Related papers: DNA nanotechnology: understanding and optimisation…
In most of the cases, the experimental study of Nanotechnology involves high cost for Laboratory set-up and the experimentation processes were also slow. So, one cannot rely on experimental nanotechnology alone. As such, the Computer-Based…
DNA strand displacement (SD) reactions are central to the operation of many synthetic nucleic acid systems, including molecular circuits, sensors, and machines. Over the years, a broad set of design frameworks has emerged to accommodate…
We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models$\unicode{x2014}$oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes…
We present a theoretical discussion of a self-assembly scheme which makes it possible to use DNA to uniquely encode the composition and structure of micro- and nanoparticle clusters. These anisotropic DNA-decorated clusters can be further…
Neural Architecture Search (NAS), aiming at automatically designing neural architectures by machines, has been considered a key step toward automatic machine learning. One notable NAS branch is the weight-sharing NAS, which significantly…
We present a quantitative, multi-scale coarse-grained model of DNA coated colloids. The parameters of this model are transferable and are solely based on experimental data. As a test case, we focus on nano-sized colloids carrying…
With recent high-throughput technology we can synthesize large heterogeneous collections of DNA structures, and also read them all out precisely in a single procedure. Can we use these tools, not only to do things faster, but also to devise…
Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…
Developing physics-based models for molecular simulation requires fitting many unknown parameters to diverse experimental datasets. Traditionally, this process is piecemeal and difficult to reproduce, leading to a fragmented landscape of…
Ordered nanoarrays, i.e. regular patterns of quantum structures at the nanometre scale, have recently been synthesized in a wide range of systems. Here I explore a possible route to technological exploitation: assuming a simple form of…
While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule…
DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of…
Synthetic molecular motors are an appealing means to control motion at the nanoscale, but understanding their behaviour as single-molecule actuators and integrating them into larger, functional systems remain technical challenges.…
Dynamic walking on bipedal robots has evolved from an idea in science fiction to a practical reality. This is due to continued progress in three key areas: a mathematical understanding of locomotion, the computational ability to encode this…
The mechanism of threshold elongation (overstretching) of DNA macromolecules under the action of external force is studied within the framework of phenomenological approach. When considering the task it is taken into account that…
Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for {\it de novo} genome assembly,…
The quest for realizing and manipulating ever smaller man-made movable structures and dynamical machines has spurred tremendous endeavors, led to important discoveries, and inspired researchers to venture to new grounds. Scientific feats…
Partial-assistance exoskeletons hold significant potential for gait rehabilitation by promoting active participation during (re)learning of normative walking patterns. Typically, the control of interaction torques in partial-assistance…
In this work, we present an automated platform for trapping and stretching individual micro- and nanoscale objects in solution using electrokinetic forces. The platform can trap objects at the stagnation point of a planar elongational…
The dynamics of individual DNA molecules in semidilute solutions undergoing planar extensional flow is simulated using a multi-particle Brownian dynamics algorithm, which incorporates hydrodynamic and excluded volume interactions in the…