genetic code regarding its overall robustness. In this
paper, we extend these results by investigating the role of amino acid
frequencies in the optimality of the genetic code. When measuring the relative
fitness of the natural code with respect to a random code, it is indeed natural
to assume that a translation error affecting a frequent amino acid is less
favorable than that of a rare one, at equal mutation cost. We find that taking
the amino acid frequency into account accordingly decreases the fraction of
random codes that beat the natural code, making the latter comparatively even
more robust. This effect is particularly pronounced when more refined measures
of the amino acid substitution cost are used than hydrophobicity. To show this,
we devise a new cost function by evaluating with computer experiments the
change in folding free energy caused by all possible single-site mutations in a
set of known protein structures. With this cost function, we estimate that of
the order of one random code out of 100 millions is more fit than the natural
code when taking amino acid frequencies into account. The genetic code seems
therefore structured so as to minimize the consequences of translation errors
on the 3D structure and stability of proteins.Comment: 31 pages, 2 figures, postscript fil
Probing empirical contact networks by simulation of spreading dynamics
Disease, opinions, ideas, gossip, etc. all spread on social networks. How
these networks are connected (the network structure) influences the dynamics of
the spreading processes. By investigating these relationships one gains
understanding both of the spreading itself and the structure and function of
the contact network. In this chapter, we will summarize the recent literature
using simulation of spreading processes on top of empirical contact data. We
will mostly focus on disease simulations on temporal proximity networks --
networks recording who is close to whom, at what time -- but also cover other
types of networks and spreading processes. We analyze 29 empirical networks to
illustrate the methods
A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family.
Conformational ensembles are increasingly recognized as a useful representation to describe fundamental relationships between protein structure, dynamics and function. Here we present an ensemble of ubiquitin in solution that is created by sampling conformational space without experimental information using "Backrub" motions inspired by alternative conformations observed in sub-Angstrom resolution crystal structures. Backrub-generated structures are then selected to produce an ensemble that optimizes agreement with nuclear magnetic resonance (NMR) Residual Dipolar Couplings (RDCs). Using this ensemble, we probe two proposed relationships between properties of protein ensembles: (i) a link between native-state dynamics and the conformational heterogeneity observed in crystal structures, and (ii) a relation between dynamics of an individual protein and the conformational variability explored by its natural family. We show that the Backrub motional mechanism can simultaneously explore protein native-state dynamics measured by RDCs, encompass the conformational variability present in ubiquitin complex structures and facilitate sampling of conformational and sequence variability matching those occurring in the ubiquitin protein family. Our results thus support an overall relation between protein dynamics and conformational changes enabling sequence changes in evolution. More practically, the presented method can be applied to improve protein design predictions by accounting for intrinsic native-state dynamics
Fractal fractal dimensions of deterministic transport coefficients
If a point particle moves chaotically through a periodic array of scatterers
the associated transport coefficients are typically irregular functions under
variation of control parameters. For a piecewise linear two-parameter map we
analyze the structure of the associated irregular diffusion coefficient and
current by numerically computing dimensions from box-counting and from the
autocorrelation function of these graphs. We find that both dimensions are
fractal for large parameter intervals and that both quantities are themselves
fractal functions if computed locally on a uniform grid of small but finite
subintervals. We furthermore show that there is a simple functional
relationship between the structure of fractal fractal dimensions and the
difference quotient defined on these subintervals.Comment: 16 pages (revtex) with 6 figures (postscript
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