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To explain the differentiation of stem cells in terms of dynamical systems theory, models of interacting cells with intracellular protein expression dynamics are analyzed and simulated. Simulations were carried out for all possible protein…
The mechanical properties of cells are dominated by the cytoskeleton, an interconnected network of long elastic filaments. The connections between the filaments are provided by crosslinking proteins, which constitute, next to the filaments,…
The G-protein coupled receptors EP2 and EP4 both transduce the signal of the lipid messenger Prostaglandin E2 (PGE2). Changes in the cell response to PGE2 can have important effects on immunity and development of diseases, however, a…
Multiple dynamic pathways always exist in biological networks, but their robustness against internal fluctuations and relative stability have not been well recognized and carefully analyzed yet. Here we try to address these issues through…
Pluripotent embryonic stem cells are of paramount importance for biomedical research thanks to their innate ability for self-renewal and differentiation into all major cell lines. The fateful decision to exit or remain in the pluripotent…
Motivated by an ongoing collaboration with clinical oncologists and pathologists, we develop a hybrid partial differential equation--ordinary differential equation (PDE--ODE) framework that captures (i) competition between susceptible and…
The influence of the synaptic channel properties on the stability of delayed activity maintained by recurrent neural network is studied. The duration of excitatory post-synaptic current (EPSC) is shown to be essential for the global…
Many organisms possess both a cell cycle to control DNA replication and a circadian clock to anticipate changes between day and night. In some cases, these two rhythmic systems are known to be coupled by specific, cross-regulatory…
The interaction of condensed phase systems with external electric fields is crucial in myriad processes in nature and technology ranging from the field-directed motion of cells (galvanotaxis), to energy storage and conversion systems…
The phenomena of stochasticity in biochemical processes have been intriguing life scientists for the past few decades. We now know that living cells take advantage of stochasticity in some cases and counteract stochastic effects in others.…
Large-scale force generation is essential for biological functions such as cell motility, embryonic development, and muscle contraction. In these processes, forces generated at the molecular level by motor proteins are transmitted by…
DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve…
Signaling pathways are responsible for the regulation of cell processes, such as monitoring the external environment, transmitting information across membranes, and making cell fate decisions. Given the increasing amount of biological data…
Complex dynamical systems are often modeled as networks, with nodes representing dynamical units which interact through the network's links. Gene regulatory networks, responsible for the production of proteins inside a cell, are an example…
Predicting lithium-ion battery degradation is worth billions to the global automotive, aviation and energy storage industries, to improve performance and safety and reduce warranty liabilities. However, very few published models of battery…
In this work we numerically calculate the electric current through three kinds of DNA sequences (telomeric, \lambda-DNA, and p53-DNA) described by different heuristic models. A bias voltage is applied between two zig-zag edged graphene…
Recent research shows that a faulty or sub-optimally operating metabolic network can often be rescued by the targeted removal of enzyme-coding genes--the exact opposite of what traditional gene therapy would suggest. Predictions go as far…
Whether live cell membranes show miscibility phase transitions (MPTs), and if so, how they fluctuate near the transitions remain outstanding unresolved issues in physics and biology alike. Motivated by these questions we construct a generic…
Reconstruction of gene regulatory networks is the process of identifying gene dependency from gene expression profile through some computation techniques. In our human body, though all cells pose similar genetic material but the activation…
The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…