Search results for "biological physics"
showing 10 items of 153 documents
Characterisation of Chlorophyll a and Chlorophyll b Monomers in Various Solvent Environments with Ultrafast Spectroscopy
1998
In photosynthesis the energy from the sun is captured by light harvesting chlorophyll pigments and converted to stable chemical energy, by the photochemical reaction center. Photosynthetic energy transfer in the antenna systems of green plants has previously been studied by ultrafast time resolved spectroscopy. The characteristics of the chlorophyll pigments itself is important to study in order to understand the dynamics on a femtosecond timescale. One way to study the energy transfer is to use transient absorption spectroscopy and follow the increase or decrease in the transient absorption signal with time (1). Another way to study the energy transfer is to monitor the change in dichroism…
Excitonic energy level structure and pigment-protein interactions in the recombinant water-soluble chlorophyll protein. II. Spectral hole-burning exp…
2011
Persistent spectral hole burning at 4.5 K has been used to investigate the excitonic energy level structure and the excited state dynamics of the recombinant class-IIa water-soluble chlorophyll-binding protein (WSCP) from cauliflower. The hole-burned spectra are composed of four main features: (i) a narrow zero-phonon hole (ZPH) at the burn wavelength, (ii) a number of vibrational ZPHs, (iii) a broad low-energy hole at ~665 and ~683 nm for chlorophyll b- and chlorophyll a-WSCP, respectively, and (iv) a second satellite hole at ~658 and ~673 nm for chlorophyll b- and chlorophyll a-WSCP, respectively. The doublet of broad satellite holes is assigned to an excitonically coupled chlorophyll dim…
The Structure of Cholesterol in Lipid Rafts
2014
Rafts, or functional domains, are transient nano- or mesoscopic structures in the plasma membrane and are thought to be essential for many cellular processes such as signal transduction, adhesion, trafficking and lipid/protein sorting. Observations of these membrane heterogeneities have proven challenging, as they are thought to be both small and short-lived. With a combination of coarse-grained molecular dynamics simulations and neutron diffraction using deuterium labeled cholesterol molecules we observe raft-like structures and determine the ordering of the cholesterol molecules in binary cholesterol-containing lipid membranes. From coarse-grained computer simulations, heterogenous membra…
A nonlinear electronic circuit mimicking the neuronal activity in presence of noise
2013
We propose a nonlinear electronic circuit simulating the neuronal activity in a noisy environment. This electronic circuit is ruled by the set of Bonhaeffer-Van der Pol equations and is excited with a white gaussian noise, that is without external deterministic stimuli. Under these conditions, our circuits reveals the Coherence Resonance signature, that is an optimum of regularity in the system response for a given noise intensity.
Spontaneous Spatiotemporal Ordering of Shape Oscillations Enhances Cell Migration
2019
The migration of cells is relevant for processes such as morphogenesis, wound healing, and invasion of cancer cells. In order to move, single cells deform cyclically. However, it is not understood how these shape oscillations influence collective properties. Here we demonstrate, using numerical simulations, that the interplay of directed motion, shape oscillations, and excluded volume enables cells to locally "synchronize" their motion and thus enhance collective migration. Our model captures elongation and contraction of crawling ameboid cells controlled by an internal clock with a fixed period, mimicking the internal cycle of biological cells. We show that shape oscillations are crucial f…
Flow properties and hydrodynamic interactions of rigid spherical microswimmers.
2017
We analyze a minimal model for a rigid spherical microswimmer and explore the consequences of its extended surface on the interplay between its self-propulsion and flow properties. The model is the first order representation of microswimmers, such as bacteria and algae, with rigid bodies and flexible propelling appendages. The flow field of such a microswimmer at finite distances significantly differs from that of a point-force (Stokeslet) dipole. For a suspension of microswimmers, we derive the grand mobility matrix that connects the motion of an individual swimmer to the active and passive forces and torques acting on all the swimmers. Our investigation of the mobility tensors reveals tha…
Complex Formation between Polyelectrolytes and Oppositely Charged Oligoelectrolytes
2016
We study the complex formation between one long polyanion chain and many short oligocation chains by computer simulations. We employ a coarse-grained bead-spring model for the polyelectrolyte chains, and model explicitly the small salt ions. We systematically vary the concentration and the length of the oligocation, and examine how the oligocations affects the chain conformation, the static structure factor, the radial and axial distribution of various charged species, and the number of bound ions in the complex. At low oligocation concentration, the polyanion has an extended structure. Upon increasing the oligocation concentration, the polyanion chain collapses and forms a compact globule,…
Non-equilibrium Markov state modeling of periodically driven biomolecules
2019
Molecular dynamics simulations allow to study the structure and dynamics of single biomolecules in microscopic detail. However, many processes occur on time scales beyond the reach of fully atomistic simulations and require coarse-grained multiscale models. While systematic approaches to construct such models have become available, these typically rely on microscopic dynamics that obey detailed balance. In vivo, however, biomolecules are constantly driven away from equilibrium in order to perform specific functions and thus break detailed balance. Here we introduce a method to construct Markov state models for systems that are driven through periodically changing one (or several) external p…
Infrared nanospectroscopic mapping of DNA molecules on mica surface
2022
Significant efforts have been done in last two decades to develop nanoscale spectroscopy techniques owning to their great potential for single-molecule structural detection and in addition, to resolve open questions in heterogeneous biological systems, such as protein-DNA complexes. Applying AFM-IR technique has become a powerful leverage for obtaining simultaneous absorption spectra with a nanoscale spatial resolution for studied proteins, however the IR-AFM investigation of DNA molecules on surface, as a benchmark for a nucleoprotein complexes nanocharacterization, has remained elusive. Herein, we demonstrate methodological approach for acquisition of IR-AFM mapping modalities with corres…
Ab initio determination of the ionization potentials of DNA and RNA nucleobases
2006
Quantum chemical high level ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute vertical and adiabatic ionization potentials of the five canonical DNA and RNA nucleobases: uracil, thymine, cytosine, adenine, and guanine. Several states of their cations have been also calculated. The present results represent a systematic compendium of these magnitudes, establishing theoretical reference values at a level not reported before, calibrating computational strategies, and guiding the assignment of the features in the experimental photoelectron spectra. Daniel.Roca@uv.es Mercedes.Rubio@uv.es Manuela.Merchan@uv.es Luis.Serrano@uv.es