- Modeling of Organic Reaction Mechanisms
- Modeling Self-Assembly
- IBM Research Almaden ARC ANGELS Student Seminar Series
Dr. Spike Narayan
Science & Technology
"Mind, like a parachute, works best when open"
"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
Almaden Institute 2012 : Superconductivity 297K
Science and Technology welcomes researchers from academia and industry to present their work in Almaden's Science Colloquium Series.
Science and Technology staff who are interested in inviting researchers for this series are encouraged to contact Gavin Jones (firstname.lastname@example.org) or Greg Wallraff (email@example.com) to arrange presentations.
Topic: Biodegradable Polymeric Nanoparticles for Toner Applications
Speaker: Andrew J. Myles, Ph. D. (NINT)
Date: 1/22/2016 Time: 10:30 AM - 11:00 AM
Location: Auditorium A
Abstract: As a principal investigator on a NINT-Xerox collaborative research project, Dr. Myles and his team developed methodologies for the synthesis and self-assembly of polymeric nanomaterials.
A novel, scalable process was developed to generate biodegradable ABC triblock copolymers, involving one-pot, neat, organocatalytic ring opening polymerization that does not require stringent reaction conditions, such as removal of water and oxygen, while still maintaining low polydispersities and high molecular weight control. Varying the length of each block allows control over the self-assembly process in aqueous mixtures to form well defined polymeric nanoparticles, opening up a new class of materials for toner applications.
Topic: FluidFM: Combining Atomic Force Microscopy and Nanofluidics in a Liquid Delivery System: 3D Manipulations from Single Cells to Metals
Speaker: Pablo Dorig, Ph. D. (Cytosurge)
Date: 3/4/2016 Time: 10:30 AM - 11:30 AM
Location: Auditorium A
Abstract: The FluidFM instrumentation is a fluid delivery system interfaced with atomic force microscopy (AFM) enabling nm-placement precision of femtoliter-volumes of material. The result is a precisely controlled nanopipette with openings down to 300 nm. This allows liquid delivery in air or under liquid of femtoliter fluid volumes from closed micro-channels. The system also performs gentle manipulation of microscopic objects while grasping them with underpressure. Possible applications range from single cell injection and biophysical measurements through to 3D metal micro printing.
Topic: Combinatorial Optimization with Coherent Ising Machines
Speaker: Yoshio Yamamoto (Stanford University and ImPACT, Japan)
Date: 3/11/2016 Time: 10:30 AM - 11:30 AM
Location: Auditorium A
Abstract: A novel method that achieves combinatorial optimization using degenerate optical parametric oscillator (DOPO) network is introduced. The DOPO network implements the Ising Hamiltonian as an effective network loss and finds the ground state by exploiting the quantum parallel search, entanglement based filtering and quantum-to-classical crossover at the oscillation threshold. The benefits of the new principle compared to the simulated annealing and quantum annealing will be discussed. A coherent Ising machine is realized by the fiber-based DOPO and the measurement-feedback FPGA circuit with number of Ising spins ranging from N=100 to N=10,000. The performance is compared with the theoretical prediction based on the quantum theory of the DOPO network.
Topic: Electrochemical Ion Insertion Reactions
Speaker: William Chueh (Stanford University)
Date: 3/25/2016 Time: 10:30 AM - 11:30 AM
Abstract: Electrochemistry plays a crucial role in virtually all energy storage and conversion technologies, such as batteries, fuel cells, and artificial leaves. Ion insertion processes, such as those involving lithium and oxygen ions in solids, are ubiquitous. Unlike electrochemical reactions on metal surfaces, intercalation involves the two-way traffic of ions and electrons. However, despite the importance of intercalation reactions, the fundamental nature of these processes remains mysterious. We are employing in-situ spectroscopy, microscopy, and computation to shed light on the detailed kinetics and thermodynamics of intercalation reactions. In this talk, I will present new insights on two important classes of reactions (1) insertion of oxygen ions in ferrate-perovskite fuel cell electrocatalysts, and (2) intercalation of lithium ions in lithium iron phosphate olivine battery electrodes.
Insertion of oxygen ions into perovskite material is crucial reaction in electrodes for solid-oxide fuel cells and electrolyzer. It is usually assumed that the electron transfer reaction takes place between oxygen adsorbate and the transition metal atoms on the surface, the latter serving as the redox-active centers. Using operando X-ray absorption spectroscopy, we show that oxygen ion is a redox-active center in transition-metal perovskites, and participates directly in the electron transfer reaction.
Another important insertion reaction is the intercalation of lithium into lithium-ion battery electrodes. Using LiFePO4 as a model system and single-particle spectro-imaging, we investigated the heterogeneity of the intercalation reaction. We found that, contrary to intuition, the heterogeneity of the intercalation reaction actually decreases with current. We explain the phenomenon using a phase-field porous electrode model.
Topic: Towards Practical Quantum Chemistry on a Quantum Computer
Speaker: Ryan Babbush, Ph. D. (Google Research)
Date: 4/8/2016 Time: 10:30 AM - 11:30 AM
Location: Auditorium A
Abstract: As small quantum computers come increasingly close to viability there has been substantial renewed interest in quantum algorithms for modeling chemistry and strongly correlated materials due to low qubit requirements and industrial importance. After a brief review, I will discuss recent work which has dramatically reduced the asymptotic cost of these algorithms. However, while industrial efforts to engineer a quantum memory will soon produce a quantum computer with more physical qubits than can be simulated classically, we are still many years away from having the same number of error-corrected logical qubits. This raises the question of whether shallow (and somewhat noisy) quantum circuits can be used to study classically intractable fermionic systems. I will discuss the promising possibility that parameterized quantum circuits could be trained to model such systems if optimized with respect to a variational principle. Finally, I will review a recent experimental demonstration of these algorithms and discuss prospects for larger demonstrations in the next several years.
Topic: Force and Function: How do Biomolecules do it?
Speaker: Hermann Gaub (Ludwig Maximillian University)
Date: 4/22/2016 Time: 10:30 AM - 11:30 AM
Location: Auditorium A
Abstract: Molecular interactions are the basis of life, and forces play a crucial role in both the assembly and the structural integrity, as well as the dynamics of all living systems. The regulation of bio-molecular complexes, the maintenance of cellular structures, and even cell signaling are all controlled by mechanical forces. At the molecular level, the relationships between these forces and their biological functions have become accessible through various single molecule force spectroscopy techniques developed in recent years. A deeper understanding of the physics of these relationships has emerged from the very fruitful combination of the high resolution and precision of such experiments together with the insight in structural rearrangements from all-atom Molecular Dynamics Calculations. In this talk, a general overview on this field will be given, followed by a report on recent discoveries: The activation mechanisms of two prominent intracellular force sensors, Myosin Light Chain Kinase and Titin Kinase were elucidated. The clamp-mechanism of catch bonds between Cohesin and Dockerins in Cellulosome complexes could be resolved. Novel strategies for parallelization of force-measuring assays will be discussed, and a new chip based strategy will be introduced starting out from genes and providing direct access to the mechanics of the encoded proteins in a single step process. Finally, the use of molecular force balances for the analysis of DNA-protein interactions will be presented.
Topic: Redesigning the Interface Between Fresh Produce and the Environment for Sustainable Agriculture
Speaker: James Rogers, PhD (Apeel Sciences)
Date: 7/01/2016 Time: 10:30 AM - 11:30 AM
Location: Auditorium A
Abstract: Apeel Sciences creates products from natural plant extracts that allow growers to reduce reliance on pesticides, increase produce quality, and provide superior shelf life even when optimal temperature control is not possible. As the world confronts the implications of an ever-expanding population, agriculture will need to evolve in order to improve the efficiency of natural resource use. In the US, the majority of fresh water is consumed for irrigation while 40% of fresh produce is lost to spoilage before it can be used. This means we are literally “throwing away” a portion of our available freshwater supply, not to mention the added negative environmental consequences of pesticide usage associated with growing the huge fraction of produce that ultimately ends up in landfills. Apeel's innovative technologies protect crops and help to significantly reduce spoilage, which in turn reduces water use, lowers energy costs, and helps preserve natural ecosystems. Using agricultural byproducts – parts of the plant that are normally discarded – Apeel creates products that fortify the surfaces of fresh fruits and vegetables, forming an ultra-thin barrier that camouflages crops and shields produce from both biotic and abiotic stressors. Made from 100% plant material, Apeel’s protective formulas are invisible, tasteless, edible and durable.
Topic: Energy Efficient Computing by Redox-based Memristive Oxide Elements
Speaker: Rainer Waser (Electronic Materials Research Lab, Jülich/Aachen)
Date: 7/08/2016 Time: 10:30 AM - 11:30 AM
Abstract: Redox-Based Resistive Switching Memories (ReRAM), also called nanoionic memories or memristive elements, are widely considered to provide a potential leap beyond the limits of Flash (with respect to write speed, write energies) and DRAM (with respect to scalability, retention times) as well as energy-efficient approaches to neuromorphic concepts.
In this seminar talk, the ultra-high non-linearity of the switching kinetics of redox-based resistive switching devices will be discussed with an emphasis on the so-called valence change mechanism (VCM) typically encountered as a bipolar switching in metal oxides. The involved electrochemical and physical processes can be either electric field/voltage enhanced or accelerated by a local increase in temperature due to Joule heating. The analysis of the published SET switching kinetics data of VCM-type ReRAM systems showed that their nonlinearity is mainly dominated by temperature-accelerated ion hopping, controlled by the local power during the switching process. The gradual RESET transition can be explained in terms of temperature-accelerated ion movement with counter-acting ion drift and diffusion processes. It will be shown that a designated combination of oxides can significantly improve the long-term kinetics, i.e. the retention time, by tailoring the ion diffusion properties in the oxide layers.
To evaluate the energy-relevant parameters, the analysis must be extended from a discrete single cell to a complete circuit such as an array. In particular, the impact of parasitics such as the bit line capacitance per cell and technical boundary conditions such as supply voltages or minimum sense voltage levels have to be considered. If we consider a typical ReRAM stack based on a VCM cell and scale the feature size in vertical and lateral dimensions, the non-linearity further improves and the switching energy decreases.
In the area of the application of redox-based memristive elements for neuromorphic computing the aim is to realize computational tasks in brain-like multi-parallel manner. The use of ultimately scaled nano-crossbar array or dedicated circuits could pave the path to energy-efficient solutions, for instance through implementing associative networks.
Topic: Shadow Microscope, Image Processing and Applications
Speaker: Thomas Zimmerman, Ph.D. (IBM Research - Almaden)
Date: 9/16/2016 Time: 10:30 AM - 11:30 AM
Abstract: Conventional microscopes uses a series of lenses to magnify the view of objects. A shadow microscope uses a point light source (e.g. LED) to cast shadows of aquatic life placed on top of an imager sensor to provide high definition images without the bulk, weight and cost of conventional microscopes. By using structured light, the 3D location and shape of the aquatic life can be determined. In this talk I will give a live demonstration of the shadowgram microscope and image processing developed to track and identify microzooplankton organisms and discuss some of the goals and applications of the shadow microscope project.
Topic: Microbiome Studies at Almaden (Part I)
Speaker: Gregory Wallraff, Ph.D. (IBM Research - Almaden)
Date: 9/30/2016 Time: 10:30 AM - 11:30 AM
Location: J2 - 109
Abstract: Microbiomes are characteristic microbial communities that occupy specific ecological niches. Mosquitos, keyboards, oil wells, dogs, bathroom floors and tide pools all have microbiomes which impact the host organism and other organisms in the environment. For example the human gut microbiome has been implicated in such diverse conditions such as obesity, intestinal disorders and autism.
The advent of high throughput DNA sequencing has enabled microbiologists to study these complex microbial communities in ways impossible previously. The high volumes of sequencing data produced, the demands posed by the bioinformatics and data analysis and the necessity of correlating the metagenomics results with environmental metadata data all present interesting computational challenges. Microbiome studies of this type are becoming of increasing interest in many industries most particularly health care.
In this presentation we will present a status update on the following microbiome experiments.
- “Sequence the Lab” A survey of the Almaden Indoor Microbiome
- Evaluation of IBM Antimicrobial Polymers – A test of efficacy of biocidal polymers against a microbial community
- Citrus Greening Studies – A metagenomic evaluation of the Citrus Microbiome under different disease treatment protocols.
We will describe our experimental design and sampling protocols. Initial results from DNA and RNA extraction and quantification and qPCR characterization of the bacterial populations will be described. A description of bioinformatics procedures used in the analysis of the 16s and DNA and RNA shotgun sequencing results will be described by Robert Prill in a subsequent presentation.