Search results for "Biological physics"
showing 10 items of 153 documents
Diamond Magnetic Microscopy of Malarial Hemozoin Nanocrystals.
2019
Magnetic microscopy of malarial hemozoin nanocrystals was performed using optically detected magnetic resonance imaging of near-surface diamond nitrogen-vacancy centers. Hemozoin crystals were extracted from $Plasmodium$-$falciparum$-infected human blood cells and studied alongside synthetic hemozoin crystals. The stray magnetic fields produced by individual crystals were imaged at room temperature as a function of applied field up to 350 mT. More than 100 nanocrystals were analyzed, revealing the distribution of their magnetic properties. Most crystals ($96\%$) exhibit a linear dependence of stray field magnitude on applied field, confirming hemozoin's paramagnetic nature. A volume magneti…
Gyrification from constrained cortical expansion
2014
The exterior of the mammalian brain - the cerebral cortex - has a conserved layered structure whose thickness varies little across species. However, selection pressures over evolutionary time scales have led to cortices that have a large surface area to volume ratio in some organisms, with the result that the brain is strongly convoluted into sulci and gyri. Here we show that the gyrification can arise as a nonlinear consequence of a simple mechanical instability driven by tangential expansion of the gray matter constrained by the white matter. A physical mimic of the process using a layered swelling gel captures the essence of the mechanism, and numerical simulations of the brain treated a…
Dynamics of the Selkov oscillator.
2018
A classical example of a mathematical model for oscillations in a biological system is the Selkov oscillator, which is a simple description of glycolysis. It is a system of two ordinary differential equations which, when expressed in dimensionless variables, depends on two parameters. Surprisingly it appears that no complete rigorous analysis of the dynamics of this model has ever been given. In this paper several properties of the dynamics of solutions of the model are established. With a view to studying unbounded solutions a thorough analysis of the Poincar\'e compactification of the system is given. It is proved that for any values of the parameters there are solutions which tend to inf…
Counting individual 41Ca atoms with a magneto-optical trap
2003
Atom Trap Trace Analysis (ATTA), a novel method based upon laser trapping and cooling, is used to count individual atoms of 41Ca present in biomedical samples with isotopic abundance levels between 10^-8 and 10^-10. ATTA is calibrated against Resonance Ionization Mass Spectrometry, demonstrating a good agreement between the two methods. The present ATTA system has a counting efficiency of 2x10^-7. Within one hour of observation time, its 3-sigma detection limit on the isotopic abundance of 41Ca reaches 4.5x10^-10.
Anomalous surface diffusion of protons on lipid membranes.
2014
AbstractThe cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of −13.0 ± 0.5 kJ mol−1. The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive re…
Retrieving infinite numbers of patterns in a spin-glass model of immune networks
2013
The similarity between neural and immune networks has been known for decades, but so far we did not understand the mechanism that allows the immune system, unlike associative neural networks, to recall and execute a large number of memorized defense strategies {\em in parallel}. The explanation turns out to lie in the network topology. Neurons interact typically with a large number of other neurons, whereas interactions among lymphocytes in immune networks are very specific, and described by graphs with finite connectivity. In this paper we use replica techniques to solve a statistical mechanical immune network model with `coordinator branches' (T-cells) and `effector branches' (B-cells), a…
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…
Counterion-Mediated Crossing of the Cyanine Limit in Crystals and Fluid Solution: Bond Length Alternation and Spectral Broadening Unveiled by Quantum…
2020
Absorption spectra of cyanine⊕·Br⊖ salts show a remarkable solvent dependence in non/polar solvents, exhibiting narrow, sharp band shapes in dichloromethane but broad features in toluene; this chan...
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…
A PHENOMENOLOGICAL OPERATOR DESCRIPTION OF INTERACTIONS BETWEEN POPULATIONS WITH APPLICATIONS TO MIGRATION
2013
We adopt an operatorial method based on the so-called creation, annihilation and number operators in the description of different systems in which two populations interact and move in a two-dimensional region. In particular, we discuss diffusion processes modeled by a quadratic hamiltonian. This general procedure will be adopted, in particular, in the description of migration phenomena. With respect to our previous analogous results, we use here fermionic operators since they automatically implement an upper bound for the population densities.