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Metabolic flux balance analyses are a standard tool in analysing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place unrealistic…
Many natural processes occur over characteristic spatial and temporal scales. This paper presents tools for (i) flexibly and scalably coarse-graining cellular automata and (ii) identifying which coarse-grainings express an automaton's…
Quantum computation based on quantum cellular automata (QCA) can greatly reduce the control and precision necessary for experimental implementations of quantum information processing. A QCA system consists of a few species of qubits in…
Advanced photonic tools may enable researchers and clinicians to visualize, track, control and manipulate biological processes at the single-cell level in space and time. Biological systems are complex and highly organized on both spatial…
In-vivo, real-time study of the local and collective cellular biomechanical responses requires the fine and selective manipulation of the cellular environment. One innovative pathway is the use of photoactive bio-substrates such as…
We experimentally demonstrate coherent control of the nonlinear response of optical second harmonic generation in resonant nanostructures beyond the weak-field regime. Contrary to common perception, we show that maximizing the intensity of…
The development of autonomous molecular computers capable of making independent decisions in vivo regarding local drug administration may revolutionize medical science. Recently Benenson at el (2004) have envisioned one form such a ``smart…
We show that a wide variety of non-linear cellular automata (CAs) can be decomposed into a quasidirect product of linear ones. These CAs can be predicted by parallel circuits of depth O(log^2 t) using gates with binary inputs, or O(log t)…
The essential ingredient for studying the phenomena of emergence is the ability to generate and manipulate emergent systems that span large scales. Cellular automata are the model class particularly known for their effective scalability but…
Cellular automata are arrays of finite state machines that can exist in a finite number of states. These machines update their states simultaneously based on specific local rules that govern their interactions. This framework provides a…
We report a study of a system which involves an enzymatic cascade realizing an AND logic gate, with an added photochemical processing of the output allowing to make the gate's response sigmoid in both inputs. New functional forms are…
Recent years have witnessed the growing scholarly interest in the next-generation general-purpose computers. Various innovative computing modes have been proposed, such as optical, quantum phenomena, and DNA-based modes. Sequential logic…
Neural Cellular Automata (NCAs) are bio-inspired dynamical systems in which identical cells iteratively apply a learned local update rule to self-organize into complex patterns, exhibiting regeneration, robustness, and spontaneous dynamics.…
Quantum Hamiltonian Computing is a recent approach that uses quantum systems, in particular a single molecule, to perform computational tasks. Within this approach, we present explicit methods to construct logic gates using two different…
The development of attosecond technology has enabled the real-time observation of coherent electron motion in atoms, molecules and condensed phases. Experimentally, it is now possible to generate laser pulses of durations of only a few tens…
Quantum coherent control of slow light for all-optical switching is investigated in a multi-level system of solids for an understanding of self-induced ultraslow light. In an optical population shelving system of a rare-earth doped solid,…
Non-Markovian quantum evolution of the electronic subsystem in a laser-driven molecule is characterized through the appearance of negative decoherence rates in the canonical form of the electronic master equation. For a driven molecular…
Cellular automata are interacting classical bits that display diverse emergent behaviors, from fractals to random-number generators to Turing-complete computation. We discover that quantum cellular automata (QCA) can exhibit complexity in…
Reaction systems are a formal model that has been introduced to investigate the interactive behaviors of biochemical reactions. Based on the formal framework of reaction systems, we propose new computing models called reaction automata that…
Quantum coherent control of ultrafast bond making and the subsequent molecular dynamics is crucial for the realization of a new photochemistry, where a shaped laser field is actively driving the chemical system in a coherent way from the…