Related papers: Nanosecond chain dynamics of single-stranded nucle…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a novel…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
Stacking interactions in single stranded nucleic acids give rise to configurations of an annealed rod-coil multiblock copolymer. Theoretical analysis identifies the resulting signatures for long homopolynucleotides: A non monotonous…
Monte Carlo simulations of a simple lattice model of protein folding show two distinct regimes depending on the chain length. The first regime well describes the folding of small protein sequences and its kinetic counterpart appears to be…
The nuclear spin, being much more isolated from the environment than its electronic counterpart, enables quantum experiments with prolonged coherence times and presents a gateway towards uncovering the intricate dynamics within an atom.…
Nucleic acids are negatively charged macromolecules and their structure properties are strongly coupled to metal ions in solutions. In this paper, the salt effects on the flexibility of single stranded (ss) nucleic acid chain ranging from…
Protein dynamics has been investigated on a wide range of time scales. Nano- and picosecond dynamics have been assigned to local fluctuations, while slower dynamics have been attributed to larger conformational changes. However, it is…
The objective of the present study was to develop an understanding of short single-stranded DNA (ssDNA) to assist the development of new DNA-based biosensors. A ssDNA model containing twelve bases was constructed from the 130-145 codon…
We study the spontaneous nucleation and crystallization of linear and cyclic chains of flexibly connected hard spheres using extensive molecular dynamics simulations. To this end, we present a novel event-driven molecular dynamics…
A new formalism for calculation of the partition function of single stranded nucleic acids is presented. Secondary structures and the topology of structure elements are the level of resolution that is used. The folding model deals with…
We study the coupled dynamics of primary and secondary structure formation (i.e. slow genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and and…
Successful assembly of suspended nanoscale rod-like particles depends on fundamental phenomena controlling rotational and translational diffusion. Despite the significant developments in fluidic fabrication of nanostructured materials, the…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
We study the elastic behaviour of a supercoiled DNA molecule. The simplest model is that of a rod like chain, involving two elastic constants, the bending and the twist rigidities. We show that this model is singular and needs a small…
We study the conformations of a semiflexible chain, confined in nano-scaled spherical cavities, under two distinct processes of confinement. Radial contraction and packaging are employed as two confining procedures. The former method is…
Single-chain nanoparticles (SCNPs) are a new class of macromolecular objects, synthesized through purely intramolecular cross-linking of single polymer chains. We use a multi-scale hydrodynamics simulation approach to study, for the first…
Because the constant extension ensemble of single chain molecule is not always equivalent with constant force ensemble, a model of double-stranded conformations, as in RNA molecules and $\beta$-sheets in proteins, with fixed extension…
Biomolecules exhibit dynamic conformations critical to their functions, yet observing these processes at the single-molecule level under native conditions remains a formidable challenge. While surface immobilization has been widely used to…