Search results for "FOS: Biological sciences"
showing 10 items of 164 documents
Field theoretic study of bilayer membrane fusion: I. Hemifusion mechanism
2003
Self-consistent field theory is used to determine structural and energetic properties of metastable intermediates and unstable transition states involved in the standard stalk mechanism of bilayer membrane fusion. A microscopic model of flexible amphiphilic chains dissolved in hydrophilic solvent is employed to describe these self-assembled structures. We find that the barrier to formation of the initial stalk is much smaller than previously estimated by phenomenological theories. Therefore its creation it is not the rate limiting process. The barrier which is relevant is associated with the rather limited radial expansion of the stalk into a hemifusion diaphragm. It is strongly affected by…
How molecular knots can pass through each other
2014
We propose a mechanism in which two molecular knots pass through each other and swap positions along a polymer strand. Associated free energy barriers in our simulations only amount to a few $k_{B}T$, which may enable the interchange of knots on a single DNA strand.
Protein search for multiple targets on DNA
2016
Protein-DNA interactions are crucial for all biological processes. One of the most important fundamental aspects of these interactions is the process of protein searching and recognizing specific binding sites on DNA. A large number of experimental and theoretical investigations have been devoted to uncovering the molecular description of these phenomena, but many aspects of the mechanisms of protein search for the targets on DNA remain not well understood. One of the most intriguing problems is the role of multiple targets in protein search dynamics. Using a recently developed theoretical framework we analyze this question in detail. Our method is based on a discrete-state stochastic appro…
Monolayer curvature stabilizes nanoscale raft domains in mixed lipid bilayers
2013
According to the lipid raft hypothesis, biological lipid membranes are laterally heterogeneous and filled with nanoscale ordered "raft" domains, which are believed to play an important role for the organization of proteins in membranes. However, the mechanisms stabilizing such small rafts are not clear, and even their existence is sometimes questioned. Here we report the observation of raft-like structures in a coarse-grained molecular model for multicomponent lipid bilayers. On small scales, our membranes demix into a liquid ordered (lo) and a liquid disordered (ld) phase. On large scales, phase separation is suppressed and gives way to a microemulsion-type state that contains nanometer si…
Evolutionary dynamics of imatinib-treated leukemic cells by stochastic approach
2008
The evolutionary dynamics of a system of cancerous cells in a model of chronic myeloid leukemia (CML) is investigated by a statistical approach. Cancer progression is explored by applying a Monte Carlo method to simulate the stochastic behavior of cell reproduction and death in a population of blood cells which can experience genetic mutations. In CML front line therapy is represented by the tyrosine kinase inhibitor imatinib which strongly affects the reproduction of leukemic cells only. In this work, we analyze the effects of a targeted therapy on the evolutionary dynamics of normal, first-mutant and cancerous cell populations. Several scenarios of the evolutionary dynamics of imatinib-tr…
Analysis of DNA sequence variation within marine species using Beta-coalescents
2013
We apply recently developed inference methods based on general coalescent processes to DNA sequence data obtained from various marine species. Several of these species are believed to exhibit so-called shallow gene genealogies, potentially due to extreme reproductive behaviour, e.g. via Hedgecock's "reproduction sweepstakes". Besides the data analysis, in particular the inference of mutation rates and the estimation of the (real) time to the most recent common ancestor, we briefly address the question whether the genealogies might be adequately described by so-called Beta coalescents (as opposed to Kingman's coalescent), allowing multiple mergers of genealogies. The choice of the underlying…
Strong absorption and ultrafast localisation in NaBiS2 nanocrystals with slow charge-carrier recombination.
2022
Funder: AiF Project, no: ZIM-KK5085302DF0
The evolution and changing ecology of the African hominid oral microbiome
2021
Significance The microbiome plays key roles in human health, but little is known about its evolution. We investigate the evolutionary history of the African hominid oral microbiome by analyzing dental biofilms of humans and Neanderthals spanning the past 100,000 years and comparing them with those of chimpanzees, gorillas, and howler monkeys. We identify 10 core bacterial genera that have been maintained within the human lineage and play key biofilm structural roles. However, many remain understudied and unnamed. We find major taxonomic and functional differences between the oral microbiomes of Homo and chimpanzees but a high degree of similarity between Neanderthals and modern humans, incl…
Visual information flow in Wilson-Cowan networks.
2020
In this paper, we study the communication efficiency of a psychophysically tuned cascade of Wilson-Cowan and divisive normalization layers that simulate the retina-V1 pathway. This is the first analysis of Wilson-Cowan networks in terms of multivariate total correlation. The parameters of the cortical model have been derived through the relation between the steady state of the Wilson-Cowan model and the divisive normalization model. The communication efficiency has been analyzed in two ways: First, we provide an analytical expression for the reduction of the total correlation among the responses of a V1-like population after the application of the Wilson-Cowan interaction. Second, we empiri…
Brain reaction times: Linking individual and collective behaviour through Physics modelling
2019
An individual's reaction time data to visual stimuli have usually been represented in Experimental Psychology by means of an ex-Gaussian function (EGF). In most previous works, researchers have mainly aimed at finding a meaning for the parameters of the EGF function in relation to psychological phenomena. We will focus on interpreting the reaction times (RTs) of a group of individuals rather than a single person's RT, which is relevant for the different contexts of social sciences. In doing so, the same model as for the Ideal Gases (IG) (an inanimate system of non-interacting particles) emerges from the experimental RT data. Both systems are characterised by a collective parameter which is …