10,093 research outputs found
A New Algorithm for Protein Design
We apply a new approach to the reverse protein folding problem. Our method
uses a minimization function in the design process which is different from the
energy function used for folding. For a lattice model, we show that this new
approach produces sequences that are likely to fold into desired structures.
Our method is a significant improvement over previous attempts which used the
energy function for designing sequences.Comment: 10 pages latex 2.09 no figures. Use uufiles to decod
Piezoelectric and optical setup to measure an electrical field: Application to the longitudinal near-field generated by a tapered coax
We propose a new setup to measure an electrical field in one direction. This
setup is made of a piezoelectric sintered lead zinconate titanate film and an
optical interferometric probe. We used this setup to investigate how the shape
of the extremity of a coaxial cable influences the longitudinal electrical
near-field generated by it. For this application, we designed our setup to have
a spatial resolution of 100 um in the direction of the electrical field.
Simulations and experiments are presented
Statistical Properties of Contact Maps
A contact map is a simple representation of the structure of proteins and
other chain-like macromolecules. This representation is quite amenable to
numerical studies of folding. We show that the number of contact maps
corresponding to the possible configurations of a polypeptide chain of N amino
acids, represented by (N-1)-step self avoiding walks on a lattice, grows
exponentially with N for all dimensions D>1. We carry out exact enumerations in
D=2 on the square and triangular lattices for walks of up to 20 steps and
investigate various statistical properties of contact maps corresponding to
such walks. We also study the exact statistics of contact maps generated by
walks on a ladder.Comment: Latex file, 15 pages, 12 eps figures. To appear on Phys. Rev.
Information Loss in Coarse Graining of Polymer Configurations via Contact Matrices
Contact matrices provide a coarse grained description of the configuration
omega of a linear chain (polymer or random walk) on Z^n: C_{ij}(omega)=1 when
the distance between the position of the i-th and j-th step are less than or
equal to some distance "a" and C_{ij}(omega)=0 otherwise. We consider models in
which polymers of length N have weights corresponding to simple and
self-avoiding random walks, SRW and SAW, with "a" the minimal permissible
distance. We prove that to leading order in N, the number of matrices equals
the number of walks for SRW, but not for SAW. The coarse grained Shannon
entropies for SRW agree with the fine grained ones for n <= 2, but differs for
n >= 3.Comment: 18 pages, 2 figures, latex2e Main change: the introduction is
rewritten in a less formal way with the main results explained in simple
term
Protein design in a lattice model of hydrophobic and polar amino acids
A general strategy is described for finding which amino acid sequences have
native states in a desired conformation (inverse design). The approach is used
to design sequences of 48 hydrophobic and polar aminoacids on three-dimensional
lattice structures. Previous studies employing a sequence-space Monte-Carlo
technique resulted in the successful design of one sequence in ten attempts.
The present work also entails the exploration of conformations that compete
significantly with the target structure for being its ground state. The design
procedure is successful in all the ten cases.Comment: RevTeX, 12 pages, 1 figur
Design of Force Fields from Data at Finite Temperature
We investigate the problem of how to obtain the force field between atoms of
an experimentally determined structure. We show how this problem can be
efficiently solved, even at finite temperature, where the position of the atoms
differs substantially from the ground state. We apply our method to systems
modeling proteins and demonstrate that the correct potentials can be recovered
even in the presence of thermal noise.Comment: 10 pages, 1 postcript figure, Late
A Solvable Model of Secondary Structure Formation in Random Hetero-Polymers
We propose and solve a simple model describing secondary structure formation
in random hetero-polymers. It describes monomers with a combination of
one-dimensional short-range interactions (representing steric forces and
hydrogen bonds) and infinite range interactions (representing polarity forces).
We solve our model using a combination of mean field and random field
techniques, leading to phase diagrams exhibiting second-order transitions
between folded, partially folded and unfolded states, including regions where
folding depends on initial conditions. Our theoretical results, which are in
excellent agreement with numerical simulations, lead to an appealing physical
picture of the folding process: the polarity forces drive the transition to a
collapsed state, the steric forces introduce monomer specificity, and the
hydrogen bonds stabilise the conformation by damping the frustration-induced
multiplicity of states.Comment: 24 pages, 14 figure
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