Search results for "biological physics"
showing 10 items of 153 documents
Ultrafast myoglobin structural dynamics observed with an X-ray free-electron laser.
2014
Light absorption can trigger biologically relevant protein conformational changes. The light-induced structural rearrangement at the level of a photoexcited chromophore is known to occur in the femtosecond timescale and is expected to propagate through the protein as a quake-like intramolecular motion. Here we report direct experimental evidence of such ‘proteinquake’ observed in myoglobin through femtosecond X-ray solution scattering measurements performed at the Linac Coherent Light Source X-ray free-electron laser. An ultrafast increase of myoglobin radius of gyration occurs within 1 picosecond and is followed by a delayed protein expansion. As the system approaches equilibrium it underg…
Anergy in self-directed B lymphocytes from a statistical mechanics perspective
2012
The ability of the adaptive immune system to discriminate between self and non-self mainly stems from the ontogenic clonal-deletion of lymphocytes expressing strong binding affinity with self-peptides. However, some self-directed lymphocytes may evade selection and still be harmless due to a mechanism called clonal anergy. As for B lymphocytes, two major explanations for anergy developed over three decades: according to "Varela theory", it stems from a proper orchestration of the whole B-repertoire, in such a way that self-reactive clones, due to intensive interactions and feed-back from other clones, display more inertia to mount a response. On the other hand, according to the `two-signal …
Transient frailty induced by cell division. Observation, reasons and implications
2021
We know that stress-factors, e.g. X-rays, have an effect on cells that is more lethal in rapid exponential growth than in stationary phase. It is this effect which makes radiotherapy effective in cancer treatment. This stress effect can be explained in two ways: (a) more vulnerability in the growth phase, (b) improved protection capacity and repair mechanisms in the stationary phase. Although the two explanations do not exclude each other, they are very different in the sense that (a) is a general mechanism whereas (b) is strain and stress-factor dependent. In this paper we explore major facets of (a). Firstly, we emphasize that (a) can account for known experimental stress-factor evidence.…
Is there an infant mortality in bacteria?
2021
This manuscript proposes a significant step in our long-run investigation of infant mortality across species. Since 2016 (Berrut et al. 2016) a succession of studies (Bois et al. 2019) have traced infant mortality from organisms of high complexity (e.g. mammals) down to unicellular organisms. Infant mortality may be considered as a filtering process through which organisms with potentially lethal congenital defects are eliminated. Such defects may have many causes but here we focus particularly on mishaps resulting from non-optimal conditions in the production of proteins, enzymes and other crucial macromolecules. The statistical signature of infant mortality consists in a falling age-speci…
Multiplexed vortex beam-based optical tweezers
2023
The design and implementation of a multiplexed spiral phase mask in an experimental optical tweezer setup are presented. This diffractive optical element allows the generation of multiple concentric vortex beams with independent topological charges. The generalization of the phase mask for multiple concentric vortices is also shown. The design for a phase mask of two multiplexed vortices with different topological charges is developed. We experimentally show the transfer of angular momentum to the optically trapped microparticles by enabling orbiting dynamics around the optical axis independently within each vortex. The angular velocity of the confined particles versus the optical power in …
A probabilistic model for crystal growth applied to protein deposition at the microscale
2018
A probabilistic discrete model for 2D protein crystal growth is presented. This model takes into account the available space and can describe growing processes of different nature due to the versatility of its parameters which gives the model great flexibility. The accuracy of the simulation is tested against a real protein (SbpA) crystallization experiment showing high agreement between the proposed model and the actual images of the nucleation process. Finally, it is also discussed how the regularity of the interface (i.e. the curve that separates the crystal from the substrate) affects to the evolution of the simulation.
Cell-sized confinements alter molecular diffusion in concentrated polymer solutions due to length-dependent wetting of polymers
2023
Living cells are characterized by the micrometric confinement of various macromolecules at high concentrations. Using droplets containing binary polymer blends as artificial cells, we previously showed that cell-sized confinement causes phase separation of the binary polymer solutions because of the length-dependent wetting of the polymers. Here we demonstrate that the wetting-induced heterogeneity of polymers also emerges in single-component polymer solutions. The resulting heterogeneity leads to a slower transport of small molecules at the center of cell-sized droplets than that in bulk solutions. This heterogeneous distribution is observed when longer polymers with lower wettability are …
Growth of immobilized DNA by polymerase: bridging nanoelectrodes with individual dsDNA molecules.
2011
We present a method for controlled connection of gold electrodes with dsDNA molecules (locally on a chip) by utilizing polymerase to elongate single-stranded DNA primers attached to the electrodes. Thiol-modified oligonucleotides are directed and immobilized to nanoscale electrodes by means of dielectrophoretic trapping, and extended in a procedure mimicking PCR, finally forming a complete dsDNA molecule bridging the gap between the electrodes. The technique opens up opportunities for building from the bottom-up, for detection and sensing applications, and also for molecular electronics.
On the role of interfacial hydrogen bonds in "on-water" catalysis.
2014
Numerous experiments have demonstrated that many classes of organic reactions exhibit increased reaction rates when performed in heterogeneous water emulsions. Despite enormous practical importance of the observed "on-water" catalytic effect and several mechanistic studies, its microscopic origins remains unclear. In this work, the second generation Car-Parrinello molecular dynamics method is extended to self-consistent charge density-functional based tight-binding in order to study "on-water" catalysis of the Diels-Alder reaction between dimethyl azodicarboxylate and quadricyclane. We find that the stabilization of the transition state by dangling hydrogen bonds exposed at the aqueous inte…
Recent achievements in ab initio modelling of liquid water
2013
The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water cluste…