相关论文: Conformational properties of neutral and charged a…
A method to reconstruct the energy landscape of small peptides is presented with reference to a 2d off--lattice model. The starting point is a statistical analysis of the configurational distances between generic minima and directly…
The ability of a protein to recognise multiple independent target conformations was demonstrated in [1]. Here we consider the recognition of correlated configurations, which we apply to funnel design for a single conformation. The maximum…
Thermodynamics of helix-coil transitions in amino-acid homo-oligomers are studied by the recently proposed multicanonical algorithms. Homo-oligomers of length 10 are considered for three characteristic amino acids, alanine (helix former),…
We present arguments that the structure of the spectrum of the supersymmetric matrix model with 16 real supercharges in the large N limit is rather nontrivial, involving besides the natural energy scale ~\lambda^{1/3} = (g^2 N)^{1/3} also a…
The adsorption of highly \textit{oppositely} charged flexible polyelectrolytes (PEs) on a charged planar substrate is investigated by means of Monte Carlo (MC) simulations. We study in detail the equilibrium structure of the first few PE…
We calculate the quartet potential energy surface for Li+NH and use it to calculate elastic and spin-relaxation cross sections for collisions in magnetically trappable spin-stretched states. The potential is strongly anisotropic but…
We describe a numerical study of the potential energy landscape for the two-dimensional XY model (with no disorder), considering up to 100 spins and CPU and GPU implementations of local optimization, focusing on minima and saddles of index…
We present a computational scheme for extracting the energy level alignment of a metal/molecule interface, based on constrained density functional theory and local exchange and correlation functionals. The method, applied here to benzene on…
We present a non-linear Thomas-Fermi theory which describes the electric charge screening in the system including two charged substrate layers separated by a few-layered graphene film. We show that by increasing the charge at the…
An application of quantum size carbon structures--graphenes as electrodes of supercapacitors is studied. A fundamental limit of energy and power density arising from quantum nature of objects due to singularity in graphene density of states…
The conformations available to polypeptides are determined by the interatomic forces acting on the peptide units, whereby backbone torsion angles are restricted as described by the Ramachandran plot. Although typical proteins are composed…
The qualitative solvent- and temperature-dependent conformational behavior of a peptide in the proximity of solid substrates with different adsorption properties is investigated by means of a simple lattice model. The resulting pseudophase…
We derive structural and binding energy trends for twenty amino acids, their dipeptides, and their interactions with the divalent cations Ca$^{2+}$, Ba$^{2+}$, Sr$^{2+}$, Cd$^{2+}$, Pb$^{2+}$, and Hg$^{2+}$. The underlying data set consists…
We used DFT to study the energetics of the decomposition of alane, AlH3, on the Si(001) surface, as the acceptor complement to PH3. Alane forms a dative bond with the raised atoms of silicon surface dimers, via the Si atom lone pair. We…
One of the major challenges towards understanding and further utilizing the properties and functional behaviors of grain boundaries (GB) is the complexity of general GBs with mixed tilt and twist characters. Here, we report the correlations…
We studied polyelectrolyte adsorption on a repulsive charged surface by scaling analysis. At low ionic strength and low surface charge density in which a single polyelectrolyte is able to be adsorbed onto the surface, different regimes in…
The link between the energy surface of bulk systems and their dynamical properties is generally difficult to establish. Using the activation-relaxation technique (ART nouveau), we follow the change in the barrier distribution of a model of…
Polycyclic aromatic compounds (PACs) constitute an important class of molecules found in various environments and are considered important pollutants of the Earth's atmosphere. In particular, functionalization of PACs modify the ring…
Microscopic calculations based on realistic nuclear hamiltonians, while yielding accurate results for the energies of the ground and low-lying excited states of nuclei with $A \leq 12$, fail to reproduce the empirical equilibrium properties…
We develop and analyze a variational model for multi-ply (i.e., multi-layered) paperboard. The model consists of a number of elastic sheets of a given thickness, which -- at the expense of an energy per unit area -- may delaminate. By…