4,806 research outputs found
Maximum entropy models for antibody diversity
Recognition of pathogens relies on families of proteins showing great
diversity. Here we construct maximum entropy models of the sequence repertoire,
building on recent experiments that provide a nearly exhaustive sampling of the
IgM sequences in zebrafish. These models are based solely on pairwise
correlations between residue positions, but correctly capture the higher order
statistical properties of the repertoire. Exploiting the interpretation of
these models as statistical physics problems, we make several predictions for
the collective properties of the sequence ensemble: the distribution of
sequences obeys Zipf's law, the repertoire decomposes into several clusters,
and there is a massive restriction of diversity due to the correlations. These
predictions are completely inconsistent with models in which amino acid
substitutions are made independently at each site, and are in good agreement
with the data. Our results suggest that antibody diversity is not limited by
the sequences encoded in the genome, and may reflect rapid adaptation to
antigenic challenges. This approach should be applicable to the study of the
global properties of other protein families
A mesoscopic ring as a XNOR gate: An exact result
We describe XNOR gate response in a mesoscopic ring threaded by a magnetic
flux . The ring is attached symmetrically to two semi-infinite
one-dimensional metallic electrodes and two gate voltages, viz, and
, are applied in one arm of the ring which are treated as the inputs of
the XNOR gate. The calculations are based on the tight-binding model and the
Green's function method, which numerically compute the conductance-energy and
current-voltage characteristics as functions of the ring-to-electrode coupling
strength, magnetic flux and gate voltages. Our theoretical study shows that,
for a particular value of () (, the elementary
flux-quantum), a high output current (1) (in the logical sense) appears if both
the two inputs to the gate are the same, while if one but not both inputs are
high (1), a low output current (0) results. It clearly exhibits the XNOR gate
behavior and this aspect may be utilized in designing an electronic logic gate.Comment: 8 pages, 5 figure
Constructing explicit magnetic analogies for the dynamics of glass forming liquids
By defining a spatially varying replica overlap parameter for a supercooled
liquid referenced to an ensemble of fiducial liquid state configurations we
explicitly construct a constrained replica free energy functional that maps
directly onto an Ising Hamiltonian with both random fields and random
interactions whose statistics depend on liquid structure. Renormalization group
results for random magnets when combined with these statistics for the
Lennard-Jones glass suggest that discontinuous replica symmetry breaking would
occur if a liquid with short range interactions could be equilibrated at a
sufficiently low temperature where its mean field configurational entropy would
vanish, even though the system strictly retains a finite configurational
entropy
Modeling transport through single-molecule junctions
Non-equilibrium Green's functions (NEGF) formalism combined with extended
Huckel (EHT) and charging model are used to study electrical conduction through
single-molecule junctions. Analyzed molecular complex is composed of asymmetric
1,4-Bis((2'-para-mercaptophenyl)-ethinyl)-2-acetyl-amino-5-nitro-benzene
molecule symmetrically coupled to two gold electrodes [Reichert et al., Phys.
Rev. Lett. Vol.88 (2002), pp. 176804]. Owing to this model, the accurate values
of the current flowing through such junction can be obtained by utilizing basic
fundamentals and coherently deriving model parameters. Furthermore, the
influence of the charging effect on the transport characteristics is
emphasized. In particular, charging-induced reduction of conductance gap,
charging-induced rectification effect and charging-generated negative value of
the second derivative of the current with respect to voltage are observed and
examined for molecular complex.Comment: 8 pages, 3 figure
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