Related papers: Stacking and Hydrogen Bonding. DNA Cooperativity a…
A combination of Fourier transform infrared and phase transition measurements as well as molecular computer simulations, and thermodynamic modeling were performed to probe the mechanisms by which guanidinium salts influence the stability of…
Most helix-coil transition theories can be characterized by a set of three parameters: energetic, describing the (free) energy cost of forming a helical state in one repeating unit; entropic, accounting for the decrease of entropy due to…
Polymer-grafted nanoparticles (PGNPs) can provide property profiles than cannot be obtained individually by polymers or nanoparticles (NPs). Here, we have studied the mixing--demixing transition of symmetric copolymer melts of…
The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…
We report circular dichroism measurements on the helix-coil transition of poly(L-glutamic acid) in solution with polyethylene glycol (PEG) as a crowding agent. Using small angle neutron scattering, PEG solutions have been characterized and…
During the melting transition of dimyristoyl phosphatidylglycerol (DMPG), the order of the lipid chains and the three-dimensional, vesicular structural arrangement change simultaneously. These changes result in peculiar heat capacity…
Mesoscopic structure of the periodically alternating layers of stretched homopolymer chains surrounded by perpendicularly oriented oligomeric tails is studied for the systems with both strong (ionic) and weak (hydrogen) interactions. We…
By means of multicanonical computer simulations, we investigate thermodynamic properties of the aggregation of interacting semiflexible polymers. We analyze a mesoscopic bead-stick model, where nonbonded monomers interact via Lennard-Jones…
DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have…
In a recent work we proposed a coarse-grained methodology for studying the response of peptides when simulated at different values of pH; in this work we extend the methodology to analyze the pH-dependent behavior of coiled coils. This…
The theory of transition between $\alpha$-helix, $\beta$-sheet and random coil conformation of a protein is discussed through a simple model, that includes both short and long-range interactions. Besides the bonding parameter and helical…
The design of hydrogels that combine mechanical robustness with dynamic reconfigurability remains a fundamental challenge, as increasing crosslink dissociation rates compromise network integrity. This limitation is addressed through the…
Extensive molecular dynamics computer simulations have been conducted for ethanol-water liquid mixtures in the water-rich side of the composition range, with 10, 20 and 30 mol % of the alcohol, at temperatures between room temperature and…
Lithium and sodium are the only solids that are known to lose crystalline order upon cooling. The seemingly-disordered low-temperature phase shows signatures of various close-packed structures. The lack of order has been attributed to a…
We study the dynamics of DNA hairpin formation using oxDNA, a nucleotide-level coarse-grained model of DNA. In particular, we explore the effects of the loop stacking interactions and non-native base pairing on the hairpin closing times. We…
A simplified model for the closed circular DNA (ccDNA) is proposed to describe some specific features of the helix-coil transition in such molecule. The Hamiltonian of ccDNA is related to the one introduced earlier for the linear DNA. The…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
We introduce a simple and predictive model for determining the phase stability of ternary phospholipid-cholesterol mixtures. Assuming that competition between the liquid and gel order of the phospholipids is the main driving force behind…
We investigate the dynamics of the collapse of a single copolymer chain, when the solvent quality is suddenly quenched from good to poor. We employ Brownian dynamics simulations of a bead-spring chain model and incorporate fluctuating…