Related papers: Extracting bulk properties of self-assembling syst…
\textit{Ab initio} quantum Monte Carlo (QMC) methods in principle allow for the calculation of exact properties of correlated many-electron systems, but are in general limited to the simulation of a finite number of electrons $N$ in…
When fluids are confined in nanopores, many of their properties deviate from bulk. These include bulk modulus, or compressibility, which determines the mechanical properties of fluid-saturated porous solids. Such properties are of…
Using a numerical approach based on the coupling of the discrete and finite element methods, we explore the variation of the bulk modulus K of soft particle assemblies undergoing isotropic compression. As the assemblies densify under…
New model equations are derived for dynamics of self-aggregation of finite-size particles. Differences from standard Debye-Huckel and Keller-Segel models are: the mobility of particles depends on the configuration of their neighbors and…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
It is shown that a small system in thermodynamic equilibrium with a finite thermostat can have a q-exponential probability distribution which closely depends on the energy nonextensivity and the particle number of the thermostat. The…
We study a two-species bidirectional exclusion process, and a single species variant, which is motivated by the motion of organelles and vesicles along microtubules. Specifically, we are interested in the clustering of the particles and…
Due to the equivalence of the statistical ensembles thermostatic properties of physical systems with short-range interactions can be calculated in different ensembles leading to the same physics. In particular, the ensemble equivalence…
A few decades after Hill's work on nano-thermodynamics, the development of a thermodynamic framework, to account consistently for the fluctuations of small systems due to their interactions with the surrounding environment, is still…
It has been widely realized that Monte Carlo methods (approximation via a sample ensemble) may fail in large scale systems. This work offers some theoretical insight into this phenomenon in the context of the particle filter. We demonstrate…
At present, many laboratories are performing experiments to simulate theoretical models of strongly correlated systems using cold atoms in optical lattices, a program referred to as "Quantum Simulation". It is hoped that these experiments…
The impact of confinement on self-assembly of particles interacting with short-range attraction and long-range repulsion (SALR) potential is studied for thermodynamic states corresponding to local ordering of clusters or layers in the bulk.…
We present a thermodynamic theory for a generic population of $M$ individuals distributed into $N$ groups (clusters). We construct the ensemble of all distributions with fixed $M$ and $N$, introduce a selection functional that embodies the…
A class of models with applications to swarm behavior as well as many other types of spatially extended complex biological and physical systems is studied. Internal fluctuations can play an active role in the organization of the phase…
We compute probability distributions of trajectory observables for reversible and irreversible growth processes. These results reveal a correspondence between reversible and irreversible processes, at particular points in parameter space,…
Multifarious assembly models consider multiple structures assembled from a shared set of components, reflecting the efficient usage of components in biological self-assembly. These models are subject to a high-dimensional parameter space,…
We show and interpret three examples of nontrivial results obtained in numerical simulations of many-body systems: exponential convergence of low-lying energy eigenvalues in the process of progressive truncation of huge shell-model…
The energy of a finite system thermally connected to a thermal reservoir may fluctuate, while the temperature is a constant representing a thermodynamic property of the reservoir. The finite system can also be used as a thermometer for the…
A new approach to describe comminution processes in general ball mills as a macroscopic canonical ensemble is proposed. Using hamiltonian method, the model is able to take simultaneously into account the internal dynamics from mechanical…
The fluctuation theorem characterizes the distribution of the dissipation in nonequilibrium systems and proves that the average dissipation will be positive. For a large system with no external source of fluctuation, fluctuations in…