Search results for "Biological physics"
showing 10 items of 153 documents
Phospholipid monolayers at water∣oil interfaces: theoretical modelling of surface pressure–molecular area isotherms
1998
Abstract The phospholipid adsorption and surface pressure–molecular area isotherms at interfaces are interpreted theoretically from two-dimensional (2D) lattice and real gas models that incorporate a minimum number of adjustable parameters. The first model is based on the lattice statistics of binary solutions and the molecular parameters introduced are the energy changes involved in the mixing process of the phospholipid and organic solvent molecules and the effective phospholipid head area. The surface pressure is interpreted in terms of the difference between the two liquid surface tensions. The second model makes use of (i) a non-localised adsorption model with a square-well potential e…
Exciton description of chlorosome to baseplate excitation energy transfer in filamentous anoxygenic phototrophs and green sulfur bacteria.
2013
A description of intra-chlorosome and from chlorosome to baseplate excitation energy transfer in green sulfur bacteria and in filamentous anoxygenic phototrophs is presented. Various shapes and sizes, single and multiwalled tubes, cylindrical spirals and lamellae of the antenna elements mimicking pigment organization in chlorosomes were generated by using molecular mechanics calculations, and the absorption, LD, and CD spectra of these were predicted by using exciton theory. Calculated absorption and LD spectra were similar for all modeled antenna structures; on the contrary, CD spectra turned out to be sensitive to the size and pigment orientations in the antenna. It was observed that, bri…
Modelling excitonic energy transfer in the photosynthetic unit of purple bacteria
2009
Abstract Molecular mechanics and quantum chemical configuration interaction calculations in combination with exciton theory were used to predict vibronic energies and eigenstates of light harvesting antennae and the reaction centre and to evaluate excitation energy transfer rates in the photosynthetic unit of purple bacteria. Excitation energy transfer rates were calculated by using the transition matrix formalism and exciton basis sets of the interacting antenna systems. Energy transfer rates of 600–800 fs from B800 ring to B850 ring in the LH2 antenna, 3–10 ps from LH2 to LH2 antenna, 2–8 ps from LH2 to LH1 antenna and finally 30–70 ps from LH1 to the reaction centre were obtained. Depend…
Crystal structure of meso-tetrakis(4-nitrophenyl)porphyrin nitrobenzene disolvate
2014
The porphyrin core of the title centrosymmetric compound, C44H26N8O8·2C6H5NO2, is approximately planar, the maximum deviation being 0.069 (3) Å. The planes of the benzene rings of the nitrophenyl substituents are almost perpendicular to the porphyrin mean plane, making dihedral angles of 73.89 (9) and 89.24 (9)°. The two pyrrole ring H atoms are equally disordered over the four pyrrole ring N atoms. In the crystal, weak C—H...O and C—H...N hydrogen bonds link the porphyrin molecules into a three-dimensional supramolecular network. The nitrobenzene solvent molecules are linked by weak C—H...O hydrogen bonds into supramolecular chains propagating along thea-axis direction.
Control of the electronic energy transfer pathway between two single fluorophores by dual pulse excitation.
2009
We report on the control of the energy transfer pathway in individual donor-acceptor dyads by proper timing of light pulses matching the donor and acceptor transition frequencies, respectively. Excitation of both chromophores at virtually the same time induces efficient singlet-singlet annihilation, whereby excitation energy effectively flows from the acceptor to the donor. The dual pulse excitation scheme implemented here allows for all-optical switching of the fluorescence intensity at the single-molecule level. The population of higher excited states at the donor site was found to significantly increase the photobleaching probability.
Structure of Polymer Brushes in Cylindrical Tubes: A Molecular Dynamics Simulation
2006
Molecular Dynamics simulations of a coarse-grained bead-spring model of flexible macromolecules tethered with one end to the surface of a cylindrical pore are presented. Chain length $N$ and grafting density $\sigma$ are varied over a wide range and the crossover from ``mushroom'' to ``brush'' behavior is studied for three pore diameters. The monomer density profile and the distribution of the free chain ends are computed and compared to the corresponding model of polymer brushes at flat substrates. It is found that there exists a regime of $N$ and $\sigma$ for large enough pore diameter where the brush height in the pore exceeds the brush height on the flat substrate, while for large enoug…
Conformations, Transverse Fluctuations and Crossover Dynamics of a Semi-Flexible Chain in Two Dimensions
2014
We present a unified scaling description for the dynamics of monomers of a semiflexible chain under good solvent condition in the free draining limit. We consider both the cases where the contour length $L$ is comparable to the persistence length $\ell_p$ and the case $L\gg \ell_p$. Our theory captures the early time monomer dynamics of a stiff chain characterized by $t^{3/4}$ dependence for the mean square displacement(MSD) of the monomers, but predicts a first crossover to the Rouse regime of $t^{2\nu/{1+2\nu}}$ for $\tau_1 \sim \ell_p^3$, and a second crossover to the purely diffusive dynamics for the entire chain at $\tau_2 \sim L^{5/2}$. We confirm the predictions of this scaling descr…
A Characterization of Quintic Helices
2005
A polynomial curve of degree 5, @a, is a helix if and only if both @[email protected]^'@? and @[email protected]^'@[email protected]^''@? are polynomial functions.
Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics
2013
Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins. WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics. It still suffers however from the same limitation, i.e. the non trivial choice of pertinent collective variables (CVs). To circumvent this problem, we couple WTmetaD with a set of CVs generated from a dihedral Principal Component Analysis (dPCA) on the Ramachadran dihedral angles describing the backbone structure of the protein. The dPCA provides a generic method to extract relevant CVs built from internal coordinates. We illustrate the robustness of this …
Dynamics of closed ecosystems described by operators
2014
Abstract We adopt the so-called occupation number representation , originally used in quantum mechanics and recently adopted in the description of several classical systems, in the analysis of the dynamics of some models of closed ecosystems. In particular, we discuss two linear models, for which the solution can be found analytically, and a nonlinear system, for which we produce numerical results. We also discuss how a dissipative effect could be effectively implemented in the model.