| 4/4 |
Dr. Lev Tsimring
(Synthetic Biology Inst., UCSD) |
Statistical Theory of Asymmetric Damage Segregation in Clonal Cell Populations (Abstract) |
| 4/11 |
Prof. Weitao Chen
(Math, UC Riverside) |
A Mechanochemical Coupled Model to Understand Budding Behavior in Aging Yeast (Abstract) |
| 4/18 |
Prof. Ruth Williams
(Math, UCSD) |
Title: Stochastic Analysis of Chemical Reaction Networks with Applications to Epigenetic Cell Memory. (Abstract) |
| 5/9 |
Prof. Feng Fu
(Math, Dartmouth College) |
Evolutionary Dynamics of Human Behavior (Abstract) |
|
5/16
(4:00 - 5:00
Math Colloquium) |
Prof. Paul Newton
(USC) |
Control of Evolutionary Mean Field Games and Tumor Cell Population Models (Abstract) |
| 5/23 |
Dr. Pearson Miller
(Flatiron Institute) |
Hierarchical Control of Biological Self-Organization (Abstract) |
|
6/6
(4:00 - 5:00
Math Colloquium) |
Prof. Yoichiro Mori
(Math/Biology, U Penn) |
| 1/25 (Room: AP&M 5829) |
Prof. Bo Li
(Math & qBio Program, UCSD) |
Variational Implicit Solvation and Fast Algorithms for Molecular Binding and Unbinding (Abstract) |
|
2/1
Cancelled |
Prof. Natalia Komarova
(Math, UCSD) |
Mathematical Methods in Evolution and Medicine (Abstract) |
| 2/8 |
Prof. Dominik Wodarz
(Biology, UCSD) |
Mathematical Models of Tissue Homeostasis and Stem-Cell Driven Cancer Growth (Abstract) |
|
2/15
(4:00 - 5:00
Math Colloquium) |
Prof. Nigel Goldenfeld
(Physics, UCSD) |
Topological Scaling Laws and the Mathematics of Evolution (Abstract) |
| 2/22 |
Prof. Jason Schweinsberg
(Math, UCSD) |
Using Coalescent Theory to Estimate the Growth Rate of a Tumor (Abstract) |
| 3/14 |
Prof. Natalia Komarova
(Math, UCSD) |
Mathematical Methods in Evolution and Medicine (Abstract) |
| 1/12 |
Prof. Christopher Miles
(Math, UC Irvine) |
Inferring RNA Dynamic Rates from Spatial Stochastic Snapshots
(Abstract) |
| 2/16 |
Prof. Tomas Gedeon
(Math, Montana State U.) |
Combinatorial Description of Dynamics of Gene Regulatory Networks Based on Network Structure (Abstract) |
| 3/2 |
Mr. Harish Kannan
(Math, UC San Diego) |
Spatiotemporal Dynamics of Metabolite Gradients Control the Emergent Morphology of a Bacterial Colony on Hard Agar (Abstract) |
| 9/22 | Organizational meeting. | |
| 11/23 | Thanksgiving Holiday. No seminar. | |
| 12/1 |
Prof. Alexandra Jilkine
(Applied Math, U. Notre Dame) |
Modeling Diffusion-Coupled Oscillations in Cell Polarity (Abstract) |
| 5/26 |
Prof. Gabriel Silva
(Bioengineering, UCSD) |
Exploring Categorical Models of Generative Neural Properties from Computable Local Dynamics (Abstract) |
| 1/27 |
Prof. German Enciso
(Math, UC Irvine) |
Absolutely Robust Control Modules in Chemical Reaction Networks (Abstract) |
| 2/3 |
Prof. Johnatan (Yonatan) Aljadeff
(Neuro biology, UCSD) |
Multiplicative Shot Noise: A New Route to Stability of Plastic Networks (Abstract) |
| 2/17 |
Prof. Edward Stites
(Salk Inst. for Biological Studies) |
Modeling the Biochemical Activities of Cancer Causing Mutations to Understand Why Some Patients Respond to Treatment (and Why Some Do Not) |
| 2/24 |
Prof. Arshad Desai
(Cell & Developmental Biology, UCSD) |
Two-ness and Time in the Cell
(Abstract) |
| 3/10 |
Prof. Henry Abarbanel
(Physics & SIO, UCSD) |
Reduced, Biophysically Based, Models for Neurons to Use as Computationally Efficient Elements of Large Functional Biological Networks (Abstract) |
| 9/23 | Organizational meeting. | |
| 9/30 |
Dr. Mauricio del Razo Sarmina
(Univ. of Amsterdam, Netherlands) |
Multiscale Molecular Kinetics by Coupling Markov State Models and Reaction Diffusion Dynamics (Abstract) |
| 10/14 |
Dr. Lev Tsimring
(Inst. Biocircuts, UCSD) |
Fate Decision Landscape in Single-Cell Aging |
| 11/4 |
Dr. Nida Obatake
(Inst. for Defense Analyses) and UCSD |
Algebraic and Geometric Methods in the Study of Chemical Reaction Networks (Abstract) |
| 11/11 | Veterans Day Holiday. No seminar. | |
| 11/25 | Thanksgiving Holiday. No seminar. | |
| 1/7 | Organizational meeting. | |
| 1/14 |
Prof. Philippe Robert
(INRIA, Paris, France) |
Stochastic Models of Neural Synaptic Plasticity
(Abstract)
|
| 2/25 |
Prof. Sergey Kryazhimskiy
(Biology, UCSD) |
Emergence and propagation of epistasis in metabolic networks (Abstract) |
| 10/1 |
Organizational meeting.
Zoom meeting ID: 934 5874 0734 |
|
| 10/8 |
Prof. Bo Li
(Math & qBio, UCSD) |
Variational Implicit-Solvent Predictions of the Ligand-Receptor (Un)Binding Kinetics
(Abstract)
Zoom meeting ID: 919 9546 7983 |
| 10/22 |
Dr. Patrick Murphy
(Bioengineering, Rice Univ.) |
Modeling Rapid Diffusion State Switching during Cellular Polarization of a C. Elegans Zygote (Abstract) |
| 10/29 |
Prof. Issac Klapper
(Math, Temple Univ.) |
Modeling Microbial Community Metabolism
(Abstract)
|
| 11/12 |
Prof. Tianyu Zhang
(Math, Montana State Univ.) |
Multiscale Flux-Based Modeling of Microbial Communities
(Abstract)
|
| 12/3 |
Dr. Shuang Liu
(Los Alamos National Lab) |
Numerical Simulations of Reaction-Diffusion Equations with
Free Boundaries for Spreading Behavior of Invasive Species
(Abstract)
|
Date |
Speaker |
Title & Abstract |
| 1/16 |
Prof. Bo Li
(Math & qBio, UCSD) |
Modeling and Simulation of Bacterial Colony Growth with Cell-Cell Mechanical Interactions
Abstract |
|
1/23
Joint with Biomech Seminar |
Prof. Mark Alber
(Math/qBio modeling, UC Riverside) |
Multi-Scale Modeling of Deformation of Blood Clots
Abstract |
| 2/6 |
Dr. Nehemiah Zewde
(Salk Inst) |
Computational Modeling of the Complement System Under Homeostasis, Renal Disease, Meningococcal Infection, and Therapeutic Interventions
Abstract |
|
2/13
|
Prof. Paul Bressloff
(Math, U. Utah) |
Biological Pattern Formation: Beyond Classical Diffusion-Based Morphogenesis
Abstract |
Date |
Speaker |
Title & Abstract |
| 4/4 |
Prof. Chengcheng Huang
(Math, Univ. Pittsburgh) |
Circuit Models of Low Dimensional Shared Variability in Cortical Networks
Abstract |
| 5/2 |
Prof. Joanna Trylska
(Biophys. Univ. Warsaw, Poland) |
Coarse-Grained Models to Simulate Dynamics of Biomolecules
Abstract |
| 5/9 |
Prof. Andreas Carlson
(Math, Univ. Oslo, Norway) |
Protein Organisation during Immune Cell Adhesion and Energy Barriers during Formation of
Intraluminal Vesicles
Abstract |
|
5/23
(Special place: AP&M 5829) Jointly with Diff. Geom. Seminar |
Prof. Joel Hass
(Math, UC Davis) |
New Applications of Geometry in Biology
Abstract |
| 6/6 |
Prof. Isaac Klapper
(Math, Temple Univ.) |
Linking Microbial Metabolism to Microbial Community Environment
Abstract |
| 6/7 |
Prof. Chuan Xue
(Math, Ohio State Univ.) |
Spatial Pattern Formation in Reaction-Diffusion Models: A Computational Approach
Abstract |
|
1:00 - 2:00, Friday, 6/14
1:00 - 2:00, AP&M B402A |
Ms. Gaoyang Bridget Fan
(Math, Univ. of Utah) |
Modeling the Role of Feedback in the Adaptive Response of Bacterial Quorum Sensing
Abstract |
Date |
Speaker |
Title & Abstract |
| 1/10 |
Prof. Yanxiang Zhao
(Math, The George Washington Univ.) |
A Phase Field Model of Cell Migration
Abstract |
|
Math Colloq.
4:00 - 5:00, 1/15 (special time) |
Prof. Chuan Xue
(Math, Ohio State Univ.) |
Multiscale Problems in Cell Biology
Abstract |
|
Math Dept event
3:00 - 6:15, 2/7 NSB Auditorium |
Prof. Ingrid Daubechies
(Duke Univ.) Prof. Simon Tavare (Columbia Univ.) |
Mathematicians Helping Art Conservators and Art Historians
(more info) Some Statistical Problems in Cancer Genomics (more info) |
| 3/7 (AP&M 5829) |
Prof. Joachim Dzubiella
(Physics, Univ. Freiberg, Germany) |
Resonance Effects in Diffusion-Influenced Bimolecular Reactions
Abstract |
| 3/14 |
Dr. Yuansheng Cao
(Biophysics, UCSD) |
Nonequilibrium Thermodynamics of Biochemical Clocks: From Single to Synchronized Oscillators
Abstract |
Date |
Speaker |
Title & Abstract |
| 10/25 |
Prof. Bo Li
(Math, UCSD) |
Predict Ligand-Receptor Binding/Unbinding Kinetics with
Variational Implicit-Solvent Model and the String Method
Abstract |
| 4:00 - 5:00, 12/12 (special time) |
Prof. Carina Curto
(Math, Penn State Univ.) |
Mathematics and Neuroscience |
Date |
Speaker |
Title & Abstract |
| 4/26 |
Prof. Gurol Suel
(Biology, UCSD) |
The Microbial Brain: Electrochemical Signaling in Bacterial Communities
Abstract |
|
5/17
(AP&M 5829) |
Prof. Shibin Dai
(Math, Uni. Alabama) |
Title: Degenerate FCH Functional and Defects in Amphiphilic Structures
Abstract |
|
5/31
(AP&M 5829) |
Dr. Wouter-Jan Rappel
(Biophys., UCSD) |
Title:
Eukaryotic Cell Motility: Insights from Modeling and Experiments
Abstract |
Date |
Speaker |
Title & Abstract |
| 1/11 | Organizational meeting. | |
| 1/25 |
Dr. Lev Tsimring
(BioCircuits Inst., UCSD) |
Gene Conversion Facilitates Adaptive Evolution on Rugged Fitness Landscapes
Abstract |
| 2/8 |
Prof. David Saintillan
(MAE, UCSD) |
From Bacteria to Chromosomes: Hydrodynamic Self-Organization of Biological Active Matter
Abstract |
|
3/1
Cancelled |
Prof. Joachim Dzubiella
(Helmholtz Inst., Humboldt Univ., Berlin) |
Cancelled
Influence of Charge Fluctuations on Electrostatic Binding Kinetics Abstract |
|
3:00 - 4:00,
3/6
AP&M 6402 Special Time & Place! |
Dr. Ji Hyun Bak
(Biophys., KIAS) |
How the Nose is Optimized: Statistical Design Principles of Olfactory Receptors
Abstract |
| 3/15 |
Prof. Xu Yang
(Math, UCSB) |
Mean-Field Models for Chemotaxis
Abstract |
Date |
Speaker |
Title & Abstract |
| 10/5 | Organizational meeting. | |
| 10/26 |
Mr. Liyang Xiong
(Phys. & The BioCircuits Inst., UCSD) |
Coexistence and Pattern Formation in Bacterial Mixtures with Contact-Dependent Killing and
Long-Range Inhibition
Abstract |
| 11/2 |
Prof. Brian Camley
(Biophys., Johns Hopkins Univ.) |
Collective Gradient Sensing:
Fundamental Bounds, Cluster Mechanics, and Cell-to-Cell Variability
Abstract |
| 11/16 |
Prof. Ruth Williams
(Math, UCSD) |
Reflected Diffusions and (Bio)Chemical Reaction Networks
Abstract |
| 11/23 | Thanksgiving Holiday. No seminar. | |
| 11/30 |
Dr. Morgan Chabanon
(MAE, UCSD) |
Bending, Stretching, and Breaking Membranes: The Biophysics of In- and Out-of-Equilibrium
Lipid Bilayer Processes
Abstract |
| 12/7 |
Dr. Thomas Fai
(Applied Sci./Engineering, Harvard) |
Special Department of Mathematics Coloquium
Title: The Lubricated Immersed Boundary Method Abstract |
June 2007 - September 2017
Informal Seminars on
Mathematics and Biochemistry-Biophysics (MBB)
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
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
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
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
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
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.
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
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
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.
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.
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
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
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
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
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
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
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.)
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.
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. | |