Nexus between in silico and in vivo models to enhance clinical translation of nanomedicine
In cancer, one of the main barriers to effective chemotherapy is inefficient drug delivery. The
delivery of drugs to solid tumors involves various biochemical, biophysical, and mechanical …
delivery of drugs to solid tumors involves various biochemical, biophysical, and mechanical …
Methods of model reduction for large-scale biological systems: a survey of current methods and trends
TJ Snowden, PH van der Graaf, MJ Tindall - Bulletin of mathematical …, 2017 - Springer
Complex models of biochemical reaction systems have become increasingly common in the
systems biology literature. The complexity of such models can present a number of …
systems biology literature. The complexity of such models can present a number of …
Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems
Biologically related processes operate across multiple spatiotemporal scales. For
computational modeling methodologies to mimic this biological complexity, individual scale …
computational modeling methodologies to mimic this biological complexity, individual scale …
A hybrid mechanistic-empirical model for in silico mammalian cell bioprocess simulation
In cell culture processes cell growth and metabolism drive changes in the chemical
environment of the culture. These environmental changes elicit reactor control actions, cell …
environment of the culture. These environmental changes elicit reactor control actions, cell …
Metabolic kinetic modeling provides insight into complex biological questions, but hurdles remain
Highlights•Constraint-based models are useful but do not always sufficiently answer a
question.•Kinetic models provide deeper insight into behavior of complex metabolic …
question.•Kinetic models provide deeper insight into behavior of complex metabolic …
[HTML][HTML] Model reduction of genome-scale metabolic models as a basis for targeted kinetic models
RP van Rosmalen, RW Smith, VAPM Dos Santos… - Metabolic …, 2021 - Elsevier
Constraint-based, genome-scale metabolic models are an essential tool to guide metabolic
engineering. However, they lack the detail and time dimension that kinetic models with …
engineering. However, they lack the detail and time dimension that kinetic models with …
Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry
Most of the fascinating phenomena studied in cell biology emerge from interactions among
highly organized multimolecular structures embedded into complex and frequently dynamic …
highly organized multimolecular structures embedded into complex and frequently dynamic …
Emergence and propagation of epistasis in metabolic networks
S Kryazhimskiy - Elife, 2021 - elifesciences.org
Epistasis is often used to probe functional relationships between genes, and it plays an
important role in evolution. However, we lack theory to understand how functional …
important role in evolution. However, we lack theory to understand how functional …
Complex and detailed balancing of chemical reaction networks revisited
The characterization of the notions of complex and detailed balancing for mass action
kinetics chemical reaction networks is revisited from the perspective of algebraic graph …
kinetics chemical reaction networks is revisited from the perspective of algebraic graph …
A modular approach for modeling the cell cycle based on functional response curves
J De Boeck, J Rombouts, L Gelens - PLoS computational biology, 2021 - journals.plos.org
Modeling biochemical reactions by means of differential equations often results in systems
with a large number of variables and parameters. As this might complicate the interpretation …
with a large number of variables and parameters. As this might complicate the interpretation …