Related papers: Spontaneous dimensional reduction and novel ground…
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…
We report about a mechanism for surface localization, present in finite defect-free polyatomic lattices described by a tight binding model. Numerical diagonalization and degenerated perturbation theory show that there is a minimum number of…
Phase-separated biomolecular condensates exhibit a wide range of dynamical properties, which depend on the sequences of the constituent proteins and RNAs. However, it is unclear to what extent condensate dynamics can be tuned without also…
With the help of a simple 20 letters, lattice model of heteropolymers, we investigate the energy landscape in the space of designed good-folder sequences. Low-energy sequences form clusters, interconnected via neutral networks, in the space…
The equilibrium conformations of a flexible permanent magnetic chain that consists of a sequence of linked magnetic colloidal nanoparticles with short-ranged Lennard-Jones attractive interactions (Stockmayer polymer) are thoroughly analysed…
Folding channels and free-energy landscapes of hydrophobic-polar heteropolymers are discussed on the basis of a minimalistic off-lattice coarse-grained model. We investigate how rearrangements of hydrophobic and polar monomers in a…
This thesis is a theoretical analysis of sample two- and one-dimensional systems. The two-dimensional examples are the quantum Hall liquid and anomalous paired states. The most widely accepted effective theory of the quantum Hall liquid is…
We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and…
In this letter, we study the effects of weak off-diagonal disorder on conjugated polymers with a doubly degenerate ground-state. We find that disorder induces a finite density of neutral solitons in the lattice dimerization of a polymer…
Atomically thin 2-dimensional heterostructures are a promising, novel class of materials with groundbreaking properties. The possiblity of choosing the many constituent components and their proportions allows optimizing these materials to…
Large multidimensionality of high-throughput datasets pertaining to cell signaling and gene regulation renders it difficult to extract mechanisms underlying the complex kinetics involving various biochemical compounds (e.g., proteins,…
Strongly interacting electrons in layered materials give rise to a plethora of emergent phenomena, such as unconventional superconductivity. heavy fermions, and spin textures with non-trivial topology. Similar effects can also be observed…
We study equilibrium shapes and shape transformations of a confined semiflexible chain inside a soft lipid tubule using simulations and continuum theories. The deformed tubular shapes and chain conformations depend on the relative magnitude…
We present the results of a self-consistent, unified molecular dynamics study of simple model heteropolymers in the continuum with emphasis on folding, sequence design and the determination of the interaction parameters of the effective…
We numerically study a simple fluid composed of particles having a hard-core repulsion, complemented by two short-ranged attractive (sticky) spots at the particle poles, which provides a simple model for equilibrium polymerization of linear…
This thesis is about the study of complex systems through simple models. Our work evidences the relevance of this kind of modeling in science, which provides us with a better understanding of nature at minimum cost. The fundamentals tools…
Optimum ground states are constructed in two dimensions by using so called vertex state models. These models are graphical generalizations of the well-known matrix product ground states for spin chains. On the hexagonal lattice we obtain a…
We investigate the crystallization of a single, flexible homopolymer chain using transition path sampling (TPS). The chain consists of N identical spherical monomers evolved according to Langevin dynamics. While neighboring monomers are…
In a variety of situations, isolated polymer molecules are found in a vacuum and here we examine their properties. Angular momentum conservation is shown to significantly alter the average size of a chain and its conservation is only broken…
The concepts of globule and random coil were developed to describe the phases of homopolymers and then used to characterize the denatured state of structured cytosolic proteins and intrinsically disordered proteins. Using multi-scale…