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Self-assembly of proteins is a biological phenomenon which gives rise to spontaneous formation of amyloid fibrils or polymers. The starting point of this phase, called nucleation exhibits an important variability among replicated…
Peptides are ubiquitous and important biologically derived molecules, that have been found to self-assemble to form a wide array of structures. Extensive research has explored the impacts of both internal chemical composition and external…
Simulation models often have parameters as input and return outputs to understand the behavior of complex systems. Calibration is the process of estimating the values of the parameters in a simulation model in light of observed data from…
We propose a method that allows us to develop tableaux modulo theories using the principles of superdeduction, among which the theory is used to enrich the deduction system with new deduction rules. This method is presented in the framework…
We develop a multi-scale approach to simulate hydrated nanobio systems under realistic condi- tions (e.g., nanoparticles and protein solutions at physiological conditions over time-scales up to hours). We combine atomistic simulations of…
We present a rejection method based on recursive covering of the probability density function with equal tiles. The concept works for any probability density function that is pointwise computable or representable by tabular data. By the…
Many useful tasks in data science and machine learning applications can be written as simple variations of matrix multiplication. However, users have difficulty performing such tasks as existing matrix/vector libraries support only a…
In this paper we investigate the computational power of the polygonal tile assembly model (polygonal TAM) at temperature 1, i.e. in non-cooperative systems. The polygonal TAM is an extension of Winfree's abstract tile assembly model (aTAM)…
Autonomous assembly is a crucial capability for robots in many applications. For this task, several problems such as obstacle avoidance, motion planning, and actuator control have been extensively studied in robotics. However, when it comes…
A well-rounded introduction to work in a STEM laboratory is vital to scientific education. Besides the ability to use available instrumentation for sample characterization, students should also be imparted knowledge in the steps of…
Many tasks require finding groups of elements in a matrix of numbers, symbols or class likelihoods. One approach is to use efficient bi- or tri-linear factorization techniques including PCA, ICA, sparse matrix factorization and plaid…
De novo genome assembly focuses on finding connections between a vast amount of short sequences in order to reconstruct the original genome. The central problem of genome assembly could be described as finding a Hamiltonian path through a…
In this paper we introduce the \emph{robust random number generation} problem where the goal is to design an abstract tile assembly system (aTAM system) whose terminal assemblies can be split into $n$ partitions such that a resulting…
We propose a multi-scale analysis method for studying arithmetic properties of integer sets, such as primality. Our approach organizes information through a hierarchy of nested sequences, where each level enables a hierarchical expression…
It is widely accepted that self-assembling building blocks is one of the promising ways for engineering new materials. Recent years reveal substantial progress in fabricating colloidal particles, polymer blocks and supramolecular aggregates…
Any quantum program on a realistic quantum device must be compiled into an executable form while taking into account the underlying hardware constraints. Stringent restrictions on architecture and control imposed by physical platforms make…
Self-assembly of nanoscale synthetic subunits is a promising bottom-up strategy for fabrication of functional materials. Here, we introduce a design principle for DNA origami nanoparticles of 50-nm size, exploiting modularity, to make a…
Mutation analysis is an effective technique to evaluate a test suite adequacy in terms of revealing unforeseen bugs in software. Traditional source- or IR-level mutation analysis is not applicable to the software only available in binary…
We prove a Pumping Lemma for the noncooperative abstract Tile Assembly Model, a model central to the theory of algorithmic self-assembly since the beginning of the field. This theory suggests, and our result proves, that small differences…
Self-assembly is one of the prevalent strategies used by living systems to fabricate ensembles of precision nanometer-scale structures and devices. The push for analogous approaches to create synthetic nanomaterials has led to the…