Ab Initio Molecular Dynamics on the Electronic Boltzmann Equilibrium Distribution

We prove that for a combined system of classical and quantum particles, it is possible to write a dynamics for the classical particles that incorporates in a natural way the Boltzmann equilibrium population for the quantum subsystem. In addition, these molecular dynamics do not need to assume that the electrons immediately follow the nuclear motion (in contrast to any adiabatic approach), and do not present problems in the presence of crossing points between different potential energy surfaces (conical intersections or spin-crossings). A practical application of this molecular dynamics to study the effect of temperature in molecular systems presenting (nearly) degenerate states - such as the avoided crossing in the ring-closure process of ozone - is presented.Comment: published in New J. Phy

Ensemble density-functional theory for ab-initio molecular dynamics of metals and finite-temperature insulators

A new method is presented for performing first-principles molecular-dynamics simulations of systems with variable occupancies. We adopt a matrix representation for the one-particle statistical operator Gamma, to introduce a ``projected'' free energy functional G that depends on the Kohn-Sham orbitals only and that is invariant under their unitary transformations. The Liouville equation [ Gamma , H ] = 0 is always satisfied, guaranteeing a very efficient and stable variational minimization algorithm that can be extended to non-conventional entropic formulations or fictitious thermal distributions.Comment: 5 pages, two-column style with 2 postscript figures embedded. Uses REVTEX and epsf macros. Also available at http://www.physics.rutgers.edu/~dhv/preprints/index.html#nm_meta

Hereditary sensory neuropathy type I

Hereditary sensory neuropathy type I (HSN I) is a slowly progressive neurological disorder characterised by prominent predominantly distal sensory loss, autonomic disturbances, autosomal dominant inheritance, and juvenile or adulthood disease onset. The exact prevalence is unknown, but is estimated as very low. Disease onset varies between the 2nd and 5th decade of life. The main clinical feature of HSN I is the reduction of sensation sense mainly distributed to the distal parts of the upper and lower limbs. Variable distal muscle weakness and wasting, and chronic skin ulcers are characteristic. Autonomic features (usually sweating disturbances) are invariably observed. Serious and common complications are spontaneous fractures, osteomyelitis and necrosis, as well as neuropathic arthropathy which may even necessitate amputations. Some patients suffer from severe pain attacks. Hypacusis or deafness, or cough and gastrooesophageal reflux have been observed in rare cases. HSN I is a genetically heterogenous condition with three loci and mutations in two genes (SPTLC1 and RAB7) identified so far. Diagnosis is based on the clinical observation and is supported by a family history. Nerve conduction studies confirm a sensory and motor neuropathy predominantly affecting the lower limbs. Radiological studies, including magnetic resonance imaging, are useful when bone infections or necrosis are suspected. Definitive diagnosis is based on the detection of mutations by direct sequencing of the SPTLC1 and RAB7 genes. Correct clinical assessment and genetic confirmation of the diagnosis are important for appropriate genetic counselling and prognosis. Differential diagnosis includes the other hereditary sensory and autonomic neuropathies (HSAN), especially HSAN II, as well as diabetic foot syndrome, alcoholic neuropathy, neuropathies caused by other neurotoxins/drugs, immune mediated neuropathy, amyloidosis, spinal cord diseases, tabes dorsalis, lepra neuropathy, or decaying skin tumours like amelanotic melanoma. Management of HSN I follows the guidelines given for diabetic foot care (removal of pressure to the ulcer and eradication of infection, followed by the use of specific protective footwear) and starts with early and accurate counselling of patients about risk factors for developing foot ulcerations. The disorder is slowly progressive and does not influence life expectancy but is often severely disabling after a long duration of the disease

Molecular genetics and pathophysiology of 17 beta-hydroxysteroid dehydrogenase 3 deficiency.

Autosomal recessive mutations in the 17 beta-hydroxysteroid dehydrogenase 3 gene impair the formation of testosterone in the fetal testis and give rise to genetic males with female external genitalia. Such individuals are usually raised as females, but virilize at the time of expected puberty as the result of increases in serum testosterone. Here we describe mutations in 12 additional subjects/families with this disorder. The 14 mutations characterized to date include 10 missense mutations, 3 splice junction abnormalities, and 1 small deletion that results in a frame shift. Three of these mutations have occurred in more than 1 family. Complementary DNAs incorporating 9 of the 10 missense mutations have been constructed and expressed in reporter cells; 8 of the 9 missense mutations cause almost complete loss of enzymatic activity. In 2 subjects with loss of function, missense mutations testosterone levels in testicular venous blood were very low. Considered together, these findings strongly suggest that the common mechanism for testosterone formation in postpubertal subjects with this disorder is the conversion of circulating androstenedione to testosterone by one or more of the unaffected 17 beta-hydroxysteroid dehydrogenase isoenzymes

A Self-Consistent First-Principles Technique Having Linear Scaling

An algorithm for first-principles electronic structure calculations having a computational cost which scales linearly with the system size is presented. Our method exploits the real-space localization of the density matrix, and in this respect it is related to the technique of Li, Nunes and Vanderbilt. The density matrix is expressed in terms of localized support functions, and a matrix of variational parameters, L, having a finite spatial range. The total energy is minimized with respect to both the support functions and the elements of the L matrix. The method is variational, and becomes exact as the ranges of the support functions and the L matrix are increased. We have tested the method on crystalline silicon systems containing up to 216 atoms, and we discuss some of these results.Comment: 12 pages, REVTeX, 2 figure

A novel approach to phylogenetic tree construction using stochastic optimization and clustering

BACKGROUND: The problem of inferring the evolutionary history and constructing the phylogenetic tree with high performance has become one of the major problems in computational biology. RESULTS: A new phylogenetic tree construction method from a given set of objects (proteins, species, etc.) is presented. As an extension of ant colony optimization, this method proposes an adaptive phylogenetic clustering algorithm based on a digraph to find a tree structure that defines the ancestral relationships among the given objects. CONCLUSION: Our phylogenetic tree construction method is tested to compare its results with that of the genetic algorithm (GA). Experimental results show that our algorithm converges much faster and also achieves higher quality than GA

Composition Dependence of the Structure and Electronic Properties of Liquid Ga-Se Alloys Studied by Ab Initio Molecular Dynamics Simulation

Ab initio molecular dynamics simulation is used to study the structure and electronic properties of the liquid Ga-Se system at the three compositions Ga$_2$Se, GaSe and Ga$_2$Se$_3$, and of the GaSe and Ga$_2$Se$_3$ crystals. The calculated equilibrium structure of GaSe crystal agrees well with available experimental data. The neutron-weighted liquid structure factors calculated from the simulations are in reasonable agreement with recent neutron diffraction measurements. Simulation results for the partial radial distribution functions show that the liquid structure is closely related to that of the crystals. A close similarity between solid and liquid is also found for the electronic density of states and charge density. The calculated electronic conductivity decreases strongly with increasing Se content, in accord with experimental measurements.Comment: REVTeX, 8 pages and 12 uuencoded PostScript figures, submitted to Phys. Rev. B. corresponding author: [email protected]

The Structure, Dynamics and Electronic Structure of Liquid Ag-Se Alloys Investigated by Ab Initio Simulation

Ab initio molecular-dynamics simulations have been used to investigate the structure, dynamics and electronic properties of the liquid alloy Ag(1-x)Se(x) at 1350 K and at the three compositions x=0.33, 0.42 and 0.65. The calculations are based on density-functional theory in the local density approximation and on the pseudopotential plane-wave method. The reliability of the simulations is confirmed by detailed comparisons with very recent neutron diffraction results for the partial structure factors and radial distribution functions (RDF) of the stoichiometric liquid Ag2Se. The simulations show a dramatic change of the Se-Se RDF with increasing Se content. This change is due to the formation of Se clusters bound by covalent bonds, the Se-Se bond length being almost the same as in pure c-Se and l-Se. The clusters are predominantly chain-like, but for higher x a large fraction of 3-fold coordinated Se atoms is also found. It is shown that the equilibrium fractions of Se present as isolated atoms and in clusters can be understood on a simple charge-balance model based on an ionic interpretation. The Ag and Se diffusion coefficients both increase with Se content, in spite of the Se clustering. An analysis of the Se-Se bond dynamics reveals surprisingly short bond lifetimes of less than 1 ps. The changes in the density of states with composition arise directly from the formation of Se-Se covalent bonds. Results for the electronic conductivity obtained using the Kubo-Greenwood approximation are in adequate agreement with experiment for l-Ag2Se, but not for the high Se contents. Possible reasons for this are discussed.Comment: 14 pages, Revtex, 14 Postscript figures embedded in the tex

Genes for hereditary sensory and autonomic neuropathies: a genotype–phenotype correlation

Hereditary sensory and autonomic neuropathies (HSAN) are clinically and genetically heterogeneous disorders characterized by axonal atrophy and degeneration, exclusively or predominantly affecting the sensory and autonomic neurons. So far, disease-associated mutations have been identified in seven genes: two genes for autosomal dominant (SPTLC1 and RAB7) and five genes for autosomal recessive forms of HSAN (WNK1/HSN2, NTRK1, NGFB, CCT5 and IKBKAP). We performed a systematic mutation screening of the coding sequences of six of these genes on a cohort of 100 familial and isolated patients diagnosed with HSAN. In addition, we screened the functional candidate gene NGFR (p75/NTR) encoding the nerve growth factor receptor. We identified disease-causing mutations in SPTLC1, RAB7, WNK1/HSN2 and NTRK1 in 19 patients, of which three mutations have not previously been reported. The phenotypes associated with mutations in NTRK1 and WNK1/HSN2 typically consisted of congenital insensitivity to pain and anhidrosis, and early-onset ulcero-mutilating sensory neuropathy, respectively. RAB7 mutations were only found in patients with a Charcot-Marie-Tooth type 2B (CMT2B) phenotype, an axonal sensory-motor neuropathy with pronounced ulcero-mutilations. In SPTLC1, we detected a novel mutation (S331F) corresponding to a previously unknown severe and early-onset HSAN phenotype. No mutations were found in NGFB, CCT5 and NGFR. Overall disease-associated mutations were found in 19% of the studied patient group, suggesting that additional genes are associated with HSAN. Our genotype–phenotype correlation study broadens the spectrum of HSAN and provides additional insights for molecular and clinical diagnosis