Related papers: Sampling rare switching events in biochemical netw…
We apply the "weighted ensemble" (WE) simulation strategy, previously employed in the context of molecular dynamics simulations, to a series of systems-biology models that range in complexity from one-dimensional to a system with 354…
The digital nature of genes combined with the associated low copy numbers of proteins regulating them is a significant source of stochasticity, which affects the phase of biochemical oscillations. We provide a theoretical framework for…
We study the stochastic dynamics of a system of interacting species in a stochastic environment by means of a continuous-time Markov chain with transition rates depending on the state of the environment. Models of gene regulation in systems…
Cell fate determination, the process through which cells commit to differentiated states is commonly mediated by gene regulatory motifs with mutually exclusive expression states. The classical deterministic picture for cell fate…
In this paper, we consider the problem of optimal exogenous control of gene regulatory networks. Our approach consists in adapting an established reinforcement learning algorithm called the fitted Q iteration. This algorithm infers the…
Key features of biological activity can often be captured by transitions between a finite number of semi-stable states that correspond to behaviors or decisions. We present here a broad class of dynamical systems that are ideal for modeling…
Dynamic gene-regulatory networks are complex since the number of potential components involved in the system is very large. Estimating dynamic networks is an important task because they compromise valuable information about interactions…
We present a self-consistent field approximation to the problem of the genetic switch composed of two mutually repressing/activating genes. The protein and DNA state dynamics are treated stochastically and on equal footing. In this approach…
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant…
Multiple phenotypic states often arise in a single cell with different gene-expression states that undergo transcription regulation with positive feedback. Recent experiments have shown that at least in E. coli, the gene state switching can…
Single-cell data reveal the presence of biological stochasticity between cells of identical genome and environment, in particular highlighting the transcriptional bursting phenomenon. To account for this property, gene expression may be…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
Ring topologies of repressing genes have qualitatively different long-term dynamics if the number of genes is odd (they oscillate) or even (they exhibit bistability). However, these attractors may not fully explain the observed behavior in…
The development of substrates with a switchable wettability is on a fast pace. The limit of switching frequencies and contact angle differences between substrate states are steadily pushed further. We investigate the behavior of a droplet…
With potential relevance to biomechanics, an interesting problem in statistical mechanics not previously solved is a binary mechanical model system. Discrete chemical states of proteins are often associated with discrete metastable…
We present a time dependent variational method to learn the mechanisms of equilibrium reactive processes and efficiently evaluate their rates within a transition path ensemble. This approach builds off variational path sampling methodology…
Understanding the dynamics of complex molecular processes is often linked to the study of infrequent transitions between long-lived stable states. The standard approach to the sampling of such rare events is to generate an ensemble of…
Considerable evidence suggests that anticipating sudden shifts from one state to another in bistable dynamical systems is a challenging task, examples include ecosystems, financial markets, complex diseases, etc. In this paper, we…
Riboswitches, RNA elements found in the untranslated region, regulate gene expression by binding to target metaboloites with exquisite specificity. Binding of metabolites to the conserved aptamer domain allosterically alters the…
Biochemical reaction networks are subjected to large fluctuations attributable to small molecule numbers, yet underlie reliable biological functions. Most theoretical approaches describe them as purely deterministic or stochastic dynamical…