Search results for "Biomolecule"
showing 10 items of 666 documents
How Well Can Coarse-Grained Models of Real Polymers Describe Their Structure? The Case of Polybutadiene
2015
Coarse-graining of chemical structure of macromolecules in the melt is investigated using extensive molecular dynamics simulation data which are based on a united atom force-field model of polybutadiene. Systematically increasing the number, n, of the united atoms approximated by an effective coarse-grained monomer, we study the influence of degree of coarse-graining on the structure functions such as the segment-segment intermolecular and intramolecular correlation functions. These results are compared to Monte Carlo simulations of the corresponding coarse-grained bead-spring model and Chen-Kreglewski potential for chain molecules. In contrast to the atomistic chemically realistic model of…
Single-molecule FRET studies of counterion effects on the free energy landscape of human mitochondrial lysine tRNA.
2011
The folding energy landscape of RNA is greatly affected by interactions between the RNA and counterions that neutralize the backbone negative charges and may also participate in tertiary contacts. Valence, size, coordination number, and electron shell structure can all contribute to the energetic stabilization of specific RNA conformations. Using single-molecule fluorescence resonance energy transfer (smFRET), we have examined the folding properties of the RNA transcript of human mitochondrial tRNA(Lys), which possesses two different folded states in addition to the unfolded one under conditions of thermodynamic equilibrium. We have quantitatively analyzed the degree of RNA tertiary structu…
Incoherent elastic and quasi-elastic neutron scattering investigation of hemoglobin dynamics.
2005
In this work we investigate the dynamic properties of hemoglobin in glycerolD(8)/D(2)O solution using incoherent elastic (ENS) and quasi-elastic (QENS) neutron scattering. Taking advantage of complementary energy resolutions of backscattering spectrometers at ILL (Grenoble), we explore motions in a large space-time window, up to 1 ns and 14 A; moreover, in order to cover the harmonic and anharmonic protein dynamics regimes, the elastic experiments have been performed over the wide temperature interval of 20-300 K. To study the dependence of the measured dynamics upon the protein quaternary structure, both deoxyhemoglobin (in T quaternary conformation) and carbonmonoxyhemoglobin (in R quater…
Determination of association constants towards carbon nanotubes† †Electronic supplementary information (ESI) available: Synthetic details and charact…
2015
We describe a simple procedure for the determination of association constants between soluble molecules and insoluble and heterogeneous carbon nanotube samples.
Determination of the relative quantum yields of the conformational species of autoassociating polypeptide gramicidin A in organic solvent using combi…
1987
Abstract A simple, novel method is proposed for the accurate determination of the relative quantum yields of each of the interconverting conformational species of the autoassociating polypeptide gramicidin A in organic solution. The method is based on fitting the experimental results obtained independently from fluorescence emission spectroscopy and high performance liquid chromatography. The fluorescence parameters obtained are discussed in terms of the structural features of the individual conformational species. The advantages of this approach and its possible application to other different organic solvents or to other autoassociating polypeptides are also considered.
Bifurcation of Singularities Near Reversible Systems
1994
In this paper we study generic unfoldings of certain singularities in the class of all C ∞ reversible systems on R 2.
A New Monte Carlo Method for the Titration of Molecules and Minerals
2007
The charge state of molecules and solid/liquid interfaces is of paramount importance in the understanding of the reactivity and the physico-chemical properties of many systems. In this work, we porpose a new Monte Carlo method in the grand canonical ensemble using the primitive model, which allows us to simulate the titration behavior of macromolecules or solids at constant pH. The method is applied to the charging process of colloidal silica particles dispersed in a sodium salt solution for various concentrations and calcium silicate hydrate nano-particles in a calcium hydroxide solution. An excellent agreement is found between the experimental and simulated results.
Field-induced ferromagnetism due to magneto-striction in 1-D helical chains
2016
Two homochiral copper(II) helices, [Cu(μ1,3-N3)(L1)]n (1) and [Cu(μ1,3-NCO)(L2)]n (2), with end-to-end pseudohalide bridges, were synthesized using two N2O donor achiral Schiff bases via spontaneous chiral resolution. Field-induced ferromagnetic ordering due to magneto-striction in homochiral 1-D helix [Cu(μ1,3-N3)(L1)]n (1) is reported for the first time. At temperatures below 5.5 K, under a magnetic field of 1 T, orthogonality between the magnetic orbitals of copper centres increases significantly due to the contraction of lattice parameters, giving rise to long-range ferromagnetic ordering in the helical chain. The magneto-dielectric results are also indicative of the observed magneto-st…
Intermolecular coupling influence on conformations of molecules in solution
1994
Abstract The influence of non-specific intermolecular interactions on conformational equilibria of organic molecules is investigated with the help of the London-Debye-Keesom pair coupling potentials. It is shown that in a series of apolar solvents equilibrium constant logarithms are proportional to ζα ≡ Z αs/ R 6s,d, and in a series of polar solvents equilibrium constants logarithms are proportional to ζμ ≡ Z μ2s/ R 6s,d, where Z is the average number of neighbours of a solute molecule in the first coordination sphere, αs is the polarizability, μs the dipole moment of solvent molecules, and R s,d = R s + R d is the sum of the radii of spherical volumes per molecule of solvent (s) and dissol…
Computer simulations of DNA stretching
2006
Abstract In this chapter we will give short review of computer modelling/simulations of DNA manipulation as a complementary tool to current single molecule manipulation experiments in order to follow the impact on molecular structure during the manipulation experiments. As an example we report molecular dynamics simulations of a 22 base-pair DNA fragment in an explicit water solution with counter-ions to mimic a torsionally unconstrained single-molecule stretching experiment. Positions of the O5′ and O3′ atoms at one end of the 22-mer were fixed while an external linearly increasing tensile force was applied on the corresponding atoms at the other end. Changes in the intramolecular potentia…