Related papers: DNA Self-Assembly and Computation Studied with a C…
We present a coarse-grained model of DNA-functionalized colloids that is computationally tractable. Importantly, the model parameters are solely based on experimental data. Using this highly simplified model, we can predict the phase…
Certain sequences of peptoid polymers (synthetic analogs of peptides) assemble into bilayer nanosheets via a nonequilibrium assembly pathway of adsorption, compression, and collapse at an air-water interface. As with other large-scale…
We use an elastic rod model with contact to study the extension versus rotation diagrams of single supercoiled DNA molecules. We reproduce quantitatively the supercoiling response of overtwisted DNA and, using experimental data, we get an…
DNA oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed by 196 nucleotides) and to explore the…
We study theoretically a new generic scheme of programmable self-assembly of nanoparticles into clusters of desired geometry. The problem is motivated by the feasibility of highly selective DNA-mediated interactions between colloidal…
This paper presents a molecular mechanics study for new nanorobotic structures using molecular dynamics (MD) simulations coupled to virtual reality (VR) techniques. The operator can design and characterize through molecular dynamics…
In living systems, DNA undergoes continuous and rhythmic mechanical remodeling through condensation, looping, and disentangling to regulate gene expression, segregate chromosomes, and guide morphogenesis. Here, we demonstrate a purely…
We present a statistical mechanical model of aggregation in colloidal systems with DNA mediated interactions. We obtain a general result for the two-particle binding energy in terms of the hybridization free energy $\Delta G$ of DNA and two…
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…
We introduce and numerically study a model designed to mimic the bulk behavior of a system composed of single-stranded DNA dendrimers. Complementarity of the base sequences of different strands results in the formation of strong cooperative…
Inspired by biology's most sophisticated computer, the brain, neural networks constitute a profound reformulation of computational principles. Remarkably, analogous high-dimensional, highly-interconnected computational architectures also…
In the context of the recently developed "equation-free" approach to the computer-assisted analysis of complex systems, we illustrate the computation of coarsely self-similar solutions. Dynamic renormalization and fixed point algorithms for…
We construct and analyze monomeric and multimeric models of the stochastic disassembly of a single nucleosome. Our monomeric model predicts the time needed for a number of histone-DNA contacts to spontaneously break, leading to dissociation…
A hypercomplex representation of DNA is proposed to facilitate comparison of DNA sequences with fuzzy composition. Using hypercomplex number representation, conventional sequence analysis method, such as, dot matrix analysis, dynamic…
Physics-constrained data-driven computing is an emerging computational paradigm that allows simulation of complex materials directly based on material database and bypass the classical constitutive model construction. However, it remains…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
The article demonstrates a technique for fabricating a structure with the inclusion of suspended DNA threads and manipulating them using composite nanotweezers with shape memory effect. This technique could be suitable for stretching of…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (rarely accessed data), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
Statistical analysis of DNA mixtures is known to pose computational challenges due to the enormous state space of possible DNA profiles. We propose a Bayesian network representation for genotypes, allowing computations to be performed…
Multilevel self-assembly involving small structured groups of nano-particles provides new routes to development of functional materials with a sophisticated architecture. Apart from the inter-particle forces, the geometrical shapes and…