Related papers: Shape-free theory for the self-assembly kinetics i…
The paper analyses stochastic systems describing reacting molecular systems with a combination of two types of state spaces, a finite-dimensional, and an infinite dimenional part. As a typical situation consider the interaction of larger…
This work extends the results of the recently developed theory of a rather complete thermodynamic formalism for discrete-state, continuous-time Markov processes with and without detailed balance. We aim at investigating the question that…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
We describe a computational model for studying the complexity of self-assembled structures with active molecular components. Our model captures notions of growth and movement ubiquitous in biological systems. The model is inspired by…
Controlling the topology of structures self-assembled from a set of heterogeneous building blocks is highly desirable for many applications, but is poorly understood theoretically. Here we show that the thermodynamic theory of self-assembly…
Self-assembly is traditionally described as the process through which an initially disordered system relaxes towards an equilibrium ordered phase only driven by local interactions between its building blocks. However, This definition is too…
Self-assembly in natural and synthetic molecular systems can create complex aggregates or materials whose properties and functionality rises from their internal structure and molecular arrangement. The key microscopic features that control…
The use of reduced models for investigating the self-assembly dynamics underlying protein shell formation in spherical viruses is described. The spontaneous self-assembly of these polyhedral, supramolecular structures, in which icosahedral…
The simulated self-assembly of molecular building blocks into functional complexes is a key area of study in computational biology and materials science. Self-assembly simulations of proteins using physically-motivated potentials for…
An irreversible thermodynamical theory of solids is presented where the kinematic quantities are defined in an automatically objective way. Namely, auxiliary elements like reference frame, reference time and reference configuration are…
A general formulation of stochastic thermodynamics is presented for open systems exchanging energy and particles with multiple reservoirs. By introducing a partition in terms of "macrostates" (e.g. sets of "microstates"), the consequence on…
A kinetic theory of vacuum particle creation under the action of an inertial mechanism is constructed within a nonpertrubative dynamical approach. At the semi-phenomenological level, the inertial mechanism corresponds to quantum field…
There are two paradigms to study nanoscale engines in stochastic and quantum thermodynamics. Autonomous models, which do not rely on any external time-dependence, and models that make use of time-dependent control fields, often combined…
We propose a concept of autonomous energy transducer at a molecular scale, where output is produced with small input energy, of the same order of the thermal energy, without restriction of magnitude or timing of input, and without any…
To study materials phenomena simultaneously at various length scales, descriptions in which matter can be coarse grained to arbitrary levels, are necessary. Attempts to do this in the static regime (i.e. zero temperature) have already been…
We analyze an autonomous micro-engine as a closed quantum mechanical system, including the work it performs and the fuel it consumes. Our model system shows by example that it is possible to transfer energy steadily and spontaneously…
Working in a three-dimensional variant of Winfree's abstract Tile Assembly Model, we show that, for an arbitrary finite, connected shape $X \subset \mathbb{Z}^2$, there is a tile set that uniquely self-assembles into a 3D representation of…
Building structures with hierarchical order through the self-assembly of smaller blocks is not only a prerogative of nature, but also a strategy to design artificial materials with tailored functions. We explore in simulation the…
Theories of phase change and self-assembly often invoke the idea of a `quasiequilibrium', a regime in which the nonequilibrium association of building blocks results nonetheless in a structure whose properties are determined solely by an…
We introduce a simple zero-range process with constant rates and one fast rate for a particular occupation number, which diverges with the system size. Surprisingly, this minor modification induces a condensation transition in the…