### Table of Contents

## List of Past DPD Club Meeting Topics

## 05/25/17

Speaker: Drs. Yin-Jia Zhang (Department of Chemistry, Brown University) & Yu-Hang Tang (Division of Applied Mathematics, Brown University)

Title: Accelerating DFT-based atomistic geometry calculations using Artificial Neural Networks and the AMP package.

Reference:

1. A. Khorshidi and A. Peterson (2016). AMP: A modular approach to machine learning in atomistic simulations. Comput Phys Commun, 207: 310-324.

## 04/27/17

*Speaker: Dr. Alireza Yazdani

Title: Multiscale Modeling of Blood Clotting in Flow using DPD.

*Speaker: Dr. Hung-Yu Chang

Title: Gene Therapy in a Patient with Sickle Cell Disease

Reference:

1. J. Ribeil, et al. (2017). Gene Therapy in a Patient with Sickle Cell Disease. N Engl J Med, 376: 848-855.

2. B. P. Frédéric, H. S. Martin, and D. C. Rees. (2017) Sickle Cell Disease. N Engl J Med, 376: 1561-1573.

## 04/06/17

- Speaker: Dr. Safa Jamali (Department of Mechanical Engineering, MIT)

Title: Connecting Microstructure to Macroscopic Properties in Complex Fluids: Towards Design of Soft Materials with Tunable Properties

Abstract: The field of complex fluids encompasses a wide class of materials, which exhibit unusual mechanical responses to an applied stress or strain. In virtually all complex fluids, this rich and unusual mechanical response originates from a microstructure that responds to different applied stress or strain in specific and varied ways. Thus understanding the microstructure – macroscopic behavior relationship is a crucial step for systematically designing complex fluid materials for novel applications. The complex fluid landscape can be subdivided based on the particle-level interactions that govern their underlying microstructure and the resulting macro rheology. For example, viscosity of a dense suspension of repulsive or neutral colloidal particles progressively increases with increasing the rate of deformation. This behavior is called Shear-Thickening behavior, and is best exemplified by someone’s ability to run on a pool of cornstarch and water, and sinking in while standing still. On the other hand, a distinct hallmark of attractive Brownian particles, even at small and intermediate concentrations, is their ability to self-assemble into percolated networks that span over the sample size. These structures show a rich time and rate dependent response to applied deformation/forces such as yielding, shear banding, microphase separation and flow heterogeneities, etc. I will present a computational framework to bridge the gap between microstructure to macroscopic properties of complex fluids, using hydrodynamics and statistical mechanics: First I will discuss the role of hydrodynamics, friction and particle geometry/deformability in shear-thickening fluids, and secondly, the role of microstructural evolutions of attractive systems in defining their mechanical response.

## 03/09/17

- Speaker: Kang-Sahn Kim (Department of Chemistry, KAIST-Korea Advanced Institute of Science and Technology)

Title: Estimation of shear viscosity for simple and complex fluids using equilibrium MD simulations: statistical errors and system size effects.

## 02/23/17

- Speaker: Peiyuan Gao (Advanced Computing, Mathematics & Data Division, PNNL)

Title: Individual chain dynamics of polybutadiene melt under shear. - Speaker: Xuejin Li

Title: In silico prediction and characterization of sickle cell anemia: Successes and challenges.

## 01/26/17

- Speaker: Xiaojie Wu (Department of Mathematics, Pennsylvania State University)

Title: From atomistic simulation to continuum mechanics: theoretical connections and coarse-graining methods (atomistic-based boundary element method)

Abstract: Molecular dynamics is an extremely powerful tool to investigate the phenomena in material science. A system with a large number of particles usually behaves like continuous materials and the dynamics follows continuum mechanics model, (i.e. elasticity or elastodynamics). However, the precise definitions of many continuum quantities in molecular dynamics, such as stress, heat flux are still challenging. Formulas with high order of accuracy will be introduced.

## 01/19/17

- Speaker: Xuhui Meng

Title: A generalized multiscale modeling approach coupled pore- and Darcy-scale models for flow and reactive transport in porous media. - Speaker: Xiaocheng Shang

Title: Adaptive thermostat: A more accurate and efficient approach in measuring viscosity in nonequilibrium simulations.

## 12/08/16

- Speaker: Lifei Zhao

Title: A multiscale method coupling particle and continuum models for viscoelastic flows with free surface. - Speaker: Yixiang Deng

Title: Fluctuating lattice Boltzmann equation: theoretical derivation and algorithm introduction.

## 12/01/16

- Speaker: Minglang Yin

Title: Dissipative particle dynamics study of a flexible filament in confined shear flow. - Speaker: Liu Yang

Title: Systematic parameter influence in stochastic mesoscopic modelling.

## 11/17/16

- Speaker: Zhizhong Chen

Title: Introduction of poiseuille flow as a numerical viscometer. - Speaker: Zhen Li

Title: A solution to arbitrary-shaped geometries in dissipative particle dynamics.

## 11/10/16

- Speaker: Minglang Yin

Title: Dissipative particle dynamics study of a flexible filament in confined shear flow. - Speaker: Hung-Yu Chang

Title: Biomechanics and biorheology of diabetic red blood cell {\em in-silico}.

## 11/03/16

- Speaker: Xuhui Meng

Title: Numerical Simulation of Reactive Flow in Porous Media using the Lattice Boltzmann Method.

## 10/20/16

- Speakers: Yu-Hang Tang, Zhen Li and Yuta Yoshimoto

Title: Coarse-grained simulations of cis- and trans-polybutadiene: A bottom-up approach. - Speakers: Xuejin Li and Hung-Yu Chang

Title: Review on red cell club meeting 2016.

## 10/13/16

- Speaker: Liu Yang

Title: Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics. - Speaker: He Li

Title: Review on particle-based models for red blood cell and its membrane.

## 10/06/16

- Speaker: Xiaocheng Shang

Title: Statistical mechanics of dissipative particle dynamics and beyond. - Speaker: Zhen Li

Title: Extended Markovian system for modeling non-Markovian dynamics.

## 09/29/16

- Speaker: Xuejin Li

Title: Applications of DPD: From simple fluids to blood flow modeling.

## 09/22/16

- Speaker: Zhen Li

Title: New methods beyond traditional dissipative particle dynamics. - Speaker: Hung-Yu Chang

Title: How the spleen filters blood?

## 09/15/16

- Speaker: Zhen Li

Title: Theoretical foundation and parameterization of dissipative particle dynamics. - Speaker: Yu-Hang Tang

Title: OpenRBC: A fast simulator of red blood cells at protein-resolution.

## 08/25/16

- Speaker: Prof. Dr. Gastone Castellani (Department of Physics and Astronomy, Bologna University)

Title: Noise and networks in biological systems: statistical connections and modeling perspectives.

Abstract: Noise in biological systems is pervasive. Each biological process is accompanied by a certain degree of noise. One of the most advanced methods to describe noise is the so called Master Equation. I will describe this approach and how this method can be used in cases of given topologies such as complex networks as in the protein-protein interaction networks.

## 08/19/16

- Speaker: Dr. Yuta Yoshimoto (Department of Mechanical Engineering, University of Tokyo)

Title: Coarse-grained dynamics incorporating non-Markovian nature of particle motions.

Abstract: We derive the equation of motion for non-Markovian dissipative particle dynamics (NMDPD) by introducing the memory effects on the time evolution of the system. For the validation of our formulation, we construct NMDPD models from high-density Lennard-Jones systems, in which the typical time scales of the coarse-grained particle motions and the fluctuating forces are not fully separable. The NMDPD models reproduce the temperatures, diffusion coefficients, and viscosities of the corresponding molecular dynamics systems more accurately than the dissipative particle dynamics models based on a Markovian approximation. - Speaker: Alireza Yazdani

Title: Seamless multiscale modeling of blood clotting using DPD.

## 08/04/16

- Speaker: Xin Bian (边鑫)

Title: Generalized fluctuating hydrodynamics of molecular dynamics. - Speaker: Lu Lu (陆路) & He Li

Title: Mesoscopic adaptive resolution scheme (MARS) for sickle hemoglobin fiber interactions via dynamic coarse-graining.

## 07/14/16

- Speaker: Xiaocheng Shang

Title: An overview of thermostats: From molecular dynamics to machine learning.

Abstract:*Classical molecular dynamics (MD) tracks the motion of individual atoms determined by Newton's law in the microcanonical ($NVE$) ensemble, where energy $E$ (i.e., the Hamiltonian of the system), as well as the total number of particles in the system, $N$, and the volume of the system, $V$, are conserved. However, constant energy is not the appropriate setting of a real-world laboratory environment. In most cases, one wishes instead to sample the canonical ($NVT$) ensemble, where temperature $T$, as an intensive variable, is conserved, by using ``thermostat'' techniques. In this talk, I will give you an overview of the thermostats techniques. I will also give you a flavor of how these techniques have been used originally in MD and recently in large-scale machine learning applications.* - Speaker: Myrto Perdikari

Title: Molecular dynamics meets supramolecular electronics.

## 05/26/16

- Speaker: Hung-Yu Chang

Title: Red blood cell deformability in diabetes mellitus.

Reference:

1. Agrawal, R., et al. Assessment of red blood cell deformability in type 2 diabetes mellitus and diabetic retinopathy by dual optical tweezers stretching technique. Scientific reports, 2016, 6: 15873.

2. Brown, C. D., et al. Association of reduced red blood cell deformability and diabetic nephropathy. Kidney international, 2005, 67: 295.

3. Tsukada, K., et al. Direct measurement of erythrocyte deformability in diabetes mellitus with a transparent microchannel capillary model and high-speed video camera system. Microvascular research, 2001, 61: 231.

4. Buys, A. V., et al. Changes in red blood cell membrane structure in type 2 diabetes: a scanning electron and atomic force microscopy study. Cardiovascular diabetology, 2013, 12: 25. - Speaker: Ansel Blumers

Title: Benchmarks - Red Blood Cell with Transport-DPD on GPU

Abstract:*Red blood cells (RBCs) dynamical simulation used to be done on CPU in our group. With the rise of demand on large simulation size and functionality, speed becomes a major concern. To alleviate the bottleneck, graphical accelerators (GPU) can be incorporated to aid the CPU and boost the speed. I will present a comparison of CPU and GPU simulation benchmark result.*

## 04/14/16

- Speaker: He Li

Title: A brief introduction on hereditary spherocytosis (HS) and elliptocytosis (HE) in blood disorder. - Speaker: Zhen Li

Title: A comparative study of coarse-graining methods for polymeric fluids.

Abstract:*We construct effective coarse-grained (CG) models for polymeric fluids by employing two coarse-graining strategies. The first one is a forward-coarse-graining procedure by the Mori-Zwanzig (MZ) projection while the other one applies a reverse-coarse-graining procedure, such as the iterative Boltzmann inversion (IBI) and the stochastic parametric optimization. More specifically, we perform molecular dynamics (MD) simulations of star polymer melts to provide the atomistic fields to be coarse-grained. Each molecule of star polymer with internal degrees of freedom is coarsened into a single CG particle and the effective interactions between CG particles can be either evaluated directly from microscopic dynamics based on the MZ formalism, or obtained by the reverse methods, i.e., IBI and SPO. The forward procedure has no free parameters to tune and recovers the MD system faithfully. For the reverse procedure, we find that the parameters in CG models cannot be selected arbitrarily. If the free parameters are properly defined, the reverse CG procedure also yields an accurate effective potential. Moreover, we explain how an aggressive coarse-graining procedure introduces many-body effect, which makes the pairwise potential invalid for the same system at densities away from the training point.*

## 03/10/16

- Speaker: Yu-Hang Tang

Title: Targeted polymeric therapeutic nanoparticles: design, development and clinical translation.

Reference:

1. Kamaly N, Xiao Z, Valencia PM, Radovic-Moreno AF, Farokhzad OC. Targeted polymeric therapeutic nanoparticles: design, development and clinical translation. Chem Soc Rev, 2012, 41, 2971-3010. - Speaker: Mingge Deng

Title: Electrons that flow like a fluid.

References:

1. Moll P, et al. Evidence for hydrodynamic electron flow in PdCoO2. Science, 2016, 351: 1061-1064.

2. Bandurin D, et al. Negative local resistance caused by viscous electron backflow in graphene. Science, 2016, 351: 1055-1058.

3. Crossno J, et al. Observation of the Dirac fluid and the breakdown of the Wiedemann-Franz law in graphene. Science, 2016, 351: 1058-1061.

4. Stajic J. Electrons that flow like a fluid. Science, 2016, 351: 1038.

## 02/25/16

- Speaker: Ansel Blumers

Title: A new multiscale approach to study blood-flow in macro-circulation. - Speaker: Xuejin Li

Title: Modeling blood flow in micro-circulation.

## 02/18/16

- Speaker: He Li

Title: Multiscale modeling of red blood cells in health and disease: Can current molecular-detailed composite membrane model drive the future of whole-cell modeling? - Speaker: Yixiang Deng

Title: Capsule-train stability.

References:

1. J. B. Freund, “Leukocyte margination in a model microvessel,” Phys. Fluids 19 (2007).

2. P. J. Schmid, “Nonmodal stability theory,” Annu. Rev. Fluid Mech. 39, 129 (2007).

## 02/04/16

- Speaker: Lu Lu

Title: Nucleation and growth of fibres and gel formation in sickle cell haemoglobin.

Reference:

1. Samuel, RE, Salmon, ED and Briehl, RW. Nucleation and growth of fibres and gel formation in sickle cell haemoglobin. Nature, 1990, 345: 833-835. - Speaker: Yu-Hang Tang

Title: Doubling down on polymerization.

Reference:

1. Yu, Z, et al. Simultaneous covalent and noncovalent hybrid polymerizations. Science, 2016, 351:497-502.

## 01/28/16

- Speaker: Hung-Yu Chang

Title: Quantitative modeling of mechanics of healthy and diseased human red blood cells via optical tweezers.

Reference:

1. Zhang Y, Huang C, Kim S, Golkaram M, Dixon M, Tilley L, Li J, Zhang S, and Suresh S. 2015. Multiple stiffening effects of nanoscale knobs on human red blood cells infected with Plasmodium falciparum malaria parasite. PNAS, 112, 6068-6073.

## 01/21/16

- Speaker: Xiaocheng Shang (School of Mathematics, University of Edinburgh)

Title: Extended stochastic dynamics: theory, algorithms, and applications in multiscale modelling and data science

Abstract: We address the sampling problem in a high dimensional space, i.e. the computation of averages with respect to a defined probability density that is a function of many variables. Such sampling problems arise in many application areas, including molecular dynamics, multiscale models and Bayesian sampling techniques used in emerging machine learning applications. Of particular interest are thermostat techniques, in the setting of a stochastic-dynamical system, that preserve the canonical Gibbs ensemble defined by an exponentiated energy function. In this talk we explore theory, algorithms and numerous applications in this setting.

References:

1. Leimkuhler, B. & Shang, X. On the numerical treatment of dissipative particle dynamics and related systems. Journal of Computational Physics, 2015, 280, 72.

2. Leimkuhler, B. & Shang, X. Adaptive thermostats for noisy gradient systems. SIAM Journal on Scientific Computing, 2016, to appear. http://arxiv.org/abs/1505.06889.

3. Shang, X., Zhu, Z., Leimkuhler, B. & Storkey, A. J. Covariance-controlled adaptive Langevin thermostat for large-scale Bayesian sampling. Advances in Neural Information Processing Systems (NIPS), 2015, 28, 37. - Speaker: Mingge Deng

Title: Mesoscopic fluctuating electro-kinetics of electrolyte solutions at equilibrium

Abstract: We study the mesoscopic fluctuating electro-kinetics of electrolyte bulk solutions at equilibrium. We first derive the explicit closed form solutions of linearized fluctuation hydrodynamics and electro-kinetics equations with perturbation theory. We then also perform computer simulations of electrolyte bulk solution using both molecular dynamics (MD) and our recently developed charged Dissipative Particle Dynamics (cDPD) methods. Specifically, we find that the local fluctuations of ionic concentrations follow Gamma distributions and converge to Gaussian distributions in the continuum limit; we also examine the spatial correlations of charge density, which have finite range and interesting structures in small scales (nm), but can be viewed as delta function in the continuum limit. In the last but most importantly, we compute the temporal correlations in Fourier space of fluctuating hydrodynamics and electro-kinetics from both MD and cDPD trajectories. The results of simulations are in good agreement with linearized theories, and the temporal correlation functions of electro-kinetics decay much slower than that of hydrodynamics.

## 01/14/16

- Speaker: Alireza Yazdani

Title: Modeling blood flow and platelet’s transport in microchannels with constriction - Speaker: Yixiang Deng

Title: A brief review on the dynamic properties of vWF and its modeling

## 01/07/16

- Speaker: Lu Lu

Title: Multiscale modeling of sickle hemoglobin polymerization with dynamic coarse-graining

References:

1. Li H, Ha V & Lykotrafitis G Modeling sickle hemoglobin fibers as one chain of coarse-grained particles. Journal of Biomechanics, 2012, 45, 1947-1951.

2. Werder T, Walther JH, & Koumoutsakos P. Hybrid atomistic–continuum method for the simulation of dense fluid flows. Journal of Computational Physics, 2005, 205: 373-390.

## 12/17/15

- Speaker: Ansel Blumers

Title: A brief crash-course to neuroplasticity.

Reference:

1. Hahnloser RHR, Kozhevnikov AA, and Michale SF. An ultra-sparse code underlies the generation of neural sequences in a songbird. Nature, 2002, 419(6902): 65-70.

## 12/10/15

* Speaker: Prof. Anastasios Matzavinos

Title: A review of relative entropy rate methods for sensitivity analysis of stochastic systems.

## 12/03/15

- Speaker: Prof. Bruce Caswell

Title: Report on selected presentations at meetings of: Society of Rheology, and AIChE - Speaker: Xuejin Li

Title: Translocation of nanoparticle with different shapes across a lipid bilayer via computer simulations

References:

- Yang K & Ma YQ. Computer simulation of the translocation of nanoparticles with different shapes across a lipid bilayer. Nature Nanotechnology, 2010, 5: 579-83.
- Ding HM, Tian WD & Ma YQ. Designing nanoparticle translocation through membranes by computer simulations. ACS Nano, 2012, 6: 1230-8.
- Li YF, Li XJ, Li ZH & Gao HJ. Surface-structure-regulated penetration of nanoparticles across a cell membrane. Nanoscale, 2012, 4: 3768-75.
- Hu XL, Hu JM, Tian J, Ge ZS, Zhang GY, Luo KF & Liu SY. Polyprodrug amphiphiles: hierarchical assemblies for shape-regulated cellular internalization, trafficking, and drug delivery. Journal of American Chemical Society, 2013, 135: 17617-29.
- Dasgupta S, Auth T & Gompper G. Shape and orientation matter for the cellular uptake of nonspherical particles. Nano Letters, 2014, 14: 687-93.
- Setyawati M, Tay CY, Docter D, Stauber RH & Leong DT. Understanding and exploiting nanoparticles' intimacy with the blood vessel and blood. Chemical Society Review, 2015, 44: 8174-99.

## 11/19/15

- Speaker: Zhen Li

Title: A modified optimal prediction – revisit the last paper of Prof. David Gottlieb

References:

- Chorin, A.J., Hald, O.H., Kupferman, R. Optimal prediction with memory, Phys. D, 2002, 166:239–257.

## 11/12/15

- Speaker: He Li

Title: Platelets motion and adhesion in pathological conditions of aortic aneurysm and stenosis - Speaker: Xiaoning Zheng

Title: Phase-field method and its applications

Reference:

1. Dong S & Shen J A time-stepping scheme involving constant coefficient matrices for phase-field simulations of two-phase incompressible flows with large density ratios. Journal of Computational Physics, 2012, 231, 5788-804.

## 11/05/15

- Speaker: Hung-Yu Chang

Title: Quantitative modeling of mechanics of healthy and diseased human red blood cells via optical tweezers - Speaker: Xuejin Li

Title: Drug delivery by red blood cells

References:

1. Muzykantov VR. Drug delivery by red blood cells: vascular carriers designed by mother nature. Expert Opin Drug Deliv, 2010, 7:403-27.

2. Biagiotti S, et al. Drug delivery by red blood cells. IUBMB Life, 2011, 63:621-31.

3. Greineder, CF, et al. Advanced drug delivery systems for antithrombotic agents. Blood, 2013, 122:1565-75.

## 10/22/15

- Speaker: Xin Bian (边鑫)

Title: Multiscale coupling of particles via domain decomposition method

## 10/15/15

- Speaker: George Pashos (School of Chemical Engineering, National Technical University of Athens)

Title: Wetting on patterned surfaces: stability and transitions - Speaker: Mingge Deng

Title: Fluctuating electro-kinetics in micro- and mesoscopic electrolyte solutions

## 10/08/15

- Speaker: Alireza Yazdani

Title: A multi-fidelity method for time-scale bridging in blood clotting process - Speaker: Lu Lu

Title: Scaling in dissipative particle dynamics

## 10/01/15

- Speaker: Zhen Li

Title: Clarification of a misunderstanding on the compressibility of DPD fluids - Speaker: Yu-Hang Tang

Title: Flip-or-Slip: Self-Assembly dynamics of thermoresponsive smart materials - Speaker: Xuejin Li

Title: Thermoresponsive polymers in drug delivery

## 09/24/15

- Speaker: Nathaniel Trask

Title: A mixed meshless method for solving the Stokes equations - Speaker: Jun Yang

Title: Sickle RBC shape effect on membrane fluctuations

## 09/17/15

- Speaker: Zhen Li

Title: Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism - Speaker: Ansel Blumers

Title: Oxygen release via red blood cells in capillaries

## 08/28/15

- Speaker: He Li

Title: Developing a hybrid sickle hemoglobin (HbS) fiber model to simulate HbS fiber formation and fiber-cell membrane interactions in sickle cell disease - Speaker: Lu Lu

Title: Growth of sickle hemoglobin fiber from its nucleus: A molecular simulation study

## 08/06/15

- Speaker: Phillips Neumann (Department of Informatics, TU München)

Title: Coupling four molecular dynamics codes in a massively parallel molecular-continuum framework

## 07/31/15

- Speaker: Hung-Yu Chang (Department of Chemical Engineering, National Taiwan University)

Title: Microfludic deformability analysis of the red cell storage lesion

## 07/03/15

- Speaker: Dimitrios Papageorgiou (Department of Materials Science and Engineering, Massachusetts Institute of Technology)

Title: Characteristics of polymersomes studied by dissipative particle dynamics

## 06/15/15

- Speaker: Prof. Bruce Caswell

Title: Enzyme kinetics and a review of some literature on the clot problem

## 06/08/15

- Speaker: Zhen Li

Title: Adaptive Thermostats for Noisy Gradient Systems - Speaker: Yu-Hang Tang

Title: Visualizing Particles with Ray Tracing

## 05/22/15

- Speakers: Xuan Zhao & Mingge Deng

Title: Polymer science applications of path-integration, integral equations, and fractional calculus

## 04/17/15

- Speakers: Alireza Yazdani & He Li

Title: Some remarks on the bio-mechanics of cell adhesion

## 03/20/15

- Speakers: Changho Kim

Title: Long–time tail of the velocity autocorrelation function of a particle in a molecular fluid

## 02/20/15

- Speaker: Clark Bowman

Title: Modeling biological polymer networks and the flow of DNA in entropic wells

## 02/06/15

- Speaker: He Li

Title: Particle simulation of oxidation induced band-3 clustering in human erythrocytes - Speaker: Xuejin Li

Title: Deformability of individual sickle cells in oxygenated and deoxygenated states

## 01/30/15

## 01/23/15

- Speaker: Lu Lu

Title: Sickle hemoglobin nucleation process

## 01/16/15

- Speaker: Yu-Hang Tang

Title: Modelling temperature-induced self-assembly of thermoresponsive polymers using eDPD - Speaker: Xuejin Li

Title: Soft–spring wall based non–periodic boundary conditions for non–equilibrium molecular dynamics

## 01/09/15

- Speaker: Yu-Hang Tang

Title: Project Builder: An omnipotent particle system constructor

## 12/12/14

- Speaker: Huan Lei

Title: Modeling fluctuation hydrodynamics and hydrophobicity via mesoscopic simulation - Speaker: Zhen Li & Alireza Yazdani

Title: Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems

## 11/28/14

- Speaker: Prof. Antonios Liakopoulos (Department of Civil Engineering, University of Thessaly)

Title: Models of thermal Convection: Boussinesq, Anelastic, and Low Mach Number - Speaker: Zhen Li

Title: Mesoscopic modeling of thermoresponsive polymers in solution

## 11/07/14

- Speaker: Xin Bian (边鑫)

Title: A promising application of multiscale modeling: polymer melts

## 10/31/14

- Speaker: Xuejin Li

Title: Shape of red blood cells in contact with artificial surfaces

## 10/24/14

- Speaker: Heyrim Cho

Title: Reduced order PDF equation by using Mori-Zwanzig framework: application to stochastic Burgers equation - Speaker: Zhen Li

Title: Mori-Zwanzig guided mesoscopic modeling of complex fluids

## 10/17/14

- Speaker: Prof. Bruce Caswell

Title: Review on 86th Annual Meeting of the Society of Rheology

## 10/10/14

- Speaker: Xuejin Li

Title: Dynamics and rheology of sickle blood flow in microfluidic channels

## 10/03/14

- Speaker: Zhen Li

Title: Preserving the memory of particle interactions in a coarse-grained model - Speaker: Nathaniel Trask

Title: An overview of the finite volume particle method

## 09/19/14

- Speaker: Nathaniel Trask

Title: A conservative mesh-free scheme and generalized framework for conservation laws

## 08/21/14

- Speaker: Changho Kim

Title: A conservative mesh-free scheme and generalized framework for conservation laws

## 07/25/14

- Speaker: Alireza Yazdani

Title: Geometry effect on platelet aggregation and formation of thrombus.

## 06/27/14

- Speaker: Changho Kim

Title: Uncertainty quantification for the estimation of the velocity autocorrelation function and diffusion coefficient from MD simulations — preliminary results - Speaker: Zhen Li

Title: Effects of high-frequency components of the conservative force on MD-informed DPD modeling

Abstract: In a previous talk, I reported that the MD system of star polymer melts can be accurately reproduced by a Mori-Zwanzig guided DPD model. However, for those star polymers with long arms, the divergence in RDF between the MD and DPD models appears. Recently, we found this divergence in RDF can be corrected by employing the high-frequency components of the conservative force. In this talk I will bring a discussion about this problem.

## 06/13/14

- Speaker: Yu-Hang Tang

Title: Implementing SPH on GPU - Speaker: Mingge Deng

Title: Low-symmetric fluid particle model

## 05/30/14

- Speaker: Nat Trask

Title: A high order meshless method with compact support

## 05/19/14

- Speaker: Dr. Wenxiao Pan

Title: Smoothed particle hydrodynamics (SPH) and its applications - Speaker: Dr. Xin Bian (边鑫)

Title: Framework of concurrent multiscale coupling of Lagrangian particle methods - Speaker: Dr. Zhen Li

Title: Bottom-up construction of coarse-grained models of complex fluids.

## 05/16/14

- Speaker: Dr. Changho Kim

Title: Brownian motion in a Rayleigh gas confined in a channel: Generalized Langevin equation approach

## 05/02/14

- Speaker: Dr. Xuejin Li

Title: Large-scale coarse-grained modeling of amphiphilic self-assembly

Abstract: Amphiphilic self-assembly is in abundance in nature and is crucial to the function of cells as well as a number of human diseases including sickle cell anemia. In biological systems such as red blood cells (RBCs), the self-assembly takes place in a soft confined environment with boundaries which are not rigid but compliant, thus, the self-assembled microstructures under this soft confinement may be different from that in bulk solution and under hard confinement. However, the kinetic and dynamic details of these processes remain largely unknown. In this talk, we will present large-scale simulation results on the self-assembly of amphiphilic systems. Specifically, we shall focus on the self-assembled polymersomes (polymeric vesicles) and liposomes (lipid vesicles) in bulk solution and under hard/soft confinement. The potential research and our continue plans including modeling some interesting phenomena such as the uncoupling of cytoskeleton from lipid bilayer in sickle RBCs and the release of spectrin-free vesicles from malaria-infected and sickle RBCs will be discussed.

## 04/25/14

- Speaker: Dr. Zhen Li

Title: Coarse-Graining Analysis for Dissipative Particle Dynamics.

Abstract: In this talk, comparisons between the performances of different DPD models in reproducing static and dynamic properties of a well-defined microscopic system. These models including the original DPD, DPD with constructed force field based on MD simulations, and Fluid Particle Model (FPM) will be introduced. When a well-defined microscopic system is coarse-grained, some of the properties associated to the CG particles such as interactions along perpendicular directions and the rotational momentum of the finite-size particles are neglected. I will show some demonstrations about how these neglected properties affect the performances of coarse-grained models.

## 04/18/14

- Speaker: Nat Trask.

Title: Projection methods for stokes equations discretized with meshless collocation.

## 04/11/14

- Speaker: Dr. Alireza Yazdani.

Title: Mesoscopic modeling of platelet aggregation. - Speaker: Dr. Helen Li.

Title: Review of bias potential constructions for accelerated hyperdynamics.

## 04/04/14

- Speaker: Dr. Xuejin Li.

Title: Sickling/unsickling dynamics of individual red cells: insights from computer simulation studies. - Speaker: Dr. Mingge Deng.

Title: DPD/FPM simulation of colloidal particles.

## 03/28/14

- Speaker: Dr. Xin Bian (边鑫).

Title: Multi-resolution simulation of SPH via domain decomposition.

Abstract: Since we are generally interested in multi-scale concurrent coupling between particles methods such as SPH, SDPD, DPD, and MD, we started with SPH-SPH deterministic coupling first to identify potential obstacles of coupling particle methods. We present here one/two dimensional flows preliminary results from dual sub-domain coupling, where each side of a hybrid interface is simulated by a deterministic SPH method. We found that “solo-velocity coupling” is not sufficient and fail for certain benchmark problems. To remedy the defects, we further couple density, therefore the pressure between two sides. For now, SPH-SDPD coupling works only for one dimensional flow, such as Couette and Poiseuille flow, therefore it will not be presented for this talk. General deterministic-stochastic coupling awaits further elaboration and will be shown in near future.

## 03/21/14

- Speaker: Dr. Changho Kim.

Title: Velocity auto-correlation function of a Brownian particle in a dense fluid.

## 03/14/14

- Speaker: Dr. Zhen Li.

Title: Bottom-up coarse-graining analysis for dissipative particle dynamics.

Abstract: To analyze the bottom-up coarse-graining process from atomic systems to DPD systems, we carried out molecular dynamics simulations to derive coarse-grained force field for DPD approach directly from microscopic trajectories. DPD is considered as the effective dynamics resulting from Mori-Zwanzig projection of an underlying microscopic dynamics, and all the forces in DPD model including the conservative, dissipative and stochastic forces are extracted directly from the molecular dynamics simulations. The coarse-graining process is illustrated in the example of star polymers in a melt and the coarse-grained interactions for different coarse-graining level are obtained. Preliminary results show that the coarse-grained force field for DPD model generates structural properties consistent with the corresponding MD systems; however, DPD simulations result in a general speedup of diffusion and of other dynamical properties. - Speaker: Yu-Hang Tang.

Title: MUI progress report and request-for-comment.

## 03/07/14

- Speaker: Dr. Xuejin Li.

Title: Data-driven simulation and prediction of blood viscosity in sickle cell disease. - Speaker: Dr. Mingge Deng.

Title: Long timestep Molecular Dynamics [paper review].

## 02/21/14

- Speaker: Dr. Changho Kim.

Title: Brownian motion in a channel: memory function approach. - Speaker: Yu-Hang Tang and Shuhei Kudo.

Title: Preliminary progress report on designing a universal concurrent coupling framework.

## 02/14/14

- Speaker: Prof. Anastasios Matzavinos.

Title: Actin network mechanics and cell shape [paper review]. - Speaker: Dr. Alireza Yazdani.

Title: Thrombus biomechanics and modeling [paper review]. - Speaker: Dr. Zhen Li.

Title: Universal scaling law for atomic diffusion in condensed matter [paper review].

## 02/07/14

- Speaker: Dr. Xiu Yang.

Title: Parameter inference in mesoscopic model. - Speaker: Nathaniel Trask.

Title: Finite volume particle method [paper review].