Math-Biochem/Biophys Seminar page

Informal Seminars on
Mathematics and Biochemistry-Biophysics (MBB)
Department of Mathematics
UC San Diego

Organizers: Li-Tien Cheng and Bo Li



Spring quarter, 2017

Thursdays, 2:00 pm - 3:00 pm, AP&M 5829 (unless otherwise announced).

Date

Speaker

Title & Abstract

4/6 Organizational meeting.
4/13   Prof. Li-Tien Cheng
(Math, UCSD)
Design Ultrafast Numerical Method with Min Cut/Max Flow for Implicit Solvation
5/11   Prof. Nan Hao
(Molecular Biology, UCSD)
Multi-Generational Silencing Dynamics Control Cell Aging
Abstract
5/18   Prof. Hui Sun
(Cal State U. Long Beach & UCSD)
Multiscale Modeling and Simulation of the Growth of Bacterial Colony with Cell-Cell Mechanical Interactions
Abstract

Winter quarter, 2017

Thursdays, 2:00 pm - 3:00 pm, AP&M 5829 (unless otherwise announced).

Date

Speaker

Title & Abstract

1/12 Organizational meeting.
3/2   Mr. Yi Luo
(Math, UCSD)
Fast Methods for Solving Eikonal Equations
Abstract
3/9   Mr. Benjamin Ciotti
(Math, UCSD)
Legendre Transforms Applied to Electrostatic Energy Functionals
Abstract
3/9   Prof. Li-Tien Cheng
(Math, UCSD)
Summary of the Binary Level-Set Method for Implicit Solvation

Fall quarter, 2016

Thursdays, 2:00 pm - 3:00 pm, AP&M 5218 (unless otherwise announced).
(Note: This room is different from our usual MBB seminar room AP&M 5829.)

Date

Speaker

Title & Abstract

9/28 Organizational meeting.
10/6  


Spring quarter, 2016

Thursdays, 2:00 pm - 3:00 pm, AP&M 5829 (unless otherwise announced).

Date

Speaker

Title & Abstract

3/31 Organizational meeting.
4/21   Dr. Nuo Wang
(Chem/Biochem, UCSD)
Improving the Accuracy of Implicit-Solvent Models with Physics-Based Molecular Surfaces
Abstract
5/19   Prof. Peter Kekenes-Huskey,
(Chem, Univ. Kentucky)
Insight into Molecular through Subcellular Calcium Signaling via Multi-Scale Simulation
Abstract

Winter quarter, 2016

Thursdays, 2:00 pm - 3:00 pm, AP&M 5829 (unless otherwise announced).

Date

Speaker

Title & Abstract

1/7 Organizational meeting.
1/14   Dr. Hui Sun
(Math & Biochem, UCSD)
Dynamic Implicit Solvent Model: Understanding Solvent Stokes Flow and Interface Dynamics for Biomolecules
Abstract
1/21   Prof. Lei Zhang
(Math Ctr./Q-Bio Ctr., Peking Univ.)
Computation of Rare Events and its Applications in Biology
Abstract
2/18   Dr. Clarisse Ricci
(Biochem, UCSD)
Coarse-Graining VISM with MARTINI Forcefield: The Right Way To Go
Abstract

Fall quarter, 2015

Thursdays, 2:00 pm - 3:00 pm, AP&M 5829 (unless otherwise announced).
(We may not have seminars as one of the organizers is on leave this quarter.)

Date

Speaker

Title & Abstract

10/8 Group discussions.
     

Spring quarter, 2015

Thursdays, 2:00 pm - 3:00 pm, AP&M 5829 (unless otherwise announced).

Date

Speaker

Title & Abstract

4/2 Organizational meeting and group discussions on hybrid Brownian dynamics and partial differential equation models for biomolecular diffusion.
4/16 Prof. Dr. Joachim Dzubiella
(Soft Matter Phys., Helmholtz Center, Berlin)
Curvature Dependence of Hydrophobic Hydration Dynamics
Abstract
4/23 Dr. Shaoying (Kathy) Lu
(Bioengineering, UCSD)
Image-driven Analysis of Molecular Transport and Activation in Single Live Cells
Abstract
4/30

5/7 Dr. Gary Huber
(Biochem and HHMI, UCSD)
BrownDye: Software for Performing Brownian Dynamics on Biological Molecules
Abstract
5/14 Mr. Jiayi Wen
(Math, UCSD)
Mathematical Modeling and Computational Methods for Electrostatic Interactions with Application to Biological Molecules
Abstract
5/21 Dr. Hui Sun
(Math and Biochem, UCSD)
Numerical Simulation of Solvent Stokes Flow and Solute-Solvent Interface Dynamics
Abstract
6/4 Dr. Shenggao Zhou
(Math & Biochem, UCSD)
Incorporation of Solvent Fluctuations into Variational Implicit-Solvent Model
Abstract

Winter quarter, 2015

Thursdays, 2:00 pm - 3:00 pm, AP&M 7218 (unless otherwise announced).
(Note: This room is different from our usual MBB seminar room AP&M 5829.

Date

Speaker

Title & Abstract

1/8 Organizational meeting.
2:00 - 3:00, Tuesday, 1/20
(Special time)
Prof. Hao Ge
(Peking Univ. China)
Stochastic Processes at Single-Molecule and Single-Cell Levels
Abstract
2/19 Prof. Padmini Rangamani
(MAE, UCSD)
Viscoelastic Lipid Bilayers: Theory and Applications
Abstract
4:00 - 5:00, Thursday, 2/26, AP&M 6402 (Joint with Math Colloq. Special time/place) Prof. Hans G. Othmer
(Math, Univ. Minnesota)
From Crawlers to Swimmers - Mathematical and Computational Problems in Cell Motility  
Abstract

Fall quarter, 2014

Thursdays, 2:00 pm - 3:00 pm, AP&M 5829 (unless otherwise announced).

Date

Speaker

Title & Abstract

10/2 Organizational meeting.
2:00 - 3:00, Tuesday, 10/7
(Special time)
Pak-Wing Fok
(Math, U. Delaware)
Mathematical Modeling of Atherosclerosis
Abstract
10/9
 
11/27 No seminar. Thanksgiving Holiday.

Spring quarter, 2014

Thursdays, 2:00 pm - 3:00 pm, AP&M 7218 (unless otherwise announced).
Note: This quarter, we will meet in AP&M 7218 not AP&M 5829.

Date

Speaker

Title & Abstract

4/3 Organizational meeting.
4/17 Dr. Hui Sun
(Math & CTBP, UCSD)
Linear Stability of a Cylindrical Solute-Solvent Interface  
Abstract
5/1 Prof. Li-Tien Cheng
(Math, UCSD)
Min Cut/Max Flow for Biomolecule Shapes  
5/8 Dr. Brian Camley
(Phys. & CTBP, UCSD)
Complex Cell Motility: Collective Rotation, Persistence, and Turning  
Abstract
6/5 Department of Mathematics Colloquium by Professor Robert Krasny (Univ. Michigan, Ann Arbor).
4:00 - 5:00, AP&M 6402. See the Department of Mathematics Colloquium web site for more information.

Winter quarter, 2014

Thursdays, 2:00 pm - 3:00 pm, AP&M 5829 (unless otherwise announced).

Date

Speaker

Title & Abstract

1/9 Dr. Shenggao Zhou
(Math, Biochem, & CTBP, UCSD)
Varitional Implicit Solvation with Poisson-Boltzmann Theory  
Abstract
1/23 Mr. Jiayi Wen
(Math & CTBP, UCSD)
Mean-Field Analysis and Computation of Electrostatics with Ionic Concentration Dependent Dielectrics  
Abstract
1/23
A related event:
Math Colloq.
4:00-5:00, AP&M 6402
Dr. Jacob Bedrossian
(Courant Inst., NYU)
Inviscid Damping and the Asymptotic Stability of Planar Shear Flows in the 2D Euler Equations  
(See the abstract at the UCSD Math Department Colloquium website)
2/27 Mr. Lane Votapka
(Chem & Biochem, UCSD)
Multiscale Estimation of Binding Kinetics using Molecular Dynamics, Brownian Dynamics, and Markov State Models
Abstract
3/13 Mr. Harishankar Manikantan
(MAE, UCSD)
The sedimentation of flexible filaments
Abstract

Fall quarter, 2013

Thursdays, 2:00 pm - 3:00 pm, AP&M 5829 (unless otherwise announced).

Date

Speaker

Title & Abstract

9/26 Organizational meeting.
10/3 Prof. Daniel Tartakovsky
(MAE, UCSD)
Stochastic Operator-Splitting Method for Reaction-Diffusion Systems  
Abstract
10/10 Dr. Hui Sun
(Math & CTBP, UCSD)
Singular Solutions and Pattern Formation in Aggregation Equations  
Abstract
10/17 Prof. Arvind Baskaran
(Math, UCI)
Kinetic Density Functional Theory: A Hydrodynamic Theory to Understanding Self Assembly of Interacting Particles into Ordered Crystalline Phases  
Abstract
10/24 Prof. Xu Yang
(Math, UCSB)
Pathway Based Mean Field Models for E. Coli Chemotaxis  
Abstract
10/31 Dr. Zuojun Guo
(GNF, & CTBP UCSD)
Heterogeneous Hydration of p53/MDM2 Ccomplex: Molecular Dynamics Simulations vs. Variational Implicit Solvent Model  
Abstract
11/7 No seminar.
11/14 Prof. Li-Tien Cheng
(Math, UCSD)
The Compact Coupled Interface Method for Poisson-Type Problems in Implicit Solvation  
Abstract
11/21 Ms. Yaojun Zhang
(Phys. & CTBP, UCSD)
A Transformation for the Mechanical Fingerprints of Complex biomolecular interactions
Abstract
11/28 Thanksgiving Holiday. No seminar.
12/5 Dr. Yanxiang Zhao
(Math & CTBP, UCSD)
Periodic Migration in a Physical Model of Cells on Micropatterns  
Abstract

Spring quarter, 2013

Thursdays, 2:00 pm - 3:00 pm, AP&M 5829 (unless otherwise announced).

Date

Speaker

Title & Abstract

4/4 Department of Mathematics Colloquium by Professor Shi Jin (Univ. Wisconsin, Madison).
4:00 - 5:00, AP&M 6402. See the Department of Mathematics Colloquium web site for more information.
4/18 Mr. Tim Banham
(Math & CTBP, UCSD)
Phase Field Model for Cell Shapes: Gamma Convergence and Numerical Methods  
Abstract
5/16 Dr. Yinglong Miao
(McCammon group, HHMI, UCSD)
Title: Activation and Dynamic Network of the M2 Muscarinic Receptor  
Abstract  

Winter quarter, 2013

Thursdays, 2:00 pm - 3:00 pm, AP&M 5829 (unless otherwise announced).

Date

Speaker

Title & Abstract

1/10 Organizational meeting.
1/17 Prof. Wei Wang
(Chem, Biochem, & CTBP, UCSD)
Computional Determination of Protein-Ligand Binding Specificity
Abstract
2/7 Prof. Wenjun Ying
(Math, Shanghai Jiaotong Univ., China)
A Kernel-Free Boundary Integral Method for the Poisson-Boltzmann Equation  
Abstract
2/14 Dr. Hui Sun
(Math, UCLA)
Analytical and Numerical Methods in Aggregation Swarming Models  
Abstract
2/28 Ms. Nuo Wang
(Chem & Biochm, & CTBP, UCSD)
Title: A Few Comments on the Calculation of the Diffusion Tensor Used in Brownian Dynamics Simulations
Abstract

Fall quarter, 2012

Thursdays, 2:00 pm - 3:00 pm, AP&M 5829 (unless otherwise announced).

Date

Speaker

Title & Abstract

8/27-29/2012
AP&M 6402
(Special event)
A joint Math/Biochemistry Brainstorming workshop on biomolecular interactions

Topics: variational implicit solvation, Brwonian dyanamics, reaction kientics, continuum electrostatics, free energy calculations, host-guest systems, multiscale modeling and computations, numerial methods, etc.
10/25 No seminar. One of the organizers is out of town.
11/1 No seminar. Group meeting.
11/8 Dr. Brian Camley
(Phys. & CTBP, UCSD)
Dynamics of Multicomponent Lipid Membranes
Abstract
11/15 Prof. Li-Tien Cheng
(Math, UCSD)
High-Order Numerical Methods for Elliptic Interface Problems with Applications to Electrostatics
11/20
(Special date)
Dr. Markus Schmuck
(Math/Chem. Eng., Imperial College, UK)
Upscaling of Ionic Transport Equations in Porous and Heterogeneous Media
Abstract
11/22 Thanksgiving Holiday. No seminar.
11/29
(Special event)
Department of Mathematics Colloquium. 4:00 - 5:00, AP&M 6402
Speaker: Professor Mitchell Luskin, Department of Mathematics, Univ. Minnesota and IPAM/UCLA.
Title. Atomistic-to-Continuum Coupling Methods
Abstract. See UCSD Department of Mathematics Colloquium
12/6 Dr. Shenggao Zhou
(Math, Chem/Biochem, & CTBP, UCSD)
Variational Implicit Solvation Modeling of Host-Guest Binding: A Case Study on Cucurbit[7]uril
Abstract

Spring quarter, 2012

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

Winter quarter, 2012

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

Fall quarter, 2011

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.

Spring quarter, 2011

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

Winter quarter, 2011

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.

Fall quarter, 2010

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

Spring quarter, 2010

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.

Winter quarter, 2010

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.

Fall quarter, 2009

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.

Spring quarter, 2009

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?

Winter quarter, 2009

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 & CTBP, UCSD)
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

Fall quarter, 2008

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.)

Spring quarter, 2008

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

Winter quarter, 2008

No seminars this quarter due to the leave of one of the organizers.



Summer and Fall quarter, 2007

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.

Last updated by Bo Li on March 29, 2017. © Bo Li, 2007-2017.