Fractional-order susceptible-infected model: definition and applications to the study of COVID-19 main protease [PDF]
Fract Calc Appl Anal, 2020 We propose a model for the transmission of perturbations across the amino acids of a protein represented as an interaction network. The dynamics consists of a Susceptible-Infected (SI) model based on the Caputo fractional-order derivative.
Abadias, Luciano +2 more
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Computational and Mathematical Biophysics, 2022 The venerable process of cellular respiration is essential for cells to produce energy from glucose molecules, in order to carry out cellular work. The process is responsible for producing molecules of ATP, a molecule which is thermodynamically coupled ...
Chaturvedi Archit
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Nanoscopy of the cellular response to hypoxia by means of fluorescence resonance energy transfer (FRET) and new FRET software [PDF]
PMC Biophys, 2010 Christoph Wotzlaw +3 more
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Tropicalization and tropical equilibration of chemical reactions [PDF]
, 2012 Systems biology uses large networks of biochemical reactions to model the functioning of biological cells from the molecular to the cellular scale. The dynamics of dissipative reaction networks with many well separated time scales can be described as a ...
Grigoriev, Dima +3 more
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Improving RNA secondary structure prediction via state inference with deep recurrent neural networks
Computational and Mathematical Biophysics, 2020 The problem of determining which nucleotides of an RNA sequence are paired or unpaired in the secondary structure of an RNA, which we call RNA state inference, can be studied by different machine learning techniques.
Willmott Devin +2 more
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Modeling repulsive forces on fibres via knot energies
Computational and Mathematical Biophysics, 2014 Modeling of repulsive forces is essential to the understanding of certain bio-physical processes, especially for the motion of DNA molecules. These kinds of phenomena seem to be driven by some sort of “energy” which especially prevents the molecules from
Blatt Simon, Reiter Philipp
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Stability Analysis of Turing Patterns Generated by the Schnakenberg Model [PDF]
, 2004 We consider the following Schnakenberg model on the interval (−1, 1): ut = D1u − u + vu2 in (−1, 1), vt = D2v + B − vu2 in (−1, 1), u (−1) = u (1) = v (−1) = v (1) = 0, where D1 > 0, D2 > 0, B>0.
Iron, D, Wei, J, Winter, M
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CBSF: A New Empirical Scoring Function for Docking Parameterized by Weights of Neural Network
Computational and Mathematical Biophysics, 2019 A new CBSF empirical scoring function for the estimation of binding energies between proteins and small molecules is proposed in this report. The final score is obtained as a sum of three energy terms calculated using descriptors based on a simple ...
Syrlybaeva Raulia R., Talipov Marat R.
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Stability of cluster solutions in a cooperative consumer chain model [PDF]
, 2012 This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ Springer-Verlag Berlin Heidelberg 2012.We study a cooperative consumer chain model which consists of one producer and two consumers. It is
A Doelman +34 more
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On a Two Dimensional Reaction-Diffusion System with Hypercyclical Structure [PDF]
, 2000 We study a hypercyclical reaction-diffusion system which arises in the modeling of catalytic networks and describes the emerging of cluster states.
Wei, J, Winter, M
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