Related papers: Stacking and Hydrogen Bonding. DNA Cooperativity a…
The folding of biological macromolecules is a fundamental process of which we lack a full comprehension. Mostly studied in proteins and RNA, single-stranded DNA (ssDNA) also folds, at physiological salt conditions, by forming non-specific…
We report on extensive molecular dynamics atomistic simulations of a \textit{meta}-substituted \textit{poly}-phenylacetylene (pPA) foldamer dispersed in three solvents, water \ce{H2O}, cyclohexane \ce{cC6H12}, and \textit{n}-hexane…
First-principles calculation has been performed to investigate the stability and electronic properties of double-layer graphene heterostructure (DLGH). In this system, two graphene layers are separated by hexagonal boron-nitride (h-BN)…
Nanoconfined water plays a crucial role in nanofluidics, biology, and cutting-edge technologies. The process of melting water monolayers and quasi-two-dimensional confined water involves, as an intermediate stage, the hexatic phase--a state…
Under appropriate conditions, mixtures of cationic and neutral lipids and DNA in water condense into complexes in which DNA strands form local 2D smectic lattices intercalated between lipid bilayer membranes in a lamellar stack. These…
We study the structural and thermodynamic properties of patchy particle liquids, with a special focus on the role of "color", i.e. specific interactions between individual patches. A possible experimental realization of such "chromatic"…
We study the phase behavior of single homopolymers in a simple hydrophobic/hydrophilic off-lattice model with sequence independent local interactions. The specific heat is, not unexpectedly, found to exhibit a pronounced peak well below the…
Using extensive Molecular Dynamics simulations we study the behavior of polyelectrolytes with hydrophobic side chains, which are known to form cylindrical micelles in aqueous solution. We investigate the stability of such bundles with…
The influence of monomer-monomer interactions on the scaling exponents and shape characteristics of a single polymer chain in a selective solvent is investigated using Langevin dynamics simulations. By systematically increasing the…
DNA-coated particles are promising as building blocks for functional and finite-sized assemblies because they can be programmed with orthogonal interactions owing to the sequence-specific hybridization of DNA strands. To fully exploit this…
A statistical mechanical distance constraint model (DCM) is presented that explicitly accounts for network rigidity among constraints present within a system. Constraints are characterized by local microscopic free energy functions.…
An analysis of the glass transition of four materials with similar chemical structures is performed: PET, PEN and two PET/PEN blends (90/10 and 70/30 w/w). During the melt processing of the blends transesterification reactions yield block…
We present a possible scaling solution to pre-equilibrium evolution which interpolates between the instability present in the dense gluon system produced immediately after a heavy ion collision and the final equilibration which occurs…
In the study of dynamical systems on networks/graphs, a key theme is how the network topology influences stability for steady states or synchronized states. Ideally, one would like to derive conditions for stability or instability that…
Current experimental and theoretical studies on the effect of intermolecular interactions on molecular conduction appear to be in conflict with each other. In particular, some experimental results, e.g., the observation of 2-dimensional…
We study the temperature dependence of static and dynamic responses of Coulomb interacting particles in two-dimensional traps across the thermal crossover from an amorphous solid- to liquid-like behaviors. While static correlations, that…
A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers. The persistence length is assumed to be large compared to the monomer size but much smaller than the total chain length. Such polymers…
Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…
Microscopic mechanisms of positive charge transfer in DNA remain unclear. A quantum state of electron hole in DNA is determined by the competition of the pi-stacking interaction $b$ sharing a charge between different base pairs and the…
We define a lattice model for the interaction of a polymer with water. We solve the model in a suitable approximation. In the case of a non-polar homopolymer, for reasonable values of the parameters, the polymer is found in a non-compact…