| 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 |
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 |
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
|
Date |
Speaker |
Title & Abstract |
| 9/28 | Organizational meeting. | |
| 10/6 |
|
|
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 |
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 |
Date |
Speaker |
Title & Abstract |
| 10/8 | Group discussions. | |
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 |
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 |
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. | |
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. |
|
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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. | |
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 |
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. | |
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 |
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. |
|
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. |
|
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. |
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? |
|
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 |
|
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. | |