Related papers: Extracting bulk properties of self-assembling syst…

The eigenstate thermalization hypothesis provides a framework for understanding thermalization in isolated quantum many-body systems by characterizing statistical properties of local observables in energy eigenstates. Here we demonstrate…

Assemblies of anisotropic particles commonly appear in studies of active many-body systems. However, in two dimensions, the geometric ramifications of the finite density of such objects are not entirely understood. To fully characterize…

The theory of small-system thermodynamics was originally developed to extend the laws of thermodynamics to length scales of nanometers. Here we review this "nanothermodynamics," and stress how it also applies to large systems that subdivide…

We consider an important class of self-assembly problems and using the formalism of stochastic thermodynamics, we derive a set of design principles for growing controlled assemblies far from equilibrium. The design principles constrain the…

A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms.…

For models which exhibit a continuous phase transition in the thermodynamic limit a numerical study of small systems reveals a non-monotonic behaviour of the microcanonical specific heat as a function of the system size. This is in contrast…

A new method is proposed for a treatment of ideal quantum gases in the microcanonical ensemble near the thermodynamic limit. The method allows rigorous asymptotic calculations of the average number of particles and particle number…

In particle-in-cell simulations and some other statistical computations, the representation of modelled distributions with tracked macro-particles can become locally excessive. Merging or resampling dense clusters or highly-populated phase…

The complex small-scale statistics of turbulence are a result of the combined cascading dynamics through all scales of the flow. Predicting these statistics using fully resolved simulations at the high Reynolds numbers that typically occur…

The scaling of correlations as a function of system size provides important hints to understand critical phenomena on a variety of systems. Its study in biological systems offers two challenges: usually they are not of infinite size, and in…

We present a maximum entropy approach to analyze the internal dynamics of a small system in contact with a large bath e.g. a solute-solvent system. For the small solute, the fluctuations around the mean values of observables are not…

There is a long history in machine learning of model ensembling, beginning with boosting and bagging and continuing to the present day. Much of this history has focused on combining models for classification and regression, but recently…

We present a method which allows reduction of a size of a simulated system. The method can be applied to any system where one can define a finite set of possible states of the system and an elementary process which transforms one state of…

Boltzmann sampling based on Metropolis algorithm has been extensively used for simulating a canonical ensemble. An estimate of a mechanical property, like energy, of an equilibrium system, can be made by averaging over a large number…

In many medical and business applications, researchers are interested in estimating individualized treatment effects using data from a randomized experiment. For example in medical applications, doctors learn the treatment effects from…

Self-assembly plays an essential role in many natural processes, involving the formation and evolution of living or non-living structures, and shows potential applications in many emerging domains. In existing research and practice, there…

We present a formalism for coupling a density functional theory-based quantum simulation to a classical simulation for the treatment of simple metallic systems. The formalism is applicable to multiscale simulations in which the part of the…

We study optical spectra of finite electronic quantum systems at frequencies smaller than the plasma frequency using a quasi-classical approach. This approach includes collective effects and enables us to analyze how the nature of the…

This review article discusses some common enhanced sampling methods in relation to the process of self-assembly of biomolecules. An introduction to self-assembly and its challenges is covered followed by a brief overview of the methods and…

Modeling of physical systems includes extensive use of software packages that implement the accurate finite element method for solving differential equations considered along with the appropriate initial and boundary conditions. When the…