Search results for "Biomolecule"
showing 10 items of 666 documents
Simulated annealing with restrained molecular dynamics using a flexible restraint potential: Theory and evaluation with simulated NMR constraints
1996
A new functional representation of NMR-derived distance constraints, the flexible restraint potential, has been implemented in the program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168) for molecular structure generation. In addition, flat-bottomed restraint potentials for representing dihedral angle and vicinal scalar coupling constraints have been introduced into CONGEN. An effective simulated annealing (SA) protocol that combines both weight annealing and temperature annealing is described. Calculations have been performed using ideal simulated NMR constraints, in order to evaluate the use of restrained molecular dynamics (MD) with these target functions as implemented i…
Role of Disorder on the Dynamics of a Nonlinear Model for DNA Thermal Denaturation
1992
The dynamics of thermal denaturation of DNA is a good example in which nonlinearity coexits with disorder. The amplitude of the motions is so high that bonds break and the base sequence is inhomogeneous since it contains the genetic code. Using a simple nonlinear model, we study the role of local inhomogeneities or of extended disorder on the dynamics of the localized excitations and on the denaturation rate by numerical simulations at constrained temperature. Approximate analytical results are obtained for the trapping of the breatherlike excitations by isolated defects and the statistical mechanics of the disordered molecule.
Force probe simulations using a hybrid scheme with virtual sites.
2017
Hybrid simulations, in which a part of the system is treated with atomistic resolution and the remainder is represented on a coarse-grained level, allow for fast sampling while using the accuracy of atomistic force fields. We apply a hybrid scheme to study the mechanical unfolding and refolding of a molecular complex using force probe molecular dynamics (FPMD) simulations. The degrees of freedom of the solvent molecules are treated in a coarse-grained manner while atomistic resolution is retained for the solute. The coupling between the solvent and the solute is provided using virtual sites. We test two different common coarse-graining procedures, the iterative Boltzmann inversion method an…
Benchmark Thermochemistry of the Hydroperoxyl Radical
2004
A theoretical estimation of the enthalpy of formation for the hydroperoxyl radical is presented. These results are based on CCSD(T)/aug-cc-pCV5Z calculations extrapolated to the basis-set limit with additional corrections. Anharmonic vibrational zero-point energies, scalar relativistic, spin -orbit coupling, and diagonal BornOppenheimer corrections are further used to correct the extrapolated term energies, as well as various empirical corrections that account for correlation effects not treated at the CCSD(T) level. We estimate that ¢fH° ) 3.66 ( 0.10 kcal mol -1 (¢fH° ) 2.96 ( 0.10 kcal mol -1 ) using several reaction schemes. Significantly, it appears to be necessary to include effects o…
Molecular-dynamics simulation of a glassy polymer melt: Incoherent scattering function
1999
We report results of molecular-dynamics simulations for a glassy polymer melt consisting of short, linear bead-spring chains. It was shown in previous work that this onset of the glassy slowing down is compatible with the predictions of the mode coupling theory. The physical process of `caging' of a monomer by its spatial neighbors leads to a distinct two step behavior in the particle mean square displacements. In this work we analyze the effects of this caging process on the Rouse description of the melt's dynamics. We show that the Rouse theory is applicable for length and time scales above the typical scales for the caging process. Futhermore, the monomer displacement is compared with si…
"Table 1" of "Measurements of the charge asymmetry in top-quark pair production in the dilepton final state at $\sqrt{s}=8$ TeV with the ATLAS detect…
2017
Unfolded distribution for the inclusive $\Delta|\eta|$ observable in the fiducial volume.
Ab initio determination of the ionization potentials of DNA and RNA nucleobases
2006
Quantum chemical high level ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute vertical and adiabatic ionization potentials of the five canonical DNA and RNA nucleobases: uracil, thymine, cytosine, adenine, and guanine. Several states of their cations have been also calculated. The present results represent a systematic compendium of these magnitudes, establishing theoretical reference values at a level not reported before, calibrating computational strategies, and guiding the assignment of the features in the experimental photoelectron spectra. Daniel.Roca@uv.es Mercedes.Rubio@uv.es Manuela.Merchan@uv.es Luis.Serrano@uv.es
Inverse Conformational Selection in Lipid–Protein Binding
2021
International audience; Interest in lipid interactions with proteins and other biomolecules is emerging not only in fundamental biochemistry but also in the field of nanobiotechnology where lipids are commonly used, for example, in carriers of mRNA vaccines. The outward-facing components of cellular membranes and lipid nanoparticles, the lipid headgroups, regulate membrane interactions with approaching substances, such as proteins, drugs, RNA, or viruses. Because lipid headgroup conformational ensembles have not been experimentally determined in physiologically relevant conditions, an essential question about their interactions with other biomolecules remains unanswered: Do headgroups excha…
On the application of an experimental multipolar pseudo-atom library for accurate refinement of small-molecule and protein crystal structures
2007
International audience; With an increasing number of biomacromolecular crystal structures being measured to ultra-high resolution, it has become possible to extend to large systems experimental charge-density methods that are usually applied to small molecules. A library has been built of average multipole populations describing the electron density of chemical groups in all 20 amino acids found in proteins. The library uses the Hansen & Coppens multipolar pseudo-atom model to derive molecular electron density and electrostatic potential distributions. The library values are obtained from several small peptide or amino acid crystal structures refined against ultra-high-resolution X-ray diff…
On n–Fold Blocking Sets
1986
An n-fold blocking set is a set of n-disjoint blocking sets. We shall prove upper and lower bounds for the number of components in an n-fold blocking set in projective and affine spaces.