Related papers: Using schematic models to understand the microscop…
Tailoring nanoparticles composition and morphology is of particular interest for improving their performance for catalysis. A challenge of this approach is that the nanoparticles optimized initial structure often changes during use.…
Two dimensional (2D) photonic crystals are well known for its ability to manipulate the propagation of electromagnetic wave inside the crystal. 1D and 2D photonic crystals are relatively easier to fabricate than 3D because the former work…
We study the effects of confinement between two parallel walls on a two dimensional fluid with competing interactions which lead to the formation of particle micro-domains at the thermodynamic equilibrium (microphases or microseparation).…
Freezing of charged colloids on square or triangular two-dimensional periodic substrates has been recently shown to realize a rich variety of orientational orders. We propose a theoretical framework to analyze the corresponding structures.…
We have employed molecular dynamics simulations based on the TIP4P/2005 water model to investigate the local structural, dynamical, and dielectric properties of the two recently reported body-centered-cubic and face-centered-cubic plastic…
We have performed a multicanonical molecular dynamics simulation on a simple model protein.We have studied a model protein composed of charged, hydrophobic, and neutral spherical bead monomers.Since the hydrophobic interaction is considered…
Two dimensional crystalline membranes in isotropic embedding space exhibit a flat phase with anomalous elasticity, relevant e.g., for graphene. Here we study their thermal fluctuations in the absence of exact rotational invariance in the…
Cryogenic electron microscopy (cryo-EM) has transformed structural biology by allowing to reconstruct 3D biomolecular structures up to near-atomic resolution. However, the 3D reconstruction process remains challenging, as the 3D structures…
We introduce a computational method to discover polymorphs in molecular crystals at finite temperature. The method is based on reproducing the crystallization process starting from the liquid and letting the system discover the relevant…
The morphologies of two-dimensional (2D) crystals, nucleated, grown, and integrated within 2D elastic fluids, for instance in giant vesicle membranes, are dictated by an interplay of mechanics, permeability, and thermal contraction.…
Antimony sulfide (Sb$_2$S$_3$), a compound of earth-abundant elements with highly anisotropic, quasi-layered crystal structure, triggered growing interest as a solar absorber in photovoltaics and as a phase change material in memory…
Using a well defined soft model glass in the framework of Molecular Dynamics simulations, the inherent structures are probed by means of a recently developed deformation protocol that aims to capture the Dynamical Heterogeneities (DH), as…
We introduce a new quantity to probe the glass transition. This quantity is a linear generalized compressibility which depends solely on the positions of the particles. We have performed a molecular dynamics simulation on a glass forming…
The temperature and length scale dependence of solvation properties of spherical hard solvophobic solutes is investigated in the Jagla liquid, a simple liquid that consists of particles interacting via a spherically symmetric potential…
A multiscale scheme combining molecular dynamics (MD) and microscopic phase-field theory is proposed to study the structural phase transformations in solids with inhomogeneous strain field. The approach calculates strain response based on…
In complex crystals close to melting or at finite temperatures, different types of defects are ubiquitous and their role becomes relevant in the mechanical response of these solids. Conventional elasticity theory fails to provide a…
The influence of dimethyl sulfoxide (DMSO) on membrane thickness, multilamellar repeat distance, and phase transitions of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) was investigated by X-ray diffraction and small-angle neutron…
Smoothed Particle Hydrodynamics (SPH) is plagued by the phenomenon of tensile instability, which is the occurrence of short wavelength zero energy modes resulting in unphysical clustering of particles. The root cause of the instability is…
Chemical composition of a molecular cloud is highly sensitive to the physical properties of the cloud. In order to obtain the chemical composition around a star forming region, we carry out a two dimensional hydrodynamical simulation of the…
Structural dynamics of macromolecules is critical to their structural-function relationship. Cryogenic electron microscopy (CryoEM) provides snapshots of vitrified protein at different compositional and conformational states, and the…