Center for Soft Matter and Biological Physics Friday Discussion Meetings

Spring 2018

Organizer: Vinh Nguyen

These meetings occur on Fridays from 4:00pm to 5:00pm in Robeson 304 (unless otherwise indicated)

January 2018
January 5

Friday 4:00pm
304 Robeson Hall
(poster)

"No CSB Discussion Meeting Scheduled"

Organizer: Vinh Nguyen

January 12

Friday 4:00pm
304 Robeson Hall
(poster)

"No CSB Discussion Meeting Scheduled"

Organizer: Vinh Nguyen

January 19

Friday 4:00pm
304 Robeson Hall
(poster)

"No CSB Discussion Meeting Scheduled"

Organizer: Vinh Nguyen

January 26

Friday 4:00pm
304 Robeson Hall
(poster)

"No CSB Discussion Meeting Scheduled"

Organizer: Vinh Nguyen

February 2018
February 2

Friday 4:00pm
304 Robeson Hall
(poster)

"No CSB Discussion Meeting Scheduled"

Organizer: Vinh Nguyen

February 9

Friday 4:00pm
304 Robeson Hall
(poster)

Jacob Carroll (Department of Physics, Virginia Tech)

"Sparsely Encoding Convolutional Neural Networks II"

Neural networks are a family of models that range from the biologically inspired recurrent networks that serve as models of the brain, to the feed-forward, deep-learning networks that have been at the forefront of machine learning in recent years. This talk will continue to introduce a specific type of neural network that while biologically inspired, has been developed for the purpose of machine learning and computer science: the sparsely encoding convolutional neural network. This talk will explain how these systems are used for imaged denoising, and how finite size scaling was observed in these networks as they denoised images across many different values of sparsity. This finite size scaling implies that these systems undergo a continuous as sparsity is varied.

Organizer: Vinh Nguyen

February 16

Friday 4:00pm
304 Robeson Hall
(poster)

Priyanka (Department of Physics, Virginia Tech)

"Study of anomalous behavior in one-dimensional harmonic system"

I will start with some theoretical models which have been developed to understand the violation of Fourier's Law in the lower dimension. Anomalous transport, nonlinear temperature profile etc, are the key feature of these model. In detail, I will talk about one of these models (harmonic chain with volume exchange) and present some its analytical and numerical results. I will present exact expression of two-point function in a stationary state and also shows that the dynamics are governed by fractional Laplacian.

Organizer: Vinh Nguyen

February 23

Friday 4:00pm
304 Robeson Hall
(poster)

Weigang Liu (Department of Physics, Virginia Tech)

"A numerical study of the two-dimensional complex Ginzburg-Landau equation"

The complex Ginzburg-Landau equation with additive noise is a stochastic partial differential equation that describes a remarkably wide range of physical systems: coupled non-linear oscillators subject to external noise near a Hopf bifurcation instability; spontaneous structure formation in non-equilibrium systems, e.g., in cyclically competing populations; and driven-dissipative Bose-Einstein condensation, realized in open systems on the interface of quantum optics and many-body physics. We employ a finite-difference method to numerically solve the noisy complex Ginzburg-Landau equation on a two-dimensional domain with the goal to investigate the coarsening dynamics following a quench from a strongly fluctuating defect turbulence phase to a long-range ordered phase. We start from a simplified amplitude equation, solve it numerically, and then study the spatio-temporal behavior characterized by the spontaneous creation and annihilation of topological defects (spiral waves). We check our simulation results against the known dynamical phase diagram in this non-equilibrium system, tentatively analyze the coarsening kinetics following sudden quenches between different phases, and have begun to characterize the ensuing aging scaling behavior.

Organizer: Vinh Nguyen

March 2018
March 2

Friday 4:00pm
304 Robeson Hall
(poster)

Physics Faculty Meeting (No CSMB Discussion Meeting)

Organizer: Vinh Nguyen

March 9

Friday 4:00pm
304 Robeson Hall
(poster)

"Spring Break" (No CSB Discussion Meeting Scheduled)

Organizer: Vinh Nguyen

March 16

Friday 4:00pm
304 Robeson Hall
(poster)

CSB Faculty Meeting (No CSMB Discussion Meeting)

Organizer: Vinh Nguyen

March 23

Friday 4:00pm
304 Robeson Hall
(poster)

Ali Charkhesht (Department of Physics, Virginia Tech)

"Probing Collective Motions of Proteins and Hydration Dynamics by a Wide Range Dielectric Spectroscopy"

Studying dynamics of proteins in their biological milieu such as water is interesting because of their strong absorption in the terahertz range that contain information on their global and sub-global collective vibrational modes (conformational dynamics) and global dynamical correlations among solvent water molecules and proteins. In addition, water molecules dynamics within protein solvation layers play a major role in enzyme activity. However, due to the strong absorption of water in the gigahertz-to-terahertz frequencies, it is challenging to study properties of the solvent dynamics as well as conformational changes protein in water. In response, we have developed a highly sensitive megahertz-to-terahertz dielectric spectroscopy system to probe the hydration shells as well as large-scale dynamics of these biomolecules. . Thereby, we have deduced the conformation flexibility of proteins and compare the hydration dynamics around proteins to understand the effects of surface-mediated solvent dynamics, relationships among different measures of interfacial solvent dynamics, and protein-mediated solvent dynamics based on the complex dielectric response from 50 MHz up to 2 THz by using the system we developed. Comparing these assets of various proteins in different classes helps us shed light on the macromolecular dynamics in a biologically relevant water environment.

Organizer: Vinh Nguyen

March 30

Friday 4:00pm
304 Robeson Hall
(poster)

Physics Faculty Meeting (No CSMB Discussion Meeting)

Organizer: Vinh Nguyen

April 2018
April 6

Friday 4:00pm
304 Robeson Hall
(poster)

Physics Faculty Meeting (No CSMB Discussion Meeting)

Organizer: Vinh Nguyen

April 13

Friday 4:00pm
304 Robeson Hall
(poster)

Riya Nandi (Department of Physics, Virginia Tech)

"Short-Time Dynamics of Three-Dimensional Magnetic Systems with Heisenberg Interaction"

This project aims to explore the initial relaxation dynamics of Heisenberg ferro and anti-ferromagnets. It involves a new simulation technique of combining reversible mode coupling dynamics with the simple diffusive relaxation dynamics in order to obtain the correct dynamic exponent and identify the correct universality class. The system undergoes critical aging and relevant exponents identified. Finally, for a system with non-conserved order-parameter, i.e., the anti-ferromagnet, theory predicts non-universal initial slip exponent. This work aims to study its dependence on the width of the initial distribution of the conserved quantities. This is a work in progress, at best just beginning to show promising results.

Organizer: Vinh Nguyen

April 20

Friday 4:00pm
304 Robeson Hall
(poster)

Physics Faculty Meeting (No CSMB Discussion Meeting)

Organizer: Vinh Nguyen

April 27

Friday 4:00pm
304 Robeson Hall
(poster)

Physics Faculty Meeting (No CSMB Discussion Meeting)

Organizer: Vinh Nguyen

May 2018
May 4

Friday 4:00pm
304 Robeson Hall
(poster)

Exam Week (No CSMB Discussion Meeting)

Organizer: Vinh Nguyen

Center for Soft Matter and Biological Physics Friday Discussion Meetings

Fall 2017

Organizer: Vinh Nguyen

These meetings occur on Fridays from 4:00pm to 5:00pm in Robeson 304 (unless otherwise indicated)

September 2017
September 1

Friday 4:00pm
304 Robeson Hall

Physics Department Faculty Meeting. No talk scheduled.

September 8

Friday 4:00pm
304 Robeson Hall

CSB Center Meeting. No talk scheduled.

September 15

Friday 4:00pm
304 Robeson Hall

Discussion with Prof. Nigel Goldenfeld (J. Mark Sowers Distinguished Speaker)

Organizer: Uwe Täuber

September 22

Friday 4:00pm
304 Robeson Hall

Physics Department Faculty Meeting. No talk scheduled.

September 29

Friday 4:00pm
304 Robeson Hall

No talk scheduled.

Organizer: Vinh Nguyen

October 2017
October 6

Friday 4:00pm
304 Robeson Hall

No talk scheduled

October 13

Friday 4:00pm
304 Robeson Hall

Fall Break. No talk scheduled.

October 20

Friday 4:00pm
304 Robeson Hall

Physics Department Faculty Meeting. No talk scheduled

Organizer: Vinh Nguyen

October 27

Friday 4:00pm
304 Robeson Hall

(poster)

Jacob Carroll  (Department of Physics, Virginia Tech)

Topic: Sparsely Encoding Convolutional Neural Networks I

Neural networks are a family of models that range from the biologically inspired recurrent networks that serve as models of the brain, to the feed-forward, deep-learning networks that have been at the forefront of machine learning in recent years. This talk will introduce a specific type of neural network, that while biologically inspired, has been developed for the purpose of machine learning and computer science: the sparsely encoding convolutional neural network. This talk will explain this model in detail, and will serve as the basis for a second talk in January that will explore observed finite-size scaling in these sparsely encoding convolutional neural networks.

Organizer: Vinh Nguyen

November 2017
November 3

Friday 4:00pm
304 Robeson Hall

(poster)

Yanfei Tang   (Department of Physics, Virginia Tech)

Topic: Young-Laplace Equation

Organizer: Vinh Nguyen

November 10

Friday 4:00pm
304 Robeson Hall

(poster)

Prof. Hildegard Meyer-Ortmanns (Jacob University Bremen, Germany)

Topic: ABOUT INTERESTING CYCLES IN OSCILLATORY SYSTEMS AND IN GAMES OF WINNERLESS COMPETITION

Upon identifying physical aging in oscillatory systems we discovered two interesting phenomena in a system of repulsively coupled Kuramoto oscillators, which have a rather rich attractor space. One is the emergence of long-period orbits, whose periods are orders of magnitude longer than the period of individual oscillators. The cycles here consist of repeating temporary patterns of phase-locked motion. The other phenomenon refers to the self-similarity of these cycles, when the strength of deviations from a uniform natural frequency distribution is appropriately tuned. In connection with winnerless games of competition we search for heteroclinic cycles that are supposed to be responsible for spiral pattern formation and even hierarchies of spirals, when these games are placed on a spatial grid. Here we indicate ongoing work.

Organizer: Vinh Nguyen

November 17

Friday 4:00pm
304 Robeson Hall

Physics Department Faculty Meeting. No talk scheduled

Organizer: Vinh Nguyen

November 24

Friday 4:00pm
304 Robeson Hall

Thanksgiving Holiday. No talk scheduled.

December 2017
December 1

Friday 4:00pm
304 Robeson Hall

Chengyuan Wen (Department of Physics, Virginia Tech)

Topic: Evaporation of Liquids

Organizer: Vinh Nguyen

December 8

Friday 4:00pm
304 Robeson Hall

(Department of Physics, Virginia Tech)

Talked Canceled and Rescheduled for Future

Organizer: Vinh Nguyen

   

Center for Soft Matter and Biological Physics Summer Discussion Meetings

Summer 2017

These meetings occur on Fridays from 1:30pm to 2:30pm in Robeson 304 (unless otherwise indicated)

< 2016 | May | June | July | August | 2018 >

May 2017
May 26

Friday 1:30pm
304 Robeson Hall
 

No talk scheduled.

June 2017
June 2

Friday 1:30pm
304 Robeson Hall

CSB Seminar
Prof. P. S. Krishnaprasad   (University of Maryland)

Topic: Subriemannian geometry and finite time thermodynamics

Subriemannian geometry has its roots in optimal control problems. The Caratheodory-Chow-Rashevskii theorem on accessibility also places the subject in contact with an axiomatic approach to macroscopic thermodynamics. Explicit integrability of optimal control problems in this context is of interest. As in the case for integrability questions in mechanics, here too symmetries and conservation laws have a key role. In this talk we discuss model problems and results pertaining to such questions in isolated systems and ensembles of interacting systems. Of special interest is the problem of determining thermodynamic cycles that draw useful work from fluctuations. This work is in collaboration with PhD student Yunlong Huang, and Dr. Eric Justh of the Naval Research Laboratory.

Organizers: Vinh Nguyen

June 9

Friday 1:30pm
304 Robeson Hall
Wen Xiong   (Dept. of Biological Sciences, Virginia Tech)

Topic: Structural and functional basis of alternative endosomal ESCRT-0 protein complexes

Early endosomes represent the first sorting station for vesicular ubiquitylated cargo. Cargo transport is mediated by the endosomal sorting complex required for transport (ESCRT) machinery. Similar to the structural organization of ESCRT-0 proteins, alternative ESCRT-0 (alt-ESCRT- 0) proteins, such as Tollip and Tom1, also present multiple ubiquitin-binding domains, including the C2 and CUE (Tollip) and VHS and GAT (Tom1) domains. Tollip localizes the Tollip-Tom1 complex at endosomal compartments by association with phosphatidylinositol 3-phosphate (PtdIns(3)P) through its central C2 domain. Tom1, through its GAT domain, is recruited to endosomes by binding to Tollip's Tom1-binding domain (TBD) through an unknown mechanism. Our NMR data revealed that Tollip TBD is a natively unfolded domain that partially folds at its N-terminus when bound to the first two helices of the Tom1 GAT domain through high affinity hydrophobic contacts. Furthermore, this association abrogates binding of Tollip to PtdIns(3)P by additionally targeting its C2 domain. Binding of the Tollip C2 domain is mediated by the third helix of the Tom1 GAT domain. We propose that association with Tom1 favors Tollip's release from endosomal membranes, allowing Tollip to commit to cargo trafficking. To directly test the ability of Tom1-Tollip complexes to bind ubiquitinated cargo within a lipid bilayer, a system was developed to measure the distribution of an ubiquitin-conjugated substrate at nanometer-scale resolution using AFM so as to clarify the formation mechanism of Tom1-Tollip complex in the absence and presence of monoubiquitin and polyubiquitin chains, and the modulatory role of PtdIns(3)P. Also, we identified a conserved central hydrophobic patch at the ubiquitin surface to be the binding site for the Tom1 VHS domain. The ubiquitin hydrophobic patch is also involved in Tom1 GAT domain binding, suggesting that Tom1 can bind ubiquitin molecules through two independent sites.

Organizers: Vinh Nguyen

June 16

Friday 1:30pm
1028 Pamplin Hall
Udaya Sree Datla and Sheng Chen   (Dept. of Physics, Virginia Tech)

Topic: The spatiotemporal network dynamics of acquired resistance in engineered microecological systems

Organizers: Vinh Nguyen

June 23

Friday 1:30pm
304 Robeson Hall
Chuanhui Chen   (Dept. of Physics, Virginia Tech)

Topic: Scanning probe Microscopy Study of Molecular Nanostructures on 2D Materials

Nanostructures self-assembled from molecules adsorbed on emerging two-dimensional (2D) materials confer physical and chemical properties desirable for potential applications in photovoltaics, electronics and quantum information. In this talk, I will present our scanning tunneling microscopy (STM) study of temperature evolution of quasi-one dimensional (1D) C60 nanostructures on rippled graphene. We demonstrated that C60 molecules can be arranged into a quasi-1D chain structure through careful control of the subtle balance between the linear periodic potential of rippled graphene and the C60 surface mobility, which can transition to a more compact hexagonal close packed stripe structure by annealing at a higher temperature. I will also present the formation of sub-monolayer C60 and perylenetetracarboxylic dianhydride (PTCDA) on graphene wrinkles. Beyond graphene, I will briefly discuss our STM investigation on few-layer molybdenum disulfide (MoS2) and liquid-cell atomic force microscopy (AFM) study of Toll interacting protein (Tollip) on a lipid membrane.

Organizers: Vinh Nguyen

June 30

Friday 1:30pm
304 Robeson Hall
Wei Song   (Dept. of Biological Sciences, Virginia Tech)

Topic: Design of a Disabled-2-derived peptide to impair platelet-mediated cancer cell extravasation

Disabled-2 (Dab2) targets membranes and triggers a wide range of biological events, including endocytosis and platelet aggregation. Dab2, through its phosphotyrosine-binding (PTB) domain, inhibits platelet aggregation by competing with fibrinogen for ?IIb?3 integrin receptor binding. We have shown that the N-terminal region, including the PTB domain (N-PTB), drives Dab2 to the platelet membrane surface by binding to sulfatides through two sulfatide-binding motifs (SBM), modulating the extent of platelet aggregation. SBM peptide contains two helices when embedded in dodecylphosphocholine micelles, reversibly binds to sulfatides with moderate affinity, lies parallel to the micelle surface, and when added to a platelet mixture, reduces the number and size of sulfatide-induced aggregates. Moreover, tumor cells are reported to have the ability of aggregating platelets, which occurs following tumor cell intravasation into the vasculature, thereby facilitating tumor cell migration, invasion and arrest within the vasculature. Contributions of platelets aggregation to tumor cell survival and spread suggest platelets as a new avenue for therapy. Overall, our findings identify and structurally characterize a minimal region in Dab2 that modulates platelet homotypic interactions, all of which provide the foundation for rational design of a new generation of anti-aggregatory peptide for therapeutic purposes of cancer.

Organizers: Vinh Nguyen

July 2017
July 7

Friday 1:30pm
304 Robeson Hall
Prof. Shengfeng Cheng   (Dept. of Physics, Virginia Tech)

Topic: Evaporation as a Phenomenon and a Tool

Organizers: Vinh Nguyen

July 14

Friday 1:30pm
304 Robeson Hall
Shadi Sadat Esmaeili   (Dept. of Physics, Virginia Tech)

Topic: Breaking of Time Translation Invariance in Kuramoto Dynamics

We identify the breaking of time-translation invariance in a deterministic system of repulsively coupled Kuramoto oscillators, which are exposed to a distribution of natural frequencies. We consider grid sizes with different characteristics of the attractor space, which is by construction quite rich. This may cause long transients until the deterministic trajectories find their stationary orbits. The stationary orbits are limit cycles with periods that extend over orders of magnitude. It is the long transient times that cause the breaking of time-translation invariance in autocorrelation functions of oscillator phases. This feature disappears close to the transition to the monostable phase, where the phase trajectories are just irregular and no stationary behavior can be identified.

Organizers: Vinh Nguyen

July 21

Friday 1:30pm
304 Robeson Hall
Harmeet Singh  (Dept. Engineering Mechanics, Virginia Tedh)

Geometric singularities in the mechanics of strings and rods

We will discuss propagating geometric discontinuities in one-dimensional bodies, particularly those mediated by partial contact with obstacles that may serve as singular sources of momentum and energy. Invariance arguments and basic assumptions about contact interactions reveal counterintuitive behavior during pick-up, lay-down, impact, peeling, and other processes. Related phenomena can be found in string instruments, mooring lines, and many other systems.

Organizers: Vinh Nguyen

July 28

Friday 1:30pm
304 Robeson Hall
 

No talk scheduled.

August 2017
August 4

Friday 1:30pm
304 Robeson Hall
 

No talk scheduled.

August 11

Friday 1:30pm
304 Robeson Hall
Laura Hanzly   (Dept. of Biological Systems Engineering, Virginia Tech)

Topic: Protein Nanoscale Self-Assembly and Nanofiller Applications

Proteins can easily be manipulated to suite a variety of applications. Proteins have the capability of forming macroscopic structures as well as the ability to assemble on the nanoscale. Here, the modification and nanoscale self-assembly of the protein wheat gluten will be discussed. Interesting effects on the kinetics of self-assembly are observed when wheat gluten is assembled in mediums other than pure water. Practical applications for wheat gluten as a nanofiller in materials such as synthetic rubber are currently being investigated.

Organizers: Vinh Nguyen

August 18

Friday 1:30pm
1028 Pamplin Hall

CSB Steering Committee Meeting. No talk scheduled.

August 25

Friday 1:30pm
304 Robeson Hall
Parviz Seifpanahi Shabane   (Dept. of Physics, Virginia Tech)

Topic: Intrinsically Disordered Proteins -- What do they look like?

Organizers: Vinh Nguyen

   
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Center for Soft Matter and Biological Physics Friday Discussion Meetings

Spring 2017

Organizer: Vinh Nguyen

These meetings occur on Fridays from 4:00pm to 5:00pm in Robeson 304 (unless otherwise indicated)

January 2017
January 20

Friday 4:00pm
304 Robeson Hall

Faculty search event. No talk scheduled.

January 27

Friday 4:00pm
304 Robeson Hall

Faculty search event. No talk scheduled.

February 2017
February 3

Friday 4:00pm
304 Robeson Hall

Faculty search event. No talk scheduled.

February 10

Friday 4:00pm
304 Robeson Hall

Faculty search event. No talk scheduled.

February 17

Friday 4:00pm
304 Robeson Hall

Faculty search event. No talk scheduled.

February 24

Friday 4:00pm
304 Robeson Hall

Faculty search event. No talk scheduled.

March 2017
March 3

Friday 4:00pm
304 Robeson Hall

Faculty meeting. No talk scheduled.

March 10

Friday 4:00pm
304 Robeson Hall

Spring Break. No talk scheduled.

March 17

Friday 4:00pm
304 Robeson Hall

APS March Meeting. No talk scheduled.

March 24

Friday 4:00pm
304 Robeson Hall
Sheng Chen (Dept. of Physics, Virginia Tech)

Topic: Computational study of biodiversity with evolution and natural selection

Organizers: Vinh Nguyen and Will Mather

March 31

Friday 4:00pm
304 Robeson Hall
Heather Deter (Dept. of Physics, Virginia Tech)

Topic: Big data analysis of differential production within toxi-antitoxin systems

Organizers: Vinh Nguyen and Will Mather

April 2017
April 7

Friday 4:00pm
304 Robeson Hall

Special talk in engineering. No CSB talk scheduled.

April 14

Friday 4:00pm
304 Robeson Hall
William Ducker (Dept. of Chemical Engineering, Virginia Tech)

Topic: Micrometer-sized spheres driven into crystalline array by simple simple rubbing

Organizers: Vinh Nguyen and Will Mather

April 21

Friday 4:00pm
304 Robeson Hall

No talk scheduled.

Organizers: Vinh Nguyen and Will Mather

April 28

Friday 4:00pm
304 Robeson Hall

Faculty Meeting, No CSB Talk Scheduled

May 2017
May 5

Friday 4:00pm
304 Robeson Hall

Exam week. No CSB talk scheduled.

   

Center for Soft Matter and Biological Physics Friday Discussion Meetings

Fall 2016

Organizer: Vinh Nguyen

These meetings occur on Fridays from 4:00pm to 5:00pm in Robeson 304 (unless otherwise indicated)

August 2016
August 26

Friday 4:00pm
304 Robeson Hall

Physics Department Faculty Meeting. No talk scheduled.

September 2016
September 2

Friday 4:00pm
304 Robeson Hall

No talk scheduled.

September 9

Friday 4:00pm
304 Robeson Hall
Udaya Sree Datla (Virginia Tech)

Topic: Evolutionary dynamics in synthetic predator-prey ecologies

Organizers: Vinh Nguyen and Will Mather

September 16

Friday 4:00pm
304 Robeson Hall

Talk cancelled.

September 23

Friday 4:00pm
304 Robeson Hall
Prudvi Gaddam (Dept. of Chemical Engineering, Virginia Tech)

Topic: A liquid state thermal diode

Organizers: Vinh Nguyen and Will Mather

September 30

Friday 4:00pm
304 Robeson Hall
William Mather

Topic: Modeling Gene Networks

Organizers: Vinh Nguyen and Will Mather

October 2016
October 7

Friday 4:00pm
304 Robeson Hall

No talk scheduled.

October 14

Friday 4:00pm
304 Robeson Hall

Fall Break. No talk scheduled.

October 21

Friday 4:00pm
304 Robeson Hall

CSB Center Faculty Meeting. No talk scheduled.

October 28

Friday 4:00pm
304 Robeson Hall
Harshwardhan Chaturvedi   (Dept. of Physics, Virginia Tech)

Topic: Flux Lines in Superconductors: Planar Defects and Beyond

Organizers: Vinh Nguyen and Will Mather

November 2016
November 4

Friday 4:00pm
304 Robeson Hall
Chola Regmi   (Dept. of Physics, Virginia Tech)

Topic: Tubulin binding energies from all-atom molecular dynamics simulations

Organizers: Vinh Nguyen and Will Mather

November 11

Friday 4:00pm
304 Robeson Hall

83rd Annual Meeting of the APS Southeastern Section. No talk scheduled.

November 18

Friday 4:00pm
304 Robeson Hall

Physics Department Faculty Meeting. No talk scheduled.

November 25

Friday 4:00pm
304 Robeson Hall

Thanksgiving Holiday. No talk scheduled.

December 2016
December 2

Friday 4:00pm
304 Robeson Hall

(poster)

Bart Brown (Dept. Physics, Virginia Tech)

Topic: Noncyclic interactions: games within games

Cyclic predator prey games can create complex patterns in space and time such as domains and propagating spirals from simple microscopic rules. The coexistence of domains and spirals has been observed in a cyclic six species game where each species preys upon three others. This game is of particular interest as it exhibits the dynamical generation of multiple space and time scales. In this work we explore different interaction schemes to investigate the effects of these different scales on the patterns produced by the system and introduce a new non-cyclic game of nine species which produces spirals within spirals.

Organizers: Vinh Nguyen and Will Mather

   

Center for Soft Matter and Biological Physics Friday Discussion Meetings

Summer 2016

Organizer: Vinh Nguyen

These meetings occur on Fridays from 4:00pm to 5:00pm in Robeson 304 (unless otherwise indicated)

May 2016
May 23

Monday 1:30pm
304 Robeson Hall
Ali Charkhesht and Vinh Nguyen   (Dept. of Physics, Virginia Tech)

Topic: Protein hydration and dynamics

Organizers: Vinh Nguyen and Will Mather

May 30

Monday 1:30pm
304 Robeson Hall
 

Memorial Day. No meeting scheduled.

Organizers: Vinh Nguyen and Will Mather

June 2016
June 6

Monday 1:30pm
304 Robeson Hall
Steve Melville   (Dept. of Biological Sciences, Virginia Tech)

Topic: How do you pull a hydrophobic protein out of a membrane and put it in a fiber 1,000 times per second?

Organizers: Vinh Nguyen and Will Mather

June 13

Monday 1:30pm
304 Robeson Hall
Will Mather   (Dept. of Physics, Virginia Tech)

Topic: Whither noise? A discussion concerning the utility of stochastic modeling for cellular networks.

Biology is in the middle of a mathematical revolution, where quantitative models for complex biological systems are increasingly being used to detangle underlying molecular mechanisms. My presentation will first provide a general introduction for non-experts concerning the application of these mathematical models, and in short time, I will discuss the usefulness of stochastic (probabilistic) modeling for cellular systems. My claim is that nearly all single cell phenomena are noisy, but it is not immediately clear that the added workload required to pursue stochastic modeling ultimately pays off. I will provide supporting evidence (with caveats) in favor of this approach, which will serve as a launching pad for discussion.

Organizers: Vinh Nguyen and Will Mather

June 20

Monday 1:30pm
304 Robeson Hall
David Popham   (Dept. of Biological Sciences, Virginia Tech)

Topic: Water and solutes in bacterial spores: Effects on protein and lipid mobility

Organizers: Vinh Nguyen and Will Mather

June 27

Monday 1:30pm
304 Robeson Hall
Alexey Onufriev   (Dept. of Computer Science, Virginia Tech)

Topic: Existing water models for atomistic modeling: the bad and the ugly

Organizers: Vinh Nguyen and Will Mather

July 2016
July 4

Monday 1:30pm
304 Robeson Hall
 

Independence Day. No meeting scheduled.

Organizers: Vinh Nguyen and Will Mather

July 11

Monday 1:30pm
304 Robeson Hall
 

No meeting scheduled.

Organizers: Vinh Nguyen and Will Mather

July 18

Monday 1:30pm
304 Robeson Hall
 

No meeting scheduled.

Organizers: Vinh Nguyen and Will Mather

July 25

Monday 1:30pm
304 Robeson Hall
Justin Barone   (Dept. of Biological Systems Engineering, Virginia Tech)

Topic: Protein amyloid self-assembly

Organizers: Vinh Nguyen and Will Mather

August 2016
August 1

Monday 1:30pm
304 Robeson Hall
Shihoko Kojima   (Dept. of Biological Sciences, Virginia Tech)

Topic: Oscillators from nature - circadian clocks

Organizers: Vinh Nguyen and Will Mather

August 8

Monday 1:30pm
304 Robeson Hall
Will Mather   (Dept. of Physics, Virginia Tech)

Topic: Machine Learning, with Image Analysis in Fiji as an Example

Organizers: Vinh Nguyen and Will Mather

   
Center for Soft Matter and Biological Physics Seminars

Spring 2018

Organizer: Vinh Nguyen

These meetings occur on Mondays from 4:00pm to 5:00pm in Robeson 304.
Refreshments are served before the semnars (unless otherwise indicated)

January 2018
January 15

Monday 4:00pm
304 Robeson Hall
(poster)

Martin Luther King Holiday. No Seminar Scheduled.

January 22

Monday 4:00pm
304 Robeson Hall
(poster)

Physics Faculty Search. No CSB Seminar Scheduled

January 29

Monday 4:00pm
304 Robeson Hall
(poster)

Physics Faculty Search. No CSB Seminar Scheduled.

February 2018
February 5

Monday 4:00pm
304 Robeson Hall
(poster)

Physics Faculty Search. No CSB Seminar Scheduled

February 12

Monday 4:00pm
304 Robeson Hall
(poster)

Physics Faculty Search. No CSB Seminar Scheduled.<./b>

February 19

Monday 4:00pm
304 Robeson Hall
Joint CM Seminar
(poster)

Dr. Michael Cooney ( NASA Langley Research Center )

MEDLI2, ARCSTONE and Broadband Photodetectors for measuring radiative flux

Dr. Michael Cooney engineer in the Electronic Systems Branch, will discuss three projects he currently supports. The first is a space flight project, the Mars Entry Descent and Landing Instrumentation 2 (MEDLI2). MEDLI2 will extend and enhance the dataset from the MEDLI mission, which flew on the Mars Science Laboratory (MSL) in 2012 and was the first instrument to characterize Mars’ aero-thermal environment. MEDLI2 is scheduled to fly on the MARS 2020 mission. The second project is ARCSTONE, a lunar spectral reflectance instrument in response to the 2007 and 2017 Earth Science Decadal Surveys. Instrument intercalibration is a vital tool to maintain consistent datasets across various instruments and ensure historical continuity. The Moon is considered to be an excellent exoatmospheric calibration source, however the accuracy of the Moon as an absolute reference is limited to 5-10%. An orbiting spectrometer flying on a small satellite in low Earth orbit will provide lunar spectral reflectance with accuracy sufficient to establish an SI-traceable absolute lunar calibration standard for past, current, and future Earth weather and climate sensors. The final project is a research activity in partnership with Virginia Tech to develop broadband photodetectors for measuring radiative flux in response to the Earth Science Decadal survey. Existing Earth science radiation budget instruments rely on radiometers with relatively difficult custom manufacturing processes and slow readout speed. To provide a lower cost future mission options, photon based photosensors have the possibility to lower mission cost while enabling new mission architectures.

Host: Vinh Nguyen

February 19

Monday 5:00pm
304 Robeson Hall
Special Seminar
(poster)

Dr. Michael Cooney ( NASA Langley Research Center )

Job/Internship Possibilities at NASA Langley

Host: Vinh Nguyen

February 26

Monday 4:00pm
304 Robeson Hall
CM Seminar Only
(poster)

Prof. Sumanta Tewari (Clemson University)

"TBD"

Host: Ed Barnes

March 2018
March 5

Monday 4:00pm
304 Robeson Hall
(poster)

Spring Break Week and APS March Meeting. No Seminar Scheduled.

March 12

Monday 4:00pm
"Canceled and Rescheduled"
Joint CM Seminar
(poster)

Weigang Liu (Department of Physics, Virginia Tech)

"A study of the complex Ginzburg-Landau equation: analytical and numerical results"

Rescheduled for March 14, 2018

Host: Uwe Tauber

March 14

Wednesday 4:00pm
400 Hahn Hall, North
Joint CM Seminar
(poster)

Weigang Liu (Department of Physics, Virginia Tech)

"A study of the complex Ginzburg-Landau equation: analytical and numerical results"

The complex Ginzburg-Landau equation (CGLe) is a stochastic partial differential equation that describes a remarkably wide range of physical systems: coupled non-linear oscillators subject to external noise near a Hopf bifurcation instability; spontaneous structure formation in non-equilibrium systems, e.g., in cyclically competing populations; and driven-dissipative Bose-Einstein condensation, realized in open systems on the interface of quantum optics and many-body physics. We employ the perturbative field-theoretic renormalization group method to analytically investigate the universal critical behavior near the continuous non-equilibrium phase transition in the complex Ginzburg–Landau equation with additive white noise. We show that to first order in the dimensional expansion about the upper critical dimension, the initial-slip exponent in the complex Ginzburg–Landau equation is identical to its equilibrium model A counterpart. In our second project, we have employed a finite-difference method to numerically solve the noisy complex Ginzburg-Landau equation on a two-dimensional domain with the goal to investigate the coarsening dynamics following a quench from a strongly fluctuating defect turbulence regime to a long-range ordered phase. We study the spatio-temporal behavior characterized by the spontaneous creation and annihilation of topological defects (spiral waves). We check our simulation results against the known dynamical phase diagram in this non-equilibrium system, tentatively analyze the coarsening kinetics following sudden quenches between different phases, and have begun to characterize the ensuing aging scaling behavior. Moreover, we are currently extracting the activation energy barrier for the nucleation process of the stable spiral wave structures.

Host: Uwe Tauber

March 19

Monday 4:00pm
304 Robeson Hall
Joint CM Seminar
(poster)

Chengyuan Wen (Department of Physics, Virginia Tech)

"Evaporation of Liquids and Solutions"

Evaporation of a liquid is a ubiquitous phenomenon. It drives the water cycle and can be used for cooling. It is also a useful tool for materials fabrication such as evaporation-induced self-assembly of colloidal particles and thin-film deposition via spin coating. In the first part of this talk, we will present million-atom scale molecular dynamics (MD) simulations of the evaporation process of water. An enhancement of water density near the liquid-vapor interface is found during fast evaporation. The temperature profiles based on both translational and rotational degrees of freedom are calculated at different stages of evaporation and evaporative cooling of the liquid-vapor interface is observed, which accounts for the higher water density at the interface. The velocity distribution of water molecules in the vapor phase during evaporation is also computed at various distances relative to the interface and fit to the Maxwell-Boltzmann distribution. Results indicate that local thermal equilibrium holds in the liquid phase, though the whole system is driven out of equilibrium. In the second part of this talk, we will focus on evaporating behavior of polymer solutions. In particular, polyelectrolyte solutions show rich physical behavior because of electrostatic interactions. We use MD simulations to study the evaporation of a solution of polyanionic chains (sodium polystyrene sulfonate). The polymers are represented by MARTINI-type bead-spring chains. Water is included as an explicit solvent and described with a model taking into account polarization effects. Counterions and salts are also explicitly included as mobile single beads. Our results show that the polyelectrolyte chains form layered structures with alternating polymer-rich and counterion-rich layers, indicating that one-pot evaporation technique may be developed to fabricate multilayer polyelectrolyte films that are currently mainly produced via a layer-by-layer deposition process. We will discuss the effects of polymer concentration, salt concentration, and evaporation rate on the structure of the resulting film. Finally, we will also briefly discuss our recent study of the evaporation of polymer solutions containing both polyanionic and polycationic chains.

Host: Shengfeng Cheng

March 26

Monday 4:00pm
304 Robeson Hall
Joint CM Seminar
(poster)

Xiangwen Wang (Department of Physics, Virginia Tech)

"Data-driven modeling of heavy-tailed distributions and scaling laws in human dynamics"

Studying human behavior is of fundamental importance in many social applications. Yet, it remains a challenging problem due to the high complexity of human activities. In recent years, advances in information technology have resulted in the collection of vast amounts of human activity logs, thus enabling the quantitative modeling of human behavior. Using a variety of metrics like probability distributions, we prove the wide existence of heavy-tailed distributions and scaling laws in human behavior. In human online searches we describe the search behavior as a foraging process that takes place on the semi-infinite line. A pairwise power-law distribution respectively exponential distribution is reported for step-lengths in long-range respectively short-range displacements, indicating that the search process is a combination of Brownian-motion local phases and truncated-Levy-flight relocation phases. These results are confirmed through the analysis of mean squared displacements. In human online gambling, we view the net change of income of each player as a random walk and find that the win/loss distributions follow power laws with exponential cut-offs. The mean squared displacement of these net income random walks exhibits a transition between a super-diffusive and a diffusive regime. We present a model that allows to reproduce this behavior and identify the key features needed for observing this transition. For human movements in both real and virtual spaces, heavy-tailed step-lengths are also reported.

Host: Michel Pleimling

April 2018
April 2

Monday 4:00pm
304 Robeson Hall
Joint CM Seminar
(poster)

Ali Charkhesht (Department of Physcis, Virginia Tech)

"Probing collective motions and hydration dynamics of bio-molecules"

Studying dynamics of proteins in their biological milieu such as water is interesting because of their strong absorption in the terahertz range that contain information on their global and sub-global collective vibrational modes (conformational dynamics) and global dynamical correlations among solvent water molecules and proteins. In addition, water molecules dynamics within protein solvation layers play a major role in enzyme activity. However, due to the strong absorption of water in the gigahertz-to-terahertz frequencies, it is challenging to study properties of the solvent dynamics as well as conformational changes protein in water. In response, we have developed a highly sensitive megahertz-to-terahertz dielectric spectroscopy system to probe the hydration shells as well as large-scale dynamics of these biomolecules. . Thereby, we have deduced the conformation flexibility of proteins and compare the hydration dynamics around proteins to understand the effects of surface-mediated solvent dynamics, relationships among different measures of interfacial solvent dynamics, and protein-mediated solvent dynamics based on the complex dielectric response from 50 MHz up to 2 THz by using the system we developed. Comparing these assets of various proteins in different classes helps us shed light on the macromolecular dynamics in a biologically relevant water environment.

Host: Vinh Nguyen

April 6

"Special Seminar"
Friday, 2:30pm
210 Robeson Hall
Colloquium
(poster)

Prof. Jeff Chen (Department of Physics & Astronomy, University of Waterloo)

"The Onsager model for liquid crystals "

The Onsager model in liquid crystal theory holds the status of the Ising model for phase transitions. They both take a different view from the phenomenological Landau-de Gennes model [liquid crystals] and Landau model [phase transitions] by relating the microscopic properties to the physical world. Identifiable molecular parameters are used in the Onsager model, allowing direct interpretation of experiments and computer simulation results. While the original model was proposed 70 years ago to deal with the bulk isotropic-nematic transition, adding geometric frustrations gives the model a new life. In this talk, the solutions of the model for a number of confined systems of current interest, which display topological defects due to the frustrations between geometry and the nematic ordering field, are presented.

Host: Shengfeng Cheng

April 9

Monday 4:00pm
304 Robeson Hall

(poster)

Mengsu Chen

Exploring quantum many-body systems via lattice model and exact diagonalization

The quantum many-body problem of solving Schrodinger equation of a large number of interacting microscopic particles is generally considered impossible to tackle analytically. Numerical simulations becomes the essential tools to study these systems, especially at the strongly correlated regime. We used exact diagonalization (ED), the only unbiased numeric method, to study the newly proposed interaction-induced states such as fractional Chern insulators (FCI), topological Mott insulators (TMI), emergent kinetics on various quantum lattice model describing many physic systems including 2D materials and optical lattices. We study quantum phase transitions between different parameter regimes of Hamiltonian, and exotic properties such as fractional charges, spontaneous time-reversal symmetry breaking in these phases.

Host: Vito Scarola

April 16

Monday 4:00pm
304 Robeson Hall
Joint CM Seminar
(poster)

Professor Mark Dykman ( Physics, Michigan State University)

"Time-translation symmetry breaking in vibrational Floquet systems"

A periodically driven system has discrete time-translation symmetry with the period of the driving. Its quantum dynamics is described in terms of the Floquet states. Generally, if the system is in a Floquet state, its dynamical variables oscillate with the period of the driving. Recently much interest have attracted systems where the time symmetry is broken, the “time crystal” effect. Nonlinear oscillators, including Nano mechanical systems and modes in electromagnetic cavities, provide an ideal platform for studying this effect. We will show how the symmetry breaking occurs in an individual oscillator in the quantum coherent regime. We will then discuss the classical and quantum phase transitions to the broken-symmetry state in systems of coupled oscillators.

Host: Uwe Tauber

April 23

Monday 4:00pm
304 Robeson Hall
CM Seminar Only
(poster)

Sriram Ganeshan (Stony Brook, New York)

"Odd Surface waves in two-dimensional in-compressible fluids"

In everyday fluids, the viscosity is the measure of resistance to the fluid flow and has a dissipative character. Avron, Seiler, and Zograf showed that viscosity of a quantum Hall (QH) fluid at zero temperature is non-dissipative. This non-dissipative viscosity (also known as ‘odd’ or ‘Hall’ viscosity) is the antisymmetric component of the total viscosity tensor and can be non-zero for parity violating fluids. I will discuss free surface dynamics of a two-dimensional incompressible fluid with the odd viscosity (not quite quantum Hall hydro). For the case of incompressible fluids, the odd viscosity manifests itself through the free surface (no stress) boundary conditions. We first find the free surface wave solutions of hydrodynamics in the linear approximation and study the dispersion of such waves. As expected, the surface waves are chiral. In the limit of vanishing shear viscosity and gravity, we derive effective nonlinear Hamiltonian equations for the surface dynamics, generalizing the linear solutions to the weakly nonlinear case. In a small surface angle approximation, the equation of motion results in a new class of non-linear chiral dynamics which we dub as chiral Burgers equation. I will briefly discuss how this program can be extended to the free surface of quantum Hall hydrodynamics.


Host: Ed Barnes

April 27

"Special Seminar"
Friday, 2:30pm
210 Robeson Hall
Colloquium
(poster)

Prof. Timothy Halpin-Healy (Department of Physics, Columbia University)

"Within & Beyond the Realm of KPZ "

We discuss significant events in the recent Renaissance triggered by the enigmatic and elusive, but reach stochastic nonlinear PDE of Kardar, Parisi & Zhang, * a celebrated equation whose reach far exceeds its grasp, touching such diverse phenomena as non-equilibrium stochastic growth, optimal paths in ill-condensed matter, the dynamics of driven lattice gases, as well as the extremal statistics of random matrix eigenvalues. *J. Stat. Phys. 160, 794 (2015).

Host: Uwe Tauber

April 30

Monday 4:00pm
304 Robeson Hall
Joint CM Seminar
(poster)

Prof. Juan Vanegas (University of Vermont)

"Mechanics at the nanoscale: Local stress calculations in Biomolecular systems"

The microscopic or local stress field provides a unique connection between molecular simulations and mechanics of materials at the nanoscale. Lateral stress profiles are routinely used to understand the mechanical behavior of liquid interfaces such as lipid membranes from molecular dynamics (MD) simulations. However, the 1-dimensional stress profiles are not adequate to understand the multidimensional mechanical state in complex asymmetrical systems such as membrane proteins or other macromolecular structures. Furthermore, the fact that the microscopic stress from MD simulations is not uniquely defined is a theoretical consideration that is most often ignored, which has acute practical consequences when atomistic models are considered. I will present our recent work on the development of objective 3D local stress calculations by way of expressions that satisfy balance of linear and angular momentum for force-fields with arbitrarily high many-body interactions. I will show how some definitions of the microscopic stress violate mechanical equilibrium through various examples including defective graphene, lipid membranes, and fibrous proteins. I will also demonstrate the use of the traction vector, computed from the microscopic stress, as a powerful tool to visualize the local balance of forces at an interface. Focusing on the bacterial mechanosensitive channel MscL, I will show how the traction vector allows identification of a unique association pattern of lipids at specific sites on the MscL surface that may mediate gating of the bacterial channel by membrane tension or other stimuli.


Host: Shengfeng Cheng

May 2018
May 7

Monday 4:00pm
304 Robeson Hall
(poster)

Final Exam Week. No Seminar Scheduled.

Center for Soft Matter and Biological Physics Seminars

Fall 2017

Organizer: Vinh Nguyen

Refreshments are served before the seminars (unless otherwise indicated)

August 2017
August 28

Monday 4:00pm
304 Robeson Hall

Joint CM Seminar

(poster)

Sheng Chen
Department of Physics, Virginia Tech

Computational studies of predator-prey competition models

The two-species stochastic Lotka-Volterra model already displays very interesting non-equilibrium dynamical properties on a two-dimensional square lattice. In order to explore possible origins of biodiversity, we add a second competing predator species, which renders the system even more complex. The individual predators are characterized by randomly distributed predation efficiencies and death rates, to which Darwinian evolutionary adaptation is introduced. We find that direct competition between predator species in combination with so-called character displacement play an important role in stabilizing ecologically diverse communities.

Host: Uwe Täuber

September 2017
September 4

Monday 4:00pm
304 Robeson Hall

Holiday No Meeting

(poster)

Labor Day. No seminar scheduled.

September 11

Monday 4:00pm
304 Robeson Hall

(poster)

Seminar cancelled and rescheduled to a later date.

September 18

Monday 4:00pm
304 Robeson Hall

Joint CM Seminar

(poster)

Prof. Lauren Childs
Department of Mathematics, Virginia Tech

Simulating Within-Vector Generation of the Malaria Parasite Diversity

Plasmodium falciparum, the malaria parasite causing the most severe disease in humans, undergoes an asexual stage within the human host, and a sexual stage within the vector host, Anopheles mosquitoes. Because mosquitoes may be super-infected with parasites of different genotypes, this sexual stage of the parasite life-cycle presents the only opportunity in the full life cycle to generate large genetic differences in parasites through recombination. To investigate the role that mosquitoes' biology plays on the generation of parasite diversity, we constructed a stochastic model of parasite development within-mosquito over its lifespan. We then coupled a model of sequence diversity generation via recombination between genotypes to the stochastic parasite population model. Our two-part model framework shows that bottlenecks entering the oocyst stage decrease diversity from the initial gametocyte population in a mosquito's blood meal, but diversity increases with the possibility for recombination and proliferation in the formation of sporozoites. Furthermore, when we begin with only two distinct parasite genotypes in the initial gametocyte population, the probability of transmitting more than two unique genotypes from mosquito to human is over 50% for a wide range of initial gametocyte densities.

Host: Michel Pleimling

September 25

Monday 4:00pm
304 Robeson Hall

Joint CM Seminar

(poster)

Harsh Chaturvedi
Department of Physics, Virginia Tech

Dynamics Of Driven Vortices In Type-II Superconductors

Technical applications of type-II superconductors in external magnetic fields require an effective flux pinning mechanism to reduce Ohmic losses due to flux creep and flow. In addition, driven vortex matter subject to thermal fluctuations and quenched disorder constitutes a system far from equilibrium that yields rich phase diagrams and many novel glassy states. Using numerical and analytical techniques, we have studied in detail, the dynamical relaxation features towards the equilibrium vortex or Bose glass phases following sudden changes in externally applied electric current. Most recently, we have characterized the long-time steady-state behavior of vortices driven perpendicular to a family of parallel planar defects (that model twin boundaries found in superconducting YBCO), revealing in the process, a rich collection of novel dynamical regimes spanning a remarkably broad depinning transition region that separates the pinned and moving-lattice states of vortex matter.

Host: Uwe Täuber

October 2017
October 2

Monday 4:00pm
304 Robeson Hall

Joint CM Seminar

(poster)

Prof. Xiaowei Wu
Department of Statistics, Virginia Tech

Learning Patterns from Genomics Data through Stochastic Modeling

Next-generation sequencing (NGS) enables a large variety of genomics applications (genome sequencing, transcriptome profiling, DNA-protein interactions, epigenome characterization, etc), and opens up unprecedented opportunities to uncover the genetic architecture and mechanisms of biological processes. However, it still remains challenging to build flexible and robust statistical models for knowledge discovery from the wealth of genomics data generated by NGS. We present several typical applications of state-of-the-art nonparametric methods (e.g., NP-Bayesian clustering, functional mixed model) based on the inhomogeneous Poisson process model of genomic heterogeneity patterns. These methods provide effective solutions to the modeling and analysis of modern omics data. Findings from such applications will help biologists better understand the molecular nature of biological processes such as transcriptional regulation and trait differentiation.

Host: Uwe Täuber

October 9

Monday 4:00pm
304 Robeson Hall

(poster)

Condensed Matter seminar. No CSB seminar scheduled.

October 16

Monday 4:00pm
304 Robeson Hall

Joint CM Seminar

(poster)

Dr. Charles Reichhardt
Los Alamos National Laboratory

Skyrmion Lattices in Random and Ordered Potential Landscapes

Since the initial discovery of skyrmion lattices in chiral magnets [1], there has been a tremendous growth in this field as an increasing number of compounds are found to have extended regions of stable skyrmion lattices [2] even close to room temperature [3]. These systems have significant promise for applications due to their size scale and the low currents or drives needed to move the skyrmions [4]. Another interesting aspect of skyrmions is that the equations of motion have significant non-dissipative terms or a Magnus effect which makes them unique in terms of collective driven dynamics as compared to other systems such as vortex lattices in type-II superconductors, sliding charge density waves, and frictional systems. We examine the driven dynamics of skyrmions interacting with random and periodic substrate potentials using both continuum based modelling and particle based simulations. In clean systems we examine the range in which skyrmion motion can be explored as a function of the magnetic field and current and show that there can be a current-induced creation or destruction of skyrmions. In systems with random pinning we find that there is a finite depinning threshold and that the Hall angle shows a strong dependence on the disorder strength. We also show that features in the transport curves correlate with different types of skyrmion flow regimes including a skyrmion glass depinning/skyrmion plastic flow region as well as a transition to a dynamically reordered skyrmioncrystal at higher drives. We find that increasing the Magnus term produces a low depinning threshold which is due to a combination of skyrmions forming complex orbits within the pinning sites and skyrmion-skyrmion scattering effects. If the skyrmions are moving over a periodic substrate, with increasing drive the Hall angle changes in quantized steps which correspond to periodic trajectories of the skyrmion that lock to symmetry directions of the substrate potential. [1] S. Muhlbauer et al Science 323 915 (2009). [2] X. Z. Yu et al. Nature 465, 901-904 (2010). [3] X.Z. Yu et al Nature Materials, 10, 106 (2011). [4] A. Fert, V. Cros, and J. Sampaio Nature Nanotechnology 8, 152 (2013).

Host: Michel Pleimling

October 17

Tuesday 2:00pm
304 Robeson Hall

Special CSB Seminar

(poster)

Dr. Charles Reichhardt
Los Alamos National Laboratory

Jamming and Clogging of Passive and Active Particles in Disordered Media

There has been tremendous growth in studying nonequilibrium systems of particle assemblies which can exhibit jamming effects. In general jamming has been studied in the absence of quenched disorder. Here we examine the dynamics of active and passive matter systems interacting with random or periodic substrates and obstacle arrays, and show that it is possible to make a clear distinction between jammed systems and clogged systems. For non-active systems of particles flowing through random obstacle arrays, when the particle density is well below that at which an obstacle free system would jam, we find that the system can reach a clogged state. The clogged states can be distinguished from jammed states in that they are spatially heterogeneous, are fragile, and have a pronounced memory effect. In contrast, jammed states are much more homogeneous, robust, and have much weaker memory effects. We outline a possible scenario in which jamming is dominated by a diverging length scale associated with a critical density at point J, while clogging is associated with the coarsening of a dense area across the sample. We have also investigated clogging and jamming in active matter or self-motile particle systems. Such dynamics can effectively describe certain biological systems such as run-and-tumble bacteria or crawling cells, as well as non-biological systems such as self-driven colloids or artificial swimmers. For active matter systems driven over random disorder we find that for intermediate amounts of self-motility the system does not clog; however, for increasing self-propulsion of the particles there is a strong reduction of the mobility due to a self-clogging or self-clustering in the system that resembles the "faster is slower" effect found in certain pedestrian panic models.

Host: Michel Pleimling

October 23

Monday 4:00pm
304 Robeson Hall

(poster)



Host:

October 30

Monday 4:00pm
304 Robeson Hall

Joint CM Seminar

(poster)

Madhurima Nath
Virginia Tech Biocomplexity Institute

Statistical Mechanical Applications of Graph Dynamical Systems

Moore and Shannon's reliability polynomial can be used as a global statistic to explore the behaviour of a diffusive process on a network that represents a finite sized interacting system. It depends on both the network topology and the dynamics of the process and gives the probability that the system has a particular desired property. Due to the complexity to evaluate the exact network reliability, it has been classified as a NP-hard problem. The estimation of the reliability polynomials for large graphs is feasible using Monte-Carlo simulation. Depending on the description of the functionality, network reliability can be utilized for a number of applications ranging from epidemiology to statistical physics. For example, it serves as a measure to study the sensitivity of the outbreak of an infectious disease on a network to the structure of the network. Further, it is analogous to the partition function of a statistical mechanical system which provides insights to the interpolation between the low and high temperature limits.

Host: Uwe Täuber

November 2017
November 6

Monday 4:00pm
304 Robeson Hall

(poster)

Condensed Matter seminar. No CSB seminar scheduled.

November 9

Thursday 4:00pm
304 Robeson Hall

Special CSB Seminar

(poster)

Professor Srividya Iyer-Biswas   (Department of Physics, Purdue University)

Making the right noise

In this talk I will introduce a theoretical framework that serves as the natural representation for biochemical dynamics, and illustrate its utility in a variety of contexts.

Host: Uwe Täuber

November 13

Monday 4:00pm
304 Robeson Hall

(poster)

Condensed Matter seminar. No CSB seminar scheduled.

November 20

Monday 4:00pm
304 Robeson Hall

Holiday No Meeting

(poster)

Thanksgiving Break. No seminar scheduled.

November 27

Monday 4:00pm
304 Robeson Hall

Joint CM Seminar

(poster)

Prof. Jiangtao Cheng
Department of Mechanical Engineering, Virginia Tech

Mechanism and Universal Scaling Law for Contact Line Friction of Cassie-State Droplets on Nano-Structured Ultra-hydrophobic Surfaces

The design and optimization of micro/Nano-fluid devices or wetting-related applications necessitate the knowledge of the physical mechanisms underlying the moving contact line, which is beyond the predictive capability of the continuum theory. Here we use the molecular dynamics (MD) simulations to explore the Cassie-state wetting dynamics on nano-structured surfaces with an emphasis on the contact line friction (CLF). We find that CLF emerges as a result of the solid-liquid interactions and liquid-liquid interactions, which are termed as solid-liquid retarding and viscous damping respectively. Solid-liquid retarding is ascribed to the work of adhesion and viscous damping is related to the depletion of liquid density near the solid-liquid interface. With gradually decreased solid-liquid contact fraction (larger apparent contact angle), solid-liquid retarding remains unchanged while viscous damping is increased. A universal scaling law is derived to describe the CLF on ultra- hydrophobic surfaces before the Cassie-to-Wenzel transition. It is suggested that the non-sticking feature (smaller CLF) of nano-structured ultra-hydrophobic surfaces is indeed caused by the lowered fraction of the solid-liquid contact. Our results have revealed the genesis of CLF from an ab initio perspective and have demonstrated the effects of surface structures on dynamic wetting by justifying the dominant role of solid fraction in lowering CLF.

Host: Shengfeng Cheng

December 2017
December 4

Monday 4:00pm
304 Robeson Hall

Joint CM Seminar

(poster)

Yanfei Tang
Department of Physics, Virginia Tech

Molecular Dynamics Simulations of Drying Colloidal Films

Evaporating solvent out of a colloidal suspension is an important technology to fabricate thin-film materials. The structure of the deposited film highly depends on the drying process. For example, when the solvent evaporates fast the colloidal particles can accumulate near the receding liquid-vapor interface, a phenomenon known as skin-layer formation. In this talk, I will discuss our recent molecular dynamics simulations of a drying suspension containing a binary mixture of colloidal nanoparticles. A distinguishing feature of our work is that the solvent is modelled explicitly as a Lennard-Jones liquid, which allows us to explore the effects of solvent on the structure of the drying film. We have confirmed a recently-found “small-on-top” stratification phenomenon in which the smaller nanoparticles form a layer closer to the liquid-vapor interface and on top of the layer of the larger nanoparticles. However, our results show that density and temperature gradients can develop in the solvent during drying and these gradients have profound effects on stratification that are not revealed in previous work based on an implicit solvent model. I will also talk about theory and simulations of a nanoparticle at a liquid-vapor interface, which clarifies the physical foundation of the implicit solvent model used in literature in which the liquid-vapor interface is modeled as a potential barrier or well.

Host: Shengfeng Cheng

December 11

Monday 4:00pm
304 Robeson Hall

Joint CM Seminar

(poster)

Prof. Robert S. Hoy
University of South Florida

Thermalized soft glassy rheology

As far back as the work of Ree and Eyring in the 1950s, plastic deformation of solids has been modeled as being controlled by multiple relaxation processes with different characteristic rates. The energy landscape picture of Stillinger et. al. allows it to be simultaneously viewed as being controlled by energy minima of broadly distributed depths and statistical weights. Modern theories of plasticity such as soft glassy rheology (SGR) and shear transformation zones (STZ) connect these two ideas, viewing amorphous solids as being composed of spatially localized "plastic zones": basins in systems' energy landscapes with characteristic relaxation rates determined by the depths of their associated energy barriers. Recent studies have shown that the STZ and SGR theories are thermodynamically consistent and therefore amenable to rigorous nonequilibrium- thermodynamic treatment. However, a particularly important open problem is determining the degree to which plastic flow is thermalized, i.e. the degree to which the "slow" degrees of freedom corresponding to plastic zone configurations are in equilibrium with the "fast" degrees of freedom corresponding to localized motions of systems' constituent atoms and molecules. I will describe a recently developed continuous formulation of SGR theory corresponding to the infinite-system-size limit and including fully thermalized strain degrees of freedom, and show that it enables prediction of many physical properties that cannot be straightforwardly accessed within the standard, discrete-zone formulation. Most notably, it allows direct calculation of systems' nonequilibrium, strain-history-dependent positions on their energy landscapes, which in turn allows standard statistical mechanics to be employed for followup calculations. These in turn allow straightforward quantitative analyses of model amorphous systems' heterogeneous yielding dynamics and nonequilibrium deformation thermodynamics. As a demonstration of the method, I will illustrate the very different characters of fully-thermal and nearly-athermal plasticity by comparing results for thermalized vs. nonthermalized strain degrees of freedom and plastic flow rules.

Host:Shengfeng Cheng

Center for Soft Matter and Biological Physics Seminars

Spring 2017

Organizer: Vinh Nguyen


These seminars occur on Monday's at 4:00pm in 304 Robeson Hall (unless otherwise indicated).

Refreshments are served before the seminars

January 2017
January 16

Monday 4:00pm
304 Robeson Hall

 

Martin Luther King Holiday. No talk scheduled.

January 20

Friday 2:30pm
210 Robeson Hall

Special Colloquium

(poster)

Dr. Rana Ashkar  
Oak Ridge National Lab

Towards Switchable Topography and Tunable Fluctuations in Biomimetic Lipid Bilayers

Lipid bilayers are ubiquitous in nature; they form the backbone of cell membranes and are responsible for vital biological processes, including the regulation of protein functions and the exchange of nutrients in and out of the cell. In order to understand the function of lipid membranes and fully utilize their potential in biotechnologies, it is imperative to investigate the factors that control essential membrane processes, such as domain formation and protein recruitment. While decades of research have remarkably furthered our understanding of lipid membranes, the role of local curvature and nanoscale fluctuations remain to be the least understood. In this talk, I will present recent progress in developing a platform for topographic control of lipid bilayers, using thermoresponsive nanostructured polymer scaffolds, to explore curvature-mediated membrane phenomena, such as domain reorganization and switchable protein binding. I will also discuss ongoing experimental and computational studies on tuning nanoscale membrane fluctuations and investigating their effects on protein binding/insertion mechanisms.


Host:Vicki Soghomonian

January 27

Friday 2:30pm
210 Robeson Hall

Special Colloquium

(poster)

Dr. Liheng Cai  
Harvard University

Soft matter approaches to biology: A tale of mucus hydrogel in human lung defense

Biological systems are featured by their ability to defend themselves against external challenges. While these defense mechanisms are extensively studied in the context of life sciences, their physical aspects have largely been overlooked, although they are implicated in many important biological processes. Using knowledge and tools in soft matter and physical science, we can not only provide unique insights to biological questions that directly impact healthcare, but also in turn create new directions that broaden the scope of soft matter research. In this talk, I will discuss how soft matter physics can help understand a long-standing question for human lung defense: Why can the human lung fight against numerous inhaled infectious particulates and maintain functional through its lifetime? Contrary to the widely accepted dogma that the epithelium of human airway is lined by a physiological liquid, I discover that it is covered by a gel-like polymer brush. This brush layer protects the epithelium from small, infectious particulates that sneak through mucus hydrogel. Moreover, the brush layer enables efficient clearance of mucus out of lung by stabilizing itself against osmotic compression from the mucus. Furthermore, I will show that chronic osmotic stress from diseased mucus likely affects airway remodeling. It slows down the proliferation of epithelial cells, and more strikingly, directs the differentiation of epithelial cells to mucus producing cells, a hallmark of mucus obstructive lung diseases such as asthma, chronic obstructive pulmonary disease (COPD) and cystic fibrosis. These findings suggest that the osmotic pressure of mucus hydrogel provides a unified measure of pathogenesis of mucus obstructive lung diseases, and open new directions for the development of novel therapeutics to teat these diseases.



Host:Will Mather

February 2017
February 6

Monday 4:00pm
145 Goodwin Hall

Special Colloquium

(poster)

Dr. Jejoong Yoo  
University of Illinois Urbana-Champaign

The physics of chromosomes: from DNA loops to nucleus-scale structures

Human chromosomes in a cell's nucleus have long been thought to behave like encapsulated random polymers. Recent experiments, however, have shown that chromosomes organize into well-defined three-dimensional structures thereby controlling the cell's state. The very presence of such structures implies existence of yet unknown physical interactions that de-fine the free energy of chromosomes in a cell's nucleus and govern the free-energy change during processes such as cell development and cancer. Using high-through put molecular dynamics simulations and single-molecule experiments, we determined the free energy landscape of the fundamental structural unit of chromosome organization-a nucleosome, which is a fragment of DNA wrapped around a protein core. At a single nucleosome level, we found the nucleotide sequence of DNA and its CpG methylation to uniquely determine the orientation of the DNA loop with respect to the protein core, offering a simple physical mechanism of controlling DNA accessibility to DNA reader machinery. At a multi-nucleosome level, we found the AT content of the DNA sequence and the methylation of either DNA or the nucleosome proteins to govern association of nucleosomes into clusters. Overall, our findings suggest that intrinsic properties of DNA may play a considerable role in defining the free energy landscape and the nucleus-scale organization of chromosomes.


Host: Shengfeng Cheng

February 13

Monday 4:00pm
145 Goodwin Hall

Special Colloquium

(poster)

Dr. Maxim Lavrentovich  
University of Pennsylvania

Putting Patterns on Spheres: Pollen Grains and Cholesteric Liquid Crystal Shells

Insect egg shells, mite carapaces, pollen grain surfaces, and many other biological materials exhibit intri-cate surface patterns including stripes, spikes, pores, and ridges. Beautiful surface patterning occurs in cho-lesteric liquid crystals (CLCs), as well. I will discuss how to understand such surface patterning as a phase transition to a spatially modulated state on a sphere. On infinite, flat surfaces, the patterned states consist of uniform strips or hexagons. On the sphere, however, the patterns are more varied because they must have topological defects, which may be accommodated in many ways. In these phase transition models, the patterns have a characteristic wavelength, which has important consequences for the thermal fluctua-tions in the system, including a fluctuation-driven qualitative change in the behavior near the phase transi-tion. Focusing on spherical pollen grain development, I will describe what sets the characteristic wave-length, the influence of fluctuations, and how our simple model may be tested experimentally. CLCs also have an intrinsic, characteristic wavelength associated with the twist in the stacking of their constituent molecules. These compounds also exhibit phase transitions to spatially modulated states, over which we have good experimental control. I will discuss the behavior of spherical CLC shells and their surface patterns by drawing insights from experiments and simulations. We will end with a discussion of the nu-cleation and growth of such patterns.


Host: Vicki Soghomonian

February 20

Monday 4:00pm
145 Goodwin Hall

Special Colloquium

(poster)

Dr. Edward Banigan  
Northwestern University

Emergent length scales of the cell nucleus

The interiors of living cells are highly organized, and this internal order is critical to robust cell biological function. However, it is not well understood how few-nanometer-sized proteins dynamically generate spatiotemporal order over length scales spanning several nanometers to tens of microns. The cell nucleus and the genome contained within exemplify this problem: the same ~1 meter of DNA is packed into each ~10 micron cell nucleus, and yet, different cells differ dramati-cally in function and activity. Thus, biological function is largely governed by genome organization, and it is critical to establish biophysical mechanisms for measuring length in the nucleus. I will discuss several models for DNA on differ-ent length scales that reveal different physical mechanisms underlying intracellu-lar organization. Specifically, I will discuss experimentally motivated models for non-equilibrium DNA twist dynamics, spatial partitioning of catalytic macromol-ecules, and whole nuclear deformation. These models show how DNA mechan-ics, biomolecule diffusion and catalytic activity, and nuclear geometry and archi-tecture each determine distinct lengths for cellular phenomena on multiple scales. Together, these models illustrate how mechanical and biochemical effects at small scales may be integrated to lead to emergent phenomena that control cell nuclear and genome organization.


Host: Shengfeng Cheng

February 27

Monday 4:00pm
304 Robeson Hall

 

Faculty Meeting. No talk scheduled.

March 2017
March 6

Monday 4:00pm
304 Robeson Hall

 

Spring Break Week. No talk scheduled.

March 13

Monday 4:00pm
304 Robeson Hall

 

APS March Meeting. No talk scheduled.

March 20

Monday 4:00pm
304 Robeson Hall

Joint Condensed Matter Seminar

(poster)

Prof. Christian Ray  
University of Kansas

Regulation of Bacterial Growth in Discrete Steps and Structured Lineages


Prodigious growth is a defining feature of bacterial life. Systems of networks change growth rates in bacteria dynamically in response to changing environments. This includes surviving stresses such as antibiotics and starvation via slowing of growth. Phenotypic heterogeneity allows a small fraction of cells to enter growth arrest by randomly crossing an internal molecular threshold, a form of bet-hedging that allows the population of cells to survive even if future environments are inhospitable to actively growing cells. Therapeutic targeting of growth arrested bacteria is a critical emerging strategy during the current rising problem of antibiotic resistance and the continued challenge of treating stubborn, chronic infections. We are taking a multifaceted approach that has opened new avenues for understanding persister formation with time-lapse microscopy and computational models. Our experiments have shown a novel persister-forming condition. In this condition, bacterial cells undergo discrete shifts in growth rate that correspond to fast molecular reshuffling events. Analysis of cellular lineages in these conditions demonstrates that cellular transitions into growth arrest are not statistically independent: closely related cells are more likely to transition together. Computational models reproduce lineage correlations with a remarkably simple set of assumptions. We discuss implications of the novel persister phenotype for pathogens surviving in changing environments, and new questions raised by our results.

Host: Will Mather

March 27

Monday 4:00pm
304 Robeson Hall

Joint Condensed Matter Seminar

(poster)

Prof. Katie Mitchell-Koch  
Dept. of Chemistry, Wichita State University

How do bio molecular surfaces influence small molecule dynamics?


Our group has been using molecular dynamics simulations to study the interactions and dynamics of small molecules-solvent and substrate-at the surfaces of biomolecules. Simulations of aldehyde and alcohol substrates in the presence of the aldehyde reductase YqhD have revealed a substrate access channel that is not evident in the crystal structure. Collaborative work with Prof. Vinh Nguyen (Virginia Tech) has investigated the hydration layer dynamics around DPC micelles. Simulations coupled with GHz-to-THz measurements have shown that the slowest waters are hydrogen-bonded to the anionic phosphatidyl oxygen's, while only a modest slowdown in hydration dynamics is observed around the cationic trimethylamine groups of the zwitterionic lipids. Hydration dynamics around the enzyme Candida Antarctica lipase B (CALB) have been simulated, indicating heterogeneity in protein-water hydrogen bond lifetimes at the surface. CALB is an enzyme that is also used in organic solvents for the production of fine chemicals such as flavoring agents. Work is underway to characterize the solvation layer of CALB in organic solvents, connecting solvent dynamics to protein structure and dynamics.

Host: Vinh Nguyen

April 2017
April 3

Monday 4:00pm
304 Robeson Hall

Joint Condensed Matter Seminar

(poster)

Prof. Ting Lu  
University of Illinois at Urbana-Champaign

Bottom-up Assembly of Microbial Communities: Modeling, Analysis and Engineering


Microbes are of fundamental importance to human health, environment and agriculture. To ultimately exploit their potential for various purposes, a fundamental challenge is to decipher the basic rules of microbial community organization that is heterogeneous in space and time. My lab aims to address the challenge using a bottom-up approach that combines biophysical modeling with experimental synthetic biology. Recently, we developed a computational platform that enables individual-based simulation of microbial communities across multiple scales. We also explored how the modes of cellular social interaction and the spatial scale of interaction contribute to microbial assemblages using the platform, both of which were subsequently determined using experimental ecosystems. Using engineered cellular interactions, we further demonstrated the utility of synthetic microbial consortia for metabolic engineering applications. Our studies provide insights into the organization of complex microbial communities and illustrate the potential of synthetic communities for practical goals.

Host: Will Mather

April 10

Monday 4:00pm
304 Robeson Hall

Joint Condensed Matter Seminar

(poster)

Prof. Jiadong Zang  
University of New Hampshire

Skyrmions in Helimagnets

A Skyrmion is a topological configuration in which local spins wrap around the unit sphere for an integer number of times. After decades of theoretical discussions in high energy physics, it has been recently observed in a series of non-centrosymmetric chiral magnets. Several experiments by neutron scattering or transmission electron microscopy confirm the presence of skyrmions in a crystalline state at a finite window of magnetic field and temperature. Skyrmions show various novel properties inherent to its topological nature, such as topological Hall effect, topological stability, and ultralow critical current for movement, which offer the skyrmion promising prospects for next generation spintronic devices and information storage. In this talk, I will explain the physical origin of skyrmions in chiral magnets, and discuss our recent progress on the skyrmion physics, including skyrmions in confined geometries, new skyrmion materials, and electron transports of the skyrmion materials.

Host: Uwe Täuber

April 17

Monday 4:00pm
304 Robeson Hall

 

Condensed Matter Seminar. No CSB seminar scheduled.

April 24

Monday 4:00pm
304 Robeson Hall




No talk scheduled.

May 2017
May 1

Monday 4:00pm
304 Robeson Hall

 

Condensed Matter Seminar. No CSB seminar scheduled.

May 8

Monday 4:00pm
304 Robeson Hall

 

Final Exam Week. No talk scheduled.

June 2017
June 2

Friday, 1:30pm
304 Robeson Hall

Special Date / Time

(poster)

Prof. P. S. Krishnaprasad  
University of Maryland

Subriemannian geometry and finite time thermodynamics

Subriemannian geometry has its roots in optimal control problems. The Caratheodory-Chow-Rashevskii theorem on accessibility also places the subject in contact with an axiomatic approach to macroscopic thermodynamics. Explicit integrability of optimal control problems in this context is of interest. As in the case for integrability questions in mechanics, here too symmetries and conservation laws have a key role. In this talk we discuss model problems and results pertaining to such questions in isolated systems and ensembles of interacting systems. Of special interest is the problem of determining thermodynamic cycles that draw useful work from fluctuations. This work is in collaboration with PhD student Yunlong Huang, and Dr. Eric Justh of the Naval Research Laboratory.

Host: Uwe Täuber

   

Center for Soft Matter and Biological Physics Seminars

Fall 2016

Organizer: Vinh Nguyen


These seminars occur on Monday's at 4:00pm in 304 Robeson Hall (unless otherwise indicated)

Refreshments are served before the seminars

August 2016
August 29

Monday 4:00pm
304 Robeson Hall

(poster)

Dr. Ting Ge
University of North Carolina at Chapel Hill

Nanoparticle Motion in Entangled Melts of Linear and Non-Concatenated Ring Polymers

Fabrication and processing of polymer nanocomposites, a prominent class of hybrid materials that integrate nanoparticles (NPs) with desirable properties into polymer matrices, requires a good understanding of their viscoelastic behavior. Central to the viscoelasticity of polymer nanocomposites is the dynamical coupling between the motion of NPs and the relaxation dynamics of matrix polymers. We perform large-scale molecular dynamics simulations to compare the motion of NPs in entangled melts of linear polymers and non-concatenated ring polymers. This comparison provides a paradigm for the effects of polymer architecture on the dynamical coupling between NPs and polymers. Strongly suppressed motion of NPs with diameter d larger than the entanglement spacing a is observed in linear polymer melts before the onset of Fickian NP diffusion. The strong suppression of NP motion occurs progressively as d exceeds a, and is related to the hopping diffusion of NPs in the entanglement network. In contrast, the motion of NPs with d>a in ring polymers is not as strongly suppressed prior to Fickian diffusion. The sub-diffusive motion of NPs in ring polymers is understood through a scaling analysis of the coupling between NP motion and the self-similar entangled dynamics of non-concatenated rings.

Host: Shengfeng Cheng

September 2016
September 5

Monday 4:00pm
304 Robeson Hall

(poster)

Prof. Hans Werner Diehl
University Duisburg-Essen

Fluctuation-induced forces in confined He and ideal and imperfect Bose gases

When condensed-matter systems in which low-energy thermal fluctuations occur are confined by a pair of parallel planes or walls to a film geometry, effective forces between the planes are generated by these fluctuations. Familiar examples are 4He near the λ transition and Bose gases near the condensation transition. The cases of He or Bose gases in a 3D film geometry are particularly challenging since nontrivial dimensional crossovers of 3D bulk systems exhibiting long-range order at low temperatures to effective 2D systems without long-range order must be handled in addition to bulk, boundary, and finite-size critical behaviors. We show that exact results can be obtained for analogous n-component φ4 models in the limit n→∞ via inverse-scattering theory and other methods, and show that these results apply directly to the so-called imperfect Bose gas.

Host: Uwe T&aumluber

October 2016
October 24

Monday 4:00pm
304 Robeson Hall

(poster)

Prof. David Odde  
Department of Biomedical Engineering, University of Minnesota

Mechanisms of microtubule kinetic stabilization by the anticancer drugs paclitaxel and vinblastine

Microtubule-targeting agents (MTAs), widely used as biological probes and chemotherapeutic drugs, bind directly to tubulin subunits and suppress the characteristic microtubule self-assembly process of dynamic instability. This "kinetic stabilization" of microtubules is a universal phenotype of MTAs even though they have generally been separated based on tendency to promote either assembly or disassembly at high concentrations. Despite years of study, the molecular-level mechanisms of kinetic stabilization are still unclear. Here we integrate a computational model for microtubule assembly with nanometer-scale fluorescence microscopy measurements to identify the kinetic and thermodynamic basis of kinetic stabilization by the MTAs paclitaxel, an assembly promoter, and vinblastine, a disassembly promoter. Acquiring the highest resolution data across the largest drug concentration range in live cells to date, we identify two distinct modes of kinetic stabilization. One is truly a suppression of tubulin on-off kinetics, characteristic of vinblastine, and the other is a 'pseudo' kinetic stabilization, characteristic of paclitaxel, that nearly eliminates the energy difference between the tubulin nucleotide states. In this work we outline a kinetic and thermodynamic description of kinetic stabilization by the drugs paclitaxel and vinblastine, and further put constraints on the molecular mechanisms of other MTAs that promote in this universal phenotype. These results may help guide development of new microtubule-directed therapies for cancer and neurodegeneration.

Host: Shengfeng Cheng

November 2016
November 14

Monday 4:00pm
304 Robeson Hall

Joint with Condensed Matter

(poster)

Prof. Nicholas J. Mayhall
Department of Chemistry, Virginia Tech

Using simple ab initio methods to construct even simpler Hamiltonians: applying spin-flip methods for strong correlation and excited states.

Although ab initio quantum chemistry can be used routinely to accurately calculate energies and properties of a rather vast array of chemical systems, when the system size grows too large, or the structure too complex, standard approximations breakdown. Strong electron correlation and multiply excited electronic states represent two examples where our current methods fail to provide a robust toolset for applications. In this talk, I will discuss some recent work toward extending the spin-flip family of approximations to larger classes of problems, including exchange coupled transition metal complexes, and multiexciton states of organic molecule clusters.

Host: Vinh Nguyen

November 28

Monday 4:00pm
304 Robeson Hall

Joint with Condensed Matter

(poster)

Prof. Jing Chen
Department of Biological Sciences, Virginia Tech

Mathematical modeling of myxobacterial motility

Myxobacterium glides on substrate with two motility systems: a pili-driven, in-pack Social(S)-Motility and a single-cell based Adventurous(A)-Motility. To carry out complex "social" behaviors on the colony level, such as fruiting body formation, the myxobacteria periodically reverse, and the reversal frequency is modulated by cell-cell contact. In each single cell, motility regulators exhibit intriguing spatiotemporal patterns, including polar localization that oscillates in coordination with cell reversals, and cluster formation at the substrate interface. Previously we built a helical rotor model, which explains the cluster formation as a necessary force generation element in the A-motility mechanism. Currently we are developing an integrated model for myxobacteria motility that coherently links force generation and spatiotemporal patterns to the modulation of cell reversals. Ultimately we aim for understanding how intercellular contact confers intracellular signal to coordinate neighboring cells.

Host: Shengfeng Cheng

December 2016
December 5

Monday 4:00pm
304 Robeson Hall

Joint with Condensed Matter

(poster)

Prof. Dmitry Matyushov
Department of Physics and Molecular Sciences, Arizona State University

Electrostatic soup of biology: Production of biological energy by the fluctuating protein-water interface

Energy comes to living systems through electrons occupying high-energy states, either from food (respiratory chains) or light (photosynthesis). Electrons are transferred across the cellular membrane in a sequence of hopping events, with an overall small loss of free energy. Biology employs electrostatic fluctuations produced by the protein-water interface to overcome activation barriers for individual electron hops. Ergodicity is often broken in protein-driven reactions and thermodynamic free energies become irrelevant. Breaking the grip of thermodynamics allows for an efficient optimization between the rates of individual electron-transfer steps and the spectrum of relaxation times. Time, it appears, plays as significant role as the free energy in optimizing biology's performance.

Host: Vinh Nguyen

Center for Soft Matter and Biological Physics Seminars

Spring 2016

Organizer: Vinh Nguyen


These seminars occur on Monday's at 4:00pm in 304 Robeson Hall (unless otherwise indicated)

Refreshments are served before the seminars

March 2016
March 4

Friday 2:30pm
304 Robeson Hall

(Poster)

Curtis Ogle  Dept. of Physics, Virginia Tech

Proteolytically Coordinated Activation of Toxin-Antitoxin Modules

Chronic infections present a serious threat to the health of humans by decreasing life expectancy and quality. They have more recently been attributed to the existence of persister cells within bacterial populations which constitute a small fraction of the population capable of surviving a wide range of environmental stressors including starvation, DNA damage, and heat shock. Persis- tence also allows the survival of successive applications of antibiotics resulting in chronic infections. Persistence has been strongly linked to so-called toxin-antitoxin (TA) modules, operons with an evolutionarily conserved motif including a toxin that halts cell growth and an antitoxin that under healthy conditions neutralizes the toxin, typically by forming a complex which protects the antitoxin from rapid proteolytic degradation and performs some regulatory action on the operon. While many such modules have been identifed and studied in a wide range of organisms, little consideration of interactions between multiple modules within a single host has been made. Moreover, the multitude of different antitoxin species share a limited number of proteolytic pathways, strongly suggesting competition between antitoxins for degradation machinery. Here we present a theoretical under- standing of the dynamics of multiple toxin-antitoxin modules whose activity is coupled through proteolytic activity. Such indirect coordination between multiple TA modules may be at the heart of bacterial robustness owed to the persistent response.

Host: Will Mather

March 21

Monday 4:00pm
304 Robeson Hall

(Poster)

Prof. Nuno Araújo Universidade de Lisboa, Portuga

Self-organization of colloids under non-equilibrium conditions

The ultimate goal of Soft Matter is to synthesize materials of enhanced physical properties from the spontaneous self-organization of their individual units. A prototypical example is the use of colloids. With a typical size of the order of the wavelength of visible light, colloidal particles are not only excellent building blocks for optical materials as they are ideal for experiments, for their trajectories can be resolved using available optical techniques. Unfortunately, self-organization is usually driven out of equilibrium and the relaxation towards equilibrium involves the competition of various mechanisms occurring at different length and time scales. The investigation of these mechanisms provides valuable information on the feasibility of the desired structures while unveiling novel non-equilibrium phases that differ in significant ways from the thermodynamic ones. One focus is on identifying novel phases and constructing the equilibrium phase diagrams, based on the properties of individual particles (shape, size, and chemistry). For example, patchy colloids, characterized by highly directional pairwise interactions, set a maximal valence and determine the local particle arrangements leading to novel thermodynamic phases. The question then is, are these phases kinetically accessible? We address this question by means of Langevin dynamics simulations. We identify a crossover between fast (exponential) and slow (scale free) relaxation regimes at a critical temperature, that it is intimately related to the formation of a percolating gel. An impressive advance of experimental techniques has opened the possibility of exploring alternative assembling routes such as the use of substrates, interfaces and electromagnetic fields to collectively drive the system towards the desired structures. We study self-organization under such constraints combining Brownian dynamics simulations and a simple dynamic density functional theory. We analyze the interplay between the strength of the particle-particle and particle-substrate interactions. In addition, we analyze field driven self-organization, by investigating the switching (field on) dynamics and the relaxation times as a function of the system parameters. We also consider binary suspensions of colloids of different mobilities finding non-equilibrium demixing, where the lifetime of the demixed phase diverges when the high mobility colloids crystallize.

Host: Uwe Tauber

April 2016
April 25

Monday 4:00pm
304 Robeson Hall

(Poster)

Prof. A. Joshua Wand  University of Pennsylvania

Internal Motion and Conformational Entropy in Protein Function

At a fundamental level, biological processes are most often controlled using molecular recognition by proteins. Protein-ligand interactions impact critical events ranging from the catalytic action of enzymes, the assembly of macromolecular structures, complex signaling and allostery, transport phenomena, force generation and so on. The physical origin of high affinity interactions involving proteins continues to be the subject of intense investigation. Conformational entropy represents perhaps the last piece of the thermodynamic puzzle that governs protein structure, stability, dynamics and function. The presence and importance of internal conformational entropy in proteins has been debated for decades but has resisted experimental quantification. Over the past few years we have introduced, developed and validated an NMR-based approach that uses a dynamical proxy to determine changes in conformational entropy. This new approach, which we term the NMR "entropy meter," requires few assumptions, is empirically calibrated and is apparently robust and universal. Using this "entropy meter," it can now be quantitatively shown that proteins retain considerable conformational entropy in their native functional states and that this conformational entropy can play a decisive role in the thermodynamics of molecular recognition by proteins. Recent results show that changes conformational entropy of a protein upon binding a high affinity ligand is highly system specific and can vary from strongly inhibiting to even strongly promoting binding and everything in between. Thus one cannot possibly understand comprehensively how proteins work without knowledge of the breadth and underlying principles of the role of conformational entropy in protein function. This approach also yields information about the role of solvent entropy and rotational-translational entropy in molecular recognition by proteins. To provide a closer view of the hydration layer we employ reverse micelle encapsulation to overcome a number of artifacts that have historically hindered use of NMR to characterize the dynamics of protein-water interactions. These types of studies indicate that the hydration layer is remarkably heterogeneously dynamic, which has significant implications for the role of solvent entropy in protein-ligand interactions. Supported by the NIH and the Mathers Foundation.

Host: Vinh Nguyen

May 2016
   
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CSB 2018 Symposium pg 1-7.pdf Center Soft Matter and Biological Physics 2018 Symposium May 16 -17 ,2018 at Virginia Tech, Blacksburg, VA 24061
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CSMBP Symposium 2017-- Program.pdf Center Soft Matter and Biological Physics 2017 Symposium May 17 -18 ,2017 at Virginia Tech, Blacksburg, VA 24061
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Symposium2016.pdf Center Soft Matter and Biological Physics 2016 Symposium May 19 , 2016 at Virginia Tech, Blacksburg, VA 24061