88 research outputs found
Two center multipole expansion method: application to macromolecular systems
We propose a new theoretical method for the calculation of the interaction
energy between macromolecular systems at large distances. The method provides a
linear scaling of the computing time with the system size and is considered as
an alternative to the well known fast multipole method. Its efficiency,
accuracy and applicability to macromolecular systems is analyzed and discussed
in detail.Comment: 23 pages, 7 figures, 1 tabl
Ab initio study of alanine polypeptide chains twisting
We have investigated the potential energy surfaces for alanine chains
consisting of three and six amino acids. For these molecules we have calculated
potential energy surfaces as a function of the Ramachandran angles Phi and Psi,
which are widely used for the characterization of the polypeptide chains. These
particular degrees of freedom are essential for the characterization of
proteins folding process. Calculations have been carried out within ab initio
theoretical framework based on the density functional theory and accounting for
all the electrons in the system. We have determined stable conformations and
calculated the energy barriers for transitions between them. Using a
thermodynamic approach, we have estimated the times of characteristic
transitions between these conformations. The results of our calculations have
been compared with those obtained by other theoretical methods and with the
available experimental data extracted from the Protein Data Base. This
comparison demonstrates a reasonable correspondence of the most prominent
minima on the calculated potential energy surfaces to the experimentally
measured angles Phi and Psi for alanine chains appearing in native proteins. We
have also investigated the influence of the secondary structure of polypeptide
chains on the formation of the potential energy landscape. This analysis has
been performed for the sheet and the helix conformations of chains of six amino
acids.Comment: 24 pages, 10 figure
Synthesis of a fullerene-based one-dimensional nanopolymer through topochemical transformation of the parent nanowire
Large-scale practical applications of fullerene (C60) in nanodevices could be
significantly facilitated if the commercially-available micrometer-scale raw
C60 powder were further processed into a one-dimensional (1D) nanowire-related
polymer displaying covalent bonding as molecular interlinks and resembling
traditional important conjugated polymers. However, there has been little study
thus far in this area despite the abundant literature on fullerene. Here we
report the synthesis and characterization of such a C60-based nanowire polymer,
(-C60TMB-)n, where TMB=1,2,4-trimethylbenzene, which displays a well-defined
crystalline structure, exceptionally large length-to-width ratio and excellent
thermal stability. The material is prepared by first growing the corresponding
nanowire through a solution phase of C60 followed by a topochemical
polymerization reaction in the solid state. Gas chromatography, mass
spectrometry and 13C nuclear magnetic resonance evidence is provided for the
nature of the covalent bonding mode adopted by the polymeric chains.
Theoretical analysis based on detailed calculations of the reaction energetics
and structural analysis provides an in-depth understanding of the
polymerization pathway. The nanopolymer promises important applications in
biological fields and in the development of optical, electrical, and magnetic
nanodevices.Comment: 30 pages, 12 figures, 2 table
Evolution of electronic and ionic structure of Mg-clusters with the growth cluster size
The optimized structure and electronic properties of neutral and singly
charged magnesium clusters have been investigated using ab initio theoretical
methods based on density-functional theory and systematic post-Hartree-Fock
many-body perturbation theory accounting for all electrons in the system. We
have systematically calculated the optimized geometries of neutral and singly
charged magnesium clusters consisting of up to 21 atoms, electronic shell
closures, binding energies per atom, ionization potentials and the gap between
the highest occupied and the lowest unoccupied molecular orbitals. We have
investigated the transition to the hcp structure and metallic evolution of the
magnesium clusters, as well as the stability of linear chains and rings of
magnesium atoms. The results obtained are compared with the available
experimental data and the results of other theoretical works.Comment: 30 pages, 10 figures, 3 table
Computational reconstruction and analysis of structural models of avian cryptochrome 4
A recent study by Xu et al. (Nature,2021, 594, 535â540) provided strongevidence that cryptochrome 4 (Cry4) is a key protein to endow migratory birds with the magneticcompass sense. The investigation compared the magneticfield response of Cry4 from migratoryand nonmigratory bird species and suggested that a difference in magnetic sensitivity could exist.Thisfinding prompted an in-depth investigation into Cry4 protein differences on the structuraland dynamic levels. In the present study, the pigeon Cry4 (ClCry4) crystal structure was used toreconstruct the missing avian Cry4 protein structures via homology modeling for carefullyselected bird species. The reconstructed Cry4 structure from European robin, Eurasian blackcap,zebrafinch, chicken, and pigeon were subsequently simulated dynamically and analyzed. Thestudied avian Cry4 structures showflexibility in analogous regions pointing to similar activationmechanisms and/or signaling interaction partners. It can be concluded that the experimentallyrecorded difference in the magneticfield sensitivity of Cry4 from different birds is unlikely to bedue to solely intrinsic dynamics of the proteins but requires additional factors that have not yet been identified
Formalism for Multiphoton Plasmon Excitation in Jellium Clusters
We present a new formalism for the description of multiphoton plasmon
excitation processes in jellium clusters. By using our method, we demonstrate
that, in addition to dipole plasmon excitations, the multipole plasmons
(quadrupole, octupole, etc) can be excited in a cluster by multiphoton
absorption processes, which results in a significant difference between plasmon
resonance profiles in the cross sections for multiphoton as compared to
single-photon absorption. We calculate the cross sections for multiphoton
absorption and analyse the balance between the surface and volume plasmon
contributions to multipole plasmons.Comment: 29 pages, 1 figur
Impurity effects on the melting of Ni clusters
We demonstrate that the addition of a single carbon impurity leads to
significant changes in the thermodynamic properties of Ni clusters consisting
of more than a hundred atoms. The magnitude of the change induced is dependent
upon the parameters of the Ni-C interaction. Hence, thermodynamic properties of
Ni clusters can be effectively tuned by the addition of an impurity of a
particular type. We also show that the presence of a carbon impurity
considerably changes the mobility and diffusion of atoms in the Ni cluster at
temperatures close to its melting point. The calculated diffusion coefficients
of the carbon impurity in the Ni cluster can be used for a reliable estimate of
the growth rate of carbon nanotubes.Comment: 27 pages, 13 figure
Structure and properties of small sodium clusters
We have investigated structure and properties of small metal clusters using
all-electron ab initio theoretical methods based on the Hartree-Fock
approximation and density functional theory, perturbation theory and compared
results of our calculations with the available experimental data and the
results of other theoretical works. We have systematically calculated the
optimized geometries of neutral and singly charged sodium clusters having up to
20 atoms, their multipole moments (dipole and quadrupole), static
polarizabilities, binding energies per atom, ionization potentials and
frequencies of normal vibration modes. Our calculations demonstrate the great
role of many-electron correlations in the formation of electronic and ionic
structure of small metal clusters and form a good basis for further detailed
study of their dynamic properties, as well as structure and properties of other
atomic cluster systems.Comment: 47 pages, 16 figure
A coarse-grained Monte Carlo approach to diffusion processes in metallic nanoparticles
A kinetic Monte Carlo approach on a coarse-grained lattice is developed for the simulation of surface diffusion processes of Ni, Pd and Au structures with diameters in the range of a few nanometers. Intensity information obtained via standard two-dimensional transmission electron microscopy imaging techniques is used to create three-dimensional structure models as input for a cellular automaton. A series of update rules based on reaction kinetics is defined to allow for a stepwise evolution in time with the aim to simulate surface diffusion phenomena such as Rayleigh breakup and surface wetting. The material flow, in our case represented by the hopping of discrete portions of metal on a given grid, is driven by the attempt to minimize the surface energy, which can be achieved by maximizing the number of filled neighbor cells
Use of bio-loggers to characterize red fox behavior with implications for studies of magnetic alignment responses in free-roaming animals
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