Related papers: Combinatorial Control through Allostery
Random boolean networks are a model of genetic regulatory networks that has proven able to describe experimental data in biology. They not only reproduce important phenomena in cell dynamics, but they are also extremely interesting from a…
Linear implication can represent state transitions, but real transition systems operate under temporal, stochastic or probabilistic constraints that are not directly representable in ordinary linear logic. We propose a general modal…
Molecular communication (MC) is emerging paradigm that employs molecules as information carriers, inspired by biological signaling processes. Existing modulation schemes such as on-off keying (OOK), although simple to implement, suffer from…
Molecules provide the smallest possible circuits in which quantum interference and electron correlation can be engineered to perform logical operations, including the universal NAND gate. We investigate a chemically encoded quantum NAND…
Model predictive control (MPC) has become one of the well-established modern control methods for three-phase inverters with an output LC filter, where a high-quality voltage with low total harmonic distortion (THD) is needed. Although it is…
Computational models of biological processes provide one of the most powerful methods for a detailed analysis of the mechanisms that drive the behavior of complex systems. Logic-based modeling has enhanced our understanding and…
Biological processes, including cell differentiation, organism development, and disease progression, can be interpreted as attractors (fixed points or limit cycles) of an underlying networked dynamical system. In this paper, we study the…
Bacterial chemotactic sensing converts noisy chemical signals into running and tumbling. We analyze the static sensing limits of mixed Tar/Tsr chemoreceptor clusters in individual Escherichia coli cells using a heterogeneous…
Cells use surface receptors to estimate the concentration of external ligands. Limits on the accuracy of such estimations have been well studied for pairs of ligand and receptor species. However, the environment typically contains many…
Signal transduction within biological cells is governed by networks of interacting proteins. Communication between these proteins is mediated by signaling molecules which bind to receptors and induce stochastic transitions between different…
It is the goal of systems biology to understand the behavior of the whole in terms of the knowledge of the parts. This is hard to achieve in many cases due to the difficulty of characterizing the many constituents and their complex web of…
We investigate bistability and memory effects in a molecular junction weakly coupled to metallic leads with the latter being subject to an adiabatic periodic change of the bias voltage. The system is described by a simple Anderson-Holstein…
The asymmetric Hopfield model is used to simulate signaling dynamics in gene/transcription factor networks. The model allows for a direct mapping of a gene expression pattern into attractor states. We analyze different control strategies…
Here we propose four-terminal molecular devices as functional logic gates (AND, NOR and XOR, respectively). Such devices are composed of single organic molecule connected to gold electrodes and located in between gate terminals.…
Quantum control of the wave function of two interacting electrons confined in quasi-one-dimensional double-well semiconductor structures is demonstrated. The control strategies are based on the knowledge of the energy spectrum as a function…
he multiqubit entangled states are coherently controlled in the quantum spin systems composed of $N+1$ interacting antiferromagnetic molecular rings. The tunable intermolecular couplings arise from the local exchange interactions between…
Recent advances in biochemical computing, i.e., information processing with cascades of primarily enzymatic reactions realizing computing gates, such as AND, OR, etc., as well as progress in networking these gates and coupling of the…
In this work, we design a type of controller that consists of adding a specific set of reactions to an existing mass-action chemical reaction network in order to control a target species. This set of reactions is effective for both…
Intracellular signaling often arises from ligand-induced oligomerization of cell surface receptors. This oligomerization or clustering process is fundamentally a cooperative behavior between near-neighbor receptor molecules; the properties…
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…