The following are events associated with or of interest to the Center for Computation and Theory of Soft Materials community. 

The architecture of biological matter:
Amino acids, proteins and nucleic acids

Speaker: Jean-Louis Sikorav
High Council for Economy & Sorbonne Université

Tuesday, December 4, 2018
11:00 a.m. - 12:00 p.m.
Mechanical Engineering Conference Room - Tech B211

Abstract: DNA is the solution found by Nature for the storage and transmission of hereditary information. Why is DNA such as it is and not otherwise? This question will be addressed through a theoretical construction of the genetic material, using the language and the methods introduced in order to build the foundations of biology (1). The construction shows the necessity of molecular chirality for living processes; it establishes the unique and ideal character of DNA and improves our understanding of the structure of amino acids and proteins (2).



Past Events:

Linking the colloidal cluster morphology with the extended law of corresponding states

Speaker: Nestor Valadez-Perez
Postdoc, Illinois Institute of Technology

Monday, November 26, 2018
11:00 a.m. - 12:00 p.m.
MSE Conference Room - Cook 2058

Abstract: The clustering of spherical particles interacting with a short-range attraction has been extensively studied due to its relevance to many applications, such as the large-scale structure in amorphous materials, protein crystallization, aggregation and phase separation of protein inside cells, among others. The parameters that determine the interaction potential among particles affect the way they assemble and the morphology of clusters. It was widely accepted that the range of the attraction solely controls the fractal dimension of clusters, however recent experimental results challenged this concept by also showing the importance of the strength of attraction. In this talk it is presented a quick review of the applications of the extended law of corresponding states in colloidal systems, including the relation of local properties to this law. This physical escenario is confirmed with the reanalysis of experimental results on colloidal-polymer mixtures, previously reported in the literature.

Asymmetric Breathing Motions of Nucleosomal DNA and the Role of Histone Tails

Speaker: Sharon M. Loverde
Associate Professor, Chemistry Department,
CUNY - Staten Island, New York

Wednesday, October 10, 2018
1:00 p.m. - 2:00 p.m.
MSE Conference Room - Cook 2058

Abstract: Being the basic packaging unit of DNA, the nucleosome core particle (NCP) stabilizes as well as controls DNA accessibility during vital cellular processes. Recently reported structures of the NCP suggest that the histone octamer undergoes conformational changes during the process of DNA translocation (Bilokapic, Nature Communications, 2018). The mechanism of repositioning of the DNA around the histone octamer has been suggested to be sequence-dependent. Furthermore, the histone talks have been suggested to play a key role in this repositioning. We demonstrate with long-time all-atomistic molecular dynamics simulations (5 microseconds) that the histone tails do indeed play a critical role in nucleosome repositioning through formation of a loop of nucleosomal DNA around the histone core at high salt concentrations (2 M NaCl) (Chakraborty, Kang, and Loverde, in review).  

Biography: Sharon M. Loverde, PhD, is an Associate Professor in the Chemistry department at College of Staten Island, a senior campus at the City University of New York (CUNY).  She is also a faculty member of the Graduate Center of CUNY in the areas of Chemistry, Biochemistry, and Physics.  Dr. Loverde’s research focuses on molecular dynamics simulations of soft and biological systems.  In 2014, she received an ACS PRF New Investigator Award and in 2018 she received an NSF CAREER Award.  Dr. Loverde was an NIH NRSA Postdoctoral Fellow who worked with Dennis E. Discher (UPenn) and Michael L. Klein (Temple).  She received her PhD in Materials Science and Engineering from Northwestern University working with Monica Olvera de la Cruz. 

Soft Matter Physics at the Nanoscale

Speaker: John T. King
Center for Soft and Living Matter, Institute for Basic Science,
South Korea

Friday, September 28, 2018
3:00 p.m. - 4:00 p.m.
MSE Conference Room - Cook 2058

Abstract: A significant challenge in experimental soft matter physics is overcoming the reliance on bulk-level measurements that average over spatial and temporal heterogeneities. Rapidly advancing microscopy and spectroscopy techniques, including super-resolution fluorescence microscopy, provide access to the spatial and temporal dimensions that often govern macroscopic structure and dynamics. In this talk, two examples will be discussed: 1) nanoscale molecular transport inside protein-DNA liquid-liquid phase separated droplets, and 2) interfacial dynamics of polymers at a non-adsorbing wall.

Biography: John King leads a group at the Institute for Basic Science, Center for Soft and Living Matter (S. Korea), which focuses on understanding how molecular and macromolecular structure and dynamics manifest in the bulk-level behavior of soft materials. He joined the Institute for Basic Science following a post-doc at the University of Illinois, Urbana-Champaign (2013-2016), where he worked on super-resolution microscopy and its application to polymer physics. He received a PhD in chemistry from the University of Michigan (2009-2013) studying ultrafast multidimensional spectroscopy of liquids. 

Assembly engineering of soft-matter-based nanomaterials using molecular dynamics simulations

Speaker: Vikram Jadhao
Professor, Intellegent Systems Engineering -
School of Informatics, Computing and Engineering at Indiana University, Bloomington

Monday, September 17, 2018
3:00 p.m. - 4:00 p.m.
Tech L440

Abstract: Self-assembly is a common process in generating biological materials and provides inspiration for engineering synthetic materials with tailored structure and functionality. I will present results from coarse-grained molecular dynamics simulations of the self-assembly of soft-matter-based nanoparticles (NPs); these systems have important applications in nanomedicine and in the design of active functional materials. In the first part of this talk, I will discuss the results on the assembly of bacteriophage P22 virus-like particles (VLPs) into three-dimensional ordered array materials in the presence of oppositely-charged dendrimers via electrostatic control. Equilibrium structures (including VLP-bound dendrimer distributions) as a function of the ionic strength and VLP surface charge will be identified and correlated with experiments. I will then present results on controlling the shape of deformable nanocontainers via the modulation of surface design patterns and ionic environment, which show that surface tension modulates the relative favorability of oblate disk to prolate rod morphologies. Finally, I will present some preliminary results on the nanoscale self-assembly of deformable building blocks, in which we explore the self-assembly of Hepatitis B viral capsids based on a model involving soft capsomeres in order to understand the role of deformability in the capsid assembly and overgrowth.

Biography: Vikram Jadhao is an assistant professor in Intelligent Systems Engineering at the School of Informatics, Computing, and Engineering at Indiana University in Bloomington. Prior to joining IU, he held postdoctoral fellowships in the Department of Physics and Astronomy at Johns Hopkins University as well as the Department of Materials Science and Engineering at Northwestern University. He received his Ph.D. and M.S. in Physics from the University of Illinois at Urbana-Champaign, and his B.S. in Physics from the Indian Institute of Technology at Kharagpur. His current research interests are in soft materials, self-assembled nanostructures, bio-inspired systems, ionic solutions, and flow of polymeric materials, with applications in nanomedicine, energy devices, and electronics. He is a recipient of the NSF CAREER award.

Studies in Bio-Inspired Physics

Speaker: Yitzhak Rabin
Professor, Physics Department; Institute for Nanotechnology and Advanced materials (BINA), Bar Ilan University, Israel

Thursday, August 16, 2018
4:00 p.m. - 5:00 p.m.
Tech E311 (BME conference room)


We devise and study simple physical models that address several questions inspired by biology:

  1. Do non-specific interactions assist or hinder the formation of specific complexes?

  2. How can one suppress aggregation of intrinsically disordered proteins?

  3. How do active processes affect polymer (DNA) dynamics?

Starting with copolymer phase behavior and moving away from equilibrium

Speaker: Wei  Li
Center for Nanophase Materials Sciences Oak Ridge National Laboratory

Monday, April 16, 2018
11:00 a.m. - 12:00 p.m.
Tech L440

Abstract: The abundant phase behaviors make block copolymer systems quite intriguing for theoretical and simulation studies. According to the combination of different numbers and types of the constituting blocks, block copolymer can have unlimited varieties. How the architecture at the molecular scale affects the self-assembly morphology at the meso-scale remains an interesting question.  We present a conceptual framework to describe and categorize the phase behavior of two-component block copolymer systems. Based on self-consistent field theory studies, three major universality classes for the topology of the equilibrium phase diagram are identified. Following a bottom-up approach, we analyze the relationship between chain architecture and copolymer mean-field phase behavior.

The precise control of self-assembly over morphology and size at the nanoscale brings a new era for the applications of block copolymers. Combining with other properties, the versality of block copolymers offers a unique platform for material design. To achieve rational design, many fundamental problems need to be addressed. We will present two case studies based on coarse-grained molecular dynamics simulations. In one study, we examined effects of dipolar interactions on the thermosdynamics of microphase separation in diblock copolymer melts and compared the results with the prediction from a field theory approach. In the other study, we investigated responses of thin films containing microphase separated ionic diblock copolymers to applied electric fields.  A plausible picture was provided to interpret the experimental findings from neutron reflectometry measurements.

Mechanics of a bacterial biofilm formed at the air-liquid interface

Speaker: Dr. Eric Raspaud
Laboratoire de Physique des Solides, Université Paris

Friday, November 10, 2017
11:00a.m. - 12:00p.m.
MSE Conference Room – Cook 2058

Abstract: Bacterial biofilms consist of a complex network of biopolymers embedded with microorganisms, and together these components form a physically robust structure that enables bacteria to grow in a protected environment. This structure can help unwanted biofilms persist in situations ranging from chronic infection to the biofouling of industrial equipment, but under certain circumstances can allow the biofilm to disperse and colonize new niches. Mechanical properties are therefore a key aspect of biofilm life. We study the physical forces acting on the floating pellicles at the air-liquid interface formed by a wild type strain of Bacillus subtilis. We have recently discovered the existence of a growth-induced compressive stress present within the biofilm and we have performed mechanical experiments in which Bacillus subtilis pellicles were subjected to elongational deformations using a custom built apparatus while simultaneously tracking the force response and macroscopic structural changes. Overall, our results indicate that we must consider not only the viscoelastic, but also the viscoplastic and mechanically heterogeneous nature of these structures to understand biofilm dispersal and removal.

Hydrophobic Hydration and the Effect of NaCl Salt in the Adsorption of Surfactants on Clathrate Hydrates

Speaker: Felipe Jimenez Angeles
Reservoir Engineering Research Institute

Wednesday, September 20, 2017
11:00a.m. - 12:00p.m.
ME Conference Room – Tech B211

Abstract: Clathrate hydrates are crystalline structures of water forming cages with guest molecules. Adsorption of hydrocarbons and functional molecules on the surface of hydrates is a key in the mechanisms of hydrate inhibition. The thinking in the literature is that hydrocarbons may not adsorb at the hydrate interface, surfactants adsorb through the headgroup, and ionic surfactants adsorb more strongly than non-ionic surfactants. Hydrophobic hydration is the ordering of water molecules around hydrophobic molecules in structures similar to clathrate hydrates. Here we establish a connection between hydrophobic hydration and the affinity of molecules such as n-decane, a non-ionic surfactant, and an ionic surfactant at the surface of hydrates. The hydrophobic hydration is investigated by means of hydrogen bonding and tetra-hedral structure of water. The affinity for the hydrate surface is investigated through the free energy profile of adsorption on the hydrate surface. We observe the molecules that are favor-ably adsorbed on the surface of hydrates induce hydrophobic hydration in the bulk. On the other hand, the hydrophilic ionic surfactants disrupt hydrophobic hydration and are not favora-bly adsorbed on hydrate surfaces. We show that the idea often presented in the literature that the ionic ammonium groups are hydratephilic may not be correct. We also find that salt disrupts the hydrophobic hydration of hydrocarbons and urfactants in the aqueous phase and increases the propensity of these molecules to be adsorbed on hydrate surfaces. We find a major difference in the adsorption of ionic and non-ionic surfactants on hydrate surfaces. The non-ionic surfactants can be adsorbed by headgroup and tail while the ionic surfactants have less affinity for adsorption and cannot adsorb through the head. Our study is performed by means of molecular dynamics and steered simulations.

Salt Entropy Effects on Protein Solubility and the Hofmeister Series

Speaker: Dr. Yuba Dahal
Department of Physics, Kansas State University

Wednesday, June 21, 2017
4:00p.m. - 5:00p.m.
MSE Conference Room – Cook 2058

Past Events

Instabilities at soft interfaces: from elastocapillary snap-through to wetting dynamics on elastomers

Speaker: Aurelie Hourlier-Fargette
PhD student at the Université Pierre et Marie Curie in Paris

Thursday, November 17, 2016
11:00am - 12:00pm
Tech-B211; Mechanical Engineering Conference Room

Abstract: Capillary forces are often too weak to deform a substrate, but are able to dominate elasticity at small scales, on soft materials. A water droplet can interact in a spectacular way with slender flexible structures such as thin elastic sheets or beams, inducing wrinkling, static or dynamic folding, aggregation of fibers, or buckling. On thicker but softer materials, a droplet that does not deform macroscopically the substrate can raise a microscopic ridge at the triple line. 

The role of surface tension in the mechanics of deformable solids is a question raising a growing interest in the soft matter community. In this context, we will present two examples of instabilities featuring liquids on soft materials.

We will begin by revisiting the snap-through instability from an elastocapillary point of view. Snap-through, which is present in systems ranging from carnivorous plants to MEMS, is a well-known phenomenon in solid mechanics: when a buckled elastic beam is subjected to a transverse force, above a critical load value the buckling mode is switched. We show that capillary forces are strong enough to trigger a snap-through instability at small scales, and even counterbalance gravity for a droplet deposited below a downward buckled elastic strip. We investigate the statics and dynamics of this phenomenon, and compare droplet-induced snap-through to dry point force indentation on a buckled thin strip.

In a second part, we will focus on the dynamics of droplet sliding on elastomers. The motion of droplets on stiff surfaces has been investigated for a long time, both experimentally and theoretically, while recent studies have shown the interesting physics underlying the sliding of droplets on soft surfaces. We focus on the dynamics of water-glycerol mixture droplets sliding down vertical plates of commercial silicone elastomers, highlighting an unexpected behavior: the droplet dynamics on such a surface includes two regimes with different constant speeds. Different candidates can be responsible for the sudden speed change: bistability, chemical interaction with the substrate, softness of the material, etc. Our experiments reveal an unexpected link between microscopic phenomena at the scale of the polymer matrix and the macroscopic dynamics of a droplet. 

Short Bio: Aurelie Hourlier-Fargette is a last year PhD student at the Université Pierre et Marie Curie in Paris (Institut Jean Le Rond d’Alembert), and has a teaching position in the Physics Department at the Ecole Normale Supérieure in Paris. Her research interests are mainly experimental soft matter physics, and her PhD work focuses on elastocapillarity and wetting at soft interfaces.

Structure Prediction in Nanoparticle Superlattices

Speaker: Alex Travesset, professor in the Department of Physics and Astronomy at Iowa State University

Date: Friday, July 22, 2016
Time: 11:00am- 12:00pm
Location: Tech, Conference Room L324


Abstract: Materials whose fundamental units are nanoparticles instead of atoms or molecules offer major opportunities to overcome many of the technological challenges of our century. They display unique structures and properties that are not found in other types of materials, usually exhibiting deep underlying geometry and topological constraints. In this talk, I will focus on crystalline assemblies of nanoparticles, i.e. supercrystals. I will discuss the efforts in my group to predict the structure and dynamics of three very successful experimental strategies for the rational design of nanoparticle materials: DNA programmable self-assembly, Evaporation of solvent in nanoparticles with hydrocarbon capping ligands, and more recently, a new technique developed at Ames lab consisting in electrostatic crystallization of nanoparticles with grafted neutral (uncharged) polymers.

Short Bio: Alex Travesset is professor in the Department of Physics and Astronomy at Iowa State University and Associate Research scientist at the Ames Lab. His research interests are in the area of theoretical and computational soft condensed matter. He received his PhD from Universitat de Barcelona and had postdoc positions at Syracuse University and the University of Illinois at Urbana-Champaign.

Shmuel Rubinstein, Ph.D.,
Physics Department, Harvard University

monday, May 23, 2016, 4:00pm,
Tech, ESAM Conference Room M416

Title: The maximally crumpled state: crumpling dynamics and the evolution of damage networks

Engineering Sciences and Applied Mathematics
2145 Sheridan Road, M416, Evanston IL 60208 (847) 491-3345
***Refreshments will be served at 3:30pm in M416***

For further information see

When describing the dynamics of a sheet of paper being crumpled one may be tempted to only take the elastic response of the thin sheet into account and consider only those deformations which minimize the elastic energy of the crumpled sheet. However, most materials yield and deform plastically, leaving permanent scars in the thin sheet. Indeed, the simple process of crumpling a sheet of paper with our hands results in a complex network of interconnected permanent creases of many sizes and orientations, along which the sheet preferentially bends. Thereby, history dependence is introduced into the process. I will present an experimental study of the dynamics of crumpling. Specifically, we investigate how a crease network evolves when a thin elastoplastic sheet is repeatedly crumpled, opened up and then re-crumpled. Is there a maximally crumpled state after which the sheet can be deformed into a sphere without further plastic deformations?

Pedro González Mozuelos, Ph.D., Physics Department, Cinvestav Av. Instituto Poletécnico Nacional

monday, april 18, 2016, 2:00pm, COOK HALL, 2220 CAMPUS DR., ROOM 2058


We discuss the general theory applicable to the determination of the parameters regulating the screened Coulomb interactions among spherical macroions immersed in an electrolyte. This approach comes from implementing the precise methodology of the dressed ion theory to the proper definition of the effective direct correlation functions, which emerge from tracing-out the degrees of freedom of the microscopic ions, and thus provides rigorous definitions for the corresponding screening length, effective permittivity, and renormalized charges. Moreover, it can be profitably employed for precise and reliable calculations of these effective parameters within any practical scheme for the determination of the bulk correlations among the components of an ionic solution.

MONDAY, APRIL 4, 2016, 11:00AM, FORD ITW

Chemical Microswimmers: From Cargo Delivery to Motion Control

Microscopic agents which can self-propel through confined, liquid-filled spaces are envisioned as a key component of future lab-on-a-chip and drug delivery systems. Chemically active Janus colloids offer a realization of such agents. A Janus microswimmer works by catalytically activating, over a fraction of its surface, chemical reactions in the surrounding solution. The resulting anisotropic distribution of reactants and products drives a surface flow in a thin layer surrounding the particle leading to a directed motion. Depending on the systems, various self-propulsion mechanisms emerge such as self-electrophoresis or self-diffusiophoresis. Here only the last mechanism shall be considered.

First, the self-propulsion of a spheroidal particle which is covered by a catalyst over a cap-like region will be discussed. I will describe how the velocity of the particle depends on its shape and on the size of the catalytic cap. Next, I will show how such particles can be used as carriers of microcargo. As a model for a carrier-cargo system, I will consider a microswimmer connected by a thin rod to an inert cargo particle. It turns out that the velocity of such composite strongly depends on the relative orientation of the carrier-cargo link. Accordingly, there is an optimal configuration for the linkage. The subtlety of such carriers is underscored by the observation that a spherical particle completely covered by catalyst, which is motionless when isolated, acts as a carrier once attached to a cargo.

Finally, I will demonstrate that a chemical microswimmer approaching a planar wall reveals novel motion scenarios, including a steady “sliding” at fixed orientation and height above the wall, and motionless steady “hovering”. Hovering particles create recirculating regions of flow, and can be used to mix fluid or to trap other particles.  Sliding states, on the contrary, provide a starting point to engineer a stable and predictable motion of microswimmers. Thus, for topographically patterned walls, novel states of guided motion along the edges of the patterns emerge when the parameters of the microswimmers are such that a sliding state occurs in the absence of the patterns. Such topography-guided states emerge from a complex interplay between chemical activity of the particle, hydrodynamic interactions and the confinement of the chemical and hydrodynamic fields by the topography.

Co-sponsored by CBES 


Co(non)solvency or the puzzle of polymer properties in mixed good or poor solvents

The relation between atomistic structure, architecture, molecular weight and material properties is of basic concern of modern soft matter science. Here computer simulations on different levels of resolution play an increasingly important role. To progress further adaptive schemes are being developed, which allow for a free exchange of particles (atoms, molecules) between the different levels of resolution.                                                                                                                                                       

The extension to open systems MD (grand canonical MD) as well as recent Hamiltonian based molecular dynamics and Monte Carlo adaptive resolution methods will be explained. Typical examples include the solvation of polymers in mixed solvents, especially PNIPAM in water alcohol mixtures, which reveals an interesting coil-globule-coil transition. This conformational transition cannot be explained within the classical Flory-Huggins picture, which is the standard mean field theory for polymer solutions and mixtures. The results point towards a general design of 'smart stimuli responsive polymers'.

This work has been performed in collaboration with D. Mukherji and C. Marques.

M. Praprotnik et al. Ann. Rev. Phys. Chem. 59, (2008)

S. Fritsch et al. Phys. Rev. Lett. 108, 170602 (2012)
R. Potestio et al Phys. Rev. Lett. 110, 108301(2013)
D. Mukherji and K. Kremer Macrom. 46, 9158 (2013)
D. Mukherji, C. M. Marques, K. Kremer, Nat. Comm. 5, 4882 (2014)
D. Mukherji, C. M. Marques, T. Stuehn, K. Kremer, J. Chem. Phys. 142, 114903 (2015)                     

Monday, October 19, 2015, 11:00am  
Cook Hall, 2220 Campus Dr., Room 2058


The effective interactions between charged hydrophilic nanoparticles (CNP) in polyelectrolyte (PE) solutions are computed using a Self-Consistent Field model. The electrostatic interactions are described within the Poisson-Boltzmann approximation. The dielectric constant is chosen to be a function of the local composition of the species. Local PE and CNP’s charges are dependent on the local concentration of ionizable groups and local degrees of dissociation. A hierarchy of two- , three- and multi-body interactions between CNP’s are computed. By reducing interactions to pairwise only one can access the phase diagram of such PE/CNP systems. For such systems only gas and crystal like phases are thermodynamically stable; the fluid-like phase is metastable. MC modelling demonstrates the suppression of the phase segregation by the formation of highly anisotropic clusters of CNPs.

Victor A. Pryamitsyn (born in 1961) obtained his M.S. in Physics in 1984 from Leningrad State University, USSR and PhD in Physics and Mechanics of Polymers in 1987 from the Institute of Macromolecular Compounds, Russian Academy of Sciences. From 2002 to present he has worked as a research associate in the Department of Chemical Engineering of the University of Texas at Austin. Before coming to Texas he was working at the Department of Chemistry and Institute of Theoretical Science at University of Oregon; IRC in Polymer Science and Technology, Department of Physics and Astronomy, University of Leeds, UK; School of Chemistry University of Bristol, UK; Institute of Problems of Mechanical Engineering and Institute of Macromolecular Compounds of Russian Academy of Sciences.

Victor Pryamitsyn

The Geometry and Assembly of the Rough Endoplasmic Reticulum

Jemal Guven

The rough endoplasmic reticulum (RER) is a large intracellular membrane consisting of a number of more or less regular stacks, an architecture that reflects its function as the principal site of protein synthesis within the cell.  Recently it was discovered that adjacent sheets within these stacks are connected by helicoidal ramps.  Guven will argue that stacks are organized about a number of  dipole defects, or “parking garages”, formed by two parallel gently-pitched ramps of opposite chiralities. Viewed more closely, individual sheets are composed of a pair of lipid bilayers enclosing a lumen. Membrane-shaping proteins are concentrated along the bilayer fold which forms the inner boundary of a ramp. These same proteins also play a role in establishing the tubular geometry of the adjoining smooth ER (SER). 

This coincidence suggests a mechanism for parking garage assembly via the nucleation of dipoles at the center of three-way tubular junctions within the SER.