4,242 research outputs found
Statistical properties of contact vectors
We study the statistical properties of contact vectors, a construct to
characterize a protein's structure. The contact vector of an N-residue protein
is a list of N integers n_i, representing the number of residues in contact
with residue i. We study analytically (at mean-field level) and numerically the
amount of structural information contained in a contact vector. Analytical
calculations reveal that a large variance in the contact numbers reduces the
degeneracy of the mapping between contact vectors and structures. Exact
enumeration for lengths up to N=16 on the three dimensional cubic lattice
indicates that the growth rate of number of contact vectors as a function of N
is only 3% less than that for contact maps. In particular, for compact
structures we present numerical evidence that, practically, each contact vector
corresponds to only a handful of structures. We discuss how this information
can be used for better structure prediction.Comment: 20 pages, 6 figure
DNA Computing by Self-Assembly
Information and algorithms appear to be central to biological organization
and processes, from the storage and reproduction of genetic information to
the control of developmental processes to the sophisticated computations
performed by the nervous system. Much as human technology uses electronic
microprocessors to control electromechanical devices, biological
organisms use biochemical circuits to control molecular and chemical events.
The engineering and programming of biochemical circuits, in vivo and in
vitro, would transform industries that use chemical and nanostructured
materials. Although the construction of biochemical circuits has been
explored theoretically since the birth of molecular biology, our practical
experience with the capabilities and possible programming of biochemical
algorithms is still very young
Simulating chemistry using quantum computers
The difficulty of simulating quantum systems, well-known to quantum chemists,
prompted the idea of quantum computation. One can avoid the steep scaling
associated with the exact simulation of increasingly large quantum systems on
conventional computers, by mapping the quantum system to another, more
controllable one. In this review, we discuss to what extent the ideas in
quantum computation, now a well-established field, have been applied to
chemical problems. We describe algorithms that achieve significant advantages
for the electronic-structure problem, the simulation of chemical dynamics,
protein folding, and other tasks. Although theory is still ahead of experiment,
we outline recent advances that have led to the first chemical calculations on
small quantum information processors.Comment: 27 pages. Submitted to Ann. Rev. Phys. Che
Critical phenomena in complex networks
The combination of the compactness of networks, featuring small diameters,
and their complex architectures results in a variety of critical effects
dramatically different from those in cooperative systems on lattices. In the
last few years, researchers have made important steps toward understanding the
qualitatively new critical phenomena in complex networks. We review the
results, concepts, and methods of this rapidly developing field. Here we mostly
consider two closely related classes of these critical phenomena, namely
structural phase transitions in the network architectures and transitions in
cooperative models on networks as substrates. We also discuss systems where a
network and interacting agents on it influence each other. We overview a wide
range of critical phenomena in equilibrium and growing networks including the
birth of the giant connected component, percolation, k-core percolation,
phenomena near epidemic thresholds, condensation transitions, critical
phenomena in spin models placed on networks, synchronization, and
self-organized criticality effects in interacting systems on networks. We also
discuss strong finite size effects in these systems and highlight open problems
and perspectives.Comment: Review article, 79 pages, 43 figures, 1 table, 508 references,
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