70 research outputs found
Special issue: Dynamics of systems on the nanoscale (2018). Editorial
The structure, formation and dynamics of both animate and inanimate matter on the nanoscale are a highly interdisciplinary ïŹeld of rapidly emerging research engaging a broad community encompassing experimentalists, theorists, and technologists. It is relevant for a large variety of molecular and nanosystems of diïŹerent origin and composition and concerns numerous phenomena originating from physics, chemistry, biology, or materials science. This Topical Issue presents a collection of original research papers devoted to diïŹerent aspects of structure and dynamics on the nanoscale. Some of the contributions discuss speciïŹc applications of the research results in several modern technologies and in next generation medicine. Most of the works of this topical issue were reported at the Fifth International Conference on Dynamics of Systems on the Nanoscale (DySoN) â the premier forum for the presentation of cutting-edge research in this ïŹeld that was held in Potsdam, Germany in October of 2018
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
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
Multiscale modeling of complex molecular structure and dynamics with MBN Explorer
This book introduces readers to MesoBioNano (MBN) Explorer â a multi-purpose software package designed to model molecular systems at various levels of size and complexity. In addition, it presents a specially designed multi-task toolkit and interface â the MBN Studio â which enables the set-up of input files, controls the simulations, and supports the subsequent visualization and analysis of the results obtained. The book subsequently provides a systematic description of the capabilities of this universal and powerful software package within the framework of computational molecular science, and guides readers through its applications in numerous areas of research in bio- and chemical physics and material science â ranging from the nano- to the meso-scale. MBN Explorer is particularly suited to computing the systemâs energy, to optimizing molecular structure, and to exploring the various facets of molecular and random walk dynamics. The package allows the use of a broad variety of interatomic potentials and can, e.g., be configured to select any subset of a molecular system as rigid fragments, whenever a significant reduction in the number of dynamical degrees of freedom is required for computational practicalities. MBN Studio enables users to easily construct initial geometries for the molecular, liquid, crystalline, gaseous and hybrid systems that serve as input for the subsequent simulations of their physical and chemical properties using MBN Explorer. Despite its universality, the computational efficiency of MBN Explorer is comparable to that of other, more specialized software packages, making it a viable multi-purpose alternative for the computational modeling of complex molecular systems. A number of detailed case studies presented in the second part of this book demonstrate MBN Explorerâs usefulness and efficiency in the fields of atomic clusters and nanoparticles, biomolecular systems, nanostructured materials, composite materials and hybrid systems, crystals, liquids and gases, as well as in providing modeling support for novel and emerging technologies. Last but not least, with the release of the 3rd edition of MBN Explorer in spring 2017, a free trial version will be available from the MBN Research Center website (mbnresearch.com)
On binding specificity of (6â4) photolyase to a T(6â4)T DNA photoproduct
Different factors lead to DNA damage and if it is not repaired in due time, the damaged DNA could initiate mutagenesis and cancer. To avoid this deadly scenario, specific enzymes can scavenge and repair the DNA, but the enzymes have to bind first to the damaged sites. We have investigated this binding for a specific enzyme called (6â4) photolyase, which is capable of repairing certain UV-induced damage in DNA. Through molecular dynamics simulations we describe the binding between photolyase and the DNA and reveal that several charged amino acid residues in the enzyme, such as arginines and lysines turn out to be important. Especially R421 is crucial, as it keeps the DNA strands at the damaged site inside the repair pocket of the enzyme separated. DNA photolyase is structurally highly homologous to a protein called cryptochrome. Both proteins are biologically activated similarly, namely through flavin co-factor photoexcitation. It is, however, striking that cryptochrome cannot repair UV-damaged DNA. The present investigation allowed us to conclude on the small but, apparently, critical differences between photolyase and cryptochrome. The performed analysis gives insight into important factors that govern the binding of UV-damaged DNA and reveal why cryptochrome cannot have this functionality
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