Search results for "Physics::Biological Physics"
showing 10 items of 78 documents
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…
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.
Theoretical study of excitation transfer from modified B800 rings of the LH II antenna complex of Rps. acidophila
2002
The recently developed configuration interaction exciton model has been applied to study spectral shifts and B800 to B850 energy transfer rates in a series of modified LH2 light harvesting antenna complexes of the purple bacterium Rhodopseudomonas acidophila. Complexes, where the in vivo B800 bacteriochlorophyll a chromophores are exchanged with different tetrapyrroles including chlorophyll a were studied. Absorption spectra of the modified complexes were simulated by using quantum chemical methods to evaluate site and interaction energies and exciton theory to generate the eigenstates of the chromophore assemblies. Four experimental input parameters: the transition moment of Bchl a, the di…
Alkoxy-styryl DCDHF fluorophores
2010
A photostable dicyanomethylenedihydrofuran fluorophore which contains electron-donating alkoxy groups is described. This chromophore is highly environmentally-sensitive, which is a remarkable property for a fluorescent reporter. Its light excitation also enables, in low viscous solvents, the formation of dark states whose radical or triplet nature is ruled out.
Pore structure and function of synthetic nanopores with fixed charges: tip shape and rectification properties
2011
We present a complete theoretical study of the relationship between the structure (tip shape and dimensions) and function (selectivity and rectification) of asymmetric nanopores on the basis of previous experimental studies. The theoretical model uses a continuum approach based on the Nernst-Planck equations. According to our results, the nanopore transport properties, such as current-voltage (I-V) characteristics, conductance, rectification ratio, and selectivity, are dictated mainly by the shape of the pore tip (we have distinguished bullet-like, conical, trumpet-like, and hybrid shapes) and the concentration of pore surface charges. As a consequence, the nanopore performance in practical…
Tuning active Brownian motion with shot noise energy pulses
2009
The main aim of this work is to explore the possibility of modeling the biological energy support mediated by absorption of ATP (adenosine triphosphate) as an energetic shot noise. We develop a general model with discrete input of energy pulses and study shot-noise-driven ratchets. We consider these ratchets as prototypes of Brownian motors driven by energy-rich ATP molecules. Our model is a stochastic machine able to acquire energy from the environment and convert it into kinetic energy of motion. We present characteristic features and demonstrate the possibility of tuning these motors by adapting the mean frequency of the discrete energy inputs, which are described as a special shot noise…
Investigation of Temperature-Induced Phase Transitions in DOPC and DPPC Phospholipid Bilayers Using Temperature-Controlled Scanning Force Microscopy
2004
Under physiological conditions, multicomponent biological membranes undergo structural changes which help define how the membrane functions. An understanding of biomembrane structure-function relations can be based on knowledge of the physical and chemical properties of pure phospholipid bilayers. Here, we have investigated phase transitions in dipalmitoylphosphatidylcholine (DPPC) and dioleoylphosphatidylcholine (DOPC) bilayers. We demonstrated the existence of several phase transitions in DPPC and DOPC mica-supported bilayers by both atomic force microscopy imaging and force measurements. Supported DPPC bilayers show a broad L(beta)-L(alpha) transition. In addition to the main transition …
Hydrodynamics with spin in bacterial suspensions
2016
We describe a new kind of self-propelling motion of bacteria based on the cooperative action of rotating flagella on the surface of bacteria. Describing the ensemble of rotating flagella in the framework of the hydrodynamics with spin the reciprocal theorem of Stokesian hydrodynamics is generalized accordingly. The velocity of the self-propulsion is expressed in terms of the characteristics of the vector field of flagella orientation and it is shown that unusually high velocities of \textit{Thiovulum majus} bacteria may be explained by the cooperative action of the rotating flagella. The expressions obtained enable us to estimate the torque created by the rotary motors of the bacterium and …