Related papers: Modular Arithmetic Expressions and Primality Testi…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
We study the computational complexity of the recently proposed nubot model of molecular-scale self-assembly. The model generalises asynchronous cellular automata to have non-local movement where large assemblies of molecules can be pushed…
Proteinaceous aggregation occurs through self-assembly-- a process not entirely understood. In a recent article [1], an analytical theory for amyloid fibril growth via secondary rather than primary nucleation was presented. Remarkably, with…
Determining whether a given integer is prime or composite is a basic task in number theory. We present a primality test based on quantum order finding and the converse of Fermat's theorem. For an integer $N$, the test tries to find an…
The modular subset sum problem consists of deciding, given a modulus $m$, a multiset $S$ of $n$ integers in $0..m-1$, and a target integer $t$, whether there exists a subset of $S$ with elements summing to $t \mod m $, and to report such a…
Biomolecular condensates self-assemble when proteins and nucleic acids spontaneously demix to form droplets within the crowded intracellular milieu. This simple mechanism underlies the formation of a wide variety of membraneless…
Recurrent neural networks have been widely used to generate millions of de novo molecules in a known chemical space. These deep generative models are typically setup with LSTM or GRU units and trained with canonical SMILEs. In this study,…
We study primary submodules and primary decompositions from a differential and computational point of view. Our main theoretical contribution is a general structure theory and a representation theorem for primary submodules of an arbitrary…
We introduce staged self-assembly of Wang tiles, where tiles can be added dynamically in sequence and where intermediate constructions can be stored for later mixing. This model and its various constraints and performance measures are…
Let $A$ be an expanding matrix on ${\Bbb R}^s$ with integral entries. A fundamental question in the fractal tiling theory is to understand the structure of the digit set ${\mathcal D}\subset{\Bbb Z}^s$ so that the integral self-affine set…
The algorithmic self-assembly of shapes has been considered in several models of self-assembly. For the problem of \emph{shape construction}, we consider an extended version of the Two-Handed Tile Assembly Model (2HAM), which contains…
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…
In recent years there have been a number of proposals to utilize the specificity of DNA based interactions for potential applications in nanoscience. One interesting direction is the self-assembly of micro- and nanoparticle clusters using…
Submodular functions allow to model many real-world optimisation problems. This paper introduces approaches for computing diverse sets of high quality solutions for submodular optimisation problems. We first present diversifying greedy…
Template directed replication of nucleic acids is at the essence of all living beings and a major milestone for any origin of life scenario. We here present an idealized model of prebiotic sequence replication, where binary polymers act as…
Consider the collection of all binary matrices having a specific sequence of row and column sums and consider sampling binary matrices uniformly from this collection. Practical algorithms for exact uniform sampling are not known, but there…
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…
The recently introduced Thermodynamic Binding Networks (TBN) model was developed with the purpose of studying self-assembling systems by focusing on their thermodynamically favorable final states, and ignoring the kinetic pathways through…
Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST ``digital northern'', are important high-throughput techniques for digital gene expression measurement. As other counting or voting processes, these…
This paper presents a novel primality test based on the eigenvalue structure of circulant matrices constructed from roots of unity. We prove that an integer $n > 2$ is prime if and only if the minimal polynomial of the circulant matrix $C_n…