The particle-transfer molecular-dynamics technique is adopted to construct the Lennard-Jones fluid gas-liquid phase diagram. Detailed study of the dependence of the simulation results on the system size and the cutoff distance is performed to test the validity of the simulation technique. Both the traditional cutoff plus long-range correction (CPC) and Ewald summation methods are used in the si...

On the basis of the icosahedral and decahedral lattices, the lowest energies of the Lennard-Jones (LJ) clusters containing 562-1000 atoms with the two motifs are obtained by using a greedy search method (GSM). Energy comparison between the decahedra and icosahedra shows that icosahedral structures are predominant. However, most of the icosahedral structures with the central vacancy are more sta...

The thermodynamic and structural properties of the planar soft-sites dumbbell fluid are examined by Monte Carlo simulations and integral equation theory. The dimers are built of two Lennard-Jones segments. Site-site integral equation theory in two dimensions is used to calculate the site-site radial distribution functions for a range of elongations and densities and the results are compared wit...

The properties of noble gas systems can be greatly extended by heterogeneous mixtures of elements. The geometrical structures and energies of mixed Ar-Kr-Xe clusters were investigated using ternary Lennard-Jones (TLJ) potential. For the Ar19Kr n Xe19, Ar19Kr19Xe n , and Ar n Kr19Xe19 (n = 0-17) clusters investigated, the results show that only two minimum energy configurations exist, i.e., poly...

A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The iterative update rule contains two thermodynamic averages which are estimated by (generalized ensemble) Monte Carlo. We test the learning algorithm on a Len...

We study the relaxation dynamics of a binary Lennard-Jones liquid in the presence of an amorphous wall generated from equilibrium particle configurations. In qualitative agreement with the results presented by Kob et al. [Nat. Phys. 8, 164 (2012).] for a liquid of harmonic spheres, we find that our binary mixture shows a saturation of the dynamical length scale close to the mode-coupling temper...

The nature of Bence Jones proteins is developed by a review of the pertinent literature. This is followed by a discussion of their metabolism and catabolism under normal and abnormal clinical conditions. Various methods for the detection of Bence Jones proteins are critically reviewed and the significance of these pro­ teins in various disorders is assessed.

The off-equilibrium dynamics of a monatomic Lennard-Jones glass is numerically investigated after sudden isothermal density jumps (crunch) from well equilibrated liquid configurations towards the glassy state. The generalized fluctuation-dissipation relation has been studied and the temperature dependence of the violation factor m is found in agreement with the one step replica symmetry breakin...

We present a computational study of the thermodynamic, dynamic, and structural properties of free-standing thin films, investigated via molecular dynamics simulation of a glass-forming binary Lennard-Jones mixture. An energy landscape analysis is also performed to study glassy states. At equilibrium, species segregation occurs, with the smaller minority component preferentially excluded from th...

We compare evolutionary algorithms with minima hopping for global optimization in the field of cluster structure prediction. We introduce a new average offspring recombination operator and compare it with previously used operators. Minima hopping is improved with a softening method and a stronger feedback mechanism. Test systems are atomic clusters with Lennard-Jones interaction as well as sili...