Related papers: Stacking and Hydrogen Bonding. DNA Cooperativity a…
The basic models of helix-coil transitions in biomolecules are introduced. These include phenomenological, zipper (Bragg-Zimm) models of polypeptides, loop-entropy (Poland-Scheraga) and Hamiltonian (Peyrard-Bishop) models of homogeneous DNA…
The random arrest of the diffusion of a single particle and its return to its origin has served as the paradigmatic example of a large variety of processes undergoing stochastic resetting. While the implications and applications of…
Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy c ln m for a…
In the present paper we present results of calculations obtained with the use of the theoretical method described in our preceding paper [1] and perform detail analysis of alpha helix-random coil transition in alanine polypeptides of…
While recent efforts have shown how local structure plays an essential role in the dynamic heterogeneity of homogeneous glass-forming materials, systems containing interfaces such as thin films or composite materials remain poorly…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
A protein model with the pairwise interaction energies varying as local environment changes, i.e., including some kinds of collective effect between the contacts, is proposed. Lattice Monte Carlo simulations on the thermodynamical…
We studied solvent-driven ordering dynamics of block copolymer films supported by a densely cross-linked polymer network designed as organic hard mask (HM) for lithographic fabrications. The ordering of microphase separated domains at low…
We study the phase ordering dynamics of a two dimensional model colloidal solid using molecular dynamics simulations. The colloid particles interact with each other with a Hamaker potential modified by the presence of equatorial "patches"…
Positions of protons in DNA hydrogen bonds are fundamental for the fidelity of the replication process. Because the hydrogen bond is partially covalent the electronic structure of DNA plays an important role in the replication process.…
In this paper, we explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleotide is represented by two interaction sites corresponding to…
It has been extensively demonstrated through first principles quantum mechanics calculations that water exhibits strong hydrogen bond cooperativity. Classical molecular simulation and statistical mechanics methods typically assume pairwise…
Experiments on supported lipid bilayers featuring liquid ordered/disordered domains have shown that the spatial arrangement of the lipid domains and their chemical composition are strongly affected by the curvature of the substrate.…
Polymer behavior in mixed solvents often exhibits intriguing phenomena, such as cosolvency, where a polymer that collapses in two individually poor solvents becomes soluble in their mixture. In this study, we employ a combination of…
Tuning the heat flow is fundamentally important for the design of advanced functional materials. Here, polymers are of particular importance because they provide different pathways for the energy transfer. More specifically, the heat flow…
Motion of protein drops on crystallization media during routine handling is a major factor affecting the reproducibility of crystallization conditions. Drop stability can be enhanced by chemical patterning to more effectively pin the drop's…
Generalized hydrodynamics (GHD) is a recent theoretical approach that is becoming a go-to tool for characterizing out-of-equilibrium phenomena in integrable and near-integrable quantum many-body systems. Here, we benchmark its performance…
We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on…
We consider the thermodynamics of a uniformly charged polyelectrolyte with harmonic bonds. For such a system there is at high temperatures an approximate scaling of global properties like the end-to-end distance and the interaction energy…
Grazing Incidence X-ray Diffraction (GIXD) studies of monolayers of biomolecules at the air-water interface give quantitative information of in-plane packing, coherence lengths of the ordered diffracting crystalline domains and the…