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We consider DNA-cationic lipid complexes that form lamellar stacks of lipid bilayers with parallel DNA strands intercalated in between. We calculate the electrostatically induced elastic deformations of the lipid bilayers. It is found that…
Epitaxial growth via chemical vapor deposition is considered to be the most promising way towards synthesizing large area graphene with high quality. However, it remains a big theoretical challenge to reveal growth kinetics with atomically…
The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…
We study the percolative properties of bi-dimensional systems generated by a random sequential adsorption of line-segments on a square lattice. As the segment length grows, the percolation threshold decreases, goes through a minimum and…
Topological entanglements are abundant, and often detrimental, in polymeric systems in biology and materials science. Here we theoretically investigate the topological simplification of knots by diffusing slip-links (SLs), which may…
We introduce an off-lattice model with continuous particle distances and pair-potential interactions which allows for the efficient simulation of strained heteroepitaxial growth by means of kinetic Monte Carlo (KMC) simulations. We discuss…
Graph Convolutional Networks (GCNs) have attracted more and more attentions in recent years. A typical GCN layer consists of a linear feature propagation step and a nonlinear transformation step. Recent works show that a linear GCN can…
We have proposed and implemented a modification of the well-known wall follower algorithm to identify a backbone (a current-carrying part) of the percolation cluster. The advantage of the modified algorithm is identification of the whole…
This thesis presents the development of entropy-elastic gelatin based networks in the form of films or scaffolds. The materials have good prospects for biomedical applications, especially in the context of bone regeneration. Entropy-elastic…
The dynamics of polymer translocation through a pore has been the subject of recent theoretical and experimental works. We have considered theoretical estimates and performed computer simulations to understand the mechanism of DNA uptake…
Research shows that gene duplication followed by either repurposing or removal of duplicated genes is an important contributor to evolution of gene and protein interaction networks. We aim to identify which characteristics of a network can…
During cell division, sister chromatids are segregated by the mitotic spindle, a bipolar assembly of interdigitating antiparallel polar filaments called microtubules. Establishing a stable overlap region is essential for maintenance of…
The repton model is a simple model of the "reptation" motion by which DNA diffuses through a gel during electrophoresis. In this paper we show that the model can be mapped onto a system consisting of two types of particles with hard-sphere…
The growth dynamics of rigid biopolymers, consisting of $N$ parallel protofilaments, is investigated theoretically using simple approximate models. In our approach, the structure of a polymer's growing end and lateral interactions between…
The industrial implementation of biofuel production from lignocellulosic biomass faces a number of economic obstacles. One of these is the cost of enzymes, typically used for cellulose hydrolysis. Nature provides some hints towards the…
The intriguing properties of graphene, a two-dimensional material composed of a honeycomb lattice of carbon atoms, have attracted a great deal of interest in recent years. Specifically, the fact that electrons in graphene behave as massless…
The art of tying knots is exploited in nature and occurs in multiple applications ranging from being an essential part of scouting programs to engineering molecular knots. Biomolecular knots, such as knotted proteins, bear various cellular…
Current biophysical models for transcriptionally active chromatin view this as a polymer with sticky sites, mimicking transcription units such as promoters and enhancers which interact via the binding of multivalent complexes of…
Multilayer networks are a powerful paradigm to model complex systems, where multiple relations occur between the same entities. Despite the keen interest in a variety of tasks, algorithms, and analyses in this type of network, the problem…
Dilated Convolutions have been shown to be highly useful for the task of image segmentation. By introducing gaps into convolutional filters, they enable the use of larger receptive fields without increasing the original kernel size. Even…