Related papers: Soft Modes as a Predictive Framework for Low Dimen…
Biological systems, with many interacting components, face high-dimensional environmental fluctuations, ranging from diverse nutrient deprivations to toxins, drugs, and physical stresses. Yet, many biological control mechanisms are `simple'…
Soft set theory provides a direct framework for parameterized decision modeling by assigning to each attribute (parameter) a subset of a given universe, thereby representing uncertainty in a structured way [1, 2]. Over the past decades, the…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
Dynamical systems in the life sciences are often composed of complex mixtures of overlapping behavioral regimes. Cellular subpopulations may shift from cycling to equilibrium dynamics or branch towards different developmental fates. The…
Different subsystems of organisms adapt over many time scales, such as rapid changes in the nervous system (learning), slower morphological and neurological change over the lifetime of the organism (postnatal development), and change over…
We find that the hierarchical organization of the potential energy landscape in a model supercooled liquid can be related to a change in the spatial distribution of soft normal modes. For groups of nearby minima, between which fast…
Revealing the functional sites of biological sequences, such as evolutionary conserved, structurally interacting or co-evolving protein sites, is a fundamental, and yet challenging task. Different frameworks and models were developed to…
Biologists and physicists have a rich tradition of modeling living systems with simple models composed of a few interacting components. Despite the remarkable success of this approach, it remains unclear how to use such finely tuned models…
Living systems evolve one mutation at a time, but a single mutation can alter the effect of subsequent mutations. The underlying mechanistic determinants of such epistasis are unclear. Here, we demonstrate that the physical dynamics of a…
One of the properties that make ecological systems so unique is the range of complex behavioural patterns that can be exhibited by even the simplest communities with only a few species. Much of this complexity is commonly attributed to…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
Possibility to establish macroscopic phenomenological theory for biological systems, akin to the akin to the well-established framework of thermodynamics, is briefly reviewed. We introduce the concept of an evolutionary fluctuation-response…
Life systems are complex and hierarchical, with diverse components at different scales, yet they sustain themselves, grow, and evolve over time. How can a theory of such complex biological states be developed? Here we note that for a…
We propose an abstract conceptual framework for analysing complex security systems using a new notion of modes and mode transitions. A mode is an independent component of a system with its own objectives, monitoring data, algorithms, and…
We describe a continuous-time modelling framework for biological population dynamics that accounts for demographic noise. In the spirit of the methodology used by statistical physicists, transitions between the states of the system are…
Much of our understanding of ecological and evolutionary mechanisms derives from analysis of low-dimensional models: with few interacting species, or few axes defining "fitness". It is not always clear to what extent the intuition derived…
A challenge in global change biology is to predict how species will respond to future environmental change and to manage these responses. To make such predictions and management actions robust to novel futures, we need to accurately…
A complex system comprises multiple interacting entities whose interdependencies form a unified whole, exhibiting emergent behaviours not present in individual components. Examples include the human brain, living cells, soft matter, Earth's…
We introduce a new measure of the structure of a liquid which is the softness of the mean-field potential developed by us earlier. We find that this softness is sensitive to small changes in the structure. We then study its correlation with…
At its core, the physics paradigm adopts a reductionist approach, aiming to understand fundamental phenomena by decomposing them into simpler, elementary processes. While this strategy has been tremendously successful in physics, it has…