9,113 research outputs found
On correlation between protein secondary structure, backbone bond angles, and side-chain orientations
We investigate the fine structure of the sp3 hybridized covalent bond
geometry that governs the tetrahedral architecture around the central
C carbon of a protein backbone, and for this we develop new
visualization techniques to analyze high resolution X-ray structures in Protein
Data Bank. We observe that there is a correlation between the deformations of
the ideal tetrahedral symmetry and the local secondary structure of the
protein. We propose a universal coarse grained energy function to describe the
ensuing side-chain geometry in terms of the C carbon orientations. The
energy function can model the side-chain geometry with a sub-atomic precision.
As an example we construct the C-C structure of HP35 chicken
villin headpiece. We obtain a configuration that deviates less than 0.4 \.A in
root-mean-square distance from the experimental X-ray structure
Slow dynamics in a primitive tetrahedral network model
We report extensive Monte Carlo and event-driven molecular dynamics
simulations of the fluid and liquid phase of a primitive model for silica
recently introduced by Ford, Auerbach and Monson [J. Chem. Phys. 17, 8415
(2004)]. We evaluate the iso-diffusivity lines in the temperature-density plane
to provide an indication of the shape of the glass transition line. Except for
large densities, arrest is driven by the onset of the tetrahedral bonding
pattern and the resulting dynamics is strong in the Angell's classification
scheme. We compare structural and dynamic properties with corresponding results
of two recently studied primitive models of network forming liquids -- a
primitive model for water and a angular-constraint free model of
four-coordinated particles -- to pin down the role of the geometric constraints
associated to the bonding. Eventually we discuss the similarities between
"glass" formation in network forming liquids and "gel" formation in colloidal
dispersions of patchy particles.Comment: 9 pages, 10 figure
Modeling vitreous silica bilayers
We computer model a free-standing vitreous silica bilayer which has recently
been synthesized and characterized experimentally in landmark work. Here we
model the bilayer using a computer assembly procedure that starts from a single
layer of amorphous graphene, generated using a bond switching algorithm from an
initially crystalline graphene structure. Next each bond is decorated with an
oxygen atom and the carbon atoms are relabeled as silicon. This monolayer can
be now thought of as a two dimensional network of corner sharing triangles.
Next each triangle is made into a tetrahedron, by raising the silicon atom
above each triangle and adding an additional singly coordinated oxygen atom at
the apex. The final step is to mirror reflect this layer to form a second layer
and then attach the two layers together to form the bilayer.
We show that this vitreous silica bilayer has the additional macroscopic
degrees of freedom to easily form a network of identical corner sharing
tetrahedra if there is a symmetry plane through the center of the bilayer going
through the layer of oxygen ions that join the upper and lower layers. This has
the consequence that the upper rings lie exactly above the lower rings, which
are tilted in general. The assumption of a network of perfect corner sharing
tetrahedra leads to a range of possible densities that we have previously
characterized in three dimensional zeolites as a flexibility window. Finally,
using a realistic potential, we have relaxed the bilayer to determine the
density, and other structural characteristics such as the Si-Si pair
distribution functions and the Si-O-Si bond angle distribution, which are
compared to the experimental results obtained by direct imaging
Photonic Band Gaps in 3D Network Structures with Short-range Order
We present a systematic study of photonic band gaps (PBGs) in
three-dimensional (3D) photonic amorphous structures (PAS) with short-range
order. From calculations of the density of optical states (DOS) for PAS with
different topologies, we find that tetrahedrally connected dielectric networks
produce the largest isotropic PBGs. Local uniformity and tetrahedral order are
essential to the formation of PBGs in PAS, in addition to short-range geometric
order. This work demonstrates that it is possible to create broad, isotropic
PBGs for vector light fields in 3D PAS without long-range order.Comment: 6 pages, 8 figure
Carbon--The First Frontier of Information Processing
Information is often encoded as an aperiodic chain of building blocks. Modern
digital computers use bits as the building blocks, but in general the choice of
building blocks depends on the nature of the information to be encoded. What
are the optimal building blocks to encode structural information? This can be
analysed by substituting the operations of addition and multiplication of
conventional arithmetic with translation and rotation. It is argued that at the
molecular level, the best component for encoding discretised structural
information is carbon. Living organisms discovered this billions of years ago,
and used carbon as the back-bone for constructing proteins that function
according to their structure. Structural analysis of polypeptide chains shows
that an efficient and versatile structural language of 20 building blocks is
needed to implement all the tasks carried out by proteins. Properties of amino
acids indicate that the present triplet genetic code was preceded by a more
primitive one, coding for 10 amino acids using two nucleotide bases.Comment: (v1) 9 pages, revtex. (v2) 10 pages. Several arguments expanded to
make the article self-contained and to increase clarity. Applications pointed
out. (v3) 11 pages. Published version. Well-known properties of proteins
shifted to an appendix. Reformatted according to journal styl
A spherical model with directional interactions: I. Static properties
We introduce a simple spherical model whose structural properties are similar
to the ones generated by models with directional interactions, by employing a
binary mixture of large and small hard spheres, with a square-well attraction
acting only between particles of different size. The small particles provide
the bonds between the large ones. With a proper choice of the interaction
parameters, as well as of the relative concentration of the two species, it is
possible to control the effective valence. Here we focus on a specific choice
of the parameters which favors tetrahedral ordering and study the equilibrium
static properties of the system in a large window of densities and
temperatures. Upon lowering the temperature we observe a progressive increase
in local order, accompanied by the formation of a four-coordinated network of
bonds. Three different density regions are observed: at low density the system
phase separates into a gas and a liquid phase; at intermediate densities a
network of fully bonded particles develops; at high densities -- due to the
competition between excluded volume and attractive interactions -- the system
forms a defective network. The very same behavior has been previously observed
in numerical studies of non-spherical models for molecular liquids, such as
water, and in models of patchy colloidal particles. Differently from these
models, theoretical treatments devised for spherical potentials, e.g. integral
equations and ideal mode coupling theory for the glass transition can be
applied in the present case, opening the way for a deeper understanding of the
thermodynamic and dynamic behavior of low valence molecules and particles.Comment: 11 pages, 11 figure
Orthorhombic Phase of Crystalline Polyethylene: A Constant Pressure Path Integral Monte Carlo Study
In this paper we present a Path Integral Monte Carlo (PIMC) simulation of the
orthorhombic phase of crystalline polyethylene, using an explicit atom force
field with unconstrained bond lengths and angles. This work represents a
quantum extension of our recent classical simulation (J. Chem. Phys. 106, 8918
(1997)). It is aimed both at exploring the applicability of the PIMC method on
such polymer crystal systems, as well as on a detailed assessment of the
importance of quantum effects on different quantities. We used the
ensemble and simulated the system at zero pressure in the temperature range 25
- 300 K, using Trotter numbers between 12 and 144. In order to investigate
finite-size effects, we used chains of two different lengths, C_12 and C_24,
corresponding to the total number of atoms in the super-cell being 432 and 864,
respectively. We show here the results for structural parameters, like the
orthorhombic lattice constants a,b,c, and also fluctuations of internal
parameters of the chains, such as bond lengths and bond and torsional angles.
We have also determined the internal energy and diagonal elastic constants
c_11, c_22 and c_33. We discuss the temperature dependence of the measured
quantities and compare to that obtained from the classical simulation. For some
quantities, we discuss the way they are related to the torsional angle
fluctuation. In case of the lattice parameters we compare our results to those
obtained from other theoretical approaches as well as to some available
experimental data. In order to study isotope effects, we simulated also a
deuterated polyethylene crystal at a low temperature. We also suggest possible
ways of extending this study and present some general considerations concerning
modeling of polymer crystals.Comment: 18 pages, RevTex, 18 figures, 3 tables, submitted to Phys. Rev.
Towards a mesoscopic model of water-like fluids with hydrodynamic interactions
We present a mesoscopic lattice model for non-ideal fluid flows with
directional interactions, mimicking the effects of hydrogen-bonds in water. The
model supports a rich and complex structural dynamics of the orientational
order parameter, and exhibits the formation of disordered domains whose size
and shape depend on the relative strength of directional order and thermal
diffusivity. By letting the directional forces carry an inverse density
dependence, the model is able to display a correlation between ordered domains
and low density regions, reflecting the idea of water as a denser liquid in the
disordered state than in the ordered one
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