Search results for "molecular dynamics"
showing 10 items of 1075 documents
Functional Extrapolations to Tame Unbound Anions in Density-Functional Theory Calculations
2019
Standard flavors of density-functional theory (DFT) calculations are known to fail in describing anions, due to large self-interaction errors. The problem may be circumvented using localized basis sets of reduced size, leaving no variational flexibility for the extra electron to delocalize. Alternatively, a recent approach exploiting DFT evaluations of total energies on electronic densities optimized at the Hartree-Fock (HF) level has been reported, showing that the self-interaction-free HF densities are able to lead to an improved description of the additional electron, returning affinities in close agreement with the experiments. Nonetheless, such an approach can fail when the HF densitie…
Multiphoton Absorption of Myoglobin Nitric-Oxide complex: Relaxation by D-NEMD of a Stationary State
2012
ABSTRACT: The photodissociation and geminate recombination of nitric oxide in myoglobin, under continuous illumination, is modeled computationally. The relaxation of the photon energy into the protein matrix is also considered in a single simulation scheme that mimics a complete experimental setup. The dynamic approach to non-equilibrium molecular dynamics is used, starting from a steady state, to compute its relaxation to equilibrium. Simulations are conducted for the native form of sperm whale myoglobin and for two other mutants, V68W and L29F, illustrating a fair diversity of spatial and temporal geminate recombination processes. Energy flow to the heme and immediate protein environment …
Computational Modeling of Geminate Recombination and Energy Relaxation of Nitric Oxide in Myoglobin under Constant Illumination,
2011
Computational studies of biomolecular screening and interactions
2015
Blends of Semiflexible Polymers: Interplay of Nematic Order and Phase Separation
2021
Mixtures of semiflexible polymers with a mismatch in either their persistence lengths or their contour lengths are studied by Density Functional Theory and Molecular Dynamics simulation. Considering lyotropic solutions under good solvent conditions, the mole fraction and pressure is systematically varied for several cases of bending stiffness κ (the normalized persistence length) and chain length N. For binary mixtures with different chain length (i.e., NA=16, NB=32 or 64) but the same stiffness, isotropic-nematic phase coexistence is studied. For mixtures with the same chain length (N=32) and large stiffness disparity (κB/κA=4.9 to 8), both isotropic-nematic and nematic-nematic unmixing oc…
Conformational Changes in Acetylcholine Binding Protein Investigated by Temperature Accelerated Molecular Dynamicscottone
2014
The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer
2021
Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering…
Structure‐ and Interaction‐Based Design of Anti‐SARS‐CoV‐2 Aptamers
2022
Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. This study aims to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with …
Alignment of linear molecules by short duration laser pulses
2005
Alignment of linear molecules is efficiently induced by strong linearly polarized laser pulses. In the case of short pulses with respect to molecular rotation, periodic alignment appears in field-free conditions after the extinction of the field. This manuscript presents three techniques where the value of allows to quantify alignment without molecular dissociation nor additional alignment. They use a weak time-delayed probe pulse which experiences the optical properties of an aligned sample and shows modification of its characteristics. The first of them measures a depolarization due to the birefringence of the sample. The second one is based on the defocusing produced by the spatial distr…