Network biologists attempt to extract meaningful relationships among genes or their products from very noisy data. We argue that what we categorize as noisy data may sometimes reflect noisy biology and therefore may shield a hidden meaning about how networks evolve and how matter is organized in the cell. We present practical solutions, based on existing evolutionary and biophysical concepts, t...

Complaints on low-frequency noise were till recently fairly unexplained, but audiological research shed light on the mechanisms that enable perception of frequencies below the threshold of average normal hearing. It was shown that exposure to low-frequency sound may alter the inner ear. This results in an increase of sensitivity to low-frequency sounds, and as a result, previously imperceptible...

Spike timing-dependent plasticity is a fundamental adaptation mechanism of the nervous system. It induces structural changes of synaptic connectivity by regulation of coupling strengths between individual cells depending on their spiking behavior. As a biophysical process its functioning is constantly subjected to natural fluctuations. We study theoretically the influence of noise on a microsco...

In this paper we present an efficient method to generate realistic simulations of extracellular recordings. The method uses a hybrid and computationally simple approach, where the features of the background noise arise naturally from its biophysical process of generation. The generated data resemble the characteristics of real recordings, as quantified by the amplitude and frequency distributio...

Connectivity, or the exchange of individuals among marine populations, is a central topic in marine ecology. For most benthic marine species with complex life cycles, this exchange occurs primarily during the pelagic larval stage. The small size of larvae coupled with the vast and complex fluid environment they occupy hamper our ability to quantify dispersal and connectivity. Evidence from dire...

The impacts of such water transfers are expected to vary temporally and spatially. The aim of this paper is to specify a method to assess these impacts. Although water trading and its impacts have been discussed qualitatively in the literature; there are limited qualitative models available. In the past economists primarily modeled water trading without considering biophysical and systemic cons...

Based on the physico-biophysical considerations, mathematical analysis and some approximate formulations generally adopted in meteorology and ecology, an ecological dynamic model of grassland is developed. The model consists of three interactive variables, i.e. the biomass of living grass, the biomass of wilted grass, and the soil wetness. The major biophysical processes are represented in para...

Many fluorescent proteins are currently available for biological spectroscopy and imaging measurements, allowing a wide range of biochemical and biophysical processes and interactions to be studied at various length scales. However, in applications where a small fluorescence reporter is required or desirable, the choice of fluorophores is rather limited. As such, continued effort has been devot...

Dynamic programming algorithms solve many standard problems of RNA bioinformatics in polynomial time. In this contribution we discuss a series of variations on these standard methods that implement refined biophysical models, such as a restriction of RNA folding to canonical structures, and an extension of structural alignments to an explicit scoring of stacking propensities. Furthermore, we de...

Human spermatozoa have unusual cryobiological behaviour and improvements in their survival have not been achieved by the standard approaches of cryobiology. Conventional approaches to cryopreservation impose a linear change of temperature with time; however, the stresses that cells encounter during cryopreservation are all non-linear with time. In this paper it is shown that improved methods of...