Search results for "Biological physics"
showing 10 items of 153 documents
Excitation Transport in Helical Proteins
1994
Recent results for excitation dynamics in and IR-absorption spectrum of helical polypeptides are briefly reviewed.
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.
Action potentials induce biomagnetic fields in Venus flytrap plants
2020
Upon stimulation, plants elicit electrical signals that can travel within a cellular network analogous to the animal nervous system. It is well-known that in the human brain, voltage changes in certain regions result from concerted electrical activity which, in the form of action potentials (APs), travels within nerve-cell arrays. Electrophysiological techniques like electroencephalography, magnetoencephalography, and magnetic resonance imaging are used to record this activity and to diagnose disorders. In the plant kingdom, two types of electrical signals are observed: all-or-nothing APs of similar amplitudes to those seen in humans and animals, and slow-wave potentials of smaller amplitud…
Monitoring noise-resonant effects in cancer growth influenced by external fluctuations and periodic treatment
2007
In the paper we investigate a mathematical model describing the growth of tumor in the presence of immune response of a host organism. The dynamics of tumor and immune cells is based on the generic Michaelis-Menten kinetics depicting interaction and competition between the tumor and the immune system. The appropriate phenomenological equation modeling cell-mediated immune surveillance against cancer is of the predator-prey form and exhibits bistability within a given choice of the immune response-related parameters. Under the influence of weak external fluctuations, the model may be analyzed in terms of a stochastic differential equation bearing the form of an overdamped Langevin-like dynam…
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…