Related papers: A mathematical model of p62-ubiquitin aggregates i…
We propose a computationally lean, two-stage approach that reliably predicts self-assembly behavior of complex charged molecules on a metallic surfaces under electrochemical conditions. Stage one uses ab initio simulations to provide…
Self-assembly kinetics is usually described by approaches which assume that the shape of the aggregates has a definite form (e.g., spherical, cylindrical, cubic, etc), however that is unlikely to be the case in many finite-sized…
Control of stochastic systems is a challenging open problem in statistical physics, with potential applications in a wealth of systems from biology to granulates. Unlike most cases investigated so far, we aim here at controlling a genuinely…
A recently introduced thermodynamic model of amphiphilic molecules in solution has yielded, under certain realistic conditions, a significant presence of metastable aggregates well below the critical micelle concentration -- a phenomenon…
The three species ABC model of driven particles on a ring is generalized to include vacancies and particle-nonconserving processes. The model exhibits phase separation at high densities. For equal average densities of the three species, it…
We study a two parameter ($u,p$) extension of the conformally invariant raise and peel model. The model also represents a nonlocal and biased-asymmetric exclusion process with local and nonlocal jumps of excluded volume particles in the…
Protein aggregation is an important field of investigation because it is closely related to the problem of neurodegenerative diseases, to the development of biomaterials, and to the growth of cellular structures such as cyto-skeleton.…
This paper describes a massively parallel algebraic multigrid method based on non-smoothed aggregation. It is especially suited for solving heterogeneous elliptic problems as it uses a greedy heuristic algorithm for the aggregation that…
I consider a generic coarse-grained model suitable for the study of bulk self-assembly of liquid crystal (LC) macromolecules. The cases include LC dendrimers, gold nanoparticles modified by polymer chains with terminating LC groups and…
In this work, we study the long time asymptotics of a coagulation model which describes the evolution of a system of particles characterized by their volume and surface area. The aggregation mechanism takes place in two stages: collision…
This paper is devoted to investigate the pattern formation of a volume-filling chemotaxis model with logistic cell growth. We first apply the local stability analysis to establish sufficient conditions of destabilization for uniform…
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…
This study proposes a mixed logit model with multivariate nonparametric finite mixture distributions. The support of the distribution is specified as a high-dimensional grid over the coefficient space, with equal or unequal intervals…
A simple relation of the order of $n$ abstract objects generates an $n-2$ dimensional basis of three dimensional vectors. A cellular automaton-like model of evolution of this system is postulated. During this evolution, some quantities…
In this pedagogical study, carried out by adopting standard mathematical methods of nonlinear dynamics, we have presented some simple analytical models to understand terminal behaviour in industrial growth. This issue has also been…
In this paper, a two-dimensional model for the growth of multi-layer tumors is presented. The model consists of a free boundary problem for the tumor cell membrane and the tumor is supposed to grow or shrink due to cell proliferation or…
We first discuss the geometrical construction and the main mathematical features of the maximum-entropy-production/steepest-entropy-ascent nonlinear evolution equation proposed long ago by this author in the framework of a fully quantum…
Peptides and proteins exhibit a common tendency to assemble into highly ordered fibrillar aggregates, whose formation proceeds in a nucleation-dependent manner that is often preceded by the formation of disordered oligomeric assemblies.…
The existence of a very special ratcheting regime has recently been reported in a granular packing subjected to cyclic loading \cite{alonso04}. In this state, the system accumulates a small permanent deformation after each cycle. After a…
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…