Thursdays, 2:00 pm - 3:00 pm, AP&M 5829 (unless otherwise announced).
Date |
Speaker |
Title & Abstract |
| 4/5 | No seminar. (Osher Conference at IPAM, UCLA.) | |
| 4/12 |
Mr. Jiayi Wen
(Math & CTBP, UCSD) |
Competitive Adsorption and Ordered Packing of Counterions Near Highly Charged Surfaces: From
Mean-Field Theory to Monte Carlo Simulations
Abstract |
| 4/19 |
Prof. Burkard Duenweg
(Phys. Max-Planck, Mainz, Germany) |
Local Approaches to Electrostatics
Abstract |
| 4/26 |
Prof. Xun Jia
(Medical Phys., UCSD) |
Treatment Plan Optimization in Radiation Therapy
Abstract |
| 5/3 |
Prof. Li-Tien Cheng
(Math, UCSD) |
Binary Level-Set Shape Optimization Model
and Algorithm for Volumetric Modulated Arc Therapy in Radiotherapy Treatment
Abstract |
| 5/10 |
Mr. Michael White
(Math & CTBP, UCSD) |
Motion of a Cylindrical Dielectric Boundary
Abstract |
| 5/17 | No seminar. (Frontiers in Applied and Computational Mathematics 2012 Conference at NJIT.) | |
| 5/24 |
Dr. Zuojun Guo
(Genomics Inst. of the Novartis Res. Foundation - GNF) |
The Role of Electrostatic Interaction to the Structural Stability of Nucleic
Acid and Peptide
Abstract |
| 5/31 |
Dr. Changsun Eun
(Biochem, UCSD) |
Some Aspects of Hydrophobic Interaction Between Two Nanoscale Particles:
Water Number Fluctuation and Roughness Effect
Abstract |
| 6/7 |
|
Title:
Abstract |
Thursdays, 2:00 pm - 3:00 pm, AP&M 5829 (unless otherwise announced).
Date |
Speaker |
Title & Abstract |
| 2:00 - 3:00, Friday, 1/6 (Special time) |
Prof. Ridg Scott
(Computer Sci. & Math, Univ., Chicago) |
Models for Dielectrics at the Molecular and Continuum Scale |
|
11:30-12:30, Tuesday, 1/17
AP&M 6402 (Special time/place) |
Dr. Jianfeng Lu
(Courant Inst., NYU) |
Multiscale Analysis of Solid Materials: From Electronic Structure
Models to Continuum Theories
Abstract |
| 2/9 |
Prof. Yu-Chen Shu
(Math, National Cheng Kung Univ., Taiwan) |
Coupling Interface Method for Solving Poisson-Boltzmann Equation
Abstract |
| 3/15 |
Ms. Shenshen Wang
(Phys. & CTBP, UCSD) |
Effective Temperature and Spontaneous Collective Motion of Active Matter
Abstract |
Thursdays, 2:00 pm - 3:00 pm, AP&M 5829.
Date |
Speaker |
Title & Abstract |
| 9/22 | Organizational meeting. | |
| 9/29 |
Prof. Chauhui Tong
(Phys., Ningbo Univ., China) |
The Self-Consistent Field Study of the Adsorption of Flexible Polyelectrolytes onto Two Charged Objects
Abstract |
| 10/6 |
Dr. Yanxiang Zhao
(Math, Chem & Biochem, & CTBP, UCSD) |
A Diffuse Interface Model of Multicomponent Vesicle Adhesion and Fusion
Abstract |
| 10/13 |
Dr. Tony Kwan
(Math & CTBP, UCSD) |
Efficient Preconditioners for the Triangular Spectral Element Method
Abstract |
| 10/20 |
Mr. Shenggao Zhou
(Math, Zhejiang Univ. China, & Math & CTBP, UCSD) |
Mean-Filed Description of Ionic Size Effect with
Non-Uniform Ionic Sizes: A Numerical Approach
Abstract |
| 10/27 |
Prof. Zhenli Xu
(Math & Inst. Natural Sci., Shanghai Jiaotong Univ., & Math, UCSD) |
Image Effects in Colloidal Suspensions
Abstract |
| 11/3 | No seminar. Group meeting. | |
| 11/10 |
Ms. Helen Parks
(Math, UCSD) |
The Dynamics of a Forced Coupled Network of Active Elements
Abstract |
|
11/17
Special event |
The SIAM Conference on Analysis of PDEs will end around 2:00 pm. So there will be no
seminar today.
But Professor Robert Pego of Carnegie Mellon University will speak in the Department of Mathematics Colloquium: 4:00 pm, AP&M 6402. |
|
| 11/24 | No seminar. Thanksgiving Holiday. | |
| 12/2 | No seminar. Group meeting. | |
Thursdays, 2:00 pm - 3:00 pm, AP&M 6402, unless otherwise announced.
Date |
Speaker |
Title & Abstract |
| 3/31 | Organizational meeting. | |
|
4/7
AP&M 6218 (Special place) |
Prof. Li-Tien Cheng
(Math, UCSD) |
Numerical Methods for Elliptic Interface Problems with Applications to
Cell Motion and Continuum Electrostatics. Part I.
|
| 4/14 | No seminar/group meeting. | |
|
2:00-3:00, Tuesday, 5/3
AP&M 6218 (Special time & place) |
Prof. Li-Tien Cheng
(Math, UCSD) |
Numerical Methods for Elliptic Interface Problems with Applications to
Cell Motion and Continuum Electrostatics. Part II.
|
| 5/5 |
Prof. Tatyana Sharpee
(Biophys., Salk Inst. & UCSD) |
Maximally Informative Decision Boundaries in Neural Coding
Abstract |
|
1:00 - 2:00, Friday, 5/13
Pacific Hall 4500 (Special time & place) |
Professor Ruth Williams speaks at Center for Theoretical Biological Physics.
Title: Queueing Up for Enzymatic Processing: Correlations through Coupled Degradation. |
|
|
5/19
3:30-4:30, AP&M 5829 (Special time & place) |
Dr. Yifei Lou
(EE/CS, Gatech) |
Image Deblurring via Self-Similarity and via Sparsity
Abstract |
| 5/26 | Group meeting. | |
|
6/2
1:30-2:30, AP&M 2402 (Special time & place) |
Prof. Bo Li
(Math & CTBP, UCSD) |
Dielectric Boundary Forces in Variational Implicit-Solvent Modeling of Biomolecules
Abstract |
|
6/7
11:00-:12:00, AP&M 5829 (Special time & place) |
Prof. Jaydeep Bardhan
(Biophys., Rush Univ.) |
Boundary-Integral Methods for Fast Continuum-Model Biomolecule
Electrostatics
Abstract |
Thursdays, 2:00 pm - 3:00 pm, AP&M 5829.
Date |
Speaker |
Title & Abstract |
| 1/6 | Organizational meeting. | |
| 1/13 | Group meeting. | |
|
1/20
Joint with Math Colloq. 4:00, AP&M 5402. (Special time & place) |
Prof. Bob Eisenberg
(Biophysics, Rush Univ.) |
Ions in Channels
Abstract |
| 1/27 | Group meeting. | |
| 2/3 | Group meeting. | |
| 2/10. | No seminar/group meeting. | |
|
2/17
|
Dr. Pete Kekenes-Huskey
(Biochem, UCSD) |
Contributions of Structural t-tubule Heterogeneities and Membrane Ca2+ Flux
Localization to Local Ca2+ Signaling in Rabbit Ventricular Myocytes
Abstract |
| 2/24 | No seminar/group meeting. | |
| 3/3 | No seminar/group meeting. | |
| 3/7 - 3/10 | A "Brainstorming" workshop. | |
| 3/11 | Prof. Joe Dzubiella of Helmholtz Center Berlin and the Humboldt University Berlin will give a talk in the CTBP weekly seminar: 1:00 - 2:00, 3500 Pacific Hall. | |
Thursdays, 2:00 pm - 3:00 pm, AP&M 5829.
Date |
Speaker |
Title & Abstract |
| 9/30 | Organizational meeting. | |
| 10/7 |
Ms. Danying Shao
(Phys. & CTBP, UCSD) |
Modeling Cell Migration with Phase Field Method
Abstract |
| 10/14 | Group meeting. | |
| 10/21 |
Prof. Yunbo Kim
(Math, UCI) |
Oscillatory Component Recovery and Separation in Images by Sobolev Norms
Abstract |
|
Joint with Math Colloq.
10/28 4:00, AP&M 6402. (Special time & place) |
Prof. Chun Liu
(Math, Penn State Univ.) |
Energetic Variational Approaches in the Modeling of Ionic Solutions and Ion Channels
Abstract |
|
11/4
|
Ms. Maryannn Hohn
(Math, UCSD) |
Diffusion Equation Models and Numerical Simulations of Gene Expression |
| 11/11 | No seminar. Veterans Day Holiday. | |
| 11/18 | Group meeting. | |
| 11/25 | No seminar. Thanksgiving Holiday. | |
|
12/2
|
Prof. Ray Luo
(Biochem, UC Irvine) |
Charge-based Approach to the Poisson-Boltzmann Continuum Solvation Treatment
Abstract |
Thursdays, 2:00 pm - 3:00 pm, AP&M 5829.
Date |
Speaker |
Title & Abstract |
| 4/1/10 | Organizational meeting. | |
| 4/8/10 |
Prof. Ir. Sim Kok-Swee
(Multimedia Univ.) Malaysia |
Real-Time Auto-Probing for Breast Cancer Detection by Magnetic Resonance Imaging
Abstract |
| 4/15/10 | Group meeting. | |
| 4/29/10 | Group meeting with Steve Jiang's group. | |
| 5/20/10 | Group meeting. | |
|
10:00-11:30, 6/3
AP&M 5402. (Special time & place) |
Maryann Hohn's advancement.
Title: Some Mathematical Problems on Gene Expression. |
|
Thursdays, 2:00 pm - 3:00 pm, AP&M 5829.
Date |
Speaker |
Title & Abstract |
| 1/7/10 | Organizational meeting. | |
| 1/14/10 | Group meeting. | |
|
4:00pm, 1/28,
AP&M 6402. (Special time & place) |
Prof. Zuowei Shen of National University of Singapore will speak
in the Department of Mathematics Colloquium.
Title: Frame Based Image Restoration. See Department of Mathematics Colloquium for the abstract. |
|
| 2/4/10 | Group meeting. | |
|
Joint w/ Math Colloq.
2/18/10, AP&M 6402. (Special place) |
Prof. Greg Forest
(Math, UNC Chepel Hill) |
The Virtual Lung Project at UNC
Abstract |
| 2/25/10 |
Dr. Riccardo Baron
(Biochem & CTBP, UCSD) |
Water: Active or Passive Player in Cavity-Ligand Recognition & Binding?
Abstract |
|
1:30-2:30, 3/3/10,
EBUII, Room 479 (Special time & place) |
Prof. Tom Chou, UCLA Biomath & Math,
will speak at Biomechanics Semianr.
Title: Reconstruction of Complex Bond Potentials from Multiple Rupture Time Distributions Abstract. |
|
Thursdays, 2:00 pm - 3:00 pm, AP&M 5829.
Date |
Speaker |
Title & Abstract |
| 10/1/09 | Organizational meeting. | |
| 10/8/09 |
Prof. Bin Dong
(Math, UCSD) |
Applications of PDEs and Optimization in Medical Image and Surface Processing.
Abstract. |
| 10/15/09 |
Dr. Yohichi Suzuki
(Phys & CTBP, UCSD) |
Single-Molecule Rupture Dynamics on Multidimensional Landscapes.
Abstract. |
| 10/22/09 |
Dr. Eunjung Kim
(Math, Univ. Notre Dame) |
Multiscale Biomechanical Models for Biological Soft Tissue.
Abstract. |
| 10/29/09 |
Mr. Bo Hu
(Phys. & CTBP, UCSD) |
Stochastic Information Processing and Optimal Design in Eukaryotic Chemotaxis.
Abstract. |
| 11/5/09 |
Dr. Arijit Maitra
(Nanoengineer., UCSD) |
A Model of Dynamic Single-Molecule Force Spectroscopy that Harnesses Both Loading Rates and Device Stiffness.
Abstract. |
| 11/12/09 |
Dr. Immanuel Kalcher
(Biophys, Tech Univ Munich) |
Modeling Ion-Specific Correlations in Bulk and Confinement
Abstract. |
| 11/19/09 | No seminar. Group meeting. | |
| 11/26/09 | No seminar. Thanksgiving Holiday. | |
| 12/3/09 |
Dr. Shuangliang Zhao
(Chem. Eng., UC Riverside) |
Density Functional Theory for Solvation in Molecular Solvents.
Abstract. |
Tuesdays, 2:00 pm - 3:00 pm, AP&M 5829.
Date |
Speaker |
Title & Abstract |
| 3/31/09 | Organizational meeting. | |
|
4:00pm, Thursday, 4/9/09
AP&M 6402. (Special time & place) |
Prof. Eric Cances, Ecole des Ponts ParisTech, France,
will speak in the Math Dept Colloquium.
Title: Some Mathematical Aspects of Density Functional Theory. Abstract. |
|
| 4/14/09 |
Prof. Leonard M. Sander
(Phys., Univ. of Michigan) |
A Generalized Cahn-Hilliard Equation for Biological Applications
Abstract. |
| 4/21/09 | No seminar. One of the organizers is out of town. | |
| 4/28/09 |
Prof. Huan-Xiang Zhou
(Biophys., Florida State Univ.) |
Accurate Calculation of Binding and Folding Free Energies by a Scaled Generalized Born Method
Abstract. |
| 5/5/09 | Group meeting. | |
| 5/12/09 | No seminar and group meeting this week. | |
| 5/19/09 | Group meeting. | |
| 5/26/09 | No seminar and group meeting this week. | |
|
3:00, 6/3/09, EBU-II 479
(Special time & place) |
Penner Biomechanics Seminar, Mechanical and Aerospace Engineering Department, UCSD.
Speaker: Professor Alex Mogilner, UC Davis. Title: How Actin Treadmill, Membrane Tension and Myosin Contraction Determine Cell Shape? |
|
Tuesdays, 2:00 pm - 3:00 pm, AP&M 5829.
Date |
Speaker |
Title & Abstract |
| 1/6/09 | Organizational meeting. | |
|
4:00, Thursday,
1/15/09, AP&M 6402. (Special time & place) |
Prof. Gil Ariel, Univeristy of Texas at Austin, will give a mathematics colloquium talk.
Title: Modeling and Computation with Multiple Time Scales. Abstract |
|
|
3:00, Thursday,
1/22/09, AP&M 5829. (Special time) |
Dr. Piotr Setny
(Biophys., Univ. of Warsaw) |
Hydrophobic Effects in Vicinity of Concave Nanoscopic Objects
Abstract |
| 1/27/09 |
Dr. Zhongming Wang
(Biochem & Math, UCSD) |
A Level-Set Variational Implicit-Solvent Approach to Hydrophobic Interactions
Abstract |
| 2/3/09 |
Prof. Bo Li
(Math & |
The Poisson-Boltzmann Theory of Continuum Electrostatics with Application
to Variational Solvation of Molecules
Abstract |
|
11:00, Tuesday,
2/10/09, AP&M 2402 (Special time & place) |
Professor Ridgway Scott, Univ. of Chicago, speaks at Numerial Analysis/Computational Math seminar. Title: Mathematical Foundation for Molecular van der Waals Forces | |
| 2/17/09 |
Dr. Joanna Sulkowska
(Phys. & CTBP, UCSD) |
Dodging the Crisis of Folding Proteins with Knot |
|
2:00,
Thursday,
2/26/09, AP&M 5829 (Special time) |
Dr. Yangjin Kim
(Math. Biosci. Inst., Ohio State Univ.) |
Glioma Invasion and Microenvironment: A PDE/Multiscale Model
Abstract |
|
1:00, Friday,
3/6/09, Pacific Hall 3500 (Special time & place) |
Professor John Lowengrub, Department of Mathematics, UC Irvine,
speaks at the Center for Theoretical Biological Physics Seminar.
Title: Multiscale Models of Solid Tumor Growth and Angiogenesis |
|
Tuesdays, 2:00 pm - 3:00 pm, AP&M 5829.
Date |
Speaker |
Title & Abstract |
| 9/30/08 | Organizational meeting. | |
|
1:00 pm, Firday
10/10/08 Pacific Hall 3500 (Special time & place) |
Prof. Bo Li will give a talk
at
Center for Theoretical Biological Physics.
Title: Coupling the Level-Set Method with Variational Implicit-Solvent Models for Molecular Solvation. |
|
| 10/14/08 |
Dr. Mathias Buenemann
(Biophys., UCSD) |
Mechanical Limits of Viral Capsids
Abstract |
| 10/21/08 | No meeting this week. (One of the organizers is away this week.) | |
|
2:00pm, Thursday, 10/30/08
(Special date) |
Prof. Paul Atzberger
(Math, UCSB) |
Spatially Adaptive Stochastic Numerical Methods
for Intrinsic Fluctuations in Reaction-Diffusion System
Abstract |
| 11/4/08 | No seminar. Organizers will participate in a workshop at the IMA (Institute for Mathematics and Its Applications). | |
| 11/11/08 | No seminar. Verterans Day Holiday. | |
| 11/18/08 |
Dr. Zhongming Wang
(Math & Biochem, UCSD) |
Solutions to a Model Poisson-Nernst-Planck System and the Determination of Reaction Rates |
| 11/25/08 |
Dr. Igor Klep
(Math, UCSD) |
Sign Patterns and Determinant Expansions for Chemical Rection Networks
Abstract |
| 12/2/08 | No meeting this week. (One of the organizers is away this week.) | |
Tuesdays, 2:00 pm - 3:00 pm, AP&M 5829.
Date |
Speaker |
Title & Abstract |
| 4/1/08 | Organizational meeting | |
| 4/8/08 |
Dr. Benzhuo Lu
(HHMI, Chem-Biochem & CTBP, UCSD) |
Boundary Integral Methods for Electrostatics in Biomolecules.
Part I: An overview
Abstract |
| 4/15/08 |
Prof. Jingfang Huang
(Math, UNC-Chapel Hill, & CTBP, UCSD) |
Boundary Integral Methods for Electrostatics in Biomolecules.
Part II: Fast Multipole Methods
Abstract |
| 4/22/08 |
Dr. Ilja Khavrutskii
(HHMI, Chem-Biochem & CTBP, UCSD) |
Transition Path and Path Ensemble Optimization with Gradient-Augmented
Harmonic Fourier Beads Method
Abstract |
| 4/29/08 |
Prof. Doug Smith
(Phys Dept, UCSD) |
Single Molecule Studies of Entangled DNA Molecule Dynamics and Viral DNA Packaging |
|
Special event
4:00pm, Thursday, 5/8/08, AP&M 6402. |
Prof. Herbert Levine, Phys Dept & CTBP, UCSD,
will speak in the Math Dept Colloquium.
Title: Fluctuation-Dominated Front Motion and its Application to Laboratory-Scale Darwinian Evolution. |
|
| 5/13/08 |
Dr. Shachi Gosavi
(Phys Dept & CTBP, UCSD) |
Protein Folding, Topological Frustration and Biological Function
Abstract |
| 5/20/08 | Prof. Bo Li
(Math & CTBP, UCSD) |
Variational Implicit-Solvent Modeling and the Level-Set Computation
of Biomolecular Structures and Interactions. Part I: An Overview
Abstract |
| 5/27/08 |
Prof. Li-Tien Cheng
(Math, UCSD) |
Variational Implicit-Solvent Modeling and the Level-Set Computation
of Biomolecular Structures and Interactions. Part II: The Level-Set Method
Abstract |
| 6/3/08 |
Dr. Yuhui Cheng
(Biochem, UCSD) |
Self-Cleavage Reaction Mechanism Study in Group I Intron Ribozyme: Application of ab initio QM/MM Approach |
No seminars this quarter due to the leave of one of the organizers.
Tuesdays, 3:00 pm - 4:00 pm, AP&M 5402.
Date |
Speaker |
Title & Abstract |
|
6/14/07 (special date) |
Dr. Jianwei Che (GNF) Prof. Li-Tien Cheng (Math, UCSD) |
Biochemistry and Rational Drug Design. Level-set method. |
| 8//28/07 | Prof. Bo Li (Math & CTBP, UCSD)
Ms. Morgan Lawrenz (Biochem, UCSD) Mr. Yang Xie (MAE, UCSD) |
Level-Set Implicit Solvent Models. MD Simulations of Charged Xenon Particles
Bo Li's presentation PDF. Yang Xie's presentation PDF. |
| 9/25/07 | Prof. Bo Li
(Math & CTBP, UCSD) |
Electrostatic Free Energy and its Variations in Implicit Solvent Models
Abstract |
| 10/2/07 | Dr. Benzhuo Lu
(HHMI, and Biochem and CTBP of UCSD) |
Electrodiffusion: A continuum modeling framework for
biomolecular systems with realistic spatiotemporal resolution
Abstract |
| 10/9/07 |
Prof. Lei Ni
(Math, UCSD) |
Ricci Flow
Follow-up discussion on: Geometrical flows, molecular surfaces, and protein folding. |
| 10/16/07 | Prof. Ray Luo
(Molecular Biology & Biochem, UC Irvine) |
Scaling in Solvation: Implicit Solvent vs. Explicit Solvent
Abstract |
| 10/23/07 | Seminar cancelled due to the closure of UCSD campus. | |
| 10/30/07 |
Dr. Zeyun Yu
(Math and Biochem, UCSD) |
Molecular Mesh Generation and Processing
Abstract |
| 11/6/07 |
Dr. Yongcheng Zhou (Biochem & Math, UCSD) |
Modeling, Computation and Applications of Electrostatic Stress of Bimolecules
Abstract |
| 11/13/07 |
Prof. Gaurav Arya
(Nanoenginnering, UCSD) |
Mesoscale Modeling and Simulation of Chromatin
Abstract |
| 11/20/07 |
Prof. Olga Dudko
(Phys Dept & CTBP, UCSD) |
Single-Molecule Pulling Experiments: Theory, Analysis and Interpretation
Abstract |
| 11/27/07 |
Mr. Alex Bilik (Math, UCSD) |
Diffuse-Interface Modeling and Simulation of Solvation of Nonpolar Molecules |
|
Special event
12/3/2007 |
Professor Richard D. James of Univ. of Minnesota is giving a talk in Seminars in Mechanics and Materials. 11:00 - 12:00, Monday, Dec. 3, CMRR Auditorium. Title: Lessons on Structure from the Structure of Viruses. Abstract. | |