Research Highlights

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Visualizing Biological Specimens at Nanometer Scale Using a New Automated, More Detailed Method

The ability to locate and visualize proteins and macromolecular complexes in cells and tissues in 3D high resolution continues to be a challenge in biomedical studies. Various techniques and tools are key to this work. For example, light microscopy uses fluorescent labels to track elements of interest, but it provides an incomplete view, including only the distribution of the labeled elements. Researchers who want to collect more comprehensive 3D datasets at higher-resolution use electron microscopic tomography (EMT) to visualize all structures in the cellular or subcellular domain under investigation.

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Allostery and Protein Dynamics Across Scales

There’s long been a standard tradeoff in biochemistry: You can study overall shape (of, say, a macromolecule or an organelle) or high-resolution detail within, say, at the 10-40-nanometer scale. Seeing both at the same time would be one of today’s scientific Holy Grails.

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Biomedical Big Data Training Collaborative

For the last 5-10 years, a lot has been said and written about “big data” and the insight it’s reputed to hold – if only you can find an efficient, effective way to get at it. But big data can be a bewildering topic, as there seem to be as many types and formats of big data as there are methods to analyze it.

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Multi-scale Simulations with Applications for Drug Design

Lane Votapka, relaxed from a recent successful defense of his PhD research, sets the stage for the work he published this fall with his advisor and NBCR Director Rommie Amaro at UC San Diego: “The cell is made up of proteins and other large molecules. 

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cellPACK – a new tool to build complex systems

In collaboration with QB3 Fellow Graham Johnson at UCSF, NBCR investigators Art Olson and Michel Sanner have developed cellPACK, a new software tool to build increasingly complex systems.

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cAMP Binding Causes Protein Kinase Activation

In spite of several decades of research, scientists have been unable to describe in rigorous quantitative terms the exact sequence of events that leads to activation of Protein Kinase A (PKA) by cyclic adenosine monophosphate (cAMP). But a research team at UCSD will soon publish results that explain this mechanism for a PKA isoform essential for proper functioning of the heart.

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Experimentation and Computation Meet

A normal heart uses the complementary, alternating activities of “systolic” contraction and “diastolic” relaxation to pump blood throughout the body. So scientists are eager to understand the various factors that affect this process, including those that lead to heart disease and failure.

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Finding New Anti-Flu Compounds

By comparison with his peers, Eric Chen might be considered a veteran researcher. Currently a senior at Canyon Crest High School in northern San Diego County, he has already worked for two years in several laboratories – both computational and bench science – at UCSD and The Scripps Research Institute.

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Ilkay Altintas: Advancing Computational Research with Scientific Workflows

It was a lark that brought Ilkay Altintas to San Diego. The year was 2001. She had just finished her M.S. thesis and was working at the Middle East Technical University in Ankara, Turkey, when she discovered an open position at the San Diego Supercomputer Center (SDSC). 

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New Molecular Dynamics Method

A team of NBCR researchers recently demonstrated a new accelerated molecular dynamics (aMD) implementation that enhances sampling of the conformational space of biomolecules by several orders of magnitude. More specifically, they developed an implementation of the aMD method using the OpenMM toolkit library to produce high performance – and, as a result, longer simulation times – on graphics processing units (GPUs). 

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Nucleotide Diffusion in the Cardiac Myofilament Lattice

An NBCR research team recently published a paper investigating the spatiotemporal diffusion of adenine di- and triphosphate (ADP and ATP) nucleotides through the myofilament lattice in heart muscle. The investigation of diffusion of these biomolecules is important because they regulate cardiac energetics and coupling between cell excitation and contraction.

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Accelerated Molecular Dynamics Simulations

Using just an upgraded desktop computer equipped with a relatively inexpensive graphics processing card, a team of computer scientists and biochemists at the University of California, San Diego, has developed advanced GPU accelerated software and demonstrated for the first time that this approach can sample biological events that occur on the millisecond timescale. 

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Calcium Sparks Generation

Triggered release of Ca2+ from an individual sarcoplasmic reticulum (SR) Ca(2+) release unit (CRU) is the fundamental event of cardiac excitation-contraction coupling, and spontaneous release events (sparks) are the major contributor to diastolic Ca(2+) leak in cardiomyocytes. Previous model studies have predicted that the duration and magnitude of the spark is determined by the local CRU geometry, as well as the localization and density of Ca(2+) handling proteins. 

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Intracellular Calcium Dynamics Model

According to the Centers for Disease Control and Prevention (CDC), heart diseases are the number one cause of death in the US. Heart attacks are caused by blockages in coronary arteries, and heart failures or in severe cases, cardiac arrest, are often caused by irregular heart beats or arrhythmias.

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Myosin light chain kinase dephosphorylation

Actin-myosin interactions provide the driving force underlying each heartbeat. The current view is that actin-bound regulatory proteins play a dominant role in the activation of calcium-dependent cardiac muscle contraction. 

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New drug effective against MRSA

Millions of people die each year from bacterial infections in tuberculosis or pneumonia. The bacterium, Staphlococcus aureus, while usually harmless, may lead to ear infection, sinusitis, pneumonia, meningitis, toxic shock syndrome and a number of postsurgical infections.

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Pocket Full of Promise

Cancer remains the second leading cause of death, after heart diseases, in the US, and millions of people die from different types of cancer worldwide each year. The known tumor suppressor protein p53 is an important regulator of cell growth in normal cells and its dysfunction is closely related to tumor development and progression.

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Versatile Python API

The uPy Python extension module provides a uniform abstraction of the APIs of several 3D computer graphics programs (called hosts), including Blender, Maya, Cinema 4D, and DejaVu. A plug-in written with uPy can run in all uPy-supported hosts. 

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Active Conformational States

Lauded by Biomedical Research Community , the relaxed complex scheme (RCS) is a promising computational method for computer-aided drug discovery (CADD) that combines the advantages of docking algorithms with the dynamic structural information provided by molecular dynamics (MD) simulations.

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Attacking Chagas Disease

Projects in Scientific Computing publishes an article describing Studies with Anton, a special-purpose supercomputer designed by D. E. Shaw Research and made available at PSC, that have yielded new insights into the motion and function of proteins.

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Better Understanding of Heart Failure

Modeling Calcium Dynamics in Ventricular Myocytes with Realistic Transverse Tubules/em> What is known as cardiac remodeling (or ventricular remodeling) is not a good thing; it implies that there is a decline in the function of the heart. 

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Biomolecular Electrostatics

Scientists use a number of tools to investigate how cells develop, operate, communicate, and control their activities. Molecular interactions have several components, including biomolecular electrostatics, which is considered to be of special importance because of its long range nature and influence on polar or charged molecules (primary components in living systems).

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Major Step in Heart Modeling

A “picture” of your failing heart is worth a thousand words. The development and clinical use of patient-specific models of the heart is now a possible goal. Models have the potential to help with diagnosis and support decision-making for cardiologists and their patients. Several research groups are now working to develop multiscale models of the heart; these models integrate the many physiological functions taking place in the heart. 

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Tool Speed up for Computer-aided Drug Discovery

Found to be an efficient approach Drug discovery and design involves finding small molecules that are complementary in shape and charge to the biomolecular target with which they interact so that they will bind to it. Applying computational power to the combined chemical and biological aspects of this process is an ever-growing effort because doing so improves the speed of the process and development of effective treatments.

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Visualization and Modeling Integration

Bringing modeling and animation into one interface and improving interdisciplinary collaborations: Increasingly complex research has made it more difficult to prepare data for analysis, publication, education, and outreach. Many scientists must also wade through what seems like black-boxes with mysterious code that works “magic” to generate results with computational algorithms from diverse sources in order to supplement their laboratory (bench) work.

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