Erika C. Flint photo

Research Areas

Director

Spike Narayan

Spike Narayan

Dr. Spike Narayan
Director
Science & Technology

"Mind, like a parachute, works best when open"
- Anonymous

"Any sufficiently advanced technology is indistinguishable from magic."
- Arthur C. Clarke

"If we knew what it was we were doing, it would not be called research, would it?"
- Albert Einstein

Collaborations

  • SpinAps
  • Link to Center for Probing the Nanoscale

Almaden Institute 2012 : Superconductivity 297K

Link to Almaden Institute 2012 : Superconductivity 297K -
Synthetic Routes to Room Temperature Superconductivity

Group Name

IBM Research - Almaden Science & Technology


We share our knowledge with the world! align=
Science and Technology welcomes students from various universities to present their work in Almaden's ARC ANGELS Student Seminar Series.

If you are interested in attending, contact Greg Wallraff (gmwall@us.ibm.com)



Topic: DNA Fragility and Adaptive Evolution In Natural Populations
Speaker: Kathleen T. Xie, (Stanford University)

Date: 11/08/2013 Time: 10:30 AM - 11:00 AM
Abstract: We study the genetic basis of evolution using stickleback fish. Vertebrates have evolved a striking array of limb modifications, including complete loss of the pelvis in many groups. In sticklebacks, pelvic loss is adaptive in many freshwater populations. Previous studies have mapped the trait to the PITX1 gene, a major developmental regulator gene. Although the mutations occurred independently in different freshwater lineages, almost all map to the same location, and almost all are deletions of ~500-5,000 base pairs. We tested whether inherent DNA fragility contributes to this unusual mutational spectrum. We find that the region is capable of forming unusual DNA structures and is prone to DNA breakage. Previous studies suggest that DNA fragile sites contribute to human disease phenotypes, including cancer. Our studies suggest that DNA fragility may also be important for generating the variations that underlie major evolutionary changes in natural populations.

Topic: Recent Human Evolution As Revealed By Ancient Hominin Genomes
Speaker: Samuel Vohr, (UC Santa Cruz)

Date: 11/08/2013 Time: 11:00 AM - 11:30 AM
Abstract: Neandertals, the closest evolutionary relatives to modern humans, lived throughout Europe and western Asia before disappearing 30,000 years ago. Although Neandertals have been known to science since the 19th century, recent advances in the fields genome sequencing and ancient DNA have afforded us the opportunity to study them from a new, genetic perspective. Comparison of Neandertal genomic sequences with present-day human genetic diversity has uncovered a surprising signal of admixture (interbreeding) between Neandertals and the ancestors of all present-day non-Africans. Further examination has led to the identification genetic variants introduced into humans through Neandertals and hints of the biological basis of what makes humans unique as a species. In this presentation, I will outline the sequencing of the first draft of the Neandertal genome and some of the first discoveries that came from it.

Topic: Synthetic Biology for Cellular Nanomaterials
Speaker: Stephanie Jones, (University of California at Berkeley)

Date: 12/13/2013 Time: 10:30 AM - 11:00 AM
Abstract: Nanostructured materials have different physical properties than their bulk counterparts, properties which are dependent upon the size and shape as well as the composition of the nanostructures. The ability to develop new materials with novel, precise properties has large implications in a wide variety of fields, from energy to medicine. Traditional materials synthesis, however, depends upon harsh processing conditions and precise control over nanostructure formation is difficult. Biological organisms have found ways to mineralize inorganic materials of specific composition, morphology, and orientation under ambient conditions. The understanding and manipulation of biologically-controlled mineral growth can allow the generation of novel materials under mild conditions. Magnetotactic bacteria, a phylogenetically diverse group of magnetic field-sensing bacteria, are of particular interest as they form magnetite nanocrystals of precise shape and size and have precise control over the redox state of iron in order to form a defectless crystal lattice. Our group uses magnetotactic bacteria as a platform for understanding and engineering the production of cellular nanomaterials with applications to the synthesis and discovery of new nanoscale materials as well as the implantation of novel intracellular devices to alter or control cell behavior.

Topic: Toward Scalable Biological Computers
Speaker: Pakpoom Subsoontorn (Stanford University)

Date: 12/13/2013 Time: 11:00 AM - 11:30 AM
Abstract: Nanostructured materials have different physical properties than their bulk counterparts, properties which are dependent upon the size and shape as well as the composition of the nanostructures. The ability to develop new materials with novel, precise properties has large implications in a wide variety of fields, from energy to medicine. Traditional materials synthesis, however, depends upon harsh processing conditions and precise control over nanostructure formation is difficult. Biological organisms have found ways to mineralize inorganic materials of specific composition, morphology, and orientation under ambient conditions. The understanding and manipulation of biologically-controlled mineral growth can allow the generation of novel materials under mild conditions. Magnetotactic bacteria, a phylogenetically diverse group of magnetic field-sensing bacteria, are of particular interest as they form magnetite nanocrystals of precise shape and size and have precise control over the redox state of iron in order to form a defectless crystal lattice. Our group uses magnetotactic bacteria as a platform for understanding and engineering the production of cellular nanomaterials with applications to the synthesis and discovery of new nanoscale materials as well as the implantation of novel intracellular devices to alter or control cell behavior.

Topic: Mechanical unfolding of human telomere G-quadruplex DNA probed by integrated fluorescence and magnetic tweezers
Speaker: Xi (Salina) Long (University of California Santa Cruz)

Date: 2/14/2014 Time: 10:30 AM - 11:00 AM
Abstract: Telomeres are specialized DNA that protect the natural ends of chromosomes. The foundation of human telomere structure is a long array of tandem DNA sequences (TTAGGG), which can fold into a class of secondary structures known as G-quadruplexes (GQ). Previous studies revealed that distinct forms of GQs coexist under a single folding condition1-3. Single molecule Forster resonance energy transfer (smFRET) experiments demonstrated the folding dynamics of GQ, and suggested that inter-conversion between distinct GQ folds proceeds through an obligatory transient intermediate4. To further characterize this GQ folding intermediate we developed an integrated fluorescence and magnetic tweezers spectroscopy technique, which permits the application of a wide range of stretching forces (0.1-50 picoNewtons) to individual GQ folds, together with simultaneous detection of GQ folding and unfolding through smFRET. Here, we present our investigation of the Na+-induced anti-parallel GQ conformation. Analysis of the force-dependent rate constants for the GQ folding and unfolding reactions provided an estimate of the position of transition state for GQ unfolding along the DNA stretching coordinate. The results suggest the telomere GQ is extremely sensitive to mechanical force; only small perturbations can disrupt the entire structure. Furthermore, by comparing the GQ unfolded state with a single-stranded polyT DNA we show the unfolded GQ exhibits a significantly compacted non-native conformation reminiscent of the protein molten globule.

Topic: Beyond the Clear Pupil: Engineering New Capabilities into Optical Microscopes
Speaker: Matthew Lew (Stanford University)

Date: 2/14/2014 Time: 11:00 AM - 11:30 AM
Abstract: The basic design of optical microscopes remains unchanged since Hooke and van Leeuwenhoek peered through them four centuries ago. However, by engineering the point spread function (PSF), or the impulse response of an imaging system to a point source, we can encode more information into microscope images beyond the simple two-dimensional diffraction-limited slices through a sample common in laboratory microscopes today. The Moerner Lab utilizes the double-helix (DH) microscope, an imaging system that bends the light emitted from point objects into a double-helix shape, to measure the three-dimensional position of many fluorescent emitters simultaneously without any mechanical scanning. Combined with single-molecule photoswitching techniques like (F)PALM and STORM, the DH microscope routinely images the 3D morphology of structures within living cells with resolution beyond the diffraction limit. Recently, we have extended the capabilities of the DH microscope to measure simultaneously the 3D position and orientation of fixed single molecules. As brighter fluorescent molecules become available and newly designed PSFs more efficiently convey rich information about the sample of interest, modern microscopes will be able to probe the complex nanoscale machinery at work within living cells.