Peptide binding to a graphene sheet is studied by a coarse-grained approach. All-atom molecular dynamics (MD) is used to assess the adsorption energy (e.g. binding) of each amino acid with graphene. The relative adsorption energy of each residue is normalized to describe its coarse-grained interactions with graphene which is used as an input to a phenomenological interaction in an all-residue coarse-grained (ARCG) representation of the peptide chain. Large scale Monte Carlo (MC) simulations are performed to study the stability of peptides (P1: ¹H–²S–³S–⁴Y–⁵W–⁶Y–⁷A–⁸F–⁹N–¹⁰N–¹¹K–¹²T and P2: ¹E–²P–³L–⁴Q–⁵L–⁶K–⁷M) binding to a graphene sheet as a function of temperature. A number of local and global physical quantities are analyzed including mobility and substrate-in-contact profiles of each residue, density profiles, root mean square displacement of the center of mass of each peptide and its radius of gyration. We find that P1 has a higher probability of binding to a graphene sheet than P2 supported by both local and global physical quantities. All residues of P1 can bind to the graphene sheet at low temperatures; however, three residues ⁴Y–⁵W–⁶Y seem to anchor it most strongly at higher temperatures, which is consistent with an all-atom MD simulation.

Computer simulations are performed to study kinetic gelation on a simple cubic lattice. Two models are considered: (1) irreversible gelation in which the monomers and microgels attempt to react with their neighboring particles with a certain probability (${\mathrm{p}}_{\mathrm{b}}$) and (2) reversible gelation in which the bonds are broken with a certain probability (${\mathrm{p}}_{\mathrm{r}}$). The growth of the extent of reaction (i.e., the concentration of the bonds grown), volume fraction of the gel, weight average degree of polymerization, and the correlation length are studied as a function of ${\mathrm{p}}_{\mathrm{b}}$ and ${\mathrm{p}}_{\mathrm{r}}$. We observe that (i) the concentration of bonds grows nonlinearly with time. (ii) The critical gel time (${\mathrm{t}}_{\mathrm{c}}$) increases nonlinearly on increasing the degree of reversibility, ${\mathrm{p}}_{\mathrm{r}}$, while the critical concentration (${\mathrm{p}}_{\mathrm{c}}$) at the gel point is insensitive to ${\mathrm{p}}_{\mathrm{b}}$ and ${\mathrm{p}}_{\mathrm{r}}$. (iii) For large ${\mathrm{p}}_{\mathrm{r}}$, our data suggest that the sol-to-gel transition may be nonuniversal.

Can a layer of stacked sheets (coarse grained description of clay platelets) exfoliate in a given solvent? Computer simulations are performed to address this question with a stacked layer of four sheets. A sheet is described by a set of nodes (N) tethered together by flexible (fluctuating) bonds in a planar structure with linear scaleL_s,N=L_s²on a cubic lattice of sizeL³. The initial distance between the sheets is small and kept constant for different sets of stacked sheets. Quality of the effective solvent is controlled by a short range interaction (ε) between sheets, that is, their nodes and the empty lattice sites (ε = −2,−1, 1, 2). Nodes execute stochastic movement with the Metropolis algorithm subject to bond fluctuation and excluded volume constraints. Simulations are also performed at different temperatures. Visual analysis shows that the exfoliation depends on the size of the sheet and temperature. We find that it is easier to exfoliate smaller sheets and that the exfoliation is enhanced by raising the temperature. The exfoliation becomes very slow for large sheets at low temperatures because of longer relaxation times. Exfoliation is enhanced by increasing the attractiveness (i.e., the quality) of the solvent interaction with the platelets. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 3580–3589, 2006

A coarse-grained model is used to study the structure and dynamics of a human immunodeficiency virus-1 protease (1DIFA dimer) consisting of 198 residues in an effective solvent medium on a cubic lattice by Monte Carlo simulations for a range of interaction strengths. Energy and mobility profiles of residues are found to depend on the interaction strength and exhibit remarkable segmental symmetries in two monomers. Lowest energy residues such as Arg41 and Arg140 (most electrostatic and polar) are not the least mobile; despite the higher energy, the hydrophobic residues (Ile, Leu, and Val) are least mobile and form the core by pinning down the local segments for the globular structure. Variations in the gyration radius (Rg) and energy (Ec) of the protein show nonmonotonic dependence on the interaction strength with the smallest Rg around the largest value of Ec. Pinning of the conformations by the hydrophobic residues at high interaction strength seems to provide seed for the protein chain to collapse.

Exfoliation of a stack of sheets (a model for clay platelets) in a dynamic matrix of polymer chains is investigated by a computer simulation model. How the interplay between the thermodynamics (interaction‐driven) and conformational (structural constraints) entropy affects the exfoliation of sheets is the subject of this study. A stack of four sheets with a small initial interlayer distance constitutes the layer on a discrete lattice. The layered platelets are immersed in a matrix represented by the mobile polymer chains which occupy a fraction (concentration) of the lattice sites. Both sheets and chains are modeled by the bond‐fluctuation mechanism and execute their stochastic motion via Metropolis algorithm. An attractive and a repulsive interaction between the polymer matrix and platelets are considered. Exfoliation of the sheets is examined by varying the molecular weight of the polymer chains forming a dynamic network matrix with various degrees of entanglements. At low‐molecular weight of the polymer, exfoliation is achieved with repulsive interaction and the exfoliation is suppressed with attractive matrix as sheets stick together via polymer mediated interaction introduced by intercalated polymer chains. Increasing the molecular weight of the polymer matrix suppresses the exfoliation of sheets primarily due to enhanced entanglement—at high‐molecular weight (with the radius of gyration of polymer chains larger than the characteristic linear dimension of the platelets), the stacked (layered) morphology is arrested via entropic trapping and exfoliation ceases to occur. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 2696–2710, 2008