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Dislocation nucleation is essential to our understanding of plastic deformation, ductility and mechanical strength of crystalline materials. Molecular dynamics simulation has played an important role in uncovering the fundamental mechanisms…
A major challenge in molecular simulations is to describe denaturant-dependent folding of proteins order to make direct comparisons with {\it in vitro} experiments. We use the molecular transfer model, which is currently the only method…
Numerous studies have investigated the differences and similarities between protein structures determined by solution NMR spectroscopy and those determined by x-ray crystallography. A fundamental question is whether any observed differences…
It is well stablished that confinement of supercooled liquids in nano-pores induces various effects as a strong modification of the dynamics and a layering of the local structure. In this work we raise the issue as how these confinement…
Hyperpolarized water can be a valuable aid in protein NMR, leading to amide group 1H polarizations that are orders of magnitude larger than their thermal counterparts. Suitable procedures can exploit this to deliver 2D 1H-15N correlations…
One of the most promising applications in nanoscience is the design of new materials to improve water permeability and selectivity of nanoporous membranes. Understanding the molecular architecture behind these fascinating structures and how…
Here we report on the translocation of folded polymers through nano-pores using molecular dynamic simulations. Two cases are studied; one in which a folded molecule unfolds upon passage and one in which the folding remains intact as the…
The behavior of polyampholytes near a charged planar surface is studied by means of Monte Carlo simulations. The investigated polyampholytes are overall electrically neutral and made up of oppositely charged units (called blocks) that are…
For a comprehensive characterization of mechanical reliability of metallization layers on polymer substrates both electrical and mechanical degradation should be taken into account. Although it is evident that cracking of a conductive film…
A statistical mechanical description of flexible and semi-flexible polymer chains in a poor solvent is developed in the constant force and constant distance ensembles. We predict the existence of many intermediate states at low temperatures…
In this paper, we employ Molecular Dynamics computer simulations to study and compare the statics and dynamics of linear and circular (ring) polymer chains in entangled solutions of different densities. While we confirm that linear chain…
There have been several studies suggesting that protein structures solved by NMR spectroscopy and x-ray crystallography show significant differences. To understand the origin of these differences, we assembled a database of high-quality…
Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of…
We investigate the crystallization of crosslinked and entangled polymers under external deformation using a coarse-grained poly(vinyl alcohol) (CG-PVA) model and molecular dynamics simulations. Following uniaxial deformation, the systems…
The structure property of non-ideal Si/GaAs heterostructures that were integrated with the ultra-thin oxide (UO) tunneling interfacial layer has been systematically investigated. Si nanomembranes (NMs) were oxidized in different time…
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession…
We have used coarse-grained simulation methods to investigate the effect of stretching-induced structure orientation on the proton conductivity of Nafion-like polyelectrolyte membranes. Recent experimental data on the morphology of ionomers…
Hypotheses: Additives are commonly used to tune macromolecular conformational transitions. Among additives, trehalose is an excellent bioprotectant and among responsive polymers, PNIPAM is the most studied material. Nevertheless, their…
Refractory multi-principal element alloys (RMPEAs) are promising materials for high-temperature structural applications. Here, we investigate the role of chemical short-range ordering (CSRO) on dislocation glide in two model RMPEAs - TaNbTi…
The bioprotective nature of disaccharides is hypothesized to derive from the modification of the hydrogen bonding network of water which protects biomolecules through lowered water activity at the protein interface. Using ultrafast…