2,759 research outputs found
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
Invited commentary on "Green HEMS in mountain and remote areas: reduction of carbon footprint through drones?".
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
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
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
Kramers rate theory of ionization and dissociation of bound states
Calculating the microscopic dissociation rate of a bound state, such as a
classical diatomic molecule, has been difficult so far. The problem was that
standard theories require an energy barrier over which the bound particle (or
state) escapes into the preferred low-energy state. This is not the case when
the long-range repulsion responsible for the barrier is either absent or
screened (as in Cooper pairs, ionized plasma, or biomolecular complexes). We
solve this classical problem by accounting for entropic memory at the
microscopic level. The theory predicts dissociation rates for arbitrary
potentials and is successfully tested on the example of plasma, where it yields
an estimate of ionization in the core of Sun in excellent agreement with
experiments. In biology, the new theory accounts for crowding in
receptor-ligand kinetics and protein aggregation
Human dynamics revealed through Web analytics
When the World Wide Web was first conceived as a way to facilitate the
sharing of scientific information at the CERN (European Center for Nuclear
Research) few could have imagined the role it would come to play in the
following decades. Since then, the increasing ubiquity of Internet access and
the frequency with which people interact with it raise the possibility of using
the Web to better observe, understand, and monitor several aspects of human
social behavior. Web sites with large numbers of frequently returning users are
ideal for this task. If these sites belong to companies or universities, their
usage patterns can furnish information about the working habits of entire
populations. In this work, we analyze the properly anonymized logs detailing
the access history to Emory University's Web site. Emory is a medium size
university located in Atlanta, Georgia. We find interesting structure in the
activity patterns of the domain and study in a systematic way the main forces
behind the dynamics of the traffic. In particular, we show that both linear
preferential linking and priority based queuing are essential ingredients to
understand the way users navigate the Web.Comment: 7 pages, 8 figure
A test generation framework for quiescent real-time systems
We present an extension of Tretmans theory and algorithm for test generation for input-output transition systems to real-time systems. Our treatment is based on an operational interpretation of the notion of quiescence in the context of real-time behaviour. This gives rise to a family of implementation relations parameterized by observation durations for quiescence. We define a nondeterministic (parameterized) test generation algorithm that generates test cases that are sound with respect to the corresponding implementation relation. Also, the test generation is exhaustive in the sense that for each non-conforming implementation a test case can be generated that detects the non-conformance
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
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
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