Searcharxiv⌕ Search

SEARCH · Searcharxiv

Results for “physics.bio-ph”

Search indexed arXiv papers on artificial intelligence, large language models, computer vision and robotics. Read source abstracts and follow links to arXiv.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 271 records · Page 15Linked to original sources
arXiv2014

Noise driven emergence of cooperative behavior

Cooperative behaviors are defined as the production of common goods benefitting all members of the community at the producer's cost. They could seem to be in contradiction with natural selection, as non-cooperators have an increased fitness compared to cooperators. Understanding the emergence of cooperation has necessitated the development of concepts and models (inclusive fitness, multilevel selection, ...) attributing deterministic advantages to this behavior. In contrast to these models, we show here that cooperative behaviors can emerge by taking into account the stochastic nature of evolutionary dynamics : when cooperative behaviors increase the carrying capacity of the habitat, they also increase the genetic drift against non-cooperators. Using the Wright-Fisher models of population genetics, we compute exactly this increased genetic drift and its consequences on the fixation probability of both types of individuals. This computation leads to a simple criterion: cooperative behavior dominates when the relative increase in carrying capacity of the habitat caused by cooperators is higher than the selection pressure against them. This is a purely stochastic effect with no deterministic interpretation.

q-bio.PE↗
arXiv2014

Effects of Substrate Defects on Lipid Bilayer Compression Dynamics

In vivo and in vitro lipid bilayers are commonly supported by subcellular structures, particles, and artificial substrates. Deformation of the underlying structure can lead to large, localized deformations as the bilayer deforms to avoid stretching. In this work, we consider the effect of defects within the underlying substrate by simulating different bilayers supported by continuous and nanoporous substrates. We show that the bilayer behavior greatly depends on strain rate, and that substrate defects may contribute to the formation of nanotubes for compressed substrate.

cond-mat.soft↗
arXiv2014

Nanoplasmonic Tweezers Visualize Protein p53 Suppressing Unzipping of Single DNA-Hairpins

Here we report on the use of double-nanohole (DNH) optical tweezers as a label-free and free-solution single-molecule probe for protein-DNA interactions. Using this approach, we demonstrate the unzipping of individual 10 base pair DNA-hairpins, and quantify how tumor suppressor p53 protein delays the unzipping. From the Arrhenius behavior, we find the energy barrier to unzipping introduced by p53 to be $2\times 10^{-20}$ J, whereas cys135ser mutant p53 does not show suppression of unzipping, which gives clues to its functional inability to suppress tumor growth. This transformative approach to single molecule analysis allows for ultra-sensitive detection and quantification of protein-DNA interactions to revolutionize the fight against genetic diseases.

physics.bio-ph↗
arXiv2014

Dynamic Variation in Protein-Small Molecule Interaction Observed by Double-Nanohole Optical Trapping

The interaction of proteins with small molecules is fundamental to their function in living organisms and it is widely studied in drug development. Here we compare optical trapping dynamics of streptavidin and biotinylated streptavidin using a double nanohole optical trap in a metal film. Consistent and clearly distinct behavior is seen between the protein with and without the small molecule binding. The real-time dynamics at the single protein level are accessible with this technique, which also has advantages of not requiring tethering to a surface or the need for exogeneous markers.

physics.bio-ph↗
arXiv2014

Waving transport and propulsion in a generalized Newtonian fluid

Cilia and flagella are hair-like appendages that protrude from the surface of a variety of eukaryotic cells and deform in a wavelike fashion to transport fluids and propel cells. Motivated by the ubiquity of non-Newtonian fluids in biology, we address mathematically the role of shear-dependent viscosities on both the waving flagellar locomotion and ciliary transport by metachronal waves. Using a two-dimensional waving sheet as model for the kinematics of a flagellum or an array of cilia, and allowing for both normal and tangential deformation of the sheet, we calculate the flow field induced by a small-amplitude deformation of the sheet in a generalized Newtonian Carreau fluid up to order four in the dimensionless waving amplitude. Shear-thinning and shear-thickening fluids are seen to always induce opposite effects. When the fluid is shear-thinning, the rate of working of the sheet against the fluid is always smaller than in the Newtonian fluid, and the largest gain is obtained for antiplectic metachronal waves. Considering a variety of deformation kinematics for the sheet, we further show that in all cases transport by the sheet is more efficiency in a shear-thinning fluid, and in most cases the transport speed in the fluid is also increased. Comparing the order of magnitude of the shear-thinning contributions with past work on elastic effects as well as the magnitude of the Newtonian contributions, our theoretical results suggest that the impact of shear-dependent viscosities on transport could play a major biological role.

physics.flu-dyn↗
arXiv2014

Capillary Network, Cancer and Kleiber Law

We develop a heuristic model embedding Kleiber and Murray laws to describe mass growth, metastasis and vascularization in cancer. We analyze the relevant dynamics using different evolution equations (Verhulst, Gompertz and others). Their extension to reaction diffusion equation of the Fisher type is then used to describe the relevant metastatic spreading in space. Regarding this last point, we suggest that cancer diffusion may be regulated by Levy flights mechanisms and discuss the possibility that the associated reaction diffusion equations are of the fractional type, with the fractional coefficient being determined by the fractal nature of the capillary evolution.

physics.bio-ph↗
arXiv2014

Bright and fast voltage reporters across the visible spectrum via electrochromic FRET (eFRET)

We present a palette of brightly fluorescent genetically encoded voltage indicators (GEVIs) with excitation and emission peaks spanning the visible spectrum, sensitivities from 6 - 10% Delta F/F per 100 mV, and half-maximal response times from 1 - 7 ms. A fluorescent protein is fused to an Archaerhodopsin-derived voltage sensor. Voltage-induced shifts in the absorption spectrum of the rhodopsin lead to voltage-dependent nonradiative quenching of the appended fluorescent protein. Through a library screen, we identified linkers and fluorescent protein combinations which reported neuronal action potentials in cultured rat hippocampal neurons with a single-trial signal-to-noise ratio from 6.6 to 11.6 in a 1 kHz imaging bandwidth at modest illumination intensity. The freedom to choose a voltage indicator from an array of colors facilitates multicolor voltage imaging, as well as combination with other optical reporters and optogenetic actuators.

q-bio.BM↗
arXiv2014

Does quantum entanglement in DNA synchronize the catalytic centers of type II restriction endonucleases?

Several living systems have been examined for their apparent optimization of structure and function for quantum behavior at biological length scales. Orthodox type II endonucleases, the largest class of restriction enzymes, recognize four-to-eight base pair sequences of palindromic DNA, cut both strands symmetrically, and act without an external metabolite such as ATP. While it is known that these enzymes induce strand breaks by attacking phosphodiester bonds, what remains unclear is the mechanism by which cutting occurs in concert at the catalytic centers. Previous studies indicate the primacy of intimate DNA contacts made by the specifically bound enzyme in coordinating the two synchronized cuts. We propose that collective electronic behavior in the DNA helix generates coherent oscillations, quantized through boundary conditions imposed by the endonuclease, that provide the energy required to break two phosphodiester bonds. Such quanta may be preserved in the presence of thermal noise and electromagnetic interference through decoherence shielding, the specific complex's exclusion of water and ions surrounding the helix. Clamping energy imparted by the enzyme decoherence shield is comparable with zero-point modes of the dipole-dipole oscillations in the DNA recognition sequence. The palindromic mirror symmetry of this sequence should conserve parity during the process. Experimental data corroborate that symmetric bond-breaking ceases when the symmetry of the endonuclease complex is violated, or when environmental parameters are perturbed far from biological optima. Persistent correlation between states in DNA sequence across spatial separations of any length--a characteristic signature of quantum entanglement--may be explained by such a physical mechanism.

physics.bio-ph↗
arXiv2014

Joint fitting reveals hidden interactions in tumor growth

Tumor growth is often the result of the simultaneous development of two or more cancer cell populations. Their interaction between them characterizes the system evolution. To obtain information about these interactions we apply the recently developed vector universality (VUN) formalism to various instances of competition between tumor populations. The formalism allows us: (a) to quantify the growth mechanisms of a HeLa cell colony, describing the phenotype switching responsible for its fast expansion, (b) to reliably reconstruct the evolution of the necrotic and viable fractions in both in vitro and in vivo tumors using data for the time dependences of the total masses, and (c) to show how the shedding of cells leading to subspheroid formation is beneficial to both the spheroid and subspheroid populations, suggesting that shedding is a strong positive influence on cancer dissemination.

q-bio.TO↗
arXiv2014

Slime mould electronic oscillators

We construct electronic oscillator from acellular slime mould Physarum polycephalum. The slime mould oscillator is made of two electrodes connected by a protoplasmic tube of the living slime mould. A protoplasmic tube has an average resistance of 3~MOhm. The tube's resistance is changing over time due to peristaltic contractile activity of the tube. The resistance of the protoplasmic tube oscillates with average period of 73~sec and average amplitude of 0.6~MOhm. We present experimental laboratory results on dynamics of Physarum oscillator under direct current voltage up to 15~V and speculate that slime mould P. polycephalum can be employed as a living electrical oscillator in biological and hybrid circuits.

cs.ET↗
arXiv2014

Volume Determination of Globular Proteins by Molecular Dynamics

Molecular dynamics simulations of myoglobin and aspartate aminotransferase, with explicit solvent, are shown to accurately reproduce the experimentally measured molar volumes. Single amino-acid substitution at VAL39 of aspartate aminotransferase is known to produce large volumetric changes in the enzyme, and this effect is demonstrated in simulation as well. This molecular dynamics approach, while more computationally expensive that extant computational methods of determining the apparent volume of biological systems, is quite feasible with modern computer hardware and is shown to yield accurate volumetric data with as little as several nanoseconds of dynamics.

cond-mat.soft↗
arXiv2014

A microscopic model for hydrated biological tissues

The present work presents a density-functional microscopic model of soft biological tissue. The model was based on a prototype molecular structure from experimentally resolved collagen peptide residues and water clusters and has the objective to capture some well-known experimental features of soft tissues. It was obtained the optimized geometry, binding and coupling energies and dipole moments. The results concerning the stability of the confined water clusters, the water-water and water-collagen interactions within the CLBM framework were successfully correlated to some important trends observed experimentally in inflammatory tissues.

cond-mat.soft↗
arXiv2014

Modification of poly(L-lactide) and polycaprolactone bioresorbable polymeric materials by RF plasma discharge: a preliminary study evaluating EA-hy 926 cell attachment

Surface modification of poly(L-lactide) (L-PLA) and polycaprolactone (PCL) bioresorbable polymers by radio-frequency thermal glow discharge plasma is reported. Improved biocompatibility of L-PLA and PCL materials was obtained by employing hydroxyapatite target sputtering in Ar+ plasma as evidenced by the change of L-PLA and PCL properties from highly hydrophobic to hydrophilic, with absolute wettability obtained for both materials, and enhanced endothelial hybrid cell line EA-hy 926 attachment to modified surfaces. For the latter, surface properties that suppress adverse cellular responses (e.g. apoptosis, necrosis) were also attained. Surface roughness and surface free energy were found to increase significantly for both polymers under prolonged plasma exposure and, a longer chain aliphatic PCL were found to display a marginally better post plasma-treated biocompatibility compared to L-PLA.

cond-mat.mtrl-sci↗
arXiv2014

Origin of $1/f$ noise transition in hydration dynamics on a lipid membrane surface

Water molecules on lipid membrane surfaces are known to contribute to membrane stability by connecting lipid molecules and acting as a water bridge. Although the number of water molecules near the membrane fluctuates dynamically, the hydration dynamics has been veiled. Here we investigate residence statistics of water molecules on the surface of a lipid membrane using all-atom molecular dynamics simulations. We show that hydration dynamics on the lipid membrane exhibit $1/f^β$ noise with two different power-law exponents, $β_l < 1$ and $β_h > 1$. By constructing a dichotomous process for the hydration dynamics, we find that the process can be regarded as a non-Markov renewal process. The result implies that the origin of the $1/f$ noise transition in hydration dynamics on the membrane surface is a combination of a power-law distribution with cutoff of interoccurrence times of switching events and a long-term correlation between the interoccurrence times.

physics.bio-ph↗
arXiv2014

Universal Model of Ontogenetic Growth: Substantiation and Development of Schmalhausen's Model

A hypothesis of singleness of the growth equation for biological objects on different organizational levels and dimensional analysis are used in order to substantiate Schmalhausen's model of ontogenetic growth (the mass of a growing organism is a power function of time). It is stated that such a model is valid only in the initial period of growth. For the whole period of growth, a generalization of Schmalhausen's model is advanced; it provides the same accuracy as previously known models of quantitative description of kinetic curves. Within the scope of the developed model, a number of interesting results related to an allometry and biological time are obtained.

q-bio.QM↗
arXiv2014

Cooperation with both synergistic and local interactions can be worse than each alone

Cooperation is ubiquitous ranging from multicellular organisms to human societies. Population structures indicating individuals' limited interaction ranges are crucial to understand this issue. But it is still at large to what extend multiple interactions involving nonlinearity in payoff play a role on cooperation in structured populations. Here we show a rule, which determines the emergence and stabilization of cooperation, under multiple discounted, linear, and synergistic interactions. The rule is validated by simulations in homogenous and heterogenous structured populations. We find that the more neighbors there are the harder for cooperation to evolve for multiple interactions with linearity and discounting. For synergistic scenario, however, distinct from its pairwise counterpart, moderate number of neighbors can be the worst, indicating that synergistic interactions work with strangers but not with neighbors. Our results suggest that the combination of different factors which promotes cooperation alone can be worse than that with every single factor.

physics.bio-ph↗