Search results for "Physics::Biological Physics"
showing 10 items of 78 documents
A Theoretical Model for Excitation Energy Transfer in Chlorosomes: Lamellar and Rod-Shaped Antenna Structures
2008
A model based on exciton theory is presented for description of excitation energy transfer in chlorosomes. Three models to describe the internal organization of the pigments inside the chlorosome were considered, a stack of single-wall rods, a stack of double-wall rods and a stack of lamellae directed along the long axis of the chlorosome. Simulated absorption, circular dichroism and linear dichroism spectra of single-wall rod and the lamella structures turned out to be practically identical. It was shown that rod—rod interactions may localize the exciton states in the regions of a rod facing a neighboring rod. Such localized states provide a fast excitation energy transfer mechanism in per…
Force-dependent folding pathways in mechanically interlocked calixarene dimers via atomistic force quench simulations
2020
Single-molecule force spectroscopy and molecular simulations are well-established techniques to study the mechanical unfolding of supramolecular complexes in various fields of biomolecular physics....
Isotope Effects and Collective Excitations
1983
Isotopic substitution in the aqueous solvent is discussed as an effective method for probing the role of solvent dynamics in the stability of biomolecular conformation.
Photophysical behavior of norharmane related to proximity effect
1990
Abstract Solvent and temperature effects of fluorescence and its polarization characteristics for norharmane were studied. From the results obtained it is concluded that the fluorescent state changes from the φφ ∗ -type in a polar solvent (EPA) to nφ ∗ -type in a nonpolar solvent (MC), and also that lowest singlet excited states (φφ ∗ -type and nφ ∗ -type) interact by vibronic coupling. In the nonpolar solvent (MC) the lowest singlet excited states are very close in energy and consequently the vibronic coupling is stronger. At high temperatures, in a nonpolar solvent (MC), the emission is from both the φφ ∗ - and nφ ∗ -states due to thermal equilibration, while at low temperatures the emiss…
Mapping CO diffusion paths in Myoglobin with the Single Sweep Method
2010
The pathways of diffusion and escape of a CO molecule inside and out a myoglobin protein are investigated. Specifically, the three-dimensional potential of mean force (PMF or free energy) of the CO molecule position inside the protein is calculated by using the single-sweep method in concert with fully resolved atomistic simulations in explicit solvent.The results are interpreted under the assumption that the diffusion of the ligand can be modeled as a navigation on the PMF in which the ligand hops between the PMF local minima following the minimum free energy paths (MFEPs) with rates set by the free energy barriers that need to be crossed. We calculate all these quantities --local minima, …
Brewster angle microscopy and X-ray GID studies of morphology and crystal structure in monolayers of N-tetradecyl-γ,δ-dihydroxypentanoic acid amide
1997
First-order phase transitions from the low-density fluidlike phase to the condensed phase of monolayers of N-tetradecyl-γ,δ-dihydroxypentanoic acid amides at the air−water interface have been studied by π−A isotherms, Brewster angle microscopy (BAM), and synchrotron X-ray grazing incidence diffraction (GID). The thermodynamic differences between enantiomeric and racemic monolayers are too small to be measured. However, chiral discrimination is observable in the macroscopic domain morphology by BAM. The domains of the condensed phase grow dendritically. The characteristic shapes of domains of the pure S and R enantiomers are mirror images of each other. The domains of the racemic mixture are…
rac-(E,trans)-4-Bromo-10,10-dimethyl-9,11-dioxabicyclo[6.3.0]undec-4-ene
2020
In the title compound, a cyclooctene ring in a twist-boat conformation and a dioxolane ring with a distorted envelope conformation are annulated in a trans configuration. Alternating strands of single enantiomers build up the crystal. Within the strands, the molecules are connected by weak C—H...O hydrogen bonds.
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…