Related papers: Dynamical patterns of p53 states driven by PML
The thermodynamics of proteins indicate that folding/unfolding takes place either through stable intermediates or through a two-state process without intermediates. The rather short folding times of the two-state process indicate that…
Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…
Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. First, we introduce a new theoretical framework, reaction-diffusion system on `chemical species…
Present-day atomistic simulations generate long trajectories of ever more complex systems. Analyzing these data, discovering metastable states, and uncovering their nature is becoming increasingly challenging. In this paper, we first use…
We study the dynamics of particles in a multi-component 2d Lennard-Jones (LJ) fluid in the limiting case where {\it all the particles are different} (APD). The equilibrium properties of this APD system were studied in our earlier work…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
Gene regulatory networks with dynamics characterized by multiple stable states underlie cell fate-decisions. Quantitative models that can link molecular-level knowledge of gene regulation to a global understanding of network dynamics have…
The influence of the internal structure of a biological cell (e.g., a leukocyte) on its dynamics and rheology is not yet fully understood. By using 2D numerical simulations of a bilamellar vesicle (BLV) consisting of two vesicles as a cell…
Cytoskeletal motor proteins are involved in major intracellular transport processes which are vital for maintaining appropriate cellular function. The motor exhibits distinct states of motility: active motion along filaments, and…
This paper presents a computational solution to determine if a chemical reaction network endowed with power-law kinetics (PLK system) has the capacity for multistationarity, i.e., whether there exist positive rate constants such that the…
The activation of matrix metalloproteinase 2 (MMP2) is a crucial event during tumor metastasis and invasion, and this pathway network consists of 3 monomers. The pathway network of the activation obeys to a set of specified reaction rules.…
Protein phase transitions govern numerous diseases, including neurodegenerative disorders such as Parkinson's and Alzheimer's. In Parkinson's disease, distinct species of the protein alpha-synuclein undergo phase transitions from highly…
The exciton dynamics in a molecular heterodimer is studied as a function of differences in excitation and reorganization energies, asymmetry in transition dipole moments and excited state lifetimes. The heterodimer is composed of two…
We investigate the dynamics of a deterministic self-propelled particle endowed with coherent memory. We evidence experimentally and numerically that it exhibits several stable free states. The system is composed of a self-propelled drop…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
The May--Leonard model was introduced to examine the behavior of three competing populations where rich dynamics, such as limit cycles and nonperiodic cyclic solutions, arise. In this work, we perturb the system by adding the capability of…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
A dynamic mitigation mechanism of the two-stream instability is discussed based on a phase control for plasma and fluid instabilities. The basic idea for the dynamic mitigation mechanism by the phase control was proposed in the paper [Phys.…
DNA methylation is a primary layer of epigenetic modification that plays a pivotal role in the regulation of development, aging, and cancer. The concurrent activity of opposing enzymes that mediate DNA methylation and demethylation gives…
MicroRNAs (miRNAs) critically modulate stem cell properties like pluripotency, but the fundamental mechanism remains largely unknown. This study systematically analyzes multiple-omics data and builds a systems physical network including…