Molecular dynamics investigations on a quantum system in a thermostat

The model quantum system of fermions in a one dimensional harmonic oscillator potential is investigated by a molecular dynamics method at constant temperature. Although in quantum mechanics the equipartition theorem cannot be used like in the Nose-Hoover-thermostat it is possible to couple an additional degree of freedom to the system which acts as a thermometer and drives the system towards the desired temperature via complex time steps.Comment: 11 pages, 8 postscript figures, uses 'epsfig.sty'. Submitted to PHYSICA A. More information available at http://obelix.physik.uni-osnabrueck.de/~schnac

Nose-Hoover dynamics for coherent states

The popular method of Nose and Hoover to create canonically distributed positions and momenta in classical molecular dynamics simulations is generalized to a genuine quantum system of infinite dimensionality. We show that for the quantum harmonic oscillator, the equations of motion in terms of coherent states can easily be modified in an analogous manner to mimic the coupling of the system to a thermal bath and create a quantum canonical ensemble. Possible applications to more complex systems, especially interacting Fermion systems, are proposed.Comment: 13 pages, 3 figure

Thermodynamics of the harmonic oscillator using coherent states

The ongoing discussion whether thermodynamic properties can be extracted from a (possibly approximate) quantum mechanical time evolution using time averages is fed with an instructive example. It is shown for the harmonic oscillator how the Hilbert space or an appropriately defined phase space must be populated in terms of coherent states in order to obtain the quantum result respectively the classical one.Comment: 6 pages, 2 postscript figures, uses 'epsfig.sty'. Submitted to Europhysics Letters. Introduction changed and references added for the revised version. More information available at http://obelix.physik.uni-osnabrueck.de/~schnack

Non-finite-difference algorithm for integrating Newton's motion equations

We have presented some practical consequences on the molecular-dynamics simulations arising from the numerical algorithm published recently in paper Int. J. Mod. Phys. C 16, 413 (2005). The algorithm is not a finite-difference method and therefore it could be complementary to the traditional numerical integrating of the motion equations. It consists of two steps. First, an analytic form of polynomials in some formal parameter $\lambda$ (we put $\lambda=1$ after all) is derived, which approximate the solution of the system of differential equations under consideration. Next, the numerical values of the derived polynomials in the interval, in which the difference between them and their truncated part of smaller degree does not exceed a given accuracy $\epsilon$, become the numerical solution. The particular examples, which we have considered, represent the forced linear and nonlinear oscillator and the 2D Lennard-Jones fluid. In the latter case we have restricted to the polynomials of the first degree in formal parameter $\lambda$. The computer simulations play very important role in modeling materials with unusual properties being contradictictory to our intuition. The particular example could be the auxetic materials. In this case, the accuracy of the applied numerical algorithms as well as various side-effects, which might change the physical reality, could become important for the properties of the simulated material.Comment: 11 page

Predicting crystal structures: the Parrinello-Rahman method revisited

By suitably adapting a recent approach [A. Laio and M. Parrinello, PNAS, 99, 12562 (2002)] we develop a powerful molecular dynamics method for the study of pressure-induced structural transformations. We use the edges of the simulation cell as collective variables. In the space of these variables we define a metadynamics that drives the system away from the local minimum towards a new crystal structure. In contrast to the Parrinello-Rahman method our approach shows no hysteresis and crystal structure transformations can occur at the equilibrium pressure. We illustrate the power of the method by studying the pressure-induced diamond to simple hexagonal phase transition in a model of silicon.Comment: 5 pages, 2 Postscript figures, submitte

Nonequilibrium Microscopic Distribution of Thermal Current in Particle Systems

A nonequilibrium distribution function of microscopic thermal current is studied by a direct numerical simulation in a thermal conducting steady state of particle systems. Two characteristic temperatures of the thermal current are investigated on the basis of the distribution. It is confirmed that the temperature depends on the current direction; Parallel temperature to the heat-flux is higher than antiparallel one. The difference between the parallel temperature and the antiparallel one is proportional to a macroscopic temperature gradient.Comment: 4 page

Hydration of methanol in water. A DFT-based molecular dynamics study

We studied the hydration of a single methanol molecule in aqueous solution by first-principle DFT-based molecular dynamics simulation. The calculations show that the local structural and short-time dynamical properties of the water molecules remain almost unchanged by the presence of the methanol, confirming the observation from recent experimental structural data for dilute solutions. We also see, in accordance with this experimental work, a distinct shell of water molecules that consists of about 15 molecules. We found no evidence for a strong tangential ordering of the water molecules in the first hydration shell.Comment: 5 pages, 3 figures, submitted to Chemical Physics Letter

Familial Follicular Cell-Derived Thyroid Carcinoma

Follicular cell-derived well-differentiated thyroid cancer, papillary (PTC) and follicular thyroid carcinomas comprise 95% of all thyroid malignancies. Familial follicular cell-derived well-differentiated thyroid cancers contribute 5% of cases. Such familial follicular cell-derived carcinomas or non-medullary thyroid carcinomas (NMTC) are divided into two clinical–pathological groups. The syndromic-associated group is composed of predominately non-thyroidal tumors and includes Pendred syndrome, Warner syndrome, Carney complex (CNC) type 1, PTEN-hamartoma tumor syndrome (PHTS; Cowden disease), and familial adenomatous polyposis (FAP)/Gardner syndrome. Other conditions with less established links to the development of follicular cell-derived tumors include ataxia–telangiectasia syndrome, McCune Albright syndrome, and Peutz–Jeghers syndrome. The final group encompasses syndromes typified by NMTC, as well as pure familial (f) PTC with or without oxyphilia, fPTC with multinodular goiter, and fPTC with papillary renal cell carcinoma. This heterogeneous group of diseases does not have the established genotype–phenotype correlations known as in the familial C-cell-derived tumors or medullary thyroid carcinomas (MTC). Clinicians should have the knowledge to identify the likelihood of a patient presenting with thyroid cancer having an additional underlying familial syndrome stemming from characteristics by examining morphological findings that would alert pathologists to recommend that patients undergo molecular genetic evaluation. This review discusses the clinical and pathological findings of patients with familial PTC, such as FAP, CNC, Werner syndrome, and Pendred syndrome, and the heterogeneous group of familial PTC