scholarly journals A minimal and self-consistent in silico cell model based on macromolecular interactions

2007 ◽  
Vol 362 (1486) ◽  
pp. 1831-1839 ◽  
Author(s):  
Christoph Flamm ◽  
Lukas Endler ◽  
Stefan Müller ◽  
Stefanie Widder ◽  
Peter Schuster
Keyword(s):  
Cell Model ◽  
Reaction Network ◽  
Metabolic Reaction ◽  
Minimal Cell ◽  
Biochemical Kinetics ◽  
Biological Phenomena ◽  
Self Consistent ◽  
Basic Features ◽  
Insight Into ◽  
Modelling Approach

A self-consistent minimal cell model with a physically motivated schema for molecular interaction is introduced and described. The genetic and metabolic reaction network of the cell is modelled by multidimensional nonlinear ordinary differential equations, which are derived from biochemical kinetics. The strategy behind this modelling approach is to keep the model sufficiently simple in order to be able to perform studies on evolutionary optimization in populations of cells. At the same time, the model should be complex enough to handle the basic features of genetic control of metabolism and coupling to environmental factors. Thereby, the model system will provide insight into the mechanisms leading to important biological phenomena, such as homeostasis, (circadian) rhythms, robustness and adaptation to a changing environment. One example of modelling a molecular regulatory mechanism, cooperative binding of transcription factors, is discussed in detail.

scholarly journals Be different to be better: the effect of personality on optimal foraging with incomplete knowledge

2021 ◽  
Author(s):  
Poppy M. Jeffries ◽  
Samantha C. Patrick ◽  
Jonathan R. Potts
Keyword(s):  
Optimal Foraging ◽  
Optimal Foraging Theory ◽  
Foraging Strategy ◽  
Foraging Strategies ◽  
Partial Knowledge ◽  
Marginal Value ◽  
Animal Populations ◽  
Plausible Mechanism ◽  
Insight Into ◽  
Modelling Approach

AbstractMany animal populations include a diversity of personalities, and these personalities are often linked to foraging strategy. However, it is not always clear why populations should evolve to have this diversity. Indeed, optimal foraging theory typically seeks out a single optimal strategy for individuals in a population. So why do we, in fact, see a variety of strategies existing in a single population? Here, we aim to provide insight into this conundrum by modelling the particular case of foraging seabirds, that forage on patchy prey. These seabirds have only partial knowledge of their environment: they do not know exactly where the next patch will emerge, but they may have some understanding of which locations are more likely to lead to patch emergence than others. Many existing optimal foraging studies assume either complete knowledge (e.g. Marginal Value Theorem) or no knowledge (e.g. Lévy Flight Hypothesis), but here we construct a new modelling approach which incorporates partial knowledge. In our model, different foraging strategies are favoured by different birds along the bold-shy personality continuum, so we can assess the optimality of a personality type. We show that it is optimal to be shy (resp. bold) when living in a population of bold (resp. shy) birds. This observation gives a plausible mechanism behind the emergence of diverse personalities. We also show that environmental degradation is likely to favour shyer birds and cause a decrease in diversity of personality over time.

scholarly journals Bayesian metabolic flux analysis reveals intracellular flux couplings

2019 ◽  
Vol 35 (14) ◽  
pp. i548-i557 ◽  
Author(s):  
Markus Heinonen ◽  
Maria Osmala ◽  
Henrik Mannerström ◽  
Janne Wallenius ◽  
Samuel Kaski ◽  
...  
Keyword(s):  
Steady State ◽  
Metabolic Flux Analysis ◽  
Metabolic Flux ◽  
Reaction Network ◽  
Reaction Rates ◽  
Supplementary Information ◽  
Flux Analysis ◽  
Metabolic Reaction ◽  
Metabolic Systems ◽  
Genome Scale

AbstractMotivationMetabolic flux balance analysis (FBA) is a standard tool in analyzing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place model assumptions on fluxes due to the convenience of formulating the problem as a linear programing model, while many methods do not consider the inherent uncertainty in flux estimates.ResultsWe introduce a novel paradigm of Bayesian metabolic flux analysis that models the reactions of the whole genome-scale cellular system in probabilistic terms, and can infer the full flux vector distribution of genome-scale metabolic systems based on exchange and intracellular (e.g. 13C) flux measurements, steady-state assumptions, and objective function assumptions. The Bayesian model couples all fluxes jointly together in a simple truncated multivariate posterior distribution, which reveals informative flux couplings. Our model is a plug-in replacement to conventional metabolic balance methods, such as FBA. Our experiments indicate that we can characterize the genome-scale flux covariances, reveal flux couplings, and determine more intracellular unobserved fluxes in Clostridium acetobutylicum from 13C data than flux variability analysis.Availability and implementationThe COBRA compatible software is available at github.com/markusheinonen/bamfa.Supplementary informationSupplementary data are available at Bioinformatics online.

scholarly journals A two-step modelling approach for plasma reactors – experimental validation for CO2 dissociation in surface wave microwave plasma

2019 ◽  
Vol 4 (7) ◽  
pp. 1253-1269 ◽  
Author(s):  
Sergio H. Moreno ◽  
Andrzej I. Stankiewicz ◽  
Georgios D. Stefanidis
Keyword(s):  
Surface Wave ◽  
Performance Analysis ◽  
Experimental Validation ◽  
Microwave Plasma ◽  
Second Step ◽  
Plasma Reactors ◽  
Plasma Model ◽  
Self Consistent ◽  
Modelling Approach

Modelling approach that comprises a 2D self-consistent plasma model for discharge characterization in the first step and a 0D global plasma model for performance analysis in the second step.

Nonsuicidal Self-Injury and Its Relation to Suicidal Behavior

2014 ◽  
Author(s):  
Joseph C. Franklin ◽  
Matthew K. Nock
Keyword(s):  
Suicidal Behavior ◽  
Predictive Power ◽  
Suicide Attempts ◽  
Strong Association ◽  
Future Directions ◽  
Suicidal Intent ◽  
Self Injury ◽  
Basic Features ◽  
Insight Into ◽  
Nonsuicidal Self Injury

Nonsuicidal self-injury (NSSI) is the direct and intentional destruction of one’s own body tissue in the absence of suicidal intent. Although NSSI itself is explicitly nonsuicidal, nearly half of individuals who engage in NSSI also engage in suicidal behavior, and nearly all individuals who engage in suicidal behavior also engage in NSSI. Moreover, recent studies suggest that NSSI is one of the strongest known predictors of future suicide attempts, even exceeding the predictive power of prior suicide attempts in some instances. In this chapter we review the basic features and correlates of NSSI, evaluate the evidence for traditional models of NSSI, and discuss how an emerging model of NSSI may provide insight into the strong association between NSSI and suicidal behavior. We conclude by recommending how to evaluate when NSSI is a behavioral emergency and by noting the most crucial future directions for research on this topic.

Localization of the 4f wave-function in cesium

1996 ◽  
Vol 74 (9-10) ◽  
pp. 565-567
Author(s):  
B. N. Onwuagba
Keyword(s):  
Wave Function ◽  
Field Potential ◽  
Local Spin Density Approximation ◽  
Energy Term ◽  
Radial Part ◽  
Consistent Field ◽  
Self Consistent ◽  
Self Consistent Field ◽  
Kinetic Energy Term ◽  
Insight Into

The local spin density approximation is used in the study of the localization of the 4f wave function in cesium, by superimposing the radial part of the kinetic-energy term on the self-consistent field potential VSCF(r). The results obtained show a collapsed 4f wave function in Cs+, but not in neutral Cs, which compares favourably with the previous findings and provide good insight into the understanding of the collapsed 4f wave function in cesium.

scholarly journals Microfluidic measurement of cell motility in response to applied non-homogeneous DC electric fields

2016 ◽  
Vol 5 (2) ◽  
pp. 237-243
Author(s):  
Marisa Rio ◽  
Sharanya Bola ◽  
Richard H. W. Funk ◽  
Gerald Gerlach
Keyword(s):  
Electric Fields ◽  
Soft Lithography ◽  
Cellular Responses ◽  
Biological Processes ◽  
Biological Phenomena ◽  
Inverted Microscope ◽  
Directional Cell Migration ◽  
Insight Into ◽  
Dc Electric Fields

Abstract. Endogenous electric fields (EFs) play an important role in many biological processes. In order to gain an insight into these biological phenomena, externally applied electric fields are used to study cellular responses. In this work, we report the construction and fabrication of a direct current (DC)-electrically stimulated microfluidic biochip and its validation with murine photoreceptor-derived 661 W cells. The presented device has the particularity of offering a non-homogeneous EF environment that best resembles the endogenous electric fields in vitro. The fabrication process is relatively easy, namely by photolithography and soft lithography techniques and, furthermore, it enables live-cell imaging under an inverted microscope. First experimental results reveal cathodal directional cell migration upon applied DC EFs. In summary, the microfluidic biochip has proven biocompatibility and suitability for cellular electrotaxis experiments in non-homogeneous DC electric fields.

scholarly journals A covariate-constraint method to map brain feature space into lower dimensional manifolds

2020 ◽  
pp. 1-30
Author(s):  
Félix Renard ◽  
Christian Heinrich ◽  
Marine Bouthillon ◽  
Maleka Schenck ◽  
Francis Schneider ◽  
...  
Keyword(s):  
Brain Connectivity ◽  
Feature Space ◽  
Graph Metrics ◽  
Brain Connectome ◽  
Biological Phenomena ◽  
Number Of Patients ◽  
Population Comparison ◽  
Constraint Method ◽  
The Brain ◽  
Insight Into

Human brain connectome studies aim at both exploring healthy brains, and extracting and analyzing relevant features associated to pathologies of interest. Usually this consists in modeling the brain connectome as a graph and in using graph metrics as features. A fine brain description requires graph metrics computation at the node level. Given the relatively reduced number of patients in standard cohorts, such data analysis problems fall in the high-dimension low sample size framework. In this context, our goal is to provide a machine learning technique that exhibits flexibility, gives the investigator grip on the features and covariates, allows visualization and exploration, and yields insight into the data and the biological phenomena at stake. The retained approach is dimension reduction in a manifold1 learning methodology, the originality lying in that one (or several) reduced variables be chosen by the investigator. The proposed method is illustrated on two studies, the first one addressing comatose patients, the second one addressing young versus elderly population comparison. The method sheds light on the differences between brain connectivity graphs using graph metrics and potential clinical interpretations of theses differences.

scholarly journals Application of GIS in the Tourism Designing a Frame Work for Kerala Tourism

2010 ◽  
Vol 5 (1) ◽  
pp. 1-13
Author(s):  
Venugopal C K
Keyword(s):  
Information System ◽  
Geographic Information System ◽  
International Market ◽  
Geographic Information ◽  
Full Potential ◽  
Master Plan ◽  
The Future ◽  
Frame Work ◽  
Basic Features ◽  
Insight Into

Applications of Geographic Information System (GIS) are still in its infancy in the Kerala Tourism perspective.  THE FUTURE OF KEALA Tourism lies in implementing a GIS based solution for its applications.  Some basic features like itinerary planner and destination location finder have been implemented in the official website of Kerala Tourism.  The full potential of GIS is yet to be realised.  In order to compete in the international market this areas needs to be strengthened.  This study gives in insight into the possible implementation of a GIS based solution in the master plan of Kerala Tourism.  Also the possible outputs which such a system can generate are also examined.

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