Search results for "COMPUTATION"
showing 10 items of 7362 documents
In vivophage display: identification of organ-specific peptides using deep sequencing and differential profiling across tissues
2020
ABSTRACTIn vivophage display is widely used for identification of organ- or disease-specific homing peptides. However, the currentin vivophage biopanning approaches fail to assess biodistribution of specific peptide phages across tissues during the screen, thus necessitating laborious and time-consuming post-screening validation studies on individual peptide phages. Here, we adopted bioinformatics tools used for RNA sequencing for analysis of high throughput sequencing (HTS) data to estimate the representation of individual peptides during biopanningin vivo. The data fromin vivophage screen were analyzed using differential binding – relative representation of each peptide in the target orga…
Innovative Combination of Three Alternating Current Relaxation Techniques: Electrical Charge, Mass, and Color Impedance Spectroscopy. Part I: The Tool
2009
Technical details concerning the simultaneous acquisition of three impedance functions (electrochemical impedance spectroscopy, alternating current electrogravimetry or mass impedance, and alternating current colorimetry or color impedance) are presented. The analysis of each type of impedance function gives interesting information about the species participating during the electrochemical processes. Furthermore, obtaining three impedance functions in situ allows the crossed impedance functions to be calculated. These functions are especially useful in detecting delays between the color, mass, and electrical charge response of the system to the same perturbation, and it allows species parti…
GPU Based Molecular Dynamics Simulations of Polymer Rings in Concentrated Solution: Structure and Scaling
2011
We report on equilibrium properties of a concentrated solution of non-concatenated ring polymers by Molecular dynamics simulations using HooMD-blue, a fast implementation on graphics processor units (GPUs). We are able to identify the intermediate scaling regime for the radius of gyration Rg ∝ N as well as indication for a crossover to Rg ∝ N for rings with chain length N in our fully flexible off-lattice polymer model. This crossover takes place between a ring size of 2500 and 7500 monomers for monomer density ρ = 0.5. Our results are in agreement with recent studies for lattice and stiff off-lattice models and show once again that this scaling is not model dependent at all. Furthermore th…
Parity violation energy of biomolecules - III: RNA
2006
The energy of parity-violation associated with a typical DNA double helix is estimated with ab initio techniques. It is shown that weak-nuclear interactions do not favor the formation of the double helices found in nature. Possible implications regarding the potential effect of parity-violation interactions on the evolution of biological homochirality are discussed.
KINETICS OF POLYMER EJECTION FROM CAPSID CONFINEMENT: SCALING CONSIDERATIONS AND COMPUTER EXPERIMENT
2012
We investigate the ejection dynamics of a flexible polymer chain out of confined environment by means of scaling considerations and Monte Carlo simulations. Situations of this kind arise in different physical contexts, including a flexible synthetic polymer partially confined in a nanopore and a viral genome partially ejected from its capsid. In the case of cylindric confinement the entropic driving force which pulls the chain out of the pore is argued to be constant once a few persistent lengths are out of the pore. We demonstrate that in this case the ejection dynamics follows a [Formula: see text]-law with elapsed time t. The mean ejection time τ depends nonmonotonically on chain length…
"Dormant" secondary metal-alkyl complexes are not omnipresent.
2006
This theoretical study was inspired by the perpetual debate over the so-called “dormancy” of the active sites in propylene polymerization, i.e., a drop in their activity after a regioerror (2,1-insertion), which was reported to occur in many (although not all) catalytic systems. To explore the range of possible situations, we have selected two homogeneous systems of fundamentally different structure: an octahedral system of C 2 symmetry with a tetradentate O N N O ligand and a bridged indenyl catalyst. This choice was not accidental; it is in these two systems where the experimentalists cannot reach a consensus about dormancy. Our density-functional theory calculations explain why in certa…
Solid state NMR - A tool for studying molecular motion in polymers
1986
After an introduction describing the development of 1H, 2H, and 13C solid state NMR two sections on 13C and 2H NMR, respectively, outline the physical background as related with molecular motion. Some representative examples demonstrate the potential of recent NMR techniques in polymer dynamics studies.
Generation and transformation of the [3.3.1]propellane skeleton by thermal rearrangements
1994
Abstract In a sequence of unexpected thermal rearrangements the strained monocyclic alkyne 4 is transformed into the tricyclic system 5 which yields in a flash vacuum pyrolysis again a monocyclic compound 10 .
Photoswitchable coordination compounds
2001
Photoswitchable compounds represent an attractive class of materials in coordination chemistry. Recent progress dealing with transition metal compounds involving photo-induced changes of the magnetic and/or optical properties to long-lived metastable states are covered in the present review article. The basic photophysical phenomena together with representative examples such as nitroprusside derivatives, relevant spin crossover complexes, stilbenoid complexes and finally Prussian blue analogues are discussed. Some possible applications regarding energy and information storage are suggested at the end.
Interfaces in immiscible polymer blends: A Monte Carlo simulation approach on the CRAY T3E
1999
Polymeric materials pose a challenge for Monte Carlo simulations because of the widely spread length and time scales involved. Using large scale computer simulations we investigate the interfacial structure in a partially compatible polymer mixture. The problem is studied in the framework of a coarse grained lattice model - the bond fluctuation model on the simple cubic lattice, choosing N = 32 and lattice linear dimensions L × L × D up to 512 × 512 × 64. We employ a two dimensional geometric decomposition scheme to implement this algorithm on the CRAY T3E. The algorithm scales very well with the number of processors. The structure of polymer coils near interfaces between coexisting phases …