For more details CSWeek.lbl.gov

For more details CSWeek.lbl.gov

University of California, Berkeley – Applied Mathematics Seminar

Date:
Wednesday, February 5, 2025

Time:
11:10am- 12:00pm

Location:
939 Evans Hall – UC Berkeley Campus
Zoom: https://berkeley.zoom.us/j/98667278310

Speakers(s) and Affiliations(s):
Jacob Elafandi
University of California, Berkeley

Title:
Finite element analysis of a nematic liquid crystal Landau-de Gennes model with quartic elastic terms

Abstract:
In this talk, I will discuss the basic theory of liquid crystals, the theory of the Q-tensor model for liquid crystal dynamics, and various models of the elastic and thermotropic energy of liquid crystal samples. In particular, I will outline a model presented by Golovaty et al. in a 2020 paper which reduces to the Oseen-Frank director field model in uniaxial states. I will then show an energy stable scheme for the gradient flow of a closely related model, discuss a proof of its convergence via fixed-point iteration, and discuss a proof of the Gamma-convergence of discrete minimizers as the mesh size approaches zero. Finally, I will show the results of numerical experiments which successfully simulate isotropic-to-nematic phase transitions as expected.

Hosts of Seminar:
Zhiyan Ding, Lin Lin, Michael Lindsey, Krutika Tawri and Franziska Weber,  Mathematics Group
____________________________________________________________________
Welcome to the Applied Mathematics seminar for the Spring 2025 semester. This year, the seminar series is being organized by Zhiyan Ding ([email protected]), Lin Lin ([email protected]), Michael Lindsey ([email protected]), Krutika Tawri ([email protected]), and Franziska Weber ([email protected]). If you have any inquiries, please contact one of them.

To join the applied math seminar mailing list, click
https://groups.google.com/a/lists.berkeley.edu/forum/#!forum/appliedmathseminar/join
—
LBNL-UCB Applied Math Seminar website https://berkeleyams.lbl.gov/
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Berkeley Lab – CS Seminar
The Scientific Python project and the Berkeley Open Source Program Office

Date:
02/05/25

Time:
1:30 pm – 2:30 pm

Location:
59-4102 and zoom

Speakers(s) and Affiliations(s):
Jarrod Millman, Scientific Python Developer at BIDS and the Executive Director for Berkeley’s Open Source Program Office (OSPO)

Title:
The Scientific Python project and the Berkeley Open Source Program Office

Abstract:
With an extensive and high-quality ecosystem of libraries, scientific
Python has emerged as the leading platform for data analysis. This
ecosystem has been created and sustained by independent volunteers
with separate mailing lists, websites, roadmaps, documentation,
engineering and packaging solutions, and governance structures.
Unfortunately, this has meant that there was a lack of coordination
that resulted in duplicated effort, disorganized documentation,
breakage upon new releases, unintended performance regressions, and
user confusion.

The Scientific Python project (https://scientific-python.org/)
addresses these issues through a number of efforts:

– Providing recommendation infrastructure for community-wide policy,
– Improving common engineering infrastructure,
– Hosting shared development and community documentation,
– Maintaining a set of classroom-style lecture notes,
– Organizing a series of developer events to discuss needs,
– Writing a community vetted strategic plan, and
– Helping the community develop grant proposals.

Bio:
Jarrod Millman is a Senior Open Source Scientific Python Developer at
BIDS and the Executive Director for Berkeley’s Open Source Program
Office (OSPO). With a background in computer science, mathematics, and
statistics, and degrees from Cornell and Berkeley, Millman is a
founding member of the scientific Python ecosystem. His primary focus
is on developing and sustaining open-source, community-owned
scientific software tools. Millman serves on the steering council of
NetworkX, is a core developer of scikit-image, and was an early
contributor to NumPy, SciPy, and scikit-learn. He has co-founded
several influential initiatives to advance open and reproducible
research, including the Scientific Python project, the nonprofit
NumFOCUS, and the Neuroimaging in Python project.

Virtual Information:
https://lbnl.zoom.us/j/94777801965

Meeting ID: 947 7780 1965

Host of Seminar:
Lavanya Ramakrishnan, Scientific Data Division

For more details CSWeek.lbl.gov

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Seminar Type: Computing Sciences Area Seminar

~~~~~~~~Calendar event name~~~~~~~~~~~~~
CS Seminar: Geometric Deep Learning and Generative Modeling for Drug Discovery and 3D Biomolecular Design
~~~~~~~~Event Details Below~~~~~~~~~~~~~~
Berkeley Lab – CS Seminar
Geometric Deep Learning and Generative Modeling for Drug Discovery and 3D Biomolecular Design

Date:
02/06/25

Time:
11:00AM – 12:00PM

Location:
https://lbnl.zoom.us/j/95239048013

Speakers(s) and Affiliations(s):
ALEX MOREHEAD, UNIVERSITY OF MISSOURI-COLUMBIA

Title:
Geometric Deep Learning and Generative Modeling for Drug Discovery and 3D Biomolecular Design

Abstract:
The COVID-19 pandemic underscored the critical need for rapid drug discovery, catalyzing advances in machine learning (ML) for understanding and designing biological molecules. This domain, often referred to as AI for Science, represents a convergence of modern ML with high-impact scientific challenges. This talk will explore the emerging paradigm of integrating geometric deep learning algorithms with generative ML techniques to model dynamic 3D biomolecules. By enabling scalable, rational molecular design for applications such as drug discovery and bioengineering, these approaches simultaneously advance research in ML and biotechnology. In this seminar, I will highlight recent successes, such as advancements in modeling protein-ligand interactions, discuss current interdisciplinary challenges, and explore future directions at the intersection of AI and molecular science.

Bio:

Virtual Information:
Join Zoom Meeting
https://lbnl.zoom.us/j/95239048013

Meeting ID: 952 3904 8013

Berkeley Lab – CS Seminar

Date:
Thursday, February 6, 2025

Time:
3:00pm – 4:00pm

Location:
Shyh Wang Hall – Bldg. 59, Room 3070

Speakers(s) and Affiliations(s):
Yaniv Brick
Ben-Gurion University of the Negev, Beer-Sheva, Israel

Title:
Generalized Integral Equation Formulations for Efficient High-Frequency Wave Analysis

Abstract:
High-fidelity wave simulation of large and intricate systems has been enabled greatly thanks to advances to the numerical solution of integral equation (IE) formulations of scattering problems. Fast solution algorithms and more stable formulations have been progressively developed to combat the high computational costs and degradation in problem conditioning associated with the increase in the electrical size, model detail, and numbers of simulated scenarios. Recent research in these fronts has focused on the development of fast direct solvers, relying on algebraic compression and compressed factorization of impedance matrices. Among these, notable are the classes of first generation low-rank compression-based hierarchical matrix solvers and the more sophisticated butterfly-compression solvers. The latter exhibit superior asymptotic cost scaling, even for geometric settings that do not exhibit inherent (asymptotic) rank-deficiency, i.e., ones that are not of reduced dimensionality. The appeal of the former is in their relative simplicity and effectiveness for systems that include large quasi-planar or elongated parts. Complementary to the search for faster and more compressive algebraic structures is that for IE formulations that are of enhanced compressibility, which will be the focus of our talk (selected publications listed below). Generalized IE formulations use modified Green’s function kernels to turn, where possible, broadside wave interactions between large sub-structures, which are of fast-scaling ranks, into reduced dimensionality ones. The resulting moment matrix blocks exhibit slower scaling of the ranks and greater rank-deficiency. This translates to greater compression and faster compressed factorization and solution. In the talk, we will review the evolution of generalized IEs, discuss the various types of such formulations, and present algorithms for removal of the bottlenecks associated with the computations of their more complex IE kernels. We will then demonstrate the algorithmic utilization of the reduced effective dimensionality (e.g., by employing non-uniform and randomized field sampling technique) for the design of fast solvers.

[1] Y. Brick, V. Lomakin, and A. Boag, “Fast Green's function evaluation for sources and observers near smooth convex bodies,” IEEE Trans. Antennas Propag., vol. 62, no. 6, pp. 3374 – 3378, June 2014.

[2] A. Sharshevsky, Y. Brick, and A. Boag, “Direct solution of scattering problems using generalized source integral equations,” IEEE Trans. Antennas Propag., vol. 68, no. 7, pp. 5512-5523, July 2020.

[3] D. Zvulun, Y. Brick, and A. Boag “A generalized source integral equation for enhanced compression in three dimensions,” IEEE Trans. Antennas Propag., vol. 72, no. 12, pp. 9316-9325, Dec. 2023.

[4] Y. Dahan and Y. Brick , “Fast direct solvers with arbitrary admissibility using generalized source integral equations,” IEEE Trans. Antennas Propag., vol. 72, no. 10, pp. 7872-7882, Oct. 2024.

Bio:
Yaniv Brick received the B.Sc. (2005, magna cum laude), M.Sc. (2007, summa cum laude), and Ph.D (2015) degrees in electrical and electronics engineering from the School of Electrical Engineering, Tel Aviv University. From 2014 to 2017, he was a Post-Doctoral Fellow with the Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin. Since 2017, he has been with the School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, where he is an associate professor. He is currently a visiting scholar at the University of California San Diego Center for Memory and Recording Research (CMRR). He has been an associate editor for the IEEE Journal on Multiscale and Multiphysics Computational Techniques and the IEEE Antennas and Propagation Magazine. He is a senior member of the IEEE and the International Union of Radio Science (URSI), and a recipient of the IEEE AP-S Doctoral Research Award, the Peter O’Donnell Jr. Post-Doctoral

2 Fellowships in Computational Engineering and Sciences, the Fulbright Post-Doctoral Fellowship Program Grant, and the Fulbright Alumni Prize.

Virtual Information:
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Meeting ID: 972 2981 2706

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Meeting ID: 972 2981 2706

Host of Seminar:
Yang Liu
Scalable Solvers Group (SSG)
Applied Mathematics and Computational Research Division
Lawrence Berkeley National Laboratory

University of California, Berkeley – Applied Mathematics Seminar

Date:
Wednesday, February 12, 2025

Time:
11:10am- 12:00pm

Location:
939 Evans Hall – UC Berkeley Campus
Zoom: https://berkeley.zoom.us/j/98667278310

Speakers(s) and Affiliations(s):
Alfred Kirsch
ENPC

Title:
An (Applied) Mathematical Analysis of Dynamical Mean-Field Theory
 
Abstract:
In this talk, I will discuss the mathematical properties of the Dynamical Mean-Field Theory (DMFT), a standard approximation scheme in quantum condensed matter physics. After a general introduction and motivation, I will first define quantum one-body Green’s functions, which appear to be (operator-valued) Nevanlinna-Pick functions. I then introduce and discuss the properties of the Hubbard and Anderson Impurity Models, and indicate how DMFT relates the former to a collection of the latter in a self-consistent way.

Mathematically speaking, DMFT gives rise to a fixed-point equation that can be formulated in the set of probability measures via Cauchy-Stieltjes transforms. In the setting of the Iterated Perturbation Theory (IPT) approximation, I then prove the existence of solution(s) to this equation using a Schauder fixed-point theorem.

Finally, I will discuss the properties of an existing discretized scheme and, if time permits, propose a novel approach that bypasses analytic continuations issues.

Hosts of Seminar:
Zhiyan Ding, Lin Lin, Michael Lindsey, Krutika Tawri and Franziska Weber,  Mathematics Group
____________________________________________________________________
Welcome to the Applied Mathematics seminar for the Spring 2025 semester. This year, the seminar series is being organized by Zhiyan Ding ([email protected]), Lin Lin ([email protected]), Michael Lindsey ([email protected]), Krutika Tawri ([email protected]), and Franziska Weber ([email protected]). If you have any inquiries, please contact one of them.

To join the applied math seminar mailing list, click
https://groups.google.com/a/lists.berkeley.edu/forum/#!forum/appliedmathseminar/join
—
LBNL-UCB Applied Math Seminar website https://berkeleyams.lbl.gov/
—

University of California, Berkeley – Applied Mathematics Seminar

Date:
Wednesday, February 19, 2025

Time:
11:10am- 12:00pm

Location:
939 Evans Hall – UC Berkeley Campus
Zoom: https://berkeley.zoom.us/j/98667278310

Speakers(s) and Affiliations(s):
Hongkang Ni
Stanford University

Title:
Error Analysis of a New Eigenmatrix-Based Method for Unstructured Sparse Recovery

Abstract:
Unstructured sparse recovery problems arise in various applications, including rational approximation, spectral function estimation, and sparse deconvolution. A recently proposed method, inspired by the ESPRIT algorithm, introduces a unifying data-driven framework that effectively recovers underlying sparse structures across different sparse recovery problems. In this talk, we establish its effectiveness by presenting a framework for analyzing its error bound, following a brief introduction to the method. We then examine the rational approximation problem as a concrete example, demonstrating how the analysis applies in this setting.

Hosts of Seminar:
Zhiyan Ding, Lin Lin, Michael Lindsey, Krutika Tawri and Franziska Weber,  Mathematics Group
____________________________________________________________________
Welcome to the Applied Mathematics seminar for the Spring 2025 semester. This year, the seminar series is being organized by Zhiyan Ding ([email protected]), Lin Lin ([email protected]), Michael Lindsey ([email protected]), Krutika Tawri ([email protected]), and Franziska Weber ([email protected]). If you have any inquiries, please contact one of them.

To join the applied math seminar mailing list, click
https://groups.google.com/a/lists.berkeley.edu/forum/#!forum/appliedmathseminar/join
—
LBNL-UCB Applied Math Seminar website https://berkeleyams.lbl.gov/
—