Many-Body Physics & Biology Group

Dervis Can Vural, Assistant Professor. Physics Department, University of Notre Dame. Email: dvural@nd.edu, Room: Nieuwland Science Hall 384g

Research

People

Publications

Bulletin

Noise



Introduction

Invaders

We are a theoretical group interested in the many body behavior of physical and biological systems in which disorder and strong interactions play an important role. We specialize in statistical mechanics, disordered states of matter and evolutionary biology.

We are currently working on the following questions:

1. The rise and fall of interdependence: How do complex biological structures form, and how do they fall apart? Are these doings and undoings uniquely determined by the physical surroundings governing these systems, or are they universal?

2. Physical limits to knowledge: What is the relationship between the mathematical representation of a physical quantity, and the mathematical representation of a device that measures the physical quantity? When does a past state of a system become irrecoverable? Does a scientific model live in a platonic world or does it have any  physical footprint?

Aging, Failure and Death

agingStandard theories of aging typically focus on microscopic mechanisms such as oxidative damage or telomere shortening. However we age and die not because we run out of cells, but because small scale failures on the cellular level manifest at larger scales, leading to a macroscopic catastrophe.

We view aging as an emergent universal property of systems that consist of a large number of interdependent components (read paper). The video below shows how a large number of interdependent nodes fail.


Failure can also be viewed as a microscope that reveals the structure of a complex system. The failure times of components informs how they are interconnected. Read paper.

Recently, our experimental collaborators verified the interaction based picture of aging in synthetic tissues. Read paper.

Based on experimental observations and earlier theoretical ideas, we predict that tissues collapse through a wave of failure that propagates from outside inwards, with non-monotonic velocity. Read paper.

We organized a nice workshop surrounding these topics.

Disordered Materials

Materials such as glasses, polymers, disordered crystals, quasi-crystals and proteins lack long range order, and are thus referred as disordered solids. The standard model describing disordered solids at low temperatures postulate that these materials are composed of two level systems, i.e. atoms, or groups of atoms with two available discrete configurations.

Glass
All disordered solids universally exhibit certain properties which cannot be explained by the two level systems model.
Here is a critique of the said model, and here is a more general model, from which the universality is derived.

Evolution of Cooperation



We study how flow patterns influence the evolution of social cooperation. We have discovered that flow shear enables and promotes social behavior in microbes. Specifically, shear tears apart social communities clusters, and thereby limiting the spread of cheating strains. The videos above shows how flow patterns can shape social evolution. In a vortex, cooperative microbes can sustain only within an annular region. In a flowing pipe, they can only sustain near the boundaries, where the shear is larger than a critical amount. Everywhere else cheaters take over, causing the groups to weaken and die. Read paper.

Although cheating behavior is often devastating for social species, we have discovered that in special cases, cheating can, counterintuitively, benefit the community. This will happen, in the context of a disease or tumor, where rapid growth can be beneficial. Cheaters fueled by altruists will expand rapidly, and overwhelm the host immune system. Read paper.

Rewinding Randomness


Many astonishing facts about the origin of the universe, evolution of life, or history of civilizations will never be directly observed, but will only be inferred in the light of their manifestations in the present. Forward in time, any state of knowledge, regardless of how exact, will invariably deteriorate into an entropy maximizing probability distribution. We adresss the converse question: Given a measurement at present time, how rapidly does our knowledge fade away backwards in time? Read paper.

inversion

Theoretically relevant information such as original causes or underlying mechanisms are seldom directly observable. For example, one can easily measure the amount of proteins expressed in a cell but not necessarily know what interactions lead to the particular expression pattern. One can observe a certain species decline in numbers, but not exactly know which ecological relationship, or what triggering event causes the decline. When a virus spreads seemingly spontaneously, or when an invasive species expands its range, it is very difficult to know where it exactly came from, or its evolutionary trajectory that lead to its final success.

We develop algorithms and formulae to infer causal origins from raw empirical data, such as identifying the original trigerring event given an observed final state. Read paper.

Quantizing Temperature

Temperature is conventionally defined in terms of the number of possible" microstates, given a set of macroscopic constraints such as total energy, volume and particle number. It is a remarkable achievement of statistical mechanics, that an information theoretical, combinatoric quantity can connect so well to physical observables, such as the hight of a mercury collumn, or the volume of a baloon.

We offer an alternative view of temperature, and propose that temperature must be reformulated as a non-local non-realistic quantum variable. We demonstrate that if a large but finite system is split into two subsystems, their temperatures must get entangled. As such, an operator description of temperature becomes necessary to avoid an EPR-type causality violation. In this new picture, temperature is subject to the constraints of quantum mechanics, where its measurement must necessarily accompany a wavefunction collapse into a "temperature eigenstate". Finally, we briefly discuss the experimental implications of this non-orthodox view of temperature.
Read paper.

Ecological Evolution

Evolution of Complexity1Evolution of Complexity 2

Start with a large number of unrelated species, put them together and wait for many generations. Eventually the interactions between them evolve into a tangled web of exchanges - so much, that no species can survive in isolation. Above are connectivity matrices and phylogenetic trees of two such communities subject to different selective pressures. Higher pressures (right) leads to the formation of specialized communities. Read paper.

Model Awareness


A model need not be a passive descriptor of its subject. If the subject is affected by the model building process, the model must be updated in real time. In some cases, the very act model building can cause the otherwise correct model to fail, or cause an otherwise incorrect model to succeed. In other cases, attempting to predict the future can be detrimental to the predictor. Read paper.



We studied the dynamics of a predictive swarm aiming to maximize the uptake of some resource. A predictive agent tries to estimate what others will do, and update its behavior accordingly. All other predictive agents are doing the same, trying to predict the trajectory of agents that are trying to predict them! The video above shows a few iterations o the thoughts of a predictor, while it saysthey know that I know that they know that I know...". On the left, the resources are initialized randomly, whereas on the right resources are concentrated in two spots, one large and one small. Read paper.

Active Inferrence

Scientific inference involves obtaining the unknown properties or behavior of a system in the light of what is known, typically, without changing the system. We propose an alternative to this approach: a system can be modified in a targetted way, preferrably by a small amount, so that it becomes more predictable or more retrodictable. Read paper.