6,211 research outputs found
Theories, models, simulations: a computational challenge
In this talk I would like to illustrate with examples taken from Quantum
Field Theory and Biophysics how an intelligent exploitation of the
unprecedented power of today's computers could led not only to the solution of
pivotal problems in the theory of Strong Interactions, but also to the
emergence of new lines of interdisciplinary research, while at the same time
pushing the limits of modeling to the realm of living systems.Comment: 19 pages, 1 figure, conference pape
Frustration in Biomolecules
Biomolecules are the prime information processing elements of living matter.
Most of these inanimate systems are polymers that compute their structures and
dynamics using as input seemingly random character strings of their sequence,
following which they coalesce and perform integrated cellular functions. In
large computational systems with a finite interaction-codes, the appearance of
conflicting goals is inevitable. Simple conflicting forces can lead to quite
complex structures and behaviors, leading to the concept of "frustration" in
condensed matter. We present here some basic ideas about frustration in
biomolecules and how the frustration concept leads to a better appreciation of
many aspects of the architecture of biomolecules, and how structure connects to
function. These ideas are simultaneously both seductively simple and perilously
subtle to grasp completely. The energy landscape theory of protein folding
provides a framework for quantifying frustration in large systems and has been
implemented at many levels of description. We first review the notion of
frustration from the areas of abstract logic and its uses in simple condensed
matter systems. We discuss then how the frustration concept applies
specifically to heteropolymers, testing folding landscape theory in computer
simulations of protein models and in experimentally accessible systems.
Studying the aspects of frustration averaged over many proteins provides ways
to infer energy functions useful for reliable structure prediction. We discuss
how frustration affects folding, how a large part of the biological functions
of proteins are related to subtle local frustration effects and how frustration
influences the appearance of metastable states, the nature of binding
processes, catalysis and allosteric transitions. We hope to illustrate how
Frustration is a fundamental concept in relating function to structural
biology.Comment: 97 pages, 30 figure
Two-State Folding, Folding through Intermediates, and Metastability in a Minimalistic Hydrophobic-Polar Model for Proteins
Within the frame of an effective, coarse-grained hydrophobic-polar protein
model, we employ multicanonical Monte Carlo simulations to investigate
free-energy landscapes and folding channels of exemplified heteropolymer
sequences, which are permutations of each other. Despite the simplicity of the
model, the knowledge of the free-energy landscape in dependence of a suitable
system order parameter enables us to reveal complex folding characteristics
known from real bioproteins and synthetic peptides, such as two-state folding,
folding through weakly stable intermediates, and glassy metastability.Comment: 10 pages, 1 figur
Computational complexity of the landscape I
We study the computational complexity of the physical problem of finding
vacua of string theory which agree with data, such as the cosmological
constant, and show that such problems are typically NP hard. In particular, we
prove that in the Bousso-Polchinski model, the problem is NP complete. We
discuss the issues this raises and the possibility that, even if we were to
find compelling evidence that some vacuum of string theory describes our
universe, we might never be able to find that vacuum explicitly.
In a companion paper, we apply this point of view to the question of how
early cosmology might select a vacuum.Comment: JHEP3 Latex, 53 pp, 2 .eps figure
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