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Lipid vesicles consist of aqueous cores surrounded by a bilayer of phospholipids. Hybrid polymer-lipid vesicles incorporate both polymers and lipids, offering promising properties for developing pharmaceuticals, biosensors, and artificial…
Exchanging hydrophobic alkyl-based side chains to hydrophilic glycol-based side chains is a widely adopted method for improving mixed-transport device performance, despite the impact on solid state packing and polymer-electrolyte…
Via hydrodynamics preserving molecular dynamics simulations we study growth phenomena in a phase separating symmetric binary mixture model. We quench high-temperature homogeneous configurations to state points inside the miscibility gap,…
We implement the replica exchange molecular dynamics algorithm to study the interactions of a model peptide (WALP-16) with an explicitly represented DPPC membrane bilayer. We observe the spontaneous, unbiased insertion of WALP-16 into the…
We introduce a lattice model of protein conformations which is able to reproduce second structures of proteins (alpha--helices and beta--sheets). This model is based on the following two main ideas. First, we model backbone parts of amino…
The collective motion of membrane lipids over hundred of nanometers and nanoseconds is essential for the formation of submicron complexes of lipids and proteins in the cell membrane. These dynamics are difficult to access experimentally and…
We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with two simple effective, coarse-grained off-lattice models to study the influence of specific interactions in the models on conformational transitions…
Graphene-water interaction has been under scrutiny ever since graphene discovery and realization of its exceptional properties. Several computational and experimental reports exist that have tried to look into the interactions involved,…
Vesicles prepared in water from a series of diblock copolymers and termed "polymersomes" are physically characterized. With increasing molecular weight $\bar{M}_n$, the hydrophobic core thickness $d$ for the self-assembled bilayers of…
Particles interacting through long-range attraction and short-range repulsion given by power-laws have been widely used to model physical and biological systems, and to predict or explain many of the patterns they display. Apart from rare…
In this study, the thermal relaxation of the 20 naturally occurring amino-acids in water is investigated using transient non-equilibrium molecular-dynamics simulations. By modeling the thermal relaxation process, the relaxation times of the…
Biological molecules can form hydrogen bonds between nearby residues, leading to helical secondary structures. The associated reduction of configurational entropy leads to a temperature dependence of this effect: the "helix-coil…
We report Monte Carlo results for the fluid structure of a system of dimeric particles interacting via a core-softened potential. More specifically, dimers interact through a repulsive pair potential of inverse-power form, modified in such…
Understanding the stabilities of proteins in nanopores requires a quantitative description of confinement induced interactions between amino acid side chains. We use molecular dynamics simulations to study the nature of interactions between…
Dissipative Particle Dynamics (DPD) is becoming a popular particle based method to study flow through microchannels due to the ease with which the presence of biological cells or DNA chains can be modeled. Many Lab-On-Chip (LOC) devices…
The thermodynamic behavior and structural properties of hydrophobic-polar (HP) lattice proteins interacting with attractive surfaces are studied by means of Wang-Landau sampling. Three benchmark HP sequences (48mer, 67mer, and 103mer) are…
Thermodynamics of helix-coil transitions in amino-acid homo-oligomers are studied by the recently proposed multicanonical algorithms. Homo-oligomers of length 10 are considered for three characteristic amino acids, alanine (helix former),…
The activity of cell membrane inclusions (such as ion channels) is influenced by the host lipid membrane, to which they are elastically coupled. This coupling concerns the hydrophobic thickness of the bilayer (imposed by the length of the…
Two of the most commonly encountered friction reducing agents used in plastic sheet production are the amides known as erucamide and behenamide, which despite being almost identical chemically, lead to markedly different values of the…
A hydrated 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) lipid membrane is investigated using an all atom molecular dynamics simulation at 308K to find out the physical sources of universal slow relaxation of hydration layers.…