Related papers: Group theory of icosahedral virus capsids: a dynam…
Contagion processes have been proven to fundamentally depend on the structural properties of the interaction networks conveying them. Many real networked systems are characterized by clustered substructures representing either collections…
We present a generic computational framework for the simulation of viral capsid assembly which is quantitative and specific. Starting from PDB files containing atomic coordinates, the algorithm builds a coarse grained description of protein…
Current approaches for modeling propagation in networks (e.g., spread of disease) are unable to adequately capture temporal properties of the data such as order and duration of evolving connections or dynamic likelihoods of propagation…
Dynamical systems methods are used to investigate global behavior of the spatially flat Friedmann-Robertson-Walker cosmological model in gravitational theory with a non-minimally coupled scalar field and a constant potential function. We…
Graphical models are an important tool in exploring relationships between variables in complex, multivariate data. Methods for learning such graphical models are well developed in the case where all variables are either continuous or…
Analytical description of propagation phenomena on random networks has flourished in recent years, yet more complex systems have mainly been studied through numerical means. In this paper, a mean-field description is used to coherently…
Building on the recently derived inhomogeneous mode-coupling theory, we extend the generalised mode-coupling theory of supercooled liquids to inhomogeneous environments. This provides a first-principles-based, systematic and rigorous way of…
Learning the unique directed acyclic graph corresponding to an unknown causal model is a challenging task. Methods based on functional causal models can identify a unique graph, but either suffer from the curse of dimensionality or impose…
In this work, we introduce a novel methodology for divisive hierarchical clustering. Our divisive (``top-down'') approach is motivated by the fact that agglomerative hierarchical clustering (``bottom-up''), which is commonly used for…
The basic theory of dynamic tides in close binaries is reviewed. Particular attention is paid to resonances between dynamic tides and free oscillation modes and to the role of the apsidal-motion rate in probing the internal structure of…
Edge states protected by bulk topology of photonic crystals show robustness against short-range disorder, making robust information transfer possible. Here, topological photonic crystals under long-range deformations are investigated.…
An Ising-type Vicsek model is proposed for collective motion and sudden direction change in a population of self-propelled particles. Particles move on a linear lattice with velocity +1 or -1 in the one-dimensional model. The probability of…
We suggest and implement an approach for the bottom-up description of systems undergoing large-scale structural changes and chemical transformations from dynamic atomically resolved imaging data, where only partial or uncertain data on…
Minimal energy shapes of closed, elastic shells with twelve pentagonal disclinations introduced in otherwise hexagonally coordinated crystalline lattice are studied. The geometry and the total energy of shells are studied as a function of…
In this paper, we study the topology associated to the fractal manifold model. It turns out that this topology is actually a family of topologies that gives to the fractal manifold a structure of variable topological space. Additionally, we…
We present a practical approach to treat static and dynamical correlation accurately in large multi-configurational systems. The static correlation is accounted for using the spin-flip approach which is well known for capturing static…
Single and collective cell migration are fundamental processes critical for physiological phenomena ranging from embryonic development and immune response to wound healing and cancer metastasis. To understand cell migration from a physical…
In active matter systems, self-propelled particles can self-organize to undergo collective motion, leading to persistent dynamical behavior out of equilibrium. In cells, cytoskeletal filaments and motor proteins self-organize into complex…
In this paper we study a simple cascading process in a structured heterogeneous population, namely, a network composed of two loosely coupled communities. We demonstrate that under certain conditions the cascading dynamics in such a network…
In many virus families, tens to thousands of proteins assemble spontaneously into a capsid (protein shell) while packaging the genomic nucleic acid. This review summarizes recent advances in computational modeling of these dynamical…