Search results for "FOS: Biological sciences"
showing 10 items of 164 documents
On the thermodynamic origin of metabolic scaling
2018
The origin and shape of metabolic scaling has been controversial since Kleiber found that basal metabolic rate of animals seemed to vary as a power law of their body mass with exponent 3/4, instead of 2/3, as a surface-to-volume argument predicts. The universality of exponent 3/4 -claimed in terms of the fractal properties of the nutrient network- has recently been challenged according to empirical evidence that observed a wealth of robust exponents deviating from 3/4. Here we present a conceptually simple thermodynamic framework, where the dependence of metabolic rate with body mass emerges from a trade-off between the energy dissipated as heat and the energy efficiently used by the organi…
Narrow genetic base in forest restoration with holm oak (Quercus ilex L.) in Sicily
2007
International audience; In order to empirically assess the effect of actual seed sampling strategy on genetic diversity of holm oak (Quercus ilex) forestations in Sicily, we have analysed the genetic composition of two seedling lots (nursery stock and plantation) and their known natural seed origin stand by means of six nuclear microsatellite loci. Significant reduction in genetic diversity and significant difference in genetic composition of the seedling lots compared to the seed origin stand were detected. The female and the total effective number of parents were quantified by means of maternity assignment of seedlings and temporal changes in allele frequencies. Extremely low effective ma…
The Strategic Reference Gene: an organismal theory of inclusive fitness
2019
How to define and use the concept of inclusive fitness is a contentious topic in evolutionary theory. Inclusive fitness can be used to calculate selection on a focal gene, but it is also applied to whole organisms. Individuals are then predicted to appear designed as if to maximise their inclusive fitness, provided that certain conditions are met (formally when interactions between individuals are 'additive'). Here we argue that applying the concept of inclusive fitness to organisms is justified under far broader conditions than previously shown, but only if it is appropriately defined. Specifically, we propose that organisms should maximise the sum of their offspring (including any accrued…
Collective behavior of quorum-sensing run-and-tumble particles in confinement
2016
We study a generic model for quorum-sensing bacteria in circular confinement. Every bacterium produces signaling molecules, the local concentration of which triggers a response when a certain threshold is reached. If this response lowers the motility then an aggregation of bacteria occurs, which differs fundamentally from standard motility-induced phase separation due to the long-ranged nature of the concentration of signal molecules. We analyze this phenomenon analytically and by numerical simulations employing two different protocols leading to stationary cluster and ring morphologies, respectively.
Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding
2017
We present a dynamic coarse-graining technique that allows to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSM), which we construct from molecular dynamics simulations using the pulling coordinate as an order parameter. We obtain a sequence of MSMs as a function of the discretized pulling coordinate, and the pulling process is modeled by switching among the MSMs according to the protocol applied to unfold the complex. This way we cover seven orders of magnitude in pulling speed. In the region of rapid pulling we additionally perform steered molecular dynamics simulations and find excellen…
Conformational dynamics of a single protein monitored for 24 hours at video rate
2018
We use plasmon rulers to follow the conformational dynamics of a single protein for up to 24 h at a video rate. The plasmon ruler consists of two gold nanospheres connected by a single protein linker. In our experiment, we follow the dynamics of the molecular chaperone heat shock protein 90 (Hsp90), which is known to show “open” and “closed” conformations. Our measurements confirm the previously known conformational dynamics with transition times in the second to minute time scale and reveals new dynamics on the time scale of minutes to hours. Plasmon rulers thus extend the observation bandwidth 3–4 orders of magnitude with respect to single-molecule fluorescence resonance energy transfer a…
Mapping brain activity with flexible graphene micro-transistors
2016
arXiv:1611.05693v1.-- et al.
Simple Muscle Architecture Analysis (SMA): An ImageJ macro tool to automate measurements in B-mode ultrasound scans
2020
In vivo measurements of muscle architecture (i.e. the spatial arrangement of muscle fascicles) are routinely included in research and clinical settings to monitor muscle structure, function and plasticity. However, in most cases such measurements are performed manually, and more reliable and time-efficient automated methods are either lacking completely, or are inaccessible to those without expertise in image analysis. In this work, we propose an ImageJ script to automate the entire analysis process of muscle architecture in ultrasound images: Simple Muscle Architecture Analysis (SMA). Images are filtered in the spatial and frequency domains with built-in commands and external plugins to hi…
Weakly coupled map lattice models for multicellular patterning and collective normalization of abnormal single-cell states
2017
We present a weakly coupled map lattice model for patterning that explores the effects exerted by weakening the local dynamic rules on model biological and artificial networks composed of two-state building blocks (cells). To this end, we use two cellular automata models based on: (i) a smooth majority rule (model I) and (ii) a set of rules similar to those of Conway's Game of Life (model II). The normal and abnormal cell states evolve according with local rules that are modulated by a parameter $\kappa$. This parameter quantifies the effective weakening of the prescribed rules due to the limited coupling of each cell to its neighborhood and can be experimentally controlled by appropriate e…
Quantum field inspired model of decision making: Asymptotic stabilization of belief state via interaction with surrounding mental environment
2018
This paper is devoted to justification of quantum-like models of the process of decision making based on the theory of open quantum systems, i.e. decision making is considered as decoherence. This process is modeled as interaction of a decision maker, Alice, with a mental (information) environment ${\cal R}$ surrounding her. Such an interaction generates "dissipation of uncertainty" from Alice's belief-state $\rho(t)$ into ${\cal R}$ and asymptotic stabilization of $\rho(t)$ to a steady belief-state. The latter is treated as the decision state. Mathematically the problem under study is about finding constraints on ${\cal R}$ guaranteeing such stabilization. We found a partial solution of th…