A comparative simulation study of polymer brushes formed by grafting at a planar surface either flexible linear polymers (chain length $N_L$) or (non-catenated) ring polymers (chain length $N_R=2 N_L$) is presented. Two distinct off-lattice models ar
e studied, one by Monte Carlo methods, the other by Molecular Dynamics, using a fast implementation on graphics processing units (GPUs). It is shown that the monomer density profiles $rho(z)$ in the $z$-direction perpendicular to the surface for rings and linear chains are practically identical, $rho_R(2 N_L, z)=rho_L(N_L, z)$. The same applies to the pressure, exerted on a piston at hight z, as well. While the gyration radii components of rings and chains in $z$-direction coincide, too, and increase linearly with $N_L$, the transverse components differ, even with respect to their scaling properties: $R_{gxy}^{(L)} propto N_L^{1/2}$, $R_{gxy}^{(R)} propto N_L^{0.4}$. These properties are interpreted in terms of the statistical properties known for ring polymers in dense melts.
A modern graphics processing unit (GPU) is able to perform massively parallel scientific computations at low cost. We extend our implementation of the checkerboard algorithm for the two dimensional Ising model [T. Preis et al., J. Comp. Phys. 228, 44
68 (2009)] in order to overcome the memory limitations of a single GPU which enables us to simulate significantly larger systems. Using multi-spin coding techniques, we are able to accelerate simulations on a single GPU by factors up to 35 compared to an optimized single Central Processor Unit (CPU) core implementation which employs multi-spin coding. By combining the Compute Unified Device Architecture (CUDA) with the Message Parsing Interface (MPI) on the CPU level, a single Ising lattice can be updated by a cluster of GPUs in parallel. For large systems, the computation time scales nearly linearly with the number of GPUs used. As proof of concept we reproduce the critical temperature of the 2D Ising model using finite size scaling techniques.
We propose a new coarse-grained model for the description of liquid-vapor phase separation of colloid-polymer mixtures. The hard-sphere repulsion between colloids and between colloids and polymers, which is used in the well-known Asakura-Oosawa (AO)
model, is replaced by Weeks-Chandler-Anderson potentials. Similarly, a soft potential of height comparable to thermal energy is used for the polymer-polymer interaction, rather than treating polymers as ideal gas particles. It is shown by grand-canonical Monte Carlo simulations that this model leads to a coexistence curve that almost coincides with that of the AO model and the Ising critical behavior of static quantities is reproduced. Then the main advantage of the model is exploited - its suitability for Molecular Dynamics simulations - to study the dynamics of mean square displacements of the particles, transport coefficients such as the self-diffusion and interdiffusion coefficients, and dynamic structure factors. While the self-diffusion of polymers increases slightly when the critical point is approached, the self-diffusion of colloids decreases and at criticality the colloid self-diffusion coefficient is about a factor of 10 smaller than that of the polymers. Critical slowing down of interdiffusion is observed, which is qualitatively similar to symmetric binary Lennard-Jones mixtures, for which no dynamic asymmetry of self-diffusion coefficients occurs.
A number of recently discovered protein structures incorporate a rather unexpected structural feature: a knot in the polypeptide backbone. These knots are extremely rare, but their occurrence is likely connected to protein function in as yet unexplor
ed fashion. Our analysis of the complete Protein Data Bank reveals several new knots which, along with previously discovered ones, can shed light on such connections. In particular, we identify the most complex knot discovered to date in human ubiquitin hydrolase, and suggest that its entangled topology protects it against unfolding and degradation by the proteasome. Knots in proteins are typically preserved across species and sometimes even across kingdoms. However, we also identify a knot which only appears in some transcarbamylases while being absent in homologous proteins of similar structure. The emergence of the knot is accompanied by a shift in the enzymatic function of the protein. We suggest that the simple insertion of a short DNA fragment into the gene may suffice to turn an unknotted into a knotted structure in this protein.
