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Given an unknown dynamical system, what is the minimum number of samples needed for effective learning of its governing laws and accurate prediction of its future evolution behavior, and how to select these critical samples? In this work,…
Non-equilibrium thermodynamics has long been an area of substantial interest to ecologists because most fundamental biological processes, such as protein synthesis and respiration, are inherently energy-consuming. Microbial communities are…
Although resetting has widespread applicability, applying it to the dynamics in the presence of spatial quenched disorder, which is essential in many physical problems, is challenging. In this study, we consider a well-known one-dimensional…
Molecular systems often remain trapped for long times around some local minimum of the potential energy function, before switching to another one -- a behavior known as metastability. Simulating transition paths linking one metastable state…
Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they are forced out of the exponential state into…
Advances in methods of biological data collection are driving the rapid growth of comprehensive datasets across clinical and research settings. These datasets provide the opportunity to monitor biological systems in greater depth and at…
Transcription and translation retrieve and operationalize gene encoded information in cells. These processes are not instantaneous and incur significant delays. In this paper we study Goodwin models of both inducible and repressible operons…
Routinely navigating through an ever-changing and unsteady environment, and utilizing chemical energy, molecular motors transport the cell's crucial components, such as neurotransmitters and organelles. They generate force and pull cargo,…
Habituation - a phenomenon in which a dynamical system exhibits a diminishing response to repeated stimulations that eventually recovers when the stimulus is withheld - is universally observed in living systems from animals to unicellular…
One of the important challenges facing high resolution molecular dynamics calculations is to reproduce biological functions that occur in the macroscopic world and involve macroscopic variables. Some of these functions can be well described…
Genetic systems with multiple loci can have complex dynamics. For example, mean fitness need not always increase and stable cycling is possible. Here, we study the dynamics of a genetic system inspired by the molecular biology of…
Understanding how the effectiveness of natural photosynthetic energy harvesting systems arises from the interplay between quantum coherence and environmental noise represents a significant challenge for quantum theory. Recently it has begun…
Intracellular transport processes are essential to the healthy development of many organisms as well as more generally to healthy cellular function. The complex dynamics and interactions between protein molecules and filaments on different…
It has been suggested that major transitions in evolution require the emergence of novelties, often associated to the cooperative behaviour of previously existing objects or agents. A key innovation involves the first cooperative…
Discovering the underlying dynamics of complex systems from data is an important practical topic. Constrained optimization algorithms are widely utilized and lead to many successes. Yet, such purely data-driven methods may bring about…
This article proposes a fundamental methodological shift in the modelling of policy interventions for sustainability transitions in order to account for complexity (e.g. self-reinforcing mechanism arising from multi-agent interactions) and…
In order to respond to environmental signals, cells often use small molecular circuits to transmit information about their surroundings. Recently, motivated by concrete examples in signaling and gene regulation, a body of work has focused…
Transition interface sampling (TIS) and replica exchange TIS (RETIS) are powerful methods for computing rates of rare events inaccessible to straightforward molecular dynamics (MD) simulations. Path reweighting extends their output,…
Finding an effective medical treatment often requires a search by trial and error. Making this search more efficient by minimizing the number of unnecessary trials could lower both costs and patient suffering. We formalize this problem as…
This paper presents an algorithm for approximating certain types of dynamical systems given by a system of ordinary delay differential equations by a Boolean network model. Often Boolean models are much simpler to understand than complex…