Related papers: Crowding effect on helix-coil transition: beyond e…
The theoretical investigation of relevant turbulent transport mechanisms in H-mode pedestals is a great scientific and numerical challenge. In this study, we address this challenge by global, nonlinear gyrokinetic simulations of a full…
The densities of states are evaluated for very short chain molecules made up of overlapping monomers, using a model which has previously been shown to produce helical structure. The results of numerical calculations are presented for…
We study long polymer chains in a poor solvent, confined to the space between two parallel hard walls. The walls are energetically neutral and pose only a geometric constraint which changes the properties of the coil-globule (or…
We present the exact solution of a microscopic statistical mechanical model for the transformation of a long polypeptide between an unstructured coil conformation and an $\alpha$-helix conformation. The polypeptide is assumed to be adsorbed…
The force laws governing the extension behavior of homopolypeptides are obtained from a phenomenological free energy capable of describing the helix-coil transition. Just above the melting temperature of the free chains, T*, the plot of…
We use optical tweezers to perform stretching experiments on DNA molecules when interacting with the drugs daunomycin and ethidium bromide, which intercalate the DNA molecule. These experiments are performed in the low-force regime from…
Using computer simulations, we identify the mechanisms causing aggregation and structural arrest of colloidal suspensions interacting with a short-ranged attraction at moderate and high densities. Two different non-ergodicity transitions…
We study flexible polymer macromolecules in a crowded (porous) environment, modelling them as self-attracting self-avoiding walks (SASAW) on site-diluted percolative lattices in space dimensions d=2, 3. The influence of stretching force on…
Diffusive transport of small molecules within the internal structures of biological and synthetic material systems is complex because the crowded environment presents chemical and physical barriers to mobility. We explored this mobility…
Lubricated contacts in soft materials are important in various engineering systems and natural settings. Three major lubrication regimes are boundary (BL), mixed (ML), and elasto-hydrodynamic (EHL) lubrication, where the contact region is…
We study phase separation and transient gelation in a mixture consisting of polydisperse colloids and non-adsorbing polymers, where the ratio of the average size of the polymer to that of the colloid is approximately 0.063. Unlike what has…
The authors study the short-time dynamics of helix-forming polypeptide chains using an all-atom representation of the molecules and an implicit solvation model to approximate the interaction with the surrounding solvent. The results confirm…
A central question concerning glass-formation has been what governs the kinetic arrest of the quenched liquid - cooling reduces the thermal energy which molecules need to surmount local potential barriers, while the accompanying volume…
Hydrogel consists of a crosslinked polymer matrix imbibed with a solvent such as water at volume fractions that can exceed 90\%. They are important in many scientific and engineering applications due to their tunable physiochemical…
In a nematic gel, the appearance of nematic order is accompanied by a spontaneous elongation of the gel parallel to the nematic director. If such a gel is made chiral, it has a tendency to form a cholesteric helical texture, in which local…
The thermodynamic behavior of collapse transition in a fully flexible coarse-grained model of energy polydisperse polymer (EPP), a statistical model of random heteropolymer, is investigated in an implicit solvent by means of molecular…
We introduce a simple geometric model for a double-stranded and double-helical polymer. We study the statistical mechanics of such polymers using both analytical techniques and simulation. Our model has a single energy-scale which…
We study helix-coil transitions in an all-atom model of polyalanine. Molecules of up to length 30 residues are investigated by multicanonical simulations. Results from two implicit solvent models are compared with each other and with that…
Connecting the large-scale emergent behaviors of active materials to the microscopic properties of their constituents is a challenge due to a lack of data on the multiscale dynamics and structure of such systems. We approach this problem by…
We present an experimentally guided, multi-phase, multi-species polyelectrolyte gel model to make quantitative predictions on the electro-chemical properties of articular cartilage. The mixture theory consists of two different types of…