A5000234159- Cellular Mechanics and Interactions
- Blood properties and coagulation
- Platelet Disorders and Treatments
- Mathematical Biology Tumor Growth
- Slime Mold and Myxomycetes Research
- Microtubule and mitosis dynamics
- Nonlinear Waves and Solitons
- Gene Regulatory Network Analysis
- Plant Molecular Biology Research
- Cell Image Analysis Techniques
- Micro and Nano Robotics
- Nonlinear Photonic Systems
- Developmental Biology and Gene Regulation
- Antiplatelet Therapy and Cardiovascular Diseases
- Cell Adhesion Molecules Research
- Blood Coagulation and Thrombosis Mechanisms
- Advanced Differential Equations and Dynamical Systems
- Microbial Metabolic Engineering and Bioproduction
- Bacterial biofilms and quorum sensing
- Cancer Cells and Metastasis
- Quantum chaos and dynamical systems
- Diffusion and Search Dynamics
- Digital Imaging for Blood Diseases
- Innovative Microfluidic and Catalytic Techniques Innovation
- Plant Reproductive Biology
University of California, Riverside
2016-2025
Leiden University
2024-2025
University of Notre Dame
2009-2019
Indiana University – Purdue University Indianapolis
2011-2017
Indiana University School of Medicine
2011-2017
Cancer Research Institute
2017
Indiana University
2012-2016
University School
2015-2016
Biocom
2004-2014
University of Pennsylvania
2014
Segmentation of 3D images is a fundamental problem in biomedical image analysis. Deep learning (DL) approaches have achieved state-of-the-art segmentation perfor- mance. To exploit the contexts using neural networks, known DL methods, including convolution, 2D convolution on planes orthogonal to slices, and LSTM multiple directions, all suffer incompatibility with highly anisotropic dimensions common images. In this paper, we propose new framework for segmentation, based com- bination fully...
Abstract Motivation: CompuCell is a multi-model software framework for simulation of the development multicellular organisms known as morphogenesis. It models interaction gene regulatory network with generic cellular mechanisms, such cell adhesion, division, haptotaxis and chemotaxis. A combination state automaton stochastic local rules set differential equations, including subcellular ordinary equations extracellular reaction–diffusion partial model regulation. This in turn controls...
A two-dimensional multiscale model is introduced for studying formation of a thrombus (clot) in blood vessel. It involves components modelling viscous, incompressible plasma; non-activated and activated platelets; cells; activating chemicals; fibrinogen; vessel walls their interactions. The macroscale dynamics the flow described by continuum Navier-Stokes equations. microscale interactions between platelets, platelets fibrinogen wall are through an extended stochastic discrete cellular Potts...
Many bacteria can rapidly traverse surfaces from which they are extracting nutrient for growth. They generate flat, spreading colonies, called swarms because resemble of insects. We seek to understand how members any dense swarm spread efficiently while being able perceive and interfere minimally with the motion others. To this end, we investigate myxobacterium, Myxococcus xanthus. Individual M. xanthus cells elongated; always move in direction their long axis; constant motion, repeatedly...
Blood clot contraction plays an important role in prevention of bleeding and thrombotic disorders. Here, we unveil quantify the structural mechanisms at level single platelets. A key elementary step is sequential extension-retraction platelet filopodia attached to fibrin fibers. In contrast other cell-matrix systems which cells migrate along fibers, "hand-over-hand" longitudinal pulling causes shortening bending platelet-attached resulting formation fiber kinks. When multiple platelets...
Microtubule (MT) dynamic instability is fundamental to many cell functions, but its mechanism remains poorly understood, in part because it difficult gain information about the dimer-scale events at MT tip. To address this issue, we used a computational model of assembly that consistent with tubulin structure and biochemistry, displays instability, covers experimentally relevant spans time. It allows us correlate macroscopic behaviors (dynamic parameters) microscopic structures (tip...
In this paper we present the foundation of a unified, object-oriented, three-dimensional biomodelling environment, which allows us to integrate multiple submodels at scales from subcellular those tissues and organs. Our current implementation combines modified discrete model statistical mechanics, Cellular Potts Model, with continuum reaction–diffusion state automaton well-defined conditions for cell differentiation transitions genetic regulation. This environment rapidly compactly create...
We present COMPUCELL3D, a software framework for three-dimensional simulation of morphogenesis in different organisms. COMPUCELL3D employs biologically relevant models cell clustering, growth, and interaction with chemical fields. uses design patterns speed, efficient memory management, extensibility, flexibility to allow an almost unlimited variety simulations. have verified by building model growth skeletal pattern formation the avian (chicken) limb bud. Binaries source code are available,...
An extended multiscale model is introduced for studying the formation of platelet thrombi in blood vessels. The describes interplay between viscous, incompressible plasma, activated and non-activated platelets, as well other cells, activating chemicals, fibrinogen vessel walls. macroscale dynamics flow represented by continuous submodel form Navier–Stokes equations. microscale cell-cell interactions are described stochastic Cellular Potts Model (CPM). Simulations indicate that increase rates...
Background Major unresolved questions regarding vertebrate limb development concern how the numbers of skeletal elements along proximodistal (P-D) and anteroposterior (A-P) axes are determined shape a growing affects element formation. There is currently no generally accepted model for these patterning processes, but recent work on cartilage (chondrogenesis) indicates that precartilage tissue self-organizes into nodular patterns by cell-molecular circuitry with local auto-activating lateral...
Significance The opportunistic pathogen Pseudomonas aeruginosa utilizes both its flagellum and type IV pili (TFP) to facilitate motility, attachment, colonization. Surface motility such as swarming is thought precede biofilm formation during infection. We combined laboratory computational methods probe the physical interactions of TFP flagellar-mediated found that one cell strongly interact with other cells, which limits expansion rate. Hence, wild-type P. use cell−cell via their control...
Thromboembolism, one of the leading causes morbidity and mortality worldwide, is characterized by formation obstructive intravascular clots (thrombi) their mechanical breakage (embolization). A novel two-dimensional multi-phase computational model introduced that describes active interactions between main components clot, including platelets fibrin, to study impact various physiologically relevant blood shear flow conditions on deformation embolization a partially clot with variable...
Significance The microtubule (MT) cytoskeleton is a dynamic polymer network that plays crucial role in cell function and disease. MT assembly dynamics are precisely controlled; key regulator the destabilizer known as stathmin. Stathmin’s mechanism of action remains controversial: one well-supported model it reduces indirectly by sequestering subunits; alternative acts directly on MTs an yet unknown mechanism. We provide resolution to this debate presenting experimental evidence stathmin can...
A connection is established between discrete stochastic model describing microscopic motion of fluctuating cells, and macroscopic equations dynamics cellular density. Cells move towards chemical gradient (process called chemotaxis) with their shapes randomly fluctuating. Nonlinear diffusion equation derived from in dimensions one two using excluded volume approach. coefficient depends on fraction it demonstrated to prevent collapse very good agreement shown Monte Carlo simulations the Potts...