Biomedical subjects

O C Martin

Publications and source records attributed to O C Martin.

At least 19 recordsLinked to original sources

PubMed2006

Strong universality and algebraic scaling in two-dimensional Ising spin glasses.

At zero temperature, two-dimensional Ising spin glasses are known to fall into several universality classes. Here we consider the scaling at low but nonzero temperatures and provide numerical evidence that eta approximately equal 0 and nu approximately equal 3.5 in all cases, suggesting a unique universality class. This algebraic (as opposed to exponential) scaling holds, in particular, for the +/- J model, with or without dilutions, and for the plaquette diluted model. Such a picture, associated with an exceptional behavior at T = 0, is consistent with a real space renormalization group approach. We also explain how the scaling of the specific heat is compatible with the hyperscaling prediction.

Journal Article↗

PubMed2006

From simple to complex networks: inherent structures, barriers, and valleys in the context of spin glasses.

Given discrete degrees of freedom (spins) on a graph interacting via an energy function, what can be said about the energy local minima and associated inherent structures? Using the lid algorithm in the context of a spin glass energy function, we investigate the properties of the energy landscape for a variety of graph topologies. First, we find that the multiplicity N(s) of the inherent structures generically has a log-normal distribution. In addition, the large volume limit of ln / differs from unity, except for the Sherrington-Kirkpatrick model. Second, we find simple scaling laws for the growth of the height of the energy barrier between the two degenerate ground states and the size of the associated valleys. For finite connectivity models, changing the topology of the underlying graph does not modify qualitatively the energy landscape, but at the quantitative level the models can differ substantially.

Journal Article↗

PubMed2004

Low T scaling in the binary 2d spin glass.

We investigate 2d Ising spin glasses with binary couplings via exact computations of the partition function on lattices with periodic boundary conditions. After introducing the physical issues, we sketch the algorithm to compute the partition function as a polynomial with integer coefficients. This technique is then exploited to obtain the thermodynamic properties of the spin glass. We find an anomalous low temperature scaling of the heat capacity c(v) approximately e(-2beta) and that hyperscaling holds.

Algorithms↗

PubMed2004

Frozen glass phase in the multi-index matching problem.

The multi-index matching is an NP-hard combinatorial optimization problem; for two indices it reduces to the well understood bipartite matching problem that belongs to the polynomial complexity class. We use the cavity method to solve the thermodynamics of the multi-index system with random costs. The phase diagram is much richer than for the case of the bipartite matching problem: it shows a finite temperature phase transition to a completely frozen glass phase, similar to what happens in the random energy model. We derive the critical temperature, the ground-state energy density, and properties of the energy landscape and compare the results to numerics based on exact analysis of small systems.

Journal Article↗

PubMed2004

Critical thermodynamics of the two-dimensional +/-J Ising spin glass.

We compute the exact partition function of 2d Ising spin glasses with binary couplings. In these systems, the ground state is highly degenerate and is separated from the first excited state by a gap of size 4J. Nevertheless, we find that the low temperature specific heat density scales as exp(-2J/T), corresponding to an "effective" gap of size 2J; in addition, an associated crossover length scale grows as exp(J/T). We justify these scalings via the degeneracy of the low lying excitations and by the way low energy domain walls proliferate in this model.

Journal Article↗

PubMed2003

Temperature chaos, rejuvenation, and memory in Migdal-Kadanoff spin glasses.

We use simulations within the Migdal-Kadanoff approach to probe the scales relevant for rejuvenation and memory in Ising spin glasses. First we investigate scaling laws for domain wall free energies and extract the chaos overlap length l(T,T'). Then we perform out of equilibrium simulations that follow experimental protocols. We find that (1) a rejuvenation signal arises at a length scale significantly smaller than l(T,T'), and (2) memory survives even if equilibration goes out to length scales larger than l(T,T'). Theoretical justifications of these phenomena are then considered.

Journal Article↗

PubMed2003

Scalings of domain wall energies in two dimensional Ising spin glasses.

We study domain wall energies of two dimensional spin glasses. The scaling of these energies depends on the model's distribution of quenched random couplings, falling into three different classes. The first class is associated with the exponent theta approximately -0.28; the other two classes have theta=0, as can be justified theoretically. In contrast to previous claims, we find that theta=0 does not indicate d=d(c)(l) but rather d< or =d(c)(l), where d(c)(l) is the lower critical dimension.

Journal Article↗

PubMed2002

Absence of an equilibrium ferromagnetic spin-glass phase in three dimensions.

Using ground state computations, we study the transition from a spin glass to a ferromagnet in 3D spin glasses when changing the mean value of the spin-spin interaction. We find good evidence for replica symmetry breaking up until the critical value where ferromagnetic ordering sets in, and no ferromagnetic spin glass phase. This phase diagram is in conflict with the droplet/scaling and mean field theories of spin glasses. We also find that the exponents of the second order ferromagnetic transition do not depend on the microscopic Hamiltonian, suggesting universality of this transition.

Journal Article↗

PubMed2001

Zero-temperature responses of a 3D spin glass in a magnetic field.

We probe the energy landscape of the 3D Edwards-Anderson spin glass in a magnetic field to test for a spin glass ordering. We find that the spin glass susceptibility is anomalously large on the lattice sizes we can reach. Our data suggest that a transition from the spin glass to the paramagnetic phase takes place at B(c) approximately 0.65, though the possibility B(c) = 0 cannot be excluded. We also discuss the question of the nature of the putative frozen phase.

Journal Article↗

PubMed2001

Hierarchical approach for computing spin glass ground states.

We describe a numerical algorithm for computing spin glass ground states with a high level of reliability. The proposed method uses a population based search and applies optimization on multiple scales. Benchmarks are given leading to estimates of the performance on large lattices.

Journal Article↗

PubMed2000

Characterization and reconstitution of Drosophila gamma-tubulin ring complex subunits.

The gamma-tubulin ring complex (gammaTuRC) is important for microtubule nucleation from the centrosome. In addition to gamma-tubulin, the Drosophila gammaTuRC contains at least six subunits, three of which [Drosophila gamma ring proteins (Dgrips) 75/d75p, 84, and 91] have been characterized previously. Dgrips84 and 91 are present in both the small gamma-tubulin complex (gammaTuSC) and the gammaTuRC, while the remaining subunits are found only in the gammaTuRC. To study gammaTuRC assembly and function, we first reconstituted gammaTuSC using the baculovirus expression system. Using the reconstituted gammaTuSC, we showed for the first time that this subcomplex of the gammaTuRC has microtubule binding and capping activities. Next, we characterized two new gammaTuRC subunits, Dgrips128 and 163, and showed that they are centrosomal proteins. Sequence comparisons among all known gammaTuRC subunits revealed two novel sequence motifs, which we named grip motifs 1 and 2. We found that Dgrips128 and 163 can each interact with gammaTuSC. However, this interaction is insufficient for gammaTuRC assembly.

Amino Acid Motifs↗

PubMed2000

Spin and link overlaps in three-dimensional spin glasses.

Excitations of three-dimensional spin glasses are computed numerically. We find that one can flip a finite fraction of an LxLxL lattice with an O(1) energy cost, confirming the mean-field picture of a nontrivial spin overlap distribution P(q). These low energy excitations are not domain-wall-like, rather they are topologically nontrivial and they reach out to the boundaries of the lattice. Their surface to volume ratios decrease as L increases and may asymptotically go to zero. If so, link and window overlaps between the ground state and these excited states become "trivial."

Journal Article↗

PubMed2000

Langerhans cell deficiency in reticular dysgenesis.

Reticular dysgenesis is a rare inherited immunodeficiency characterized by the lack of blood monocytes and neutrophils and low lymphocyte counts, contrasting with normal red blood cell counts and normal or decreased platelet counts. Whether dendritic cells or macrophages, both of which derive primarily from blood monocytes, are affected in this condition remains unknown. We studied 7 patients with reticular dysgenesis. Macrophages were present in normal numbers in the dermis and in the atrophic lymphoid tissues of these patients, proving that at least some subsets of macrophages can differentiate despite very low monocyte counts. By contrast, Langerhans cells, which are CD1a-positive epidermal dendritic cells, were absent in all (n = 5) patients before bone marrow transplantation. After bone marrow transplantation, Langerhans cells were present (n = 2), suggesting that the defect is not related to keratinocyte dysfunction. A split chimeric reconstitution, characterized by the presence of autologous blood monocytes able to differentiate in vitro into CD1a-positive dendritic cells, was observed in a patient who underwent successful engraftment. These results suggest that an intrinsic cell defect is unlikely and that a bone marrow-derived factor may be defective in reticular dysgenesis; it may be responsible for the Langerhans cell defect but not involved in macrophage differentiation.

Antigens, CD↗

PubMed1999

Characterization of two related Drosophila gamma-tubulin complexes that differ in their ability to nucleate microtubules.

gamma-tubulin exists in two related complexes in Drosophila embryo extracts (Moritz, M., Y. Zheng, B.M. Alberts, and K. Oegema. 1998. J. Cell Biol. 142:1- 12). Here, we report the purification and characterization of both complexes that we name gamma-tubulin small complex (gammaTuSC; approximately 280,000 D) and Drosophila gammaTuRC ( approximately 2,200,000 D). In addition to gamma-tubulin, the gammaTuSC contains Dgrip84 and Dgrip91, two proteins homologous to the Spc97/98p protein family. The gammaTuSC is a structural subunit of the gammaTuRC, a larger complex containing about six additional polypeptides. Like the gammaTuRC isolated from Xenopus egg extracts (Zheng, Y., M.L. Wong, B. Alberts, and T. Mitchison. 1995. Nature. 378:578-583), the Drosophila gammaTuRC can nucleate microtubules in vitro and has an open ring structure with a diameter of 25 nm. Cryo-electron microscopy reveals a modular structure with approximately 13 radially arranged structural repeats. The gammaTuSC also nucleates microtubules, but much less efficiently than the gammaTuRC, suggesting that assembly into a larger complex enhances nucleating activity. Analysis of the nucleotide content of the gammaTuSC reveals that gamma-tubulin binds preferentially to GDP over GTP, rendering gamma-tubulin an unusual member of the tubulin superfamily.

Amino Acid Sequence↗

PubMed1998

Xgrip109: a gamma tubulin-associated protein with an essential role in gamma tubulin ring complex (gammaTuRC) assembly and centrosome function.

Previous studies indicate that gamma tubulin ring complex (gammaTuRC) can nucleate microtubule assembly and may be important in centrosome formation. gammaTuRC contains approximately eight subunits, which we refer to as Xenopus gamma ring proteins (Xgrips), in addition to gamma tubulin. We found that one gammaTuRC subunit, Xgrip109, is a highly conserved protein, with homologues present in yeast, rice, flies, zebrafish, mice, and humans. The yeast Xgrip109 homologue, Spc98, is a spindle-pole body component that interacts with gamma tubulin. In vertebrates, Xgrip109 identifies two families of related proteins. Xgrip109 and Spc98 have more homology to one family than the other. We show that Xgrip109 is a centrosomal protein that directly interacts with gamma tubulin. We have developed a complementation assay for centrosome formation using demembranated Xenopus sperm and Xenopus egg extract. Using this assay, we show that Xgrip109 is necessary for the reassembly of salt-disrupted gammaTuRC and for the recruitment of gamma tubulin to the centrosome. Xgrip109, therefore, is essential for the formation of a functional centrosome.

Amino Acid Sequence↗

PubMed1997

Changes in the spectral properties of a plasma membrane lipid analog during the first seconds of endocytosis in living cells.

N-[5-(5, 7-dimethyl Bodipy)-1-pentanoyl]-D-erythro-sphingosylphosphorylcholine (C5-DMB-SM), a fluorescent analog of sphingomyelin, has been used in a study of the formation of very early endosomes in human skin fibroblasts. This lipid exhibits a shift in its fluorescence emission maximum from green (approximately 515 nm) to red (approximately 620 nm) wavelengths with increasing concentrations in membranes. When cells were incubated with 5 microM C5-DMB-SM at 4 degrees C and washed, only plasma membrane fluorescence (yellow-green) was observed. When these cells were briefly (< or = 1 min) warmed to 37 degrees C to allow internalization to occur, and then incubated with defatted bovine serum albumin (back-exchanged) at 11 degrees C to remove fluorescent lipids from the plasma membrane, C5-DMB-SM was distributed in a punctate pattern throughout the cytoplasm. Interestingly, within the same cell some endosomes exhibited green fluorescence, whereas others emitted red-orange fluorescence. Furthermore, the red-orange endosomes were usually seen at the periphery of the cell, while the green endosomes were more uniformly distributed throughout the cytoplasm. This mixed population of endosomes was seen after internalization times as short as 7 s and was also seen over a wide range of C5-DMB-SM concentrations (1-25 microM). Control experiments established that the variously colored endosomes were not induced by changes in pH, membrane potential, vesicle size, or temperature. Quantitative fluorescence microscopy demonstrated that the apparent concentration of the lipid analog in the red-orange endosomes was severalfold higher than its initial concentration at the plasma membrane, suggesting selective internalization (sorting) of the lipid into a subset of early endosomes. Colocalization studies using C5-DMB-SM and either anti-transferrin receptor antibodies or fluorescently labeled low-density lipoprotein further demonstrated that this subpopulation of endosomes resulted from receptor-mediated endocytosis. We conclude that the spectral properties of C5-DMB-SM can be used to distinguish unique populations of early endosomes from one another and to record dynamic changes in their number and distribution within living cells.

Cell Membrane↗

PubMed1996

A numerical study of persistence length effects on DNA conformation in sequencing electrophoresis.

We have developed a program to evaluate the influence of DNA stiffness on molecular mobility and conformation during electrophoresis. This (currently) two-dimensional numerical study models DNA as a chain of uniformly charged beads connected to one another by elastic segments, of finite mean size, in the presence of fixed obstacles representing gel fibers. Contrary to the standard biased reptation model (BRM), our Langevin-type dynamics for the chain are microscopic and warrant studies of fine effects such as inner chain orientation. Using this model, we show that the introduction of a persistence length decreases the (saturated) mobility at high electric fields, providing strong evidence that the gel generates a friction force and not only a (dissipation-free) constraint force. We also show that the persistence length leads to an increase of the chain orientation in the field direction. This suggests that DNA stiffness causes the saturation plateau value to be reached for smaller chain sizes than those predicted by the BRM model.

DNA↗

PubMed1995

Memory capacity in large idiotypic networks.

Many models of immune networks have been proposed since the original work of Jerne [1974, Ann. Immun. (Inst. Pasteur)125C, 373-389]. Recently, a limited class of models (Weisbuch et al., 1990, J. theor. Biol 146, 483-499) have been shown to maintain immunological memory by idiotypic network interactions. We examine generalizations of these models when the networks are both large and highly connected to study their memory capacity, i.e., their ability to account for immunization to a large number of random antigens. Our calculations show that in these minimal models, random connectivities with continuously distributed affinities reduce the memory capacity to essentially nil.

Animals↗