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Biological signaling is imagined as a combination of activation and transport. The former is triggered by local molecular interactions and the latter is the result of molecular diffusion. However, other fundamental physical principles of…

Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. CRNs are widely used to describe information processing occurring in natural cellular regulatory networks, and with upcoming advances in synthetic biology,…

The performance of autonomous systems heavily relies on their ability to generate a robust representation of the environment. Deep neural networks have greatly improved vision-based perception systems but still fail in challenging…

Chemical communication, response, and feedback are key requirements for the function of adaptive materials with life-like properties. However, how communication on the single cell-level impacts the collective structural, dynamical and…

We consider the certification of temporal quantum correlations using the pseudo-density matrix (PDM), an extension of the density matrix to the time domain, where negative eigenvalues are key indicators of temporal correlations.…

Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural…

Determining cell identities in imaging sequences is an important yet challenging task. The conventional method for cell identification is via cell tracking, which is complex and can be time-consuming. In this study, we propose an innovative…

Spatiotemporal patterns are common in biological systems. For electrically-coupled cells previous studies of pattern formation have mainly used external forcing as the main bifurcation parameter. The purpose of this paper is to show that…

The design of molecules and materials with tailored properties is challenging, as candidate molecules must satisfy multiple competing requirements that are often difficult to measure or compute. While molecular structures, produced through…

The results of space-like separated measurements are independent of distant measurement settings, a property one might call two-way no-signalling. In contrast, time-like separated measurements are only one-way no-signalling since the past…

The temporal characterization of ultrafast laser pulses has become a cornerstone capability of ultrafast optics laboratories and is routine both for optimizing laser pulse duration and designing custom fields. Beyond pure temporal…

A feature of current membrane systems is the fact that objects and membranes are persistent. However, this is not true in the real world. In fact, cells and intracellular proteins have a well-defined lifetime. Inspired from these biological…

Motivated by the fact that living cells use molecular circuits (i.e. a set of chemical reactions) for information processing, this paper investigates the problem of designing molecular circuits for demodulation. In our earlier work, we use…

Biological information processing as implemented by regulatory and signaling networks in living cells requires sufficient specificity of molecular interaction to distinguish signals from one another, but much of regulation and signaling…

Sequential modelling with self-attention has achieved cutting edge performances in natural language processing. With advantages in model flexibility, computation complexity and interpretability, self-attention is gradually becoming a key…

Modeling dynamical biological systems is key for understanding, predicting, and controlling complex biological behaviors. Traditional methods for identifying governing equations, such as ordinary differential equations (ODEs), typically…

In recent years experiments have demonstrated that living cells can measure low chemical concentrations with high precision, and much progress has been made in understanding what sets the fundamental limit to the precision of chemical…

Circadian clocks play a pivotal role in orchestrating numerous physiological and developmental events. Waveform shapes of the oscillations of protein abundances can be informative about the underlying biochemical processes of circadian…

Causal modelling is a tool for generating causal explanations of observed correlations and has led to a deeper understanding of correlations in quantum networks. Existing frameworks for quantum causality tend to focus on acyclic causal…

We propose a theoretical and computational approach to investigate temporal behavior of a nonlinear polarization in perturbative regime induced by an intense and ultrashort pulsed electric field. First-principles time-dependent density…