Discretised Flux Balance Analysis for Reaction-Diffusion Simulation of Single-Cell Metabolism
Bull Math Biol. 2024 Mar 6;86(4):39. doi: 10.1007/s11538-024-01264-6.ABSTRACTMetabolites have to diffuse within the sub-cellular compartments they occupy to specific locations where enzymes are, so reactions could occur. Conventional flux balance analysis (FBA), a method based on linear programming that is commonly used to model metabolism, implicitly assumes that all enzymatic reactions are not diffusion-limited though that may not always be the case. In this work, we have developed a spatial method that implements FBA on a grid-based system, to enable the exploration of diffusion effects on metabolism. Specifically, the ...
Source: Bulletin of Mathematical Biology - March 6, 2024 Category: Bioinformatics Authors: Yin Hoon Chew Fabian Spill Source Type: research
Modelling the Effects of Growth and Remodelling on the Density and Structure of Cancellous Bone
Bull Math Biol. 2024 Mar 4;86(4):37. doi: 10.1007/s11538-024-01267-3.ABSTRACTA two-stage model is proposed for investigating remodelling characteristics in bone over time and distance to the growth plate. The first stage comprises a partial differential equation (PDE) for bone density as a function of time and distance from the growth plate. This stage clarifies the contributions to changes in bone density due to remodelling and growth processes and tracks the rate at which new bone emanates from the growth plate. The second stage consists of simulating the remodelling process to determine remodelling characteristics. Impl...
Source: Bulletin of Mathematical Biology - March 4, 2024 Category: Bioinformatics Authors: Brianna L Martin Karen J Reynolds Nicola L Fazzalari Murk J Bottema Source Type: research
Modelling the Effects of Growth and Remodelling on the Density and Structure of Cancellous Bone
Bull Math Biol. 2024 Mar 4;86(4):37. doi: 10.1007/s11538-024-01267-3.ABSTRACTA two-stage model is proposed for investigating remodelling characteristics in bone over time and distance to the growth plate. The first stage comprises a partial differential equation (PDE) for bone density as a function of time and distance from the growth plate. This stage clarifies the contributions to changes in bone density due to remodelling and growth processes and tracks the rate at which new bone emanates from the growth plate. The second stage consists of simulating the remodelling process to determine remodelling characteristics. Impl...
Source: Bulletin of Mathematical Biology - March 4, 2024 Category: Bioinformatics Authors: Brianna L Martin Karen J Reynolds Nicola L Fazzalari Murk J Bottema Source Type: research
Parameter Identifiability in PDE Models of Fluorescence Recovery After Photobleaching
Bull Math Biol. 2024 Mar 2;86(4):36. doi: 10.1007/s11538-024-01266-4.ABSTRACTIdentifying unique parameters for mathematical models describing biological data can be challenging and often impossible. Parameter identifiability for partial differential equations models in cell biology is especially difficult given that many established in vivo measurements of protein dynamics average out the spatial dimensions. Here, we are motivated by recent experiments on the binding dynamics of the RNA-binding protein PTBP3 in RNP granules of frog oocytes based on fluorescence recovery after photobleaching (FRAP) measurements. FRAP is a w...
Source: Bulletin of Mathematical Biology - March 2, 2024 Category: Bioinformatics Authors: Maria-Veronica Ciocanel Lee Ding Lucas Mastromatteo Sarah Reichheld Sarah Cabral Kimberly Mowry Bj örn Sandstede Source Type: research
Parameter Identifiability in PDE Models of Fluorescence Recovery After Photobleaching
Bull Math Biol. 2024 Mar 2;86(4):36. doi: 10.1007/s11538-024-01266-4.ABSTRACTIdentifying unique parameters for mathematical models describing biological data can be challenging and often impossible. Parameter identifiability for partial differential equations models in cell biology is especially difficult given that many established in vivo measurements of protein dynamics average out the spatial dimensions. Here, we are motivated by recent experiments on the binding dynamics of the RNA-binding protein PTBP3 in RNP granules of frog oocytes based on fluorescence recovery after photobleaching (FRAP) measurements. FRAP is a w...
Source: Bulletin of Mathematical Biology - March 2, 2024 Category: Bioinformatics Authors: Maria-Veronica Ciocanel Lee Ding Lucas Mastromatteo Sarah Reichheld Sarah Cabral Kimberly Mowry Bj örn Sandstede Source Type: research
Parameter Identifiability in PDE Models of Fluorescence Recovery After Photobleaching
Bull Math Biol. 2024 Mar 2;86(4):36. doi: 10.1007/s11538-024-01266-4.ABSTRACTIdentifying unique parameters for mathematical models describing biological data can be challenging and often impossible. Parameter identifiability for partial differential equations models in cell biology is especially difficult given that many established in vivo measurements of protein dynamics average out the spatial dimensions. Here, we are motivated by recent experiments on the binding dynamics of the RNA-binding protein PTBP3 in RNP granules of frog oocytes based on fluorescence recovery after photobleaching (FRAP) measurements. FRAP is a w...
Source: Bulletin of Mathematical Biology - March 2, 2024 Category: Bioinformatics Authors: Maria-Veronica Ciocanel Lee Ding Lucas Mastromatteo Sarah Reichheld Sarah Cabral Kimberly Mowry Bj örn Sandstede Source Type: research
Correction to: Predicting Radiotherapy Patient Outcomes with Real-Time Clinical Data Using Mathematical Modelling
Bull Math Biol. 2024 Feb 28;86(4):35. doi: 10.1007/s11538-024-01268-2.NO ABSTRACTPMID:38416252 | PMC:PMC10901960 | DOI:10.1007/s11538-024-01268-2 (Source: Bulletin of Mathematical Biology)
Source: Bulletin of Mathematical Biology - February 28, 2024 Category: Bioinformatics Authors: Alexander P Browning Thomas D Lewin Ruth E Baker Philip K Maini Eduardo G Moros Jimmy Caudell Helen M Byrne Heiko Enderling Source Type: research
Correction to: Predicting Radiotherapy Patient Outcomes with Real-Time Clinical Data Using Mathematical Modelling
Bull Math Biol. 2024 Feb 28;86(4):35. doi: 10.1007/s11538-024-01268-2.NO ABSTRACTPMID:38416252 | PMC:PMC10901960 | DOI:10.1007/s11538-024-01268-2 (Source: Bulletin of Mathematical Biology)
Source: Bulletin of Mathematical Biology - February 28, 2024 Category: Bioinformatics Authors: Alexander P Browning Thomas D Lewin Ruth E Baker Philip K Maini Eduardo G Moros Jimmy Caudell Helen M Byrne Heiko Enderling Source Type: research
Correction to: Predicting Radiotherapy Patient Outcomes with Real-Time Clinical Data Using Mathematical Modelling
Bull Math Biol. 2024 Feb 28;86(4):35. doi: 10.1007/s11538-024-01268-2.NO ABSTRACTPMID:38416252 | DOI:10.1007/s11538-024-01268-2 (Source: Bulletin of Mathematical Biology)
Source: Bulletin of Mathematical Biology - February 28, 2024 Category: Bioinformatics Authors: Alexander P Browning Thomas D Lewin Ruth E Baker Philip K Maini Eduardo G Moros Jimmy Caudell Helen M Byrne Heiko Enderling Source Type: research
First Passage Times of Long Transient Dynamics in Ecology
Bull Math Biol. 2024 Feb 23;86(4):34. doi: 10.1007/s11538-024-01259-3.ABSTRACTLong transient dynamics in ecological models are characterized by extended periods in one state or regime before an eventual, and often abrupt, transition. One mechanism leading to long transient dynamics is the presence of ghost attractors, states where system dynamics slow down and the system lingers before eventually transitioning to the true attractor. This transition results solely from system dynamics rather than external factors. This paper investigates the dynamics of a classical herbivore-grazer model with the potential for ghost attract...
Source: Bulletin of Mathematical Biology - February 23, 2024 Category: Bioinformatics Authors: Grant R Poulsen Claire E Plunkett Jody R Reimer Source Type: research
First Passage Times of Long Transient Dynamics in Ecology
Bull Math Biol. 2024 Feb 23;86(4):34. doi: 10.1007/s11538-024-01259-3.ABSTRACTLong transient dynamics in ecological models are characterized by extended periods in one state or regime before an eventual, and often abrupt, transition. One mechanism leading to long transient dynamics is the presence of ghost attractors, states where system dynamics slow down and the system lingers before eventually transitioning to the true attractor. This transition results solely from system dynamics rather than external factors. This paper investigates the dynamics of a classical herbivore-grazer model with the potential for ghost attract...
Source: Bulletin of Mathematical Biology - February 23, 2024 Category: Bioinformatics Authors: Grant R Poulsen Claire E Plunkett Jody R Reimer Source Type: research
First Passage Times of Long Transient Dynamics in Ecology
Bull Math Biol. 2024 Feb 23;86(4):34. doi: 10.1007/s11538-024-01259-3.ABSTRACTLong transient dynamics in ecological models are characterized by extended periods in one state or regime before an eventual, and often abrupt, transition. One mechanism leading to long transient dynamics is the presence of ghost attractors, states where system dynamics slow down and the system lingers before eventually transitioning to the true attractor. This transition results solely from system dynamics rather than external factors. This paper investigates the dynamics of a classical herbivore-grazer model with the potential for ghost attract...
Source: Bulletin of Mathematical Biology - February 23, 2024 Category: Bioinformatics Authors: Grant R Poulsen Claire E Plunkett Jody R Reimer Source Type: research
First Passage Times of Long Transient Dynamics in Ecology
Bull Math Biol. 2024 Feb 23;86(4):34. doi: 10.1007/s11538-024-01259-3.ABSTRACTLong transient dynamics in ecological models are characterized by extended periods in one state or regime before an eventual, and often abrupt, transition. One mechanism leading to long transient dynamics is the presence of ghost attractors, states where system dynamics slow down and the system lingers before eventually transitioning to the true attractor. This transition results solely from system dynamics rather than external factors. This paper investigates the dynamics of a classical herbivore-grazer model with the potential for ghost attract...
Source: Bulletin of Mathematical Biology - February 23, 2024 Category: Bioinformatics Authors: Grant R Poulsen Claire E Plunkett Jody R Reimer Source Type: research
3D Genome Reconstruction from Partially Phased Hi-C Data
Bull Math Biol. 2024 Feb 22;86(4):33. doi: 10.1007/s11538-024-01263-7.ABSTRACTThe 3-dimensional (3D) structure of the genome is of significant importance for many cellular processes. In this paper, we study the problem of reconstructing the 3D structure of chromosomes from Hi-C data of diploid organisms, which poses additional challenges compared to the better-studied haploid setting. With the help of techniques from algebraic geometry, we prove that a small amount of phased data is sufficient to ensure finite identifiability, both for noiseless and noisy data. In the light of these results, we propose a new 3D reconstruct...
Source: Bulletin of Mathematical Biology - February 22, 2024 Category: Bioinformatics Authors: Diego Cifuentes Jan Draisma Oskar Henriksson Annachiara Korchmaros Kaie Kubjas Source Type: research
3D Genome Reconstruction from Partially Phased Hi-C Data
Bull Math Biol. 2024 Feb 22;86(4):33. doi: 10.1007/s11538-024-01263-7.ABSTRACTThe 3-dimensional (3D) structure of the genome is of significant importance for many cellular processes. In this paper, we study the problem of reconstructing the 3D structure of chromosomes from Hi-C data of diploid organisms, which poses additional challenges compared to the better-studied haploid setting. With the help of techniques from algebraic geometry, we prove that a small amount of phased data is sufficient to ensure finite identifiability, both for noiseless and noisy data. In the light of these results, we propose a new 3D reconstruct...
Source: Bulletin of Mathematical Biology - February 22, 2024 Category: Bioinformatics Authors: Diego Cifuentes Jan Draisma Oskar Henriksson Annachiara Korchmaros Kaie Kubjas Source Type: research
