Search results for "topology."

Influence of pathway topology and functional class on the molecular evolution of human metabolic genes

2018

Metabolic networks comprise thousands of enzymatic reactions functioning in a controlled manner and have been shaped by natural selection. Thanks to the genome data, the footprints of adaptive (positive) selection are detectable, and the strength of purifying selection can be measured. This has made possible to know where, in the metabolic network, adaptive selection has acted and where purifying selection is more or less strong and efficient. We have carried out a comprehensive molecular evolutionary study of all the genes involved in the human metabolism. We investigated the type and strength of the selective pressures that acted on the enzyme-coding genes belonging to metabolic pathways …

The Drosophila Larval Locomotor Circuit Provides a Model to Understand Neural Circuit Development and Function

2021

It is difficult to answer important questions in neuroscience, such as: “how do neural circuits generate behaviour?,” because research is limited by the complexity and inaccessibility of the mammalian nervous system. Invertebrate model organisms offer simpler networks that are easier to manipulate. As a result, much of what we know about the development of neural circuits is derived from work in crustaceans, nematode worms and arguably most of all, the fruit fly, Drosophila melanogaster. This review aims to demonstrate the utility of the Drosophila larval locomotor network as a model circuit, to those who do not usually use the fly in their work. This utility is explored first by discussion…

A continued fraction based approach for the Two-photon Quantum Rabi Model

2019

We study the Two Photon Quantum Rabi Model by way of its spectral functions and survival probabilities. This approach allows numerical precision with large truncation numbers, and thus exploration of the spectral collapse. We provide independent checks and calibration of the numerical results by studying an exactly solvable case and comparing the essential qualitative structure of the spectral functions. We stress that the large time limit of the survival probability provides us with an indicator of spectral collapse, and propose a technique for the detection of this signal in the current and upcoming quantum simulations of the model. E.L. acknowledges fruitful discussions with D. Braak. I.…

Mixed topological semimetals driven by orbital complexity in two-dimensional ferromagnets

2018

The concepts of Weyl fermions and topological semimetals emerging in three-dimensional momentum space are extensively explored owing to the vast variety of exotic properties that they give rise to. On the other hand, very little is known about semimetallic states emerging in two-dimensional magnetic materials, which present the foundation for both present and future information technology. Here, we demonstrate that including the magnetization direction into the topological analysis allows for a natural classification of topological semimetallic states that manifest in two-dimensional ferromagnets as a result of the interplay between spin-orbit and exchange interactions. We explore the emerg…

Application of modern computer algebra systems in food formulations and development: A case study

2017

Abstract Background Nutritional security determines the level of public health within a population while inadequate nutrition is one of the major factors in development of various health problems. This can be alleviated with sufficient and affordable access to currently available or newly designed nutritious foods. Scope and approach Formulation of new foods can be very costly, so methods able to lower design expanses are of utmost importance to the industry. Hence, the purpose of this work was to rationalize utilization of modern computerized algebraic systems (CAS) in solving traditional problems for formulating food mixtures by food combinatoric principles (FCP). Key findings and conclus…

Biophysics of high density nanometer regions extracted from super-resolution single particle trajectories: application to voltage-gated calcium chann…

2019

AbstractThe cellular membrane is very heterogenous and enriched with high-density regions forming microdomains, as revealed by single particle tracking experiments. However the organization of these regions remain unexplained. We determine here the biophysical properties of these regions, when described as a basin of attraction. We develop two methods to recover the dynamics and local potential wells (field of force and boundary). The first method is based on the local density of points distribution of trajectories, which differs inside and outside the wells. The second method focuses on recovering the drift field that is convergent inside wells and uses the transient field to determine the…

2016

We determine knotting probabilities and typical sizes of knots in double-stranded DNA for chains of up to half a million base pairs with computer simulations of a coarse-grained bead-stick model: Single trefoil knots and composite knots which include at least one trefoil as a prime factor are shown to be common in DNA chains exceeding 250,000 base pairs, assuming physiologically relevant salt conditions. The analysis is motivated by the emergence of DNA nanopore sequencing technology, as knots are a potential cause of erroneous nucleotide reads in nanopore sequencing devices and may severely limit read lengths in the foreseeable future. Even though our coarse-grained model is only based on …

Androgen-inducible gene 1 increases the ER Ca(2+) content and cell death susceptibility against oxidative stress.

2016

Androgen-induced gene 1 (AIG1) is a transmembrane protein implicated with survival (its expression level was shown to correlate with the survival of patients suffering from hepatocellular carcinoma) and Ca(2+) signaling (over-expression of AIG1 increased transcription mediated by the Ca(2+)-dependent nuclear factor of activated T cells). We aimed to shed light on this less-studied protein and investigated its tissue expression, genomic organization, intracellular localization and membrane topology as well as its effects on cell death susceptibility and the Ca(2+) content of the endoplasmic reticulum. Immunoblotting of mouse tissues demonstrated highest expression of AIG1 in the liver, lung …

2016

AbstractThe different factors involved in the growth process of complex networks imprint valuable information in their observable topologies. How to exploit this information to accurately predict structural network changes is the subject of active research. A recent model of network growth sustains that the emergence of properties common to most complex systems is the result of certain trade-offs between node birth-time and similarity. This model has a geometric interpretation in hyperbolic space, where distances between nodes abstract this optimisation process. Current methods for network hyperbolic embedding search for node coordinates that maximise the likelihood that the network was pro…

Coarse-grained models of double-stranded DNA based on experimentally determined knotting probabilities

2018

Abstract To accurately model double-stranded DNA in a manner that is computationally efficient, coarse-grained models of DNA are introduced, where model parameters are selected by fitting the spectrum of observable DNA knots: We develop a general method to fit free parameters of coarse-grained chain models by comparing experimentally obtained knotting probabilities of short DNA chains to knotting probabilities that are computed in Monte Carlo simulations, resulting in coarse-grained DNA models which are tailored to reflect DNA topology in the best possible way. The method is exemplified by fitting ideal chain models as well as a bead-spring model with excluded volume interactions, to model …