Related papers: Theoretical description of a DNA-linked nanopartic…
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 mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
A theoretical construction of the genetic material establishes the unique and ideal character of DNA. A similar conclusion is reached for amino acids and proteins.
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…
The early promises of DNA computing to deliver a massively parallel architecture well-suited to computationally hard problems have so far been largely unkept. Indeed, it is probably fair to say that only toy problems have been addressed…
Mutually repelling particles form spontaneously ordered clusters when forced into confinement. The clusters may adopt similar spatial arrangements even if the underlying particle interactions are contrastingly different. Here we demonstrate…
We report the results from a computational study of the self-assembly of amphiphilic di-tethered nanospheres using molecular simulation. As a function of the interaction strength and directionality of the tether-tether interactions, we…
It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with…
Moving nanoparticles/atoms to study the nearfield interaction between them is one of the many approaches to explore the optical and electrical properties of these assemblies. Traditional approach included the self assembly by spinning or…
We survey our research on modeling the mechanisms of control of uniformity in growth of nanosize and colloid particles. The former are produced as nanocrystals, by burst-nucleation from solution. The latter, colloid-size particles, are…
Surface plasmon resonances generated in metallic nanostructures can be utilized to tailor electromagnetic fields. The precise spatial arrangement of such structures can result in surprising optical properties that are not found in any…
Taking advantage of the base-pairing specificity and tunability of DNA interactions, we investigate the spontaneous formation of hyperbranched clusters starting from purposely designed DNA tetravalent nanostar monomers, encoding in their…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
Star polymers with magnetically functionalized end groups are presented as a novel polymeric system whose morphology, self-aggregation, and orientation can easily be tuned by exposing these macromolecules simultaneously to an external…
We describe some of the important physical characteristics of the `pathways', i.e. dynamical processes, by which molecular, nanoscale and micron-scale self-assembly occurs. We highlight the fact that there exist features of self-assembly…
The emerging field of DNA storage employs strands of DNA bases (A/T/C/G) as a storage medium for digital information to enable massive density and durability. The DNA storage pipeline includes: (1) encoding the raw data into sequences of…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
Patterns generated by a colloidal suspension of nanospheres drying on a frictional substrate are studied by experiments and computer simulations. The obtained two-dimensional self-assembled structures are commonly used for nanosphere…
Self-associates of nucleic acid components (stacking trimers and tetramers of the base pairs of nucleic acids) and short fragments of nucleic acids are nanoparticles (linear sizes of these particles are more than 10 A. Modern…
With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, we need a revolutionary sequencing method for the…