Search results for "Physics::Biological Physics"
showing 10 items of 78 documents
Membrane-mediated Protein-protein Interaction: A Monte Carlo Study
2012
We investigate membrane-mediated interactions between transmembrane proteins using coarse-grained models. We compare the effective potential of mean force (PMF) between two proteins, which are always aligned parallel to the z-axis of the simulation box, with those PMFs obtained for proteins with fluctuating orientations. The PMFs are dominated by an oscillatory packing-driven contribution and a smooth attractive hydrophobic mismatch contribution, which vanishes if the hydrophobic length of the protein matches the thickness of the membrane. If protein orientations are allowed to fluctuate, the oscillations are greatly reduced compared to proteins with fixed orientation. Furthermore, the hydr…
Hydrodynamic synchronization of pairs of puller type magnetotactic bacteria in a high frequency rotating magnetic field.
2019
Ensembles of magnetotactic bacteria are known to interact hydrodynamically and form swarms under the influence of external magnetic fields. We describe the synchronization of puller type magnetotactic bacteria in a rotating magnetic field by representing the bacteria as hydrodynamic force dipoles. Numerical simulations show that at moderate values of the hydrodynamic interaction parameter large ensembles of asynchronously rotating bacteria randomly eject propagating doublets of synchronized bacteria. We quantitatively analyze the dynamics of the doublets and show that an important role in the formation of these propagating structures is played by the parameters characterizing the possible t…
Ewald sum for hydrodynamic interactions of rigid spherical microswimmers
2018
We derive the Ewald sum decomposition of the grand mobility tensor which captures the hydrodynamic interactions in an infinite suspension of rigid spherical microswimmers. The grand mobility tensor connects the motion of an individual swimmer to the active and passive forces and torques acting on all the swimmers, and it is calculated based on a minimal microswimmer model incorporating the swimmers' finite body size. Our results have direct applications to the Stokesian dynamics simulations of an infinite suspension of rigid-bodied microswimmers. They also provide a platform to develop more advanced methods such as particle-mesh-Ewald-sum and accelerated Stokesian dynamics simulations.
Acceptor Concentration Dependence of Förster Resonance Energy Transfer Dynamics in Dye–Quantum Dot Complexes
2014
The dynamics of the photoinduced Forster resonance energy transfer (FRET) in a perylene diimide–quantum dot organic–inorganic hybrid system has been investigated by femtosecond time-resolved absorption spectroscopy. The bidentate binding of the dye acceptor molecules to the surface of CdSe/CdS/ZnS multishell quantum dots provides a well-defined dye-QD geometry for which the efficiency of the energy transfer reaction can be easily tuned by the acceptor concentration. In the experiments, the spectral characteristics of the chosen FRET pair facilitate a selective photoexcitation of the quantum dot donor. Moreover, the acceptor related transient absorption change that occurs solely after energy…
Highly transparent and birefringent chromophores for organic photorefractive materials
1999
Abstract A series of chromophores for application in organic photorefractive (PR) materials is investigated by electro-optical absorption measurements (EOAM). This experimental technique yields information on the transition dipole moment μ ag , the ground-state dipole moment μ g , and the change of the dipole moment upon optical excitation Δ μ within the intense charge transfer (CT) band of the dyes. It is shown that the results of the EOAM experiment allow us to estimate the PR figures-of-merits (FOMs) of the chromophores by either perturbational two-level equations or Kramers–Kronig transformation. In particular, chromophores based on the heterocyclic dihydropyran and dihydropyridine grou…
Chemically selective imaging of overlapping C-H stretching vibrations with time-resolved coherent anti-stokes Raman scattering (CARS) microscopy.
2014
Chemically selective imaging of spectrally overlapping compounds is studied with a time-resolved, femtosecond approach on coherent anti-Stokes Raman scattering (CARS) microscopy taking advantage of time-dependent oscillating CARS amplitude which is sensitive to different chemical components at different time points. Chemically selective imaging is demonstrated for composite material of polypropylene (PP) matrix and om-POSS (octamethyl polyhedral oligomeric silsesquioxane) microparticles having partly overlapping CH stretching vibrations. Inverse Fourier transformation (IFT) was applied to Raman spectra of PP and om-POSS, indicating that the oscillatory structures of the vibrational decays d…
Electronic States, Absorption Spectrum and Circular Dichroism Spectrum of the Photosynthetic Bacterial LH2 Antenna of Rhodopseudomonas acidophila as …
1999
A new approach that uses a combination of semiempirical configuration interaction method and exciton theory to calculate electronic energies, eigenstates, absorption spectrum and circular dichroism (CD) spectrum of the LH2 antenna of Rhodopseudomonas acidophila is introduced. A statistical simulation that uses experimental homogeneous line widths was used to account for the inhomogeneous line width of the observed spectrum. Including the effect of orbital overlap of the close-lying pigments of the B850 ring and the effect of the pigment protein interaction in the B800 ring allowed a successful simulation of the experimental absorption and CD spectra of the antenna at room temperature. Two e…
Theoretical investigation of electronic excitation energy transfer in bichromophoric assemblies.
2008
Electronic excitation energy transfer (EET) rates in rylene diimide dyads are calculated using second-order approximate coupled-cluster theory and time-dependent density functional theory. We investigate the dependence of the EET rates on the interchromophoric distance and the relative orientation and show that Forster theory works quantitatively only for donor-acceptor separations larger than roughly 5 nm. For smaller distances the EET rates are over- or underestimated by Forster theory depending on the respective orientation of the transition dipole moments of the chromophores. In addition to the direct transfer rates we consider bridge-mediated transfer originating from oligophenylene un…
On ripples and rafts: Curvature induced nanoscale structures in lipid membranes
2014
We develop an elastic theory that predicts the spontaneous formation of nanoscale structures in lipid bilayers which locally phase separate between two phases with different spontaneous monolayer curvature. The theory rationalizes in a unified manner the observation of a variety of nanoscale structures in lipid membranes: Rippled states in one-component membranes, lipid rafts in multicomponent membranes. Furthermore, we report on recent observations of rippled states and rafts in simulations of a simple coarse-grained model for lipid bilayers, which are compatible with experimental observations and with our elastic model.
Effect of Packing on Cluster Solvation of Nanotubes
2006
It is discussed the possibility of the existence of single-wall carbon nanotubes (SWNTs) in organic solvents in the form of clusters, containing a number of SWNTs. A theory is developed based on a bundlet model for clusters, which enables describing the distribution function of clusters by size. Comparison of the calculated values of solubility with experimental data would permit obtaining energetic parameters characterizing the interaction of an SWNT with its surrounding, in a solid phase or solution. Fullerenes—SWNTs are unique objects, whose behaviour in many physical situations is characterized by remarkable peculiarities. Peculiarities in solutions show up first in that fullerenes—SWNT…