7,696 research outputs found
Long-range structural regularities and collectivity of folded proteins
Coarse-grained network models of proteins successfully predict equilibrium properties related to collective modes of motion. In this study, the network construction strategies and their systematic application to proteins are used to explain the role of network models in defining the collective properties of the system. The analysis is based on the radial distribution function, a newly defined angular distribution function and the spectral dimensions of a large set of globular proteins. Our analysis shows that after reaching a certain threshold for cut-off distance, network construction has negligible effect on the collective motions and the fluctuation patterns of the residues
Interpretation of the vibrational spectra of glassy polymers using coarse-grained simulations
The structure and vibrational density of states (VDOS) of polymer glasses are
investigated using numerical simulations based on the classical Kremer-Grest
bead-spring model. We focus on the roles of chain length and bending stiffness,
the latter being set by imposing three-body angular potentials along chain
backbones. Upon increasing the chain length and bending stiffness, structural
reorganisation leads to volumetric expansion of the material and build-up of
internal stresses. The VDOS has two dominant bands: a low frequency one
corresponding to inter- and intra-chain non-bonding interactions and a high
frequency one corresponding principally to vibrations of bonded beads that
constitute skeletal chain backbones. Upon increasing the steepness of the
angular potential, vibrational modes associated with chain bending gradually
move from the low-frequency to the high-frequency band. This redistribution of
modes is reflected in a reduction of the so-called Boson peak upon increasing
chain stiffness. Remarkably, the finer structure and the peaks of the
high-frequency band, and their variations with stiffness, can, for short
chains, be explained using an analytical solution derived for a model triatomic
molecule. For longer chains, the qualitative evolution of the VDOS with chain
stiffness is similar, although the distinct peaks observed for short chains
become increasingly smoothed-out. Our findings can be used to guide a
systematic approach to interpretation of Brillouin and Raman scattering spectra
of glassy polymers in future work, with applications in polymer processing
diagnostics.Comment: To appear in Macromolecule
Emergence of foams from the breakdown of the phase field crystal model
The phase field crystal (PFC) model captures the elastic and topological
properties of crystals with a single scalar field at small undercooling. At
large undercooling, new foam-like behavior emerges. We characterize this foam
phase of the PFC equation and propose a modified PFC equation that may be used
for the simulation of foam dynamics. This minimal model reproduces von
Neumann's rule for two-dimensional dry foams, and Lifshitz-Slyozov coarsening
for wet foams. We also measure the coordination number distribution and find
that its second moment is larger than previously-reported experimental and
theoretical studies of soap froths, a finding that we attribute to the wetness
of the foam increasing with time.Comment: 4 pages, 4 figure
More than one dynamic crossover in protein hydration water
Studies of liquid water in its supercooled region have led to many insights
into the structure and behavior of water. While bulk water freezes at its
homogeneous nucleation temperature of approximately 235 K, for protein
hydration water, the binding of water molecules to the protein avoids
crystallization. Here we study the dynamics of the hydrogen bond (HB) network
of a percolating layer of water molecules, comparing measurements of a hydrated
globular protein with the results of a coarse-grained model that has been shown
to successfully reproduce the properties of hydration water. With dielectric
spectroscopy we measure the temperature dependence of the relaxation time of
protons charge fluctuations. These fluctuations are associated to the dynamics
of the HB network of water molecules adsorbed on the protein surface. With
Monte Carlo (MC) simulations and mean--field (MF) calculations we study the
dynamics and thermodynamics of the model. In both experimental and model
analyses we find two dynamic crossovers: (i) one at about 252 K, and (ii) one
at about 181 K. The agreement of the experiments with the model allows us to
relate the two crossovers to the presence of two specific heat maxima at
ambient pressure. The first is due to fluctuations in the HB formation, and the
second, at lower temperature, is due to the cooperative reordering of the HB
network
S-Net for multi-memory multicores
Copyright ACM, 2010. This is the author's version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version was published in Proceedings of the 5th ACM SIGPLAN Workshop on Declarative Aspects of Multicore Programming: http://doi.acm.org/10.1145/1708046.1708054S-Net is a declarative coordination language and component technology aimed at modern multi-core/many-core architectures and systems-on-chip. It builds on the concept of stream processing to structure dynamically evolving networks of communicating asynchronous components. Components themselves are implemented using a conventional language suitable for the application domain. This two-level software architecture maintains a familiar sequential development environment for large parts of an application and offers a high-level declarative approach to component coordination. In this paper we present a conservative language extension for the placement of components and component networks in a multi-memory environment, i.e. architectures that associate individual compute cores or groups thereof with private memories. We describe a novel distributed runtime system layer that complements our existing multithreaded runtime system for shared memory multicores. Particular emphasis is put on efficient management of data communication. Last not least, we present preliminary experimental data
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