577 research outputs found
Chirality and Protein Folding
There are several simple criteria of folding to a native state in model
proteins. One of them involves crossing of a threshold value of the RMSD
distance away from the native state. Another checks whether all native contacts
are established, i.e. whether the interacting amino acids come closer than some
characteristic distance. We use Go-like models of proteins and show that such
simple criteria may prompt one to declare folding even though fragments of the
resulting conformations have a wrong sense of chirality. We propose that a
better condition of folding should augment the simple criteria with the
requirement that most of the local values of the chirality should be nearly
native. The kinetic discrepancy between the simple and compound criteria can be
substantially reduced in the Go-like models by providing the Hamiltonian with a
term which favors native values of the local chirality. We study the effects of
this term as a function of its amplitude and compare it to other models such as
with the side groups and with the angle-dependent potentials.Comment: To be published in a special issue of J. Phys.: Cond. Mat. (Bedlewo
Workshop
Delineation of the Native Basin in Continuum Models of Proteins
We propose two approaches for determining the native basins in off-lattice
models of proteins. The first of them is based on exploring the saddle points
on selected trajectories emerging from the native state. In the second
approach, the basin size can be determined by monitoring random distortions in
the shape of the protein around the native state. Both techniques yield the
similar results. As a byproduct, a simple method to determine the folding
temperature is obtained.Comment: REVTeX, 6 pages, 5 EPS figure
Scaling of folding properties in simple models of proteins
Scaling of folding properties of proteins is studied in a toy system -- the
lattice Go model with various two- and three- dimensional geometries of the
maximally compact native states. Characteristic folding times grow as power
laws with the system size. The corresponding exponents are not universal.
Scaling of the thermodynamic stability also indicates size-related
deterioration of the folding properties.Comment: REVTeX, 4 pages, 4 EPS figures, PRL (in press
Folding in two-dimenensional off-lattice models of proteins
Model off-lattice sequences in two dimensions are constructed so that their
native states are close to an on-lattice target. The Hamiltonian involves the
Lennard-Jones and harmonic interactions. The native states of these sequences
are determined with a high degree of certainty through Monte Carlo processes.
The sequences are characterized thermodynamically and kinetically. It is shown
that the rank-ordering-based scheme of the assignment of contact energies
typically fails in off-lattice models even though it generates high stability
of on-lattice sequences. Similar to the on-lattice case, Go-like modeling, in
which the interaction potentials are restricted to the native contacts in a
target shape, gives rise to good folding properties. Involving other contacts
deteriorates these properties.Comment: REVTeX, 9 pages, 8 EPS figure
Conductance fluctuations in the presence of spin scattering
Electron transport through disordered systems that include spin scatterers is
studied numerically. We consider three kinds of magnetic impurities: the Ising,
the XY and the Heisenberg. By extending the transfer matrix method to include
the spin degree of freedom, the two terminal conductance is calculated. The
variance of conductance is halved as the number of spin components of the
magnetic impurities increases. Application of the Zeeman field in the lead
causes a further halving of the variance under certain conditions.Comment: to be published in Phys. Rev.
Influence of Hydrodynamic Interactions on Mechanical Unfolding of Proteins
We incorporate hydrodynamic interactions in a structure-based model of
ubiquitin and demonstrate that the hydrodynamic coupling may reduce the peak
force when stretching the protein at constant speed, especially at larger
speeds. Hydrodynamic interactions are also shown to facilitate unfolding at
constant force and inhibit stretching by fluid flows.Comment: to be published in Journal of Physics: Condensed Matte
Impurity and strain effects on the magnetotransport of La1.85Sr0.15Cu(1-y)Zn(y)O4 films
The influence of zinc doping and strain related effects on the normal state
transport properties(the resistivity, the Hall angle and the orbital magneto-
resistance(OMR) is studied in a series of La1.85Sr0.15Cu(1-y)Zn(y)O4 films with
values of y between 0 and 0.12 and various degrees of strain induced by the
mismatch between the films and the substrate. The zinc doping affects only the
constant term in the temperature dependence of cotangent theta but the strain
affects both the slope and the constant term, while their ratio remains
constant.OMR is decreased by zinc doping but is unaffected by strain. The ratio
delta rho/(rho*tan^2 theta) is T-independent but decreases with impurity
doping. These results put strong constraints on theories of the normal state of
high- temperature superconductors
Disorder-induced critical behavior in driven diffusive systems
Using dynamic renormalization group we study the transport in driven
diffusive systems in the presence of quenched random drift velocity with
long-range correlations along the transport direction. In dimensions
we find fixed points representing novel universality classes of
disorder-dominated self-organized criticality, and a continuous phase
transition at a critical variance of disorder. Numerical values of the scaling
exponents characterizing the distributions of relaxation clusters are in good
agreement with the exponents measured in natural river networks
Finite Size Scaling Analysis of Exact Ground States for +/-J Spin Glass Models in Two Dimensions
With the help of EXACT ground states obtained by a polynomial algorithm we
compute the domain wall energy at zero-temperature for the bond-random and the
site-random Ising spin glass model in two dimensions. We find that in both
models the stability of the ferromagnetic AND the spin glass order ceases to
exist at a UNIQUE concentration p_c for the ferromagnetic bonds. In the
vicinity of this critical point, the size and concentration dependency of the
first AND second moment of the domain wall energy are, for both models,
described by a COMMON finite size scaling form. Moreover, below this
concentration the stiffness exponent turns out to be slightly negative \theta_S
= -0.056(6) indicating the absence of any intermediate spin glass phase at
non-zero temperature.Comment: 7 pages Latex, 5 postscript-figures include
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