Search results for "computational"
showing 10 items of 5884 documents
Design of bioactive and structurally well-defined peptides from conformationally restricted libraries
2004
Libraries of peptides and proteins can be categorized according to the function of their origin in gene- and synthetic-based libraries. Both kinds of libraries have the potential to generate the same grade of molecular diversity, although the limits imposed by the synthetic methods have been lately a matter of discussion. However, the use of synthetic strategies allows incorporation of non-natural amino acids. The development of canfonnallonally restricted synthetic peptide libraries can be considered as a point of convergence of the two methodologies. In these libraries the diversity is grafted into scaffolds that are defined by stable secondary structural motifs, and the deconvolution pro…
A bonding evolution theory study of the mechanism of [3+2] cycloaddition reactions of nitrones with electron-deficient ethylenes
2015
The mechanism of zw-type [3+2] cycloaddition (32CA) reactions of nitrones with electron-deficient (ED) ethylenes has been studied using density functional theory (DFT) methods at the MPWB1K/6-31G(d) level of theory. An exploration of the potential energy surfaces associated with the four competitive reactive channels of the 32CA reaction between C-phenyl-N-methyl nitrone and acrolein indicates that the cycloaddition reaction takes place through a one-step mechanism. This cycloaddition reaction presents a moderate meta regioselectivity and a complete endo stereoselectivity, which is diminished in dichloromethane. Analysis of the DFT reactivity indices of the reagents allows an explanation of…
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 .