Related papers: Universal two-step crystallization of DNA-function…
The crystal nucleation from liquid in most cases is too rare to be accessed within the limited timescales of the conventional molecular dynamics (MD) simulation. Here, we developed a "persistent embryo" method to facilitate crystal…
Colloidal crystals formed by size-asymmetric binary particles co-assemble into a wide variety of colloidal compounds with lattices akin to ionic crystals. Recently, a transition from a compound phase with a sublattice of small particles to…
Ultrasoft colloids typically do not spontaneously crystallize, but rather vitrify, at high concentrations. Combining in-situ rheo-SANS experiments and numerical simulations we show that shear facilitates crystallization of colloidal star…
Liquids crystallize as they cool; however, when crystallization is avoided in some way, they supercool, maintaining their liquidity, and freezing into glass at low temperatures, as ubiquitously observed. These metastable states crystallize…
The formation process of core-shell bimetallic nanoparticles synthesized by sputtering onto a substrate is observed in real time using an originally developed acoustic technique. The technique enables us to evaluate the structural change of…
Despite its fundamental and technological importance, a microscopic understanding of the crystallization process is still elusive. By computer simulations of the hard-sphere model we reveal the mechanism by which thermal fluctuations drive…
In this paper, we report dynamic Monte Carlo simulation results on the crystallization of crystalline/crystalline (A/B) symmetric binary polymer blend, wherein the melting temperature of A-polymer is higher than B-polymer. Crystallization…
Using molecular dynamics simulations, we investigate the crystallization pathways of two exemplary systems that form the same complex crystal structure but differ fundamentally in the nature of their particle interactions. One system is…
We introduce a combined Restrained MD/Parallel Tempering approach to study the difference in free energy as a function of a set of collective variables between two states in presence of unknown slow degrees of freedom. We applied this…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural…
In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors…
The translocation of a short DNA fragment through a nanopore is addressed when the perforated membrane contains an embedded electrode. Accurate numerical solutions of the coupled Poisson, Nernst-Planck, and Stokes equations for a realistic,…
We study the coalescence of nanoscale metal clusters in an inert-gas atmosphere using constant-energy molecular dynamics. The coalescence proceeds via atomic diffusion with the release of surface energy raising the temperature. If the…
DNA inside the cellular environment works under a confined space. An intense research of the transcription and replication of DNA in the confined state is structurally significant to command the self assembly of DNA in a chamber or channel.…
Despite numerous efforts from numerical approaches to complement experimental measurements, several fundamental challenges have still hindered one's ability to truly provide an atomistic picture of the nucleation process in nanocrystals.…
DNA nanocompartment is a typical DNA-based machine whose function is dependent of molecular collective effect. Fundamental properties of the device have been addressed via electrochemical analysis, fluorescent microscopy, and atomic force…
Nucleation is an activated process in which the system has to overcome a free energy barrier in order for a first-order phase transition between the metastable and the stable phases to take place. In the liquid-to-solid transition the…
We describe several unexpected phenomena, caused by a solid-solid phase transition (gel-to-crystal) typical for all main classes of lipid substances - phospholipids, triglycerides, diglycerides, alkanes, etc. We discovered that this…
Using molecular dynamics simulation, we investigate the slow dynamics of a supercooled binary mixture of soft particles interacting with a generalized Hertzian potential. At low density, it displays typical slow dynamics near its glass…