Volume 4, Issue 9, September 26, 2017
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UCLA Institute for Digital Research and Education
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Bonus Materials: Real World Applications
of Chemical Materials

 The image reflects research on theoretical description and design of heterogeneous catalytic interfaces: semiconductor surfaces decorated with small clusters of transition metals. It is essential to model these catalysts in a realistic way, i.e. in conditions of high temperature and pressure, because their structure and properties are in turn dependent on the conditions. The work is done in close collaboration with operando characterization experiments, exemplified by the STM image on the bottom left. 

Dr. Anastassia Alexandrova is living in a materials world; she is concerned with the study of new chemical materials through the use of computational design and multi-scale modeling.

To Alexandrova, associate professor at UCLA's Department of Chemistry and Biochemistry, the most interesting questions in science are related to the electronic structure and chemical bonding of materials. Through collaboration with experimental laboratories, these concerns are directed toward figuring out how functional materials, or materials which posses specific native properties or functions of their own such as magnetism or energy storage functions, work. Read more here.

News & Publications

IT Services Leadership Opportunity - Director, Customer Support Services

UCLA Information Technology Services has opened the position of Director, Customer Support Services and welcomes internal UCLA candidates to apply for this leadership opportunity. Reporting directly to the Associate Vice Chancellor, Information Technology Services, the Director will oversee an organization comprised of over thirty full time staff in the delivery of technical support, technical training, and service management services to the UCLA campus.

The summary of the position is below. To view the qualification and to apply, please visit the posting on the UCLA Career Opportunities website -- The posting will close on October 1.

IDRE-related Lectures, Seminars & Colloquia

Bioengineering Seminar: Cancer Nanotheranostics 
Xiaoyuan (Shawn) Chen, Ph.D., Senior Investigator and Chief, National Institute of Biomedical Imaging and Bioengineering, NIBIB, NIH

Wednesday, October 4
1 p.m. to 2 p.m.
Engineering V, Room 2101

Theranostics (Rx/Dx) aims to develop molecular diagnostic tests and targeted therapeutics with the goals of individualizing treatment by targeting therapy to an individual's specific disease subtype and genetic profile. It can be diagnosis followed by therapy to stratify patients who will likely respond to a given treatment; it can also be therapy followed by diagnosis to monitor early response to treatment and predict treatment efficacy; it is also possible that diagnostics and therapeutics are co-developed (nanotheranostics). This talk will give examples of designing nanobiosensors for ultrasensitive biomarker detection in vitro, applying molecular imaging techniques for in vivo measurement of cancer hallmarks, and making nanoparticle platforms for co-delivery of imaging labels and therapeutic genes and drug molecules.

 Dr. Xiaoyuan (Shawn) Chen received his Ph.D. in Chemistry from the University of Idaho (1999). After two postdocs at Syracuse University and Washington University in St. Louis, he started his Assistant Professorship at the University of Southern California in 2002 and then moved to Stanford in 2004. He moved to NIH in 2009 and became a Senior Investigator and Chief of the Laboratory of Molecular Imaging and Nanomedicine (LOMIN) at the National Institute of Biomedical Imaging and Bioengineering (NIBIB), NIH. His current research interests include development of a molecular imaging toolbox for better understanding of biology, early diagnosis of disease, monitoring therapy response, and guiding drug discovery/development. His lab puts special emphasis on high-sensitivity nanosensors for biomarker detection and theranostic nanomedicine for imaging, gene and rug delivery, and monitoring of treatment. Dr. Chen has published over 600 peer-reviewed papers (H-index > 100) and numerous books and book chapters. He is the founding editor of journal "Theranostics" (2016 IF + 8.712). He was elected as AIMBE Fellow (2017), received ACS Bioconjugate Chemistry Lecturer Award (2016), NIH Director's Award (2014), NIBIB Mentor Award (2012) and 1000 talent plan B (2010). He is also the President of Chinese-American Society of Nanomedicine and Nanobiotechnology (CASNN) and President of the Radiopharmaceutical Science Council (RPSC), Society of Nuclear Medicine and Molecular Imaging (SNMMI). 

Current and Future Requirements for Advanced Research Cyberinfrastructure -- Panel Discussion

Wednesday, October 25
11:45 a.m. to 1 p.m.
The Portal, 5628 Math Science Building

The Institute for Digital Research and Education is pleased to announce a panel discussion on current and future requirements for Advanced Research Cyberinfrastructure (ARC). The discussion will be led by the following early career researchers from various disciplines across the UCLA campus.
  • Bao Wang - Mathematics
  • Alan Farahani - Cotsen Institute of Archaeology
  • Karthik Sarma - Medical Imaging Informatics
  • Richard Sportsman - Chemistry and Biochemistry
  • Iris Chang - Material Science and Engineering
  • Francesca Albrezzi - World Arts and Cultures
About: Decades ago, it was hard to imagine the scale at which Advanced Research Cyberinfrastructure (ARC) at any university would drive the innovation and enhance its research capabilities. Today, ARC is playing an increasingly important role in research involving data, computation, communication, and information sharing. By providing cutting-edge opportunities to researchers, it enhances faculty competitiveness among peer organization. Due to the fast pace of ever-changing technology, however, envisaging the future requirements of the ARC is a daunting exercise. Infrastructure planning requires inputs from various segments across the university especially from the early career researchers who are the forefront of the use of technology in research. This panel discussion on "Current and Future Requirements for Advanced Research Cyberinfrastructure" is part of the exercise to get the feedback from the diverse community of early career researchers from the UCLA campus. Register here

IDRE-related Workshops & Events

Introduction to Stata

Monday, October 2
9 a.m. to 12 p.m.
CLICC Classroom B, 3rd Floor Powell Library

Stata is a powerful and yet easy-to-use statistical package that runs on Windows, Macintosh, and Unix platforms. This class is designed for people who are just getting started using Stata. The students in the class will have a hands-on experience using Stata for statistics, graphics, and data management. The class notes can be found at Register here

IPAM Workshop I: Optimization and Optimal Control for Complex Energy and Property Landscapes

Monday, October 2 through Friday, October 6
IPAM, 460 Portola Plaza

Computation materials design requires simultaneous optimization with respect to a variety of target functions including energy and electronic properties in a vast configuration space of structure and composition. This workshop will focus on the mathematical foundations and efficient implementation of optimization methods, such as methods based on stochastic sampling like random searches, genetic algorithms, and particle swarm algorithms, and methods that overcome low-energy barriers to explore surrounding local minima like basin hopping, simulated annealing, and replica exchange. Specific methods for energy barriers and their use in dynamics are the topics of Workshop II.

These optimization methods will be applied to structure prediction and property-based design of diverse materials for energy conversion, electronic, magnetic, and optical materials, catalysts, and pharmaceuticals. The systems that will be discussed include atomic clusters, inorganic and organic crystals, biomaterials, interfaces, and functional nano-structures.

Some of the challenges we wish to address are:
  • Formulating effective multi-objective optimization strategies for dealing with conflicting demands, such as low energy vs. desired electronic properties
  • Finding efficient descriptors and surrogate models that reliably correlate with complex quantum mechanical collective behavior. Workshop III specifically focuses on the development of surrogate models and their effective use in optimization, sampling, and dynamics.
  • Effective strategies for combining optimization methods with high-throughput screening and materials informatics.
  • Simulating the functionality of promising candidate materials under operating conditions. 
  • Streamlining the interpretation of experiments by feeding, e.g. measured spectra or scattering pattern directly into the target function of an optimization engine.
In this workshop, we will bring together experts on different optimization and stochastic optimal control methods and different types of materials applications from the fields of materials science, physics, chemistry, computer science, and applied mathematics.

This workshop will include a poster session; a request for posters will be sent to registered participants in advance of the workshop. Register here.

Introduction to SAS

Monday, October 9
9 a.m. to 12 p.m.
CLICC Classroom B, 3rd Floor Powell Library

SAS is a powerful statistical package that runs on many platforms, including Windows and UNIX. This class is designed for people who are just getting started using SAS. The students in the class will have a hands-on experience using SAS for statistics, graphics, and data management. The class notes can be found at Register here

Running Applications on Hoffman2 Cluster: An Introduction

Tuesday, October 10
10 a.m. to 12 p.m.
The Portal, 5628 Math Science Building

The Hoffman2 cluster is a powerful computational resource for the UCLA research community. This class is designed to clarify the process of porting your own applications on the cluster or using applications already available on the cluster. It also addresses how to port your workflow to the Hoffman2 and how to submit batch and run interactive applications. Register here.

Running Applications on Hoffman2 Cluster: Case Studies

Thursday, October 12
10 a.m. to 12 p.m.
The Portal, 5628 Math Science Building

This class will address the process of creating MATLAB standalone executables and running MATLAB in batch, as well as running Abaqus python scripts. Example of how to submit array jobs using Abaqus, R, and other applications. Can my simulations be submitted as array jobs? Bring your own problem. Also, Jupyter Notebooks: another way to run Python and R on Hoffman2. Register here.

Introduction to SPSS

Monday, October 16
9 a.m. to 12 p.m.
CLICC Classroom B, 3rd Floor Powell Library

SPSS is a very easy-to-use statistical package that runs on Windows, Macintosh, and UNIX platforms. This class is designed for people who are just starting to use SPSS. The students in the class will have a hands-on experience using SPSS for doing statistics, graphics, and data management. The class notes are the scripts for the class. The class notes can be found at Register here

Introduction to MPI (Message Passing Interface)

Monday, October 16
2 p.m. to 4 p.m.
The Portal, 5628 Math Science Building

MPI (message passing interface) is the de facto standard for distributed-memory parallel scientific computing. While the entire MPI API is quite extensive, this class will cover a number of key ingredients commonly used in practice. This class is useful for those who plan to start writing MPI code, and for those who would like to know how MPI works in order to operate an existing MPI code. Working knowledge of C and Fortran programming languages will be very helpful to follow the class materials.

Specifically, we will discuss:
  • MPI basics
  • One-to-one communication examples
  • Collective communication examples
  • Running MPI programs
Register here

IPAM Workshop II: Stochastic Sampling and Accelerated Time Dynamics on Multidimensional Surfaces

Monday, October 16 through Friday, October 20
IPAM, 460 Portola Plaza

In a multitude of research problems at the forefront of hard- and soft-matter simulation, adequate sampling of the energy landscape is a major challenge. Overcoming the energy barriers in the search for equilibrium states and accurately characterizing temporal evolution that occurs as a system evolves through a series of minima limit progress in understanding materials synthesis and processing, biology, colloidal engineering, and earth sciences. Despite advances in computing hardware, brute-force application of conventional molecular dynamics and Monte Carlo methods is not sufficient in many cases. Specialized algorithms and methods have been developed to navigate the energy landscape. In this workshop, we will discuss advances and challenges in methods such as transition-path sampling and transition-interface sampling, alchemical methods, umbrella sampling, identifying order parameters and collective variables, accelerated molecular dynamics, metadynamics, variational approaches, replica methods, and coarse-graining. We will bring together experts in sampling methods across disciplines including physics, chemistry, materials science, engineering, and mathematics.

This workshop will include a poster session; a request for posters will be sent to registered participants in advance of the workshop. This is a Julian Schwinger Workshop on Multiscale Physics, made possible by a gift from the Julian Schwinger Foundation for Physics Research (JSF)
Register here.

Python for Scientific Computing

Monday, October 23
2 p.m. to 4 p.m.
The Portal, 5628 Math Science Building

Python, originally developed as a general purpose programming language, has gained its popularity in the scientific community in recently years owning to its elegant and easy-to-understand syntax and powerful libraries. Python fully supports both functional and object-oriented programming styles. This class will present a number of useful features of Python in the context of scientific computing, and introduce a number of supporting packages, including numpy for array-based computations and h5py to access HDF5 files, and the use of Python in parallel computing (MPI style) Register here

Computing Environment on Linux -- I 

Thursday, October 26
2 p.m. to 4 p.m.
The Portal, 5628 Math Science Building

Part-I session of Computing Environment on Linus class is aimed to help researchers who are new to the Linux system. This two hour session will introduce basic UNIX/Linux commands, shells, as well as a few editors available on most of the flavors of Linux operating system. The user should be able to log in to a Linux system and use it to do the normal tasks after going through this session. Register here

IPAM Workshop III: Surrogate Models and Coarsening Techniques

Monday, October 30 through Friday, November 3
IPAM, 460 Portola Plaza

The accurate description of the energy landscapes of molecular and condensed materials often requires expensive evaluations of quantum-mechanical models. On the other hand, a large number of energy evaluations are needed to explore the landscapes for structure optimization, thermodynamic sampling, and rate estimation. Several methods have been developed that aim to approximate energy landscapes. These methods range from physically motivated approximate quantum mechanical and fully empirical energy models that describe the bonding of materials, to approaches from computer science such as machine-learning that are agnostic to the underlying chemical bonds. Ideally, a hierarchy of models with increasing and controllable accuracy is desirable to efficiently sample energy landscapes. Unfortunately, the origin of the current surrogate models in different scientific communities has led to a disconnect. As a result, knowledge about the different methods and their trade-offs have not penetrated the disconnected communities, hindering progress.

In this workshop, we will bring together researchers from the mathematics and computer science fields of optimization, optimal control and model development with chemists, physicists, and materials scientists working on model development, and energy landscape optimization and sampling problems. The goal is to discuss future methods and algorithms for the development of surrogate models and parallel exploration and their application in structure optimization, sampling, and dynamics.

This workshop will include a poster session; a request for posters will be sent to registered participants in advance of the workshop. 
Register here.

Computing Environment on Linux -- II

Tuesday, October 31
2 p.m. to 4 p.m.
The Portal, 5628 Math Science Building

The second session is regarding the use of Linux system for computation. It will describe the compilation and execution procedures for a given source program. A sample software code will be used to demonstrate the computing tools such as makefile, debugger, and profiler which are available under most Linux environments. Register here

IDRE Stat Consulting Group

The goal of the UCLA IDRE Statistical Consulting Group is to help UCLA faculty, staff, and graduate students perform top-notch research, with the greatest emphasis on data analysis related to grants and publications, but also including dissertation research. We provide advice and resources to enable you to develop and/or extend your statistical computing skills, helping you to independently use common statistical packages for the analysis of your research. Current hours for walk-in consulting are Monday-Thursday 12-3 PM. 

Walk-in consulting is in Math Sciences 4919. See our online schedule for days and hours.

Grant & Funding Opportunities

UCLA Office of Information Technology
Institute for Digital Research and Education
310-825-6635 |
5308 Math Sciences
Box 951557, Mail Code 155705
Los Angeles, CA 90095-1557

Barbara Woltag, Editor, IDRE Newsletter
310-794-5169 |

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