Related papers: A Stochastic Biofilm Disruption Model based on Quo…
Well-mixed chemical reaction networks (CRNs) contain many distinct chemical species with copy numbers that fluctuate in correlated ways. While those correlations are typically monitored via Monte Carlo sampling of stochastic trajectories,…
Quantum computing is of great potential for chemical system simulations. In this study, we propose an efficient protocol of quantum computer based simulation of chemical systems which enables accurate chemical reaction modeling on noisy…
Neuromorphic and quantum computing have recently emerged as promising paradigms for advancing artificial intelligence, each offering complementary strengths. Neuromorphic systems built on spiking neurons excel at processing time series data…
Biofilms are communities of bacteria that exhibit a multitude of multiscale biomechanical behaviors. Recent experimental advances have lead to characterizations of these behaviors in terms of measurements of the viscoelastic moduli of…
We present and open source a quantum circuit simulator tailored to chemistry applications. More specifically, our simulator can compute the Born-rule probabilities of samples obtained from circuits containing passive fermionic linear…
The stochastic simulation of large-scale biochemical reaction networks is of great importance for systems biology since it enables the study of inherently stochastic biological mechanisms at the whole cell scale. Stochastic Simulation…
Based on the theory of stochastic chemical kinetics, the inherent randomness and stochasticity of biochemical reaction networks can be accurately described by discrete-state continuous-time Markov chains. The analysis of such processes is,…
Spectroscopy is a crucial laboratory technique for understanding quantum systems through their interactions with electromagnetic radiation. Particularly, spectroscopy is capable of revealing the physical structure of molecules, leading to…
Adsorption is a relevant process in many fields, such as product manufacturing or pollution remediation in porous materials. Adsorption takes place at the molecular scale, amenable to be modeled by Lagrangian numerical methods. We have…
In chemical reaction networks (CRNs) with stochastic semantics based on continuous-time Markov chains (CTMCs), the typically large populations of species cause combinatorially large state spaces. This makes the analysis very difficult in…
This paper proposes a control theoretic framework to model and analyze the self-organized pattern formation of molecular concentrations in biomolecular communication networks, emerging applications in synthetic biology. In biomolecular…
Multi user orthogonal chirp spread spectrum (OCSS) can improve the spectral inefficiency of chirp spread spectrum (CSS) but is only feasible with perfect synchronism and without any channel dispersion. Asynchronism, channel dispersion, or…
We introduce quantum circuits for simulations of multi-mode state-vectors on 3D cQED processors, using matrix product state representations. The circuits are demonstrated as applied to simulations of molecular docking based on holographic…
Biofilms are complex structures which are inhabited by numerous amount of different species of microorganisms. Due to their ubiquity, they influence human life on an everyday basis. It is therefore important to understand the interactions…
The efficient simulation of quantum systems is a primary motivating factor for developing controllable quantum machines. For addressing systems with underlying bosonic structure, it is advantageous to utilize a naturally bosonic platform.…
Bioelectrochemistry is crucial for understanding biological functions and driving applications in synthetic biology, healthcare, and catalysis. However, current simulation methods fail to capture both the stochastic nature of molecular…
Bacterial biofilms mechanically behave as viscoelastic media consisting of micron-sized bacteria crosslinked to a selfproduced network of extracellular polymeric substances (EPS) embedded in water. Structural principles for numerical…
Bacterial cells are sensitive to a range of external signals used to learn the environment. These incoming external signals are then processed using a Gene Regulatory Network (GRN), exhibiting similarities to modern computing algorithms. An…
We derive a physiologically structured multiscale model for biofilm development. The model has components on two spatial scales, which induce different time scales into the problem. The macroscopic behavior of the system is modeled using…
Continuous-time Markov chains are frequently used as stochastic models for chemical reaction networks, especially in the growing field of systems biology. A fundamental problem for these Stochastic Chemical Reaction Networks (SCRNs) is to…