2,222 research outputs found
Magnetic suspension characteristics of electromagnetic actuators
Electromagnetic actuators that use a current-carrying coil (which is placed in a magnetic field) to generate mechanical force are conceptually attractive components for active control of rotating shafts. In one concept that is being tested in the laboratory, the control forces from such actuators are applied on the flexibly supported bearing housings of the rotor. Development of this concept into a practical reality requires a clear and thorough understanding of the role of electromechanical parameters of these actuators in delivering the right amount of control force at the right phase into the rotor. The electromechanical parameters of the actuators investigated are the mass of the armature, stiffness of its suspension, electrical resistance, and inductance of the coils. Improper selection of these parameters can result in degradation in their performance, leading to mistuning between the actuator and the rotor. Through a simple analysis, it is shown that use of such mistuned actuators could result in sharp fluctuations in the phase of the control force delivered into the rotor around the critical speeds. These sharp fluctuations in phase, called 'Phase Glitches', are undesirable. Hence, future designs of controllers should take into account the undesirable mistuning effects between the actuator and the rotor caused by the phase glitches
Design of Copolymeric Materials
We devise a method for designing materials that will have some desired
structural characteristics. We apply it to multiblock copolymers that have two
different types of monomers, A and B. We show how to determine what sequence of
A's and B's should be synthesised in order to give a particular structure and
morphology. %For example in a melt of such %polymers, one may wish to engineer
a body-centered %cubic structure. Using this method in conjunction with the
theory of microphase separation developed by Leibler, we show it is possible to
efficiently search for a desired morphology. The method is quite general and
can be extended to design isolated heteropolymers, such as proteins, with
desired structural characteristics. We show that by making certain
approximations to the exact algorithm, a method recently proposed by
Shakhnovich and Gutin is obtained. The problems with this method are discussed
and we propose an improved approximate algorithm that is computationally
efficient.Comment: 15 pages latex 2.09 and psfig, 1 postscript figure
Microcanonical versus Canonical Analysis of Protein Folding
The microcanonical analysis is shown to be a powerful tool to characterize
the protein folding transition and to neatly distinguish between good and bad
folders. An off-lattice model with parameter chosen to represent polymers of
these two types is used to illustrate this approach. Both canonical and
microcanonical ensembles are employed. The required calculations were performed
using parallel tempering Monte Carlo simulations. The most revealing features
of the folding transition are related to its first-order-like character,
namely, the S-bend pattern in the caloric curve, which gives rise to negative
microcanonical specific heats, and the bimodality of the energy distribution
function at the transition temperatures. Models for a good folder are shown to
be quite robust against perturbations in the interaction potential parameters.Comment: 4 pages, 4 figure
Dry and wet interfaces: Influence of solvent particles on molecular recognition
We present a coarse-grained lattice model to study the influence of water on
the recognition process of two rigid proteins. The basic model is formulated in
terms of the hydrophobic effect. We then investigate several modifications of
our basic model showing that the selectivity of the recognition process can be
enhanced by considering the explicit influence of single solvent particles.
When the number of cavities at the interface of a protein-protein complex is
fixed as an intrinsic geometric constraint, there typically exists a
characteristic fraction that should be filled with water molecules such that
the selectivity exhibits a maximum. In addition the optimum fraction depends on
the hydrophobicity of the interface so that one has to distinguish between dry
and wet interfaces.Comment: 11 pages, 7 figure
Viscosity Dependence of the Folding Rates of Proteins
The viscosity dependence of the folding rates for four sequences (the native
state of three sequences is a beta-sheet, while the fourth forms an
alpha-helix) is calculated for off-lattice models of proteins. Assuming that
the dynamics is given by the Langevin equation we show that the folding rates
increase linearly at low viscosities \eta, decrease as 1/\eta at large \eta and
have a maximum at intermediate values. The Kramers theory of barrier crossing
provides a quantitative fit of the numerical results. By mapping the simulation
results to real proteins we estimate that for optimized sequences the time
scale for forming a four turn \alpha-helix topology is about 500 nanoseconds,
whereas the time scale for forming a beta-sheet topology is about 10
microseconds.Comment: 14 pages, Latex, 3 figures. One figure is also available at
http://www.glue.umd.edu/~klimov/seq_I_H.html, to be published in Physical
Review Letter
Geometrically Reduced Number of Protein Ground State Candidates
Geometrical properties of protein ground states are studied using an
algebraic approach. It is shown that independent from inter-monomer
interactions, the collection of ground state candidates for any folded protein
is unexpectedly small: For the case of a two-parameter Hydrophobic-Polar
lattice model for -mers, the number of these candidates grows only as .
Moreover, the space of the interaction parameters of the model breaks up into
well-defined domains, each corresponding to one ground state candidate, which
are separated by sharp boundaries. In addition, by exact enumeration, we show
there are some sequences which have one absolute unique native state. These
absolute ground states have perfect stability against change of inter-monomer
interaction potential.Comment: 9 page, 4 ps figures are include
The Origin of the Designability of Protein Structures
We examined what determines the designability of 2-letter codes (H and P)
lattice proteins from three points of view. First, whether the native structure
is searched within all possible structures or within maximally compact
structures. Second, whether the structure of the used lattice is bipartite or
not. Third, the effect of the length of the chain, namely, the number of
monomers on the chain. We found that the bipartiteness of the lattice structure
is not a main factor which determines the designability. Our results suggest
that highly designable structures will be found when the length of the chain is
sufficiently long to make the hydrophobic core consisting of enough number of
monomers.Comment: 17 pages, 2 figure
Simulation of Lattice Polymers with Multi-Self-Overlap Ensemble
A novel family of dynamical Monte Carlo algorithms for lattice polymers is
proposed. Our central idea is to simulate an extended ensemble in which the
self-avoiding condition is systematically weakened. The degree of the
self-overlap is controlled in a similar manner as the multicanonical ensemble.
As a consequence, the ensemble --the multi-self-overlap ensemble-- contains
adequate portions of self-overlapping conformations as well as higher energy
ones. It is shown that the multi-self-overlap ensemble algorithm reproduce
correctly the canonical averages at finite temperatures of the HP model of
lattice proteins. Moreover, it outperforms massively a standard multicanonical
algorithm for a difficult example of a polymer with 8-stickers. Alternative
algorithm based on exchange Monte Carlo method is also discussed.Comment: 5 Pages, 4 Postscript figures, uses epsf.st
A New Monte Carlo Algorithm for Protein Folding
We demonstrate that the recently proposed pruned-enriched Rosenbluth method
(P. Grassberger, Phys. Rev. E 56 (1997) 3682) leads to extremely efficient
algorithms for the folding of simple model proteins. We test them on several
models for lattice heteropolymers, and compare to published Monte Carlo
studies. In all cases our algorithms are faster than all previous ones, and in
several cases we find new minimal energy states. In addition to ground states,
our algorithms give estimates for the partition sum at finite temperatures.Comment: 4 pages, Latex incl. 3 eps-figs., submitted to Phys. Rev. Lett.,
revised version with changes in the tex
Monte Carlo Procedure for Protein Design
A new method for sequence optimization in protein models is presented. The
approach, which has inherited its basic philosophy from recent work by Deutsch
and Kurosky [Phys. Rev. Lett. 76, 323 (1996)] by maximizing conditional
probabilities rather than minimizing energy functions, is based upon a novel
and very efficient multisequence Monte Carlo scheme. By construction, the
method ensures that the designed sequences represent good folders
thermodynamically. A bootstrap procedure for the sequence space search is
devised making very large chains feasible. The algorithm is successfully
explored on the two-dimensional HP model with chain lengths N=16, 18 and 32.Comment: 7 pages LaTeX, 4 Postscript figures; minor change
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