Abstract: In this paper we study a system composed by carbon
nanotube (CNT) and bundle of carbon nanotube (BuCNT) interacting
with a specific fatty acid as molecular probe. Full system is
represented by open nanotube (or nanotubes) and the linoleic acid
(LA) relaxing due the interaction with CNT and BuCNT. The LA has
in his form an asymmetric shape with COOH termination provoking
a close BuCNT interaction mainly by van der Waals force field. The
simulations were performed by classical molecular dynamics with
standard parameterizations.
Our results show that these BuCNT and CNT are dynamically
stable and it shows a preferential interaction position with LA
resulting in three features: (i) when the LA is interacting with CNT
and BuCNT (including both termination, CH2 or COOH), the LA is
repelled; (ii) when the LA terminated with CH2 is closer to open
extremity of BuCNT, the LA is also repelled by the interaction
between them; and (iii) when the LA terminated with COOH is
closer to open extremity of BuCNT, the LA is encapsulated by the
BuCNT. These simulations are part of a more extensive work on
searching efficient selective molecular devices and could be useful to
reach this goal.
Abstract: Nowadays, HPC, Grid and Cloud systems are evolving
very rapidly. However, the development of infrastructure solutions
related to HPC is lagging behind. While the existing infrastructure is
sufficient for simple cases, many computational problems have more
complex requirements.Such computational experiments use different
resources simultaneously to start a large number of computational
jobs.These resources are heterogeneous. They have different
purposes, architectures, performance and used software.Users need a
convenient tool that allows to describe and to run complex
computational experiments under conditions of HPC environment.
This paper introduces a modularworkflow system called SEGL
which makes it possible to run complex computational experiments
under conditions of a real HPC organization. The system can be used
in a great number of organizations, which provide HPC power.
Significant requirements to this system are high efficiency and
interoperability with the existing HPC infrastructure of the
organization without any changes.
Abstract: In this work, we incorporated a quartic bond potential
into a coarse-grained bead-spring model to study lubricant adsorption
on a solid surface as well as depletion instability. The surface tension
density and the number density profiles were examined to verify the
solid-liquid and liquid-vapor interfaces during heat treatment. It was
found that both the liquid-vapor interfacial thickness and the
solid-vapor separation increase with the temperatureT* when T*is
below the phase transition temperature Tc
*. At high temperatures
(T*>Tc
*), the solid-vapor separation decreases gradually as the
temperature increases. In addition, we evaluated the lubricant weight
and bond loss profiles at different temperatures. It was observed that
the lubricant desorption is favored over decomposition and is the main
cause of the lubricant failure at the head disk interface in our
simulations.
Abstract: Certain tRNA synthetases have developed highly accurate molecular machinery to discriminate their cognate amino acids. Those aaRSs achieve their goal via editing reaction in the Connective Polypeptide 1 (CP1). Recently mutagenesis studies have revealed the critical importance of residues in the CP1 domain for editing activity and X-ray structures have shown binding mode of noncognate amino acids in the editing domain. To pursue molecular mechanism for amino acid discrimination, molecular modeling studies were performed. Our results suggest that aaRS bind the noncognate amino acid more tightly than the cognate one. Finally, by comparing binding conformations of the amino acids in three systems, the amino acid binding mode was elucidated and a discrimination mechanism proposed. The results strongly reveal that the conserved threonines are responsible for amino acid discrimination. This is achieved through side chain interactions between T252 and T247/T248 as well as between those threonines and the incoming amino acids.