Date: 29 August 2018
2. Condensed Matter Physics Research Centre, Physics Department, Jadavpur University, Kolkata 700032, India
Abstract:
Crack patterns formed by desiccation in clay are known to give rise to characteristic patterns [1, 2]. The patterns are affected by various factors, such as the drying material, the substrate and ambient condi- tions like temperature and relative humidity. External conditions like electric fields and magnetic fields also control details of the crack patterns.
Cylindrically symmetric static DC (i.e. Direct Cur- rent) electric fields [3] and AC (Alternating Current) fields [4] can be used to tailor the crack patterns in specific geometrical arrangements. Here we describe another experiment.
We applied a uniform static electric field to an aque- ous layer of clay suspension while drying. This caused a self-assembly of the cracks into an interesting pat- tern, dictated by the energy supplied to the system.
Initially closely spaced straight cracks appear at the positive electrode. As the sample dries these cracks merge together in small groups. Several stages of this merging produces the final hierarchical pattern.
The final pattern is distinctly tree-like, or river like, consisting of hierarchical structures as shown in Fig. 1. River like crack structures have been observed and discussed previously [5], but not in dried clay pastes as we observe here. We try to analyse the patterns and explain their origin. The redistribution of mobile ions in the aqueous clay slurry is assumed to be responsible for the pattern formation. The process may be useful in producing tailored crack patterns for applications in nano-patterning.
We sincerely thank Tajkera Khatun and Sudeshna Sir- car for participating in this work and for offering valu- able suggestions.
Corresponding author: sujata.tarafdar@gmail.com
- L. Goehring, A. Nakahara, T. Dutta, S. Kitsunezaki and S. Tarafdar Desiccation Cracks and their Patterns (Wiley VCH, Weinheim, Germany 2015).
- J. Allen, Philos. Trans. R. Soc. Ser B 315, 127 (1987).
- T. Khatun, M. Dutta Choudhury, T. Dutta and S. Tarafdar, Phys. Rev. E 86, 016114 (2012).
- S. Sircar, S. Tarafdar and T. Dutta, Appl. Clay Science, 156, 69 (2018).
- D. Hull, Fractography: Observing, Measuring and In-terpreting Fracture Surface Topography (Cambridge University Press, Cambridge 1999).
Timings: 12:25 am - 12:45 pm
Abstract:
To explain experimental results showing shape, size and dynamics of E.coli chromosomes in growing cells, we consider a polymer model consisting of a circular backbone to which side-loops are attached, confined to a cylindrical cell [1, 2]. Such a model chromosome spon- taneously adopts a helical shape, which is further com- pacted by molecular crowders to occupy a nucleoid-like sub-volume (Fig. 1). With increasing cell length, the longitudinal size of the chromosome increases in a non- linear fashion to finally saturate, its morphology gradu- ally opening up while displaying an increasing number of helical turns. For shorter cells and low crowder densi- ties, the chromosome extension varies non-monotonically with cell size, which we show is associated with a ra- dial to longitudinal spatial reorganization of the crow- ders. Confinement and crowders constrain chain dynam- ics leading to anomalous diffusion. While the scaling ex- ponent for the mean squared displacement of centre of mass grows and saturates with cell length, that of indi- vidual loci displays broad distribution with a well-defined maximum. Despite several experimental efforts, in E.coli bacteria, the mechanism for chromosome segregation re- mains elusive. We propose chromosomal segregation via inter-chromosome repulsion mediated by protein produc- tion. The simulation results show good agreement with experiments.
Corresponding author: debc@iopb.res.in
- Fabai Wu, Pinaki Swain, Louis Kuijpers, Xuan Zheng, Kevin Felter, Margot Guurink, Debasish Chaudhuri, Bela Mulder, Cees Dekker, bioRxiv doi: https://doi.org/10.1101/348052.
- D. Chaudhuri and B. M. Mulder, Physical Review Letters 108, 268305 (2012).
Timings: 03:00 pm - 03:20 pm
Abstract:
Adaptive materials can change their mechanical prop- erties depending on external cues in a controlled manner. In this talk, I will describe a novel type of mechanical adaptation in cross-linked networks of F-actin, a ubiqui- tous protein found in the cytoskeleton of eukaryotic cells. We show that shear stress changes the nonlinear mechan- ical response of the network even long after that stress is removed [1]. The duration, magnitude and direction of forcing history all change this mechanical response. While such memory is long-lived, it can be erased simply by force application in the opposite direction. We also show that the observed mechanical adaptation is consis- tent with stress-dependent changes in the nematic order of the constituent filaments. This demonstrates that F- actin networks can exhibit analog read-write mechanical memory.
In disordered condensed matter systems, memory ef- fects originate from out of equilibrium nature of the materials involving slow non-exponential relaxation pro- cesses. Such effects have been observed in systems as diverse as, charge density wave conductors [2], molecular glasses [3], crumpled candy wrappers [4], superconduc- tors [5], granular and amorphous materials [6–8]. In the last part of my talk, I shall also briefly discuss about our preliminary data on non-monotonic stress-relaxation dy- namics in collagen networks (Fig. 1) in the light of other memory encoding condensed matter systems mentioned above.
I would like to thank M.L. Gardel (U. Chicago), A.J. Levine (UCLA), L.C. Foucard (UCLA) for the part of work on actin networks. I thank M.K. Firoz (RRI), S.R. Nagel (U. Chicago) and D. Hexner (U. Chicago) for the ongoing work on memory dynamics in collagen networks. I acknowledge SERB (DST) for support through a Ra- manujan Fellowship.
Corresponding author: smajumdar@rri.res.in
- S. Majumdar, L. C. Foucard, A.J. Levine, and M.L. Gardel, Soft Matter 14, 2052 (2018).
- R.M. Fleming, and L. F. Schneemeyer, Phys. Rev. B 33, 2930 (1986).
- A. Amir, Y. Orega, and Y. Imry, PNAS 109, 1850 (2012).
- Y. Lahini, et al., Phys. Rev. Lett., 118, 085501 (2017).
- P. Anderson, Phys. Rev. Lett., 9, 309 (1962).
- J. B. Knight, et al., Phys. Rev. E, 51, 3957 (1995).
- J. D. Paulsen, N. C. Keim, and S. R. Nagel, Phys. Rev. Lett., 113, 068301 (2014).
- D. Fiocco, G. Foffi, and S. Sastry, Phys. Rev. Lett., 112, 025702 (2014).
Timings: 03:20 pm - 03:40 pm
Date: 30 August 2018
Abstract:
The rich structural complexity of biological mem- branes arises from the chemical diversity of its constituents. Di↵erential inter and intra-molecular interactions result in preferential segregation and clustering of certain types of lipids and proteins, giving rise to a variety of lateral organization on the membrane surface. Recently, Edward Ly- man’s group at Delaware carried out multiple long timescales all-atom molecular dynamics simulations (tens of microseconds long) with carefully chosen lipid compositions to reproduce a variety of phases [1, 2]. We focus on the systems that exhibit liquid- ordered and liquid-disordered (Lo/Ld) co-existence. The three systems with their fractional composi- tions are (i) PSM/POPC/Chol (0.47/0.32/0.21) (ii) PSM/DOPC/Chol (0.43/0.38/0.19) (iii) DPPC/DOPC/Chol (0.37/0.36/0.27).
We analyze these trajectories and numerically calcu- late the degree of non-affineness of individual lipids in their local neighborhood and their topological re- arrangements [3]. We use these data to distinguish between the Lo and Ld regions in the membrane sys- tem at molecular length scales [4].
The three chosen systems exhibit di↵erent molecular- level sub-structures and unique Lo/Ld interface boundaries. We also explore the molecular-origin of this variety in organization using tools from simple statistical mechanics theories. And try to quantify the thermodynamics cost of arriving at a given mem- brane sub-structure using a di↵erent lipid types and compositions.
The authors thank Edward Lyman (University of Delaware, USA) for sharing the AA simulation trajec- tories, which was generously made available by D.E. Shaw Research. AS would also like to thank the IISc- Bangalore for the start-up grant and the DST, India for the Early Career Award.
Corresponding author: anand@iisc.ac.in
- A. J. Sodt, R. W. Pastor, and E. Lyman, Biophys. J, 109, 948-955 (2015)
- A. J. Sodt, M. L. Sandar, K. Gawrisch, R. W. Pastor, and E. Lyman, JACS, 136, 725-732 (2014)
- M. Falk and J. Langer, PRE, 57, 7192-7203 (1998).
- S. S. Iyer*, M. Tripathy*, and A. Srivastava, Biophys. J, 115, 117-128 (2018) *Contributed Equally
Timings: 03:20 pm - 03:40 pm
Date: 31 August 2018
Abstract:
The study of droplets of complex fluids, dried through evaporation, reviewed recently by Sefiane [1, 2] is becoming a rapidly growing field of research. The widespread interest is due to the basic physics aspect as well as promising applications in technology [3], quality control and medical diagnostics [4]. A drying droplet may exhibit a host of features, concentric ring patterns [5, 6], cracks[7, 8], and other interesting mor- phologies. A fact well known since many years is that gels provide a good medium for the growth of crystals [9].
We report a study on the kinetics of drying of a droplet of aqueous gelatin containing sodium chloride. The process of drying recorded as a video clearly shows different regimes of growth leading to a variety of crystalline patterns. Large faceted crystals of mm size form in the early stages of evaporation Fig. 1(a), followed by highly branched multi- fractal patterns with micron sized features Fig. 1(b). We simulate the growth using a simple algorithm incorporating aggre-gation and evaporation, which reproduces the cross- over between the two growth regimes Fig. 1(c - d). As evaporation proceeds, voids form in the gel film. The time development of the fluidvoid system can be characterized by the Euler number. A minimum in the Euler number marks the transition between the two regimes of growth Fig. 2 .
We sincerely thank Abhra Giri for participating in this work.
Corresponding author: sujata.tarafdar@gmail.com
tapati dutta@sxc.com, tapati mithu@yahoo.com
- K. Sefiane, Adv. Colloid Interface Sci., 206, 372381 (2014).
- Sujata Tarafdar, Yuri Yu Tarasevich, Moutushi Dutta Choudhury, Tapati Dutta, Duyang Zang, Advances in Condensed Matter Physics, Published on 01 Jan 2018, doi: 10.1155/2018/5214924
- M. Layani, M. Grouchko, O. Milo, I. Balberg, D. Azu- lay and S. Magdassi, ACS Nano,3, 35373542(2009).
- Yu. Yu. Tarasevisch, I. V. Vodolazskaya and O. P. Bon- darenko, Colloids Surf., A, 432, 99103 (2013)
- D. Kaya, V. A. Belyi and M. Muthukumar, J. Chem. Phys., 133, 114905 (2010).
- Tapati Dutta,Sujata Tarafdar and Tajkera Khatun,J. Phys. Commun. 2 055023 (2018)
- L. Pauchard, F. Parisse and C. Allain, Phys. Rev., 59, 37373740 (1999).
- Z. YongJian, L. ZhengTang, Z. Du Yang, Q. YiMeng and L. KeJun, Sci. China: Phys., Mech. Astron., 56, 17121718 (2013).
- Biswajit Roy, Moutushi Dutta Choudhuri, Tapati Dutta, Sujata Tarafdar, Applied Surface Science 357 10001006 (2015)
Timings: 12:25 am - 12:45 pm
Abstract:
The reversible-irreversible (RI) transition of particle trajectories in colloidal suspensions under cyclic shear deformation is an archetypal nonequilibrium phase transition and attracts much attentions recently. In the low density limit, the RI transition is predicted to belong to a universality class of the absorption transi- tions [1], whereas at the high densities well above the jamming transition point, φ J , it has more to do with the yielding transition of the amorphous solids [2]. The link to bridge the gap between the low and high densities is missing and the relation of the RI tran- sitions with mechanical and flowing behaviors of col- loidal suspensions are largely unexplored.
In this presentation, we show the RI transitions over a wide range of densities above and below φ J by using oscillatory sheared molecular dynamics simulations. It is revealed that the nature of the RI transitions dra- matically change across φ J . When the density is above φ J , the discontinuous RI transition and concomitant 1+ log<∆r(T)>/6 a 1.0 1.00 0.8 g 0 0.80 0.6 0.4 g c2 0.2 g c1 0 0.7 0.75 0.60 g c3 0.40 0.20 0.8 b 1 0.85 j 0.9 0.95 1 < t < d 'order_gamma_lifetime_1_modi.dat' u 1:2:3 0.8 g 0 0.6 0.4 0.2 0 0.7 yield transition are observed. Below φ J , however, the nature of the RI transition becomes surprisingly rich. We find the three distinct phases; (i) continuous RI transition at small amplitudes and low densities fol- lowed by (ii) reentrance to the reversible phase at larger strain amplitudes, and (iii) semi-discontinuous RI transitions in the vicinity of φ J . Here, we have confirmed that these results are quantitatively agreed with those obtained from the simulations in the ather- mal quasi-static (AQS) limit. We show that these transition behaviors are strongly correlated to the number of the contacts, characterized in AQS limit. This implies that these distinct transitions strongly correlated with hidden geometrical properties of par- ticle configurations.
We thank L. Berthier, K. A. Takeuchi, H. Hayakawa, and M. Otsuki for valuable discussions. The research leading to these results has received funding from JSPS Kakenhi (No. 15H06263, 16H04025, 16H04034, and 16H06018).
Corresponding author: kawasaki@nagoya-u.ac.jp
- L. Corté, P. M. Chaikin, J. P. Gollub, D. J. Pine, Ran-dom organization in periodically driven systems, Na-ture Phys. 4, 420 (2008).
- T. Kawasaki, and L. Berthier, Macroscopic yielding in jammed solids is accompanied by a nonequilibrium first-order transition in particle trajectories, Phys. Rev. E 94, 022615 (2016).
Timings:
Date: 28 August 2018
Lecture 1: Tuesday 28 August, 16:00 to 17:00
Title : Order, disorder and entropy
Abstract : Since the middle of the twentieth century, the traditional picture of entropy as a measure of disorder has shifted. However, this development is not well known outside the Statistical Mechanics community. In my talk, I will discuss example s where entropy increases with increasing order, I will briefly touch on Gibbs’ paradox and I will discuss how recently developed numerical tools allow us to compute close and distant relatives of Boltzmann’s entropy.
Date: 29 August 2018
Abstract:
The ability of atomic, colloidal, and nanoparticles to self-organize into highly ordered crystalline structures makes the prediction of crystal structures in these systems an important challenge for science. The question itself is deceivingly simple: assuming that the underlying interaction between constituent particles is known, which crystal structures are stable. In this talk, I will describe a Monte Carlo simulation method [1] combined with a triangular tesselation method [2] to describe the surface of arbitrarily shaped particles that can be employed to predict close-packed crystal structures in colloidal hard-particle systems. I will show that particle shape alone can give rise to a wide variety of structures with unusual properties [3-7], e.g., photonic band gap structures or highly diffusive crystals, but combining the choice of particle shape with external fields, like confinement [4], can enlarge the number of possible structures even more. Furthermore, I will discuss how one can reverse-engineer target structures like specific crystal structure and twist-bend nematic phases by tuning the particle shape and interactions. Finally, I will show that the self-assembly kinetics also plays a major role in the prediction and design of new structures.
KEY WORDS: colloids, self-assembly, crystal structures, hard particles, entropy
References
- L. Filion, M. Marechal, B. van Oorschot, D. Pelt, F. Smallenburg, and M. Dijkstra, Physical Review Letters 103, 188302 (2009).
- . de Graaf, R. van Roij and M. Dijkstra, Physical Review Letters 107, 155501 (2011).
- A. P. Gantapara, J. de Graaf, R. van Roij, and M. Dijkstra, Physical Review Letters 111, 015501 (2013)
- F. Smallenburg, L. Filion, M. Marechal, and M. Dijkstra, Proceedings of the National Academy of Sciences 109, 17886 (2012).
- K. Miszta, J. de Graaf, G. Bertoni, D. Dorfs, R. Brescia, S. Marras, L. Ceseracciu, R. Cingolani, R. van Roij, M. Dijkstra and L. Manna, _Nature Materials 10, 872-876 (2011)
- L. Filion, M. Hermes, R. Ni, E. C. M. Vermolen, A. Kuijk, C. G. Christova, J. C. P. Stiefelhagen, T. Vissers, A. van Blaaderen, and M. Dijkstra, Physical Review Letters 107, 168302 (2011).
- S. Dussi and M. Dijkstra, Nature Communications 7, 11175 (2016).
- B. de Nijs, S. Dussi, F. Smallenburg, J.D. Meeldijk, D.J. Groenendijk, L. Filion, A. Imhof, A. van Blaaderen, and M. Dijkstra, Nature Materials 14, 56-60 (2015).
Timings: 09:00 am - 09:45 am
Abstract:
Patchy particles are hard cores decorated with dis- crete attractive sites (patches) on their surfaces and are used as models for systems with strongly anisotropic interactions. The bonding of particles through their patches promotes the formation of large self-assembled aggregates. The interaction between two patches is specified by an energetic parameter and by the volume available for the bond (bonding volume), that sets the loss of (translational) entropy when a bond is formed [1].
Numerical simulations and theoretical calculations of the phase diagram of one-component patchy parti- cle fluids have revealed that lowering the number of patches (or valence M) depresses the critical proper- ties (critical temperature, critical density, and criti- cal pressure). Because the two-phase region shrinks, the density of the coexisting liquid also decreases with M, opening up the possibility of low density equilib- rium liquid states (empty liquids) that nevertheless have a percolated structure (network fluids). This effect is limited by the lowest possible value of the valence for which both percolation and phase sepa- ration can be found, M = 3 [2]. To overcome this limitation, we have proposed and studied two families of patchy particle models, that are expected to show an effective valence M < 3: (i) a single component system with particles that have 2 patches of type A and n patches of type B that form AA and AB bonds only (2AnB model) [3, 4] and (ii) binary mixtures, where each specie has a different number of patches and similar or dissimilar patches [5]. In this talk, I will present some of the striking results obtained for the liquid vapour phase diagrams of these models us- ing Wertheim’s theory (in most cases confirmed by Monte Carlo simulations) [1].
The phase diagram of the 2AnB model exhibits a reentrant liquid binodal (see Fig. 1), that leads to the appearance of equilibrium liquid states of arbi- trarily low densities [3, 6]. It can be shown that this reentrance is originated by the competition between two types of entropic defects that perturb the ground state. In some extreme cases, when the entropy of AB bonds is much larger than that of AA [4] or when rings of AA bonds are present [7], a closed liquid vapor coexistence region with an upper and a lower critical point is obtained.
The phase diagrams of binary mixtures of patchy par- ticles with different valences (M1 and M2) and a single energy scale (i.e., all patches identical) have a strong dependence on M1 and M2, originated by the compe- tition between the entropy of bonding and the entropy of mixing. The calculation of the critical properties of these mixtures reveals that the empty fluid regime is only obtained for (M1, M2) = (2, 3) and that, for gen- eral mixtures, the role of the entropy of mixing in de- termining the critical properties can only be neglected when M2 − M1 = 1 [5].
Corresponding author: jmtavares@fc.ul.pt
- P.I.C. Teixeira, and J.M. Tavares, Curr. Opin. Colloid Interface Sci. 30, 16 (2017).
- E. Bianchi, J. Largo, P. Tartaglia, E. Zaccarelli, and F. Sciortino, Phys. Rev. Lett. 97, 168301 (2006).
- J. Russo, J.M. Tavares, P.I.C. Teixeira, M.M. Telo da Gama, and F. Sciortino, Phys. Rev. Lett. 106, 085703 (2011).
- N.G. Almarza, J.M. Tavares, E.G. Noya, and M.M. Telo da Gama, J. Chem. Phys. 137, 244902 (2012)
- D. de las Heras, J.M. Tavares, and M.M. Telo da Gama, Soft Matter 7, 5615 (2011).
- J.M. Tavares, and P.I.C. Teixeira, Phys. Rev. E 95, 012612 (2017).
- L. Rovigatti, J.M. Tavares and F. Sciortino, Phys. Rev. Lett. 111, 168302 (2013).
Timings: 09:45 am - 10:30 am
Resources:
Abstract:
Light activated, assembly, movement and pattern for- mation of soft-matter has been studied in the context of micro- and nano-robots in fluidic environments. These processes have also gained interest in the con- text of light-activated dynamic networks that can be controlled in space and time, which further serves as interesting experimental models to study driven ac- tive matter and emergence phenomena. To this end, a variety of surface optical effects have been explored that can effectively interface soft-matter with confined optical fields.
One such optical process is excitation of surface plas- mon polaritons (SPPs). Interaction of visible light with thin-films and nanostructures made of coinage metals, such as gold and silver, can be used to excite SPPs at metal-dielectric interface. These surface elec- tromagnetic waves not only confine electric fields at sub-wavelength scale, but also facilitate thermal field gradients due to ohmic heating. In an essence, SPPs provide optical and thermal fields at metal-fluid in- terface, which can be controlled by an external laser beam.
We have been interested in interaction of soft-matter with SPPs at metal-fluid interface [1, 2]. Specifically, we have been interested in questions such as: how colloidal meso- and nano-structures behave in thermo- optical fields of SPPs? How will their assembly and dynamics alter when the dimensions of metal struc- ture change? What kind of unconventional patterns emerge due to interaction of SPPs with complex flu- ids?
In this presentation, we will introduce some relevant opto-thermal effects of SPPs and discuss how they can be harnessed to study assembly, dynamics and pattern formation of soft-matter at metal-fluid interface. Par- ticularly, we will discuss about formation of colloidal chains and networks in multiple plasmofluidic fields. We will conclude by discussing some new prospects of nanowire plasmons [3] that can confine and move colloids in a quasi-one dimensional channel.
This work was partially funded by DST Nanomission, India and AFRL, USA
Corresponding author: pavan@iiserpune.ac.in
- Partha P. Patra, Rohit Chikkaraddy, Ravi P.N. Tri- pathi, Arindam Dasgupta, G.V. Pavan Kumar, Nature Communications 5, 4357 (2014).
- Partha Pratim Patra, Rohit Cikkaraddy, Sreeja Thampi, Ravi P.N. Tripathi, G. V. Pavan Kumar, Faraday Discussion 186, 95 (2016).
- Adarsh B. Vasista, Harshvardhan Jog, Tal Heilpern, M.E. Sykes, Sunny Tiwari, Deepak K. Sharma, Shailendra K. Chaubey, G.P. Wiederrecht, S.K. Gray, G.V.Pavan Kumar, Nano Letters 18, 650-655 (2018).
Timings: 10:55 am - 11:40 am
Abstract:
2D liquid monolayer membranes of aligned rod like particles form in presence of depletion attraction in- duced by non-adsorbing polymer coils [1]. Surface ten- sion drives these monolayers to be circular in shape with edge fluctuations controlled by the chirality of the constituent rods [2]. Surprisingly, we find that fluid membranes assembled form mixtures of long and short rods are cyclic polygonal in shape with short rods forming the outer lobes and longer rods forming the inner faceted core of the polygon. We show that the origin of this anisotropic shape of membranes lies in the phenomenon of how one liquid spreads over an- other in presence of pinning sites. We outline the nec-essary and sufficient constraints on the nature of rods to obtain the stable out of equilibrium cyclic poly- gon membranes. Our results show the unique counter- intuitive scenario where disorder lead to self assembly of ordered structures.
We would like to acknowledge IISc, ISRO-STC and SERB-DST for funding this work.
Corresponding author: prerna@iisc.ac.in
- Edward Barry, and Zvonimir Dogic, Proceedings of the National Academy of Sciences 107, 10348 (2010).
- T. Gibaud et al., Nature 481, 348 (2012).
Timings: 11:40 am - 12:25 pm
Abstract:
DNA is not just the stuff of our genetic code; it is also a means to build new materials [1]. For instance, grafting DNA onto small particles can, in principle, ‘program’ the particles with information that tells them exactly how to put themselves together—they ‘self-assemble.’ Recent advances in our understand- ing of how this information is compiled into specific interparticle forces have enabled the assembly of in- teresting crystal phases [2], and could be extended to the assembly of prescribed, nonperiodic structures [3]. However, structure is just one piece of the puzzle; in actuality, self-assembly describes a transition between a disordered state and an ordered state, or a pathway on a phase diagram.
In this talk, I will present experiments showing that the information stored in DNA sequences can be used to design the entire assembly pathway. Using free DNA strands that either induce or compete with bind- ing between particles, I will show that it is possible to create suspensions with new types of phase behav- ior [4], enabled by our control of the entropy of the free strands [5]. I will also discuss preliminary ex- periments showing that we can measure directly the dynamics of transitions between different phases, us- ing a combination of techniques from droplet-based microfluidics, video microscopy, and image analysis. Going forward, this work could prove especially use- ful in nanomaterials research, where a central goal is to manufacture functional materials by growing them directly from solution.
We would like to acknowledge support from the Na- tional Science Foundation (NSF DMR-1710112).
Corresponding author: wrogers@brandeis.edu.edu
- W.B. Rogers, W.M. Shih, V.N. Manoharan, Nature Reviews Materials 1, 16008 (2016).
- Y. Wang, Y. Wang, X. Zheng, E. Ducrot, J.S. Yodh, M. Weck, D.J. Pine, Nature Comm. 6, 7253 (2015).
- Z. Zeravcic, V.N. Manoharan, M.P. Brenner, PNAS 111, 15918-15923 (2014).
- W.B. Rogers, V.N. Manoharan, Science 347, 639-642 (2015).
- J. Lowensohn, B. Oyarzun, G. Narvaez Paliza, B.M.Mognetti, W.B. Rogers, preprint.
Timings: 02:15 pm - 03:00 pm
Lecture 2: 16:00 to 17:00
Title : From self-assembly to cell recognition
Abstract : A holy grail of nano-technology is to create truly complex, multi-component structures by self-assembly. Most self-assembly has focused on the creation of "structural complexity". In my talk, I will discuss "Addressable Complexity": the creation of structures that contain hundreds or thousands of distinct building blocks that all have to find their place in a 3D structure. Experiments have demonstrated the feasibility of making such structures. Simulation and theory yield surprising insights that can inform the design of novel structures and materials. Surprisingly, the design principles for addressable self-assembly may provide a tool to distinguish different cell surfaces.
Date: 30 August 2018
oleksiyt@bnl.gov
Abstract:
The second law of thermodynamics states that the entropy of a closed system increases with time. Life represents a remarkable example of the opposite trend in an open, non-equilibrium system. Indeed, both informational and thermodynamic entropies decrease in the course of biological evolution reflecting ever-increasing complexity of living organisms and their communities \cite{schroedinger}. Conceptually, the problem of the origin of life can be viewed as a search for the simplest physical system capable of such spontaneous reduction of entropy and growth of complexity \cite{anderson}.
Self-replicating systems based on information-coding polymers are of crucial importance in biology. We have carried out a general theoretical and numerical analysis of the problem of spontaneous emergence of autocatalysis for heteropolymers capable of template-assisted ligation driven by cyclic changes in the environment \cite{JCP}. One of our key results is the existence of the first order transition between the regime dominated by free monomers and that with a self-sustaining population of sufficiently long chains. We provide a simple, mathematically tractable model supported by numerical simulations, which predicts the distribution of chain lengths and the onset of autocatalysis in terms of the overall monomer concentration and two fundamental rate constants.
The template-assisted ligation allows for heritable transmission of the information encoded in chain sequences thus opening up the possibility of long-term memory and evolvability in such systems. In order to explore this scenario, we focus at a reduced version of our original model \cite{arxiv}, by assuming that a template of just two ‘letters’ long is sufficient to catalyze a ligation of two chain ends. Within this reduced model, we can study both numerically and analytically the evolution of the sequence pool of such autocatalytic heteropolymers made of Z types of monomers (‘letters’). Remarkably we find that the sequence entropy, initially at its maximum (consistent with the Random Sequence Approximation used in \cite{JCP}), gets slowly reduced to a much lower value. A closer analysis shows that out of...
Our model, while not detailing specific chemical realization, describes a generic mechanism of formation of long autocatalytic heteropolymers. Furthermore, we show that this system is inherently unstable with respect to symmetry breaking in the sequence space. This leads to reduction of sequence entropy, signaling a spontaneous increase in the information. This can be interpreted as an onset of Darwinian behavior, and may explain future emergence of the natural selection.
The sequence information entropy in a pool of autocatalitic heteropolymers (black lines), and the natural logarithm of the number of surviving two-letter words, 2-mers (red lines) plotted vs. time in 5 different realizations of our system. b)-c) The heatmap visualizing concentrations of 2-mers at the early (b) and late (c) stages of the system’s evolution.
Acknowledgements
This research used resources of the Center for Functional Nanomaterials, which is a U.S. DOE Office of Science Facility, at Brookhaven National Laboratory under Contract No. DE-SC0012704.
- {schroedinger} Schr\"{o}dinger E. What is Life – the Physical Aspect of the Living Cell. Cambridge: Cambridge University Press.; 1944. NB: Strictly speaking, due to the exchange of energy and material with the environment, the appropriate measure of the reduction of thermodynamic entropy by living systems is the local accumulation of Gibbs free energy.
- {anderson} P. W. Anderson, Proc. Natl. Acad. Sci. U. S. A. 80, 3386 (1983)
- {JCP} A. V. Tkachenko, S. Maslov, J. Chem. Phys. 143, 04510 (2016)
- A. V. Tkachenko, S. Maslov, arXiv:1710.06385 (2017), to be published.
Timings: 09:00 am - 09:45 am
Abstract:
Structured materials self-assembled from dispersions of nanoparticles and colloids have numerous demonstrated applications including wave guides for optical computing, microlens arrays for energy harvesting, and porous electrodes for energy storage. As the particles self-assemble under a steady driving force, a thermodynamic constraint on the phase separation kinetics forces a tradeoff between quality of the self-assembled microstructure and its rate of formation. This is a key difficulty preventing adoption of self-assembled nanoparticle materials at scale. Dynamically self-assembling dispersions with interactions that vary in time do not have this constraint and offer a promising method to suppress kinetic arrest while accelerating growth of ordered nanostructures. For dispersions of polarizable dielectric or paramagnetic nanoparticles, varying the particle interactions in time is easily achieved by toggling the external electric or magnetic field on and off cyclically in time. Because of the cyclic driving force, materials formed by toggled self-assembly are dissipative and out-of-equilibrium, and therefore are classified as active matter, along with particles that swim, grow, or self-rotate. As toggled self-assembly cannot be understood in terms of equilibrium thermodynamics, new theories must be developed before it can be used to reliably fabricate nanomaterials.
I have developed a computational and theoretical model for dispersions of mutually polarizable nanoparticles in steady or toggled external fields. The model takes into account polarization from both the external field and from disturbance fields generated by induced dipoles on surrounding particles. Using Brownian dynamics simulations, I show that cyclically toggling the external field can avoid kinetic barriers and yield large, well-ordered crystalline domains in these dispersions. The rate of phase separation, local and global quality of the self-assembled structures, and range of tunable parameters leading to acceptable self-assembly are all enhanced with toggled fields compared to steady fields. Toggling can also stabilize new phases that are never observed in steady fields, such as fluid-fluid coexistence or body-centered-orthorhombic crystal. The growth mechanism and terminal structure of the dispersion are easily controlled by parameters of the toggling protocol, allowing for selection of processes that yield rapidly self-assembled, low defect structures. Although structures formed via toggled self-assembly are inherently out-of-equilibrium, I show that they can be understood in terms of equations of state valid for steady fields. I perform thermodynamic calculations that predict the out-of-equilibrium terminal states in terms of the parameters of the toggling protocol.
Timings: 09:45 am - 10:30 am
Abstract:
Many molecular processes involve ranges of length and time scales that cannot be tackled with atomic-scale simulations. Instead, coarse-grained molecular models are necessary to interrogate such systems from a theoretical point of view. We discuss a fundamental approach to the identification of such models and more generally of emergent physical behavior from many-body systems. We proposed that a quantity called the relative entropy measures the information lost upon coarse graining and is the natural thermodynamic metric for such tasks [1,2]; its minimization provides a universal variational principle for coarse-graining [3,4]. In particular, this broad statistical-mechanical framework can improve simulation models of complex biomolecular and liquid-state systems, and uncover important driving forces and degrees of freedom [4–6]. We discuss conceptual and numerical aspects of this approach and illustrate its use in several case studies, including our recent efforts to improve models of hydrophobic interactions and complex mixtures using mean-field, multibody interaction potentials inspired by embedded atom models of metallic systems [7,8].
Corresponding author: michael.gruenwald@utah.edu
- M. S. Shell, J. Chem. Phys. 129, 144108 (2008).
- M. S. Shell, in Advances in Chemical Physics, edited by S. A. Rice and A. R. Dinner (John Wiley & Sons, Inc., 2016), pp. 395–441.
- A. Chaimovich and M. S. Shell, Phys. Rev. E 81, 060104 (2010).
- A. Chaimovich and M. S. Shell, J. Chem. Phys. 134, 094112 (2011).
- S. Carmichael and M. S. Shell, J. Phys. Chem. B 116, 8383 (2012).
- A. Chaimovich and M. S. Shell, Phys. Rev. E 88, 052313 (2013).
- T. Sanyal and M. S. Shell, The Journal of Chemical Physics 145, 034109 (2016).
- T. Sanyal and M. S. Shell, J. Phys. Chem. B 122, 5678 (2018).
Timings: 11:40 am - 12:25 pm
Lecture 3: Thursday 30 August, 16:00 to 17:00
Title : Entropy production and phoretic transport
Abstract : It sounds so innocent: `Heat never spontaneously flows from cold to hot’, but almost nothing in this statement is as simple as it seems. In my talk, I will consider the microscopic mechanism by which thermal gradients cause flow along liquid/solid interfaces. In particular, I will discuss the problems in formulating a correct microscopic description of such `phoretic’ transport processes. Phoretic transport becomes increasingly relevant, as experiments probe transport in nanoscale channels. It turns out that our microscopic understanding of flows driven by thermodynamic, rather than mechanical, forces is far from complete.
Date: 31 August 2018
Abstract:
Macroscopic objects formed from particle assemblies are typically brittle, precluding their use in several ap- plications. We have demonstrated that ice-templating an aqueous dispersion of rigid colloidal particles and polymer, and crosslinking this polymer in the frozen state results in the formation of remarkably flexible colloidal assemblies[1]. Centimeter-scale monoliths prepared in this manner recover elastically after com- pression to 10% of their original size. This is remark- able when we consider that the monoliths are predom- inantly inorganic, with a particle weight fraction of 90%. Monoliths prepared in this manner are soft, with moduli in the range of tens of kPa. The Poisson ratio for monolith deformation can be calculated based on the change in sample dimensions during compression, and from the ratio of shear and Young’s moduli. The methods are consistent, and yield values close to zero. The scaling of moduli with density suggests the me- chanical response of the monolith in the linear regime is governed by thickening of the pore walls, rather than wall bending. For higher strains, there is a dra- matic increase in stress corresponding to buckling of pore walls.
The moduli of the monoliths increase linearly with temperature, indicating that the mechanical response is entropic in origin. We have demonstrated that flex- ible elastic hybrid monoliths can be prepared using different particles, different polymers and even dif- ferent crosslinking chemistries. Therefore, the me- chanical response appears to be a function largely of the microstructure developed by the preparation pro- cess viz. ice templating, followed by crosslinking in the frozen state. We demonstrate that this protocol results in the formation of a unique microstructure: polymers crosslinked in the frozen state form a mesh around particles in the pore walls[2, 3].
Subtle differences in the protocol for assembling nanoparticles play a critical role in determining their properties. Macroporous monoliths that are chemi- cally identical but that are prepared using small vari- ations in the ice templating protocol exhibit quali- tatively different mechanical behaviour, ranging from flexible elastic monoliths to plastic monoliths that fail at low compressive strains. We employ a variety of experimental techniques to characterize the structure and dynamics in these monoliths. We demonstrate that the preparation protocol modulates the spatial variation in crosslink density. Elastic scaffolds have a uniform distribution of crosslinks while scaffolds that have the same average crosslink density but spatially heterogeneous crosslinks exhibit brittle failure[2, 3].
Finally, I show that we can use the same ice tem- plating protocol to form flexible linear chain-like as- semblies that represent a convenient model system to study polymer physics. I will present results on the dynamics of active colloidal chains prepared using this protocol[4].
We would like to acknowledge SERB-Chemical En- gineering PAC, BRNS and IUSSTF for funding. KS, SC and BB acknowledge funding from CSIR and DST- Inspire.
Corresponding author: g.kumaraswamy@ncl.res.in
- R. Rajamanickam, S. Kumari, D. Kumar, S. Ghosh, J. C. Kim, G. Tae, S. Sengupta, G. Kumaraswamy, Chem. Mater. 26, 5161 (2014).
- S. Karthika, S. Patil, P. R. Rajamohanan, G. Ku-maraswamy, Langmuir 32, 11623 (2016).
- K. Suresh, R. Chulliyil, D. K. Sharma, Ketan, V. R. Kumar, A. Chowdhury, G. Kumaraswamy, Langmuir 34, 4603 (2018).
- B. Biswas, R. Manna, A. Laskar, P. B. S. Kumar, R. Adhikari, G. Kumaraswamy, ACS Nano 11, 10025 (2017).
Timings: 09:00 am - 09:45 am
Abstract:
One of the simplest systems to show phase transitions is a collection of particles that interact only through excluded volume interactions. Well known examples include hard sphere gas which undergoes a liquid-solid freezing transition and long rods which undergo an isotropic-nematic transition, or nearest neighbour ex- clusion models on lattices, also known as hard core lattice gas models. In such systems, all allowed con- figurations have equal energy and hence temperature plays no role, and phases transitions, if any, are driven by gain in entropy.
Simulations of such systems suffer from issues of equi- libration at high densities, especially when the ex- cluded volumes are large, due to long lived metastable states. This has resulted in not many accurate re- sults being known for hard core lattice gas models in three dimensions, or for two dimensional systems close to full packing. In this talk, I will elaborate upon a grand canonical Monte Carlo algorithm that implements cluster moves in an efficient manner which is able to equilibrate such systems even at the fully packed density. By implementing this algorithm, I will discuss recent results that have been obtained for sys- tems of differently shaped particles like rods, squares, cubes, plates, etc. [1, 2].
Corresponding author: rrajesh@imsc.res.in
- N. Vigneshwar, D. Dhar and R. Rajesh, J. Stat. Mech. 2017, 113304 (2017).
- D. Mandal, T. Nath and R. Rajesh, Phys. Rev. E 97, 032131 (2018).
Timings: 10:55 am - 11:40 am
Abstract:
Soft-core particles interacting via Spring-like repul- sion exhibit multiple reentrant crystallizations with various solid structures. In this talk, we will present our recent observations of the novel two-dimensional melting scenario due to the reentrance and surprising finding of quasicrystals.
According to the KTHNY theory [1–4], the melting of a two-dimensional solid is a two-stage process. There exists an intermediate phase called hexatic phase be- tween solid and liquid. Transitions from solid to hex- atic and from hexatic to liquid are both continuous. Recently, it has been reported that the hexatic-liquid transition of hard particles is discontinuous [5] and the transition can evolve from discontinuous to continuous when the softness of particles is tuned [6]. For soft- core particle systems which reach the first maximum melting temperature T m at a crossover density ρ m , we find that ρ m acts as a transition point. Hexatic-liquid transition at ρ < ρ m exhibits strong first order tran- sition features. There is a density interval in which liquid and hexatic phases coexist. The interval de- creases with increasing temperature and tends to van- ish at T m . When ρ > ρ m , however, the hexatic-liquid transition becomes continuous. Therefore, in soft-core systems with reentrant crystallization, density should affect the nature of the hexatic-liquid transition [7].
At much higher densities after several reentrance, we surprisingly observe the existence of two-dimensional quasicrystals [8]. Up to now, quasicrystals have been found in multi-component systems such as al- loys [9] and in mono-component systems with mul- tiple length scales in particle interactions [10–15] or with anisotropic particles such as tetrahedral and patchy particles [16, 17]. In all these systems, multiple length scales are present in particle size, interaction, or anisotropy, which seem to be the consensual condi- tion for quasicrystals to occur. The quasicrystals that we found are unexpectedly formed by monodisperse, isotropic particles interacting via the simple soft-core potential without multiple length scales. We find not only dodecagonal but also octagonal quasicrystals, which have not been found yet in soft quasicrystals. In our quasicrystals, particles tend to form pentagons. A pentagon surrounded by an n-fold polygon constructs the complex structural unit to develop the n-fold qua- sicrystalline order. In liquid states prior to the liquid- solid transition, we already observe some signs of the development of the quasicrystalline order, including the accumulation of pentagons and the emergence of two competing length scales. We have also verified that our quasicrystals are stable by showing that their formation is independent of history and they have the lowest inherent structure potential energy, compared with other crystalline states.
Corresponding author: ningxu@ustc.edu.cn
- J. M. Kosterlitz and D. J. Thouless, J. Phys. C: Solid State Phys. 6, 1181 (1973).
- D. R. Nelson and B. I. Halperin, Phys. Rev. B 19, 2457 (1979).
- B. I. Halperin and D. R. Nelson, Phys. Rev. Lett. 41, 121 (1978).
- A. P. Young, Phys. Rev. B 19, 1855 (1979).
- E. P. Bernard and W. Krauth, Phys. Rev. Lett. 107 155704 (2011).
- S. C. Kapfer and W. Krauth, Phys. Rev. Lett. 114, 035702 (2015).
- M. Zu, J. Liu, H. Tong, and N. Xu, Phys. Rev. Lett. 117, 085702 (2016).
- M. Zu, P. Tan, and N. Xu, Nat. Commun. 8, 2089 (2017).
- D. Shechtman, I. Blech, D. Gratias, and J. W. Cahn, Phys. Rev. Lett. 53, 1951 (1984).
- M. Engel, and H. Trebin, Phys. Rev. Lett. 98, 225505 (2007).
- C. R. Iacovella, C. R., A. S. Keys, and S. C. Glotzer, Proc. Natl. Acad. Sci. USA 108, 20935 (2011).
- A. J. Archer, A. M. Rucklidge, and E. Knobloch, Phys. Rev. Lett. 111, 165501 (2013).
- M. Dzugutov, Phys. Rev. Lett. 70, 2924 (1993).
- T. Dotera, T. Oshiro, and P. Ziherl, Nature 506, 208 (2014).
- M. Engel, P. F. Damasceno, C. L. Phillips, and S. C. Glotzer, Nat. Mater. 14, 109 (2015).
- A. Haji-Akbari et al., Nature 462, 773 (2009).
- A. Reinhard, F. Romano, J. P. K. Doye, Phys. Rev. Lett. 110, 255503 (2013).
Timings: 11:40 am - 12:25 pm
2. International Centre for Theoretical Sciences, Tata Institute of Fundamental Research, Bangalore 560012, India
3. Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA
4. Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA.
2. DAMTP, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK
Abstract:
We describe our efforts towards constructing synthetic active particle systems capable of tunable assemblies and organised structures. Active particles, including swimming microorganisms, autophoretic colloids and droplets, are known to self-organize into ordered struc- tures at fluid-solid boundaries. The entrainment of particles in the attractive parts of their spontaneous flows has been postulated as a possible mechanism underlying this phenomenon. Here, combining exper- iments, theory and numerical simulations, we demon- strate the validity of this flow-induced ordering mech- anism in a suspension of active emulsion droplets. We show that the mechanism can be controlled, with a variety of resultant ordered structures, by simply al- tering hydrodynamic boundary conditions.
Thus, for flow in Hele-Shaw cells, metastable lines or stable traveling bands can be obtained by varying the cell height. Similarly, for flow bounded by a plane, dynamic crystallites are formed. At a no-slip wall the crystallites are characterised by a continuous out- of-plane flux of particles that circulate and re-enter at the crystallite edges, thereby stabilising them. At an interface where the tangential stress vanishes the crystallites are strictly two-dimensional, with no out- of-plane flux. We rationalize these experimental re- sults by calculating, in each case, the slow viscous flow produced by the droplets and the dissipative, long- ranged, many-body active forces and torques between them. The results of numerical simulations of motion under the action of the active forces and torques are in excellent agreement with experiments. Our work [1] elucidates the mechanism of flow-induced phase sepa- ration (FIPS) in active fluids, particularly active col- loidal suspensions, and demonstrates its control by boundaries, suggesting new routes to geometric and topological phenomena in active matter.
States of self-organization maintained by entropy pro- duction were studied in the past by the Brussels school and were given the name dissipative structures [2]. Self-organization in active particles, as shown here, appears to be an example of a dissipative structure but one in which the dissipative mechanism and the resultant forces and torques are unambiguously iden- tified.
Corresponding author: Shashi Thutupalli - shashi@ncbs.res.in
- Thutupalli S, Geyer D, Singh R, Adhikari R, and Stone H A (2018) Flow-induced phase separation of active particles is controlled by boundary conditions Proc. Nat. Acad. Sci. 115 (21), 5403-5408.
- Kondepudi, D & Prigogine, I. (1998) Modern Ther-modynamics: From Heat Engines to Dissipative Struc-tures. (John Wiley & Sons).
Timings: 02:15 pm - 03:00 pm
Abstract:
Over the past decade, active hard spheres have be- come a benchmarking model system for studying the non-equilibrium physics in active matter. Although active hard spheres are intrisically out of equilibrium, we still find some equilibrium entropy-like effects in the system to drive the phase transition and self- organization in the system. In particular, I will talk about our recent work on active depletion forces [1], entropy driven active-passive demixing [2], and the formation of strongly hyperuniform fluids in systems of active hard spheres [3].
Corresponding author: r.ni@ntu.edu.sg
- R. Ni, M.A. Cohen Stuart, and P.G. Bolhuis, Phys. Rev. Lett. 114, 018302 (2015).
- Z. Ma, Q. Lei, and R. Ni, Soft Matter, 13, 8940 (2017)
- Q. Lei, M.P. Ciamarra, and R. Ni, arXiv:1802.03682 (2018)
Timings: 03:00 pm - 03:45 pm
Abstract:
We present a computational study of ligand effects in the self-assembly of non-spherical nanocrystals [1]. We focus on the two particle shapes most often found in experiments (cuboctahedral or truncated octahe- dral) and determine their assembly behavior as a function of ligand length and solvent quality. Our model, which is based on a coarse-grained description of ligands and a schematic representation of solvent effects, reproduces many of the experimentally ob- served superstructures [2–6], including superlattices with partial and short-ranged orientational alignment of nanocrystals [5, 6]. Our simulations show that small differences in nanoparticle size and shape, ligand cov- erage, and solvent conditions, can lead to markedly different self-assembled superstructures due to subtle changes in the free energetics of ligand interactions. These results help explain the large number of differ- ent reported superlattices self-assembled from seem- ingly similar particles and can serve as a guide for the self-assembly of specific superstructures.
We would like to acknowledge IISc, ISRO-STC and SERB-DST for funding this work.
∗ Corresponding author: michael.gruenwald@utah.edu
- M. A. Boles, M. Engel, and D. V. Talapin, Chem. Rev. 116, 11220 (2016).
- M. C. Weidman, D.-M. Smilgies, and W. A. Tisdale, Nat. Mater. 15, 775 (2016).
- J. J. Choi, C. R. Bealing, K. Bian, K. J. Hughes, W. Zhang, D. M. Smilgies, R. G. Hennig, J. R. En-gstrom, and T. Hanrath, J. Am. Chem. Soc. 133, 3131 (2011).
- J. Novák, R. Banerjee, A. Kornowski, M. Jankowski, A. André, H. Weller, F. Schreiber, and M. Scheele, ACS Appl. Mater. Interfaces 8, 22526 (2016).
- P. Simon, E. Rosseeva, I. A. Baburin, L. Liebscher, S. G. Hickey, R. Cardoso-Gil, A. Eychmüller, R. Kniep, and W. Carrillo-Cabrera, Angew. Chemie Int. Ed. 51, 10776 (2012).
- R. Li, K. Bian, T. Hanrath, W. A. Bassett, and Z. Wang, J. Am. Chem. Soc. 136, 12047 (2014).
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2. Centre for Theoretical Studies, Indian Institute of Technology Kharagpur, India
2. Centre for Theoretical Studies, Indian Institute of Technology Kharagpur, India
Abstract:
Swimming droplets are artificial micro swimmers that show self-propelled motion when immersed in a second liquid [1]. These systems are of tremendous interest as experimental models for biological systems, such as bacterial colonies, plankton, or fish swarms etc [2]. We study low Reynolds number locomotion of these spherical droplets of immiscible fluids as simplified hydrodynamic model of swimming micro-organisms or artificial self pro- pelling entities. We assume a unified surface activity in terms of interface conditions counting active velocity and stresses.
From analytical calculations, we highlight the charac- teristics of swimming pattern, migration velocity and on the energy dissipated by the swimmer into the medium.
The effect of thermal noise on the dynamics of these micro-swimmer has been highlighted. We also employ numerical simulations to construct trajectories and trans- port properties of the active swimmer. We show an ex- cellent agreement between the analytical and simulated behaviour of the swimmer.
Acknowledgments
The first author would like to acknowledge Indian In- stitute of Technology for the fellowship to pursue the PhD program.
- Sashi Thutupalli, Towards Autonomous Soft Matter Sys- tems Experiments on Membranes and Active Emul- sions, Doctoral Thesis (Springer Intenational Publishing Switzerland 2014).
- Eric Lauga, Annual Review of Fluid Mechanics 48, 105, (2016)
Timings:
2. Technical Vocational University Shahid Mofateh Institute, Hamedan, Iran
Abstract:
A rich variety of novel statistical properties and ordering-disordering states colloidal particle interact- ing through a long range repulsive Yukawa poten- tial, confined by a 2D periodic substrate potential is investigated[1],[2],[3],[4].
The study of ordering of colloidal particles and the variation of the statistical quantities of them resem- ble that of a KBT-like defect topological in low tem- perature phase Fig. 1, Fig. 2[5],[6]. We found a strong dependence of the substrate strength on ar- rangement of the particles and the diffusive behav- ior of them[7] .We study the equilibrium proper- ties such as order parameter, potential per energy and heat capacity through a Monte Carlo simulation Fig. 3,Fig. 4,Fig. 5,Fig. 6,Fig. 7,Fig. 8. The evolution of the correlation function for different temperatures is also studied Fig. 9. In addition, we studied the dynamic properties of particles structure through a MD simulation[8], which cannot provide by equilib- rium sampling method. Specifically, we studied the fluctuation of velocity and instantaneous temperature of particles vs time-stepsFig. 10. By studying of these quantities, We, finally come to an equilibrium steady state system, which is completely dependent to the substrate strength and density of particles.
Corresponding author: Amin Najafi - na-jafi.amin@znu.ac.ir
- C.Reichhardt and C.J.Olson Phys.Rev.Lett 88, 248301(2002).
- C.Reichhardt and C.J.Olson Reichhardt Euro- phys.Lett 68, 303(2004) .
- A.Libal , C.Reichhardt and C.J.Olsont Phys.Rev.E 75, 011403(2007).
- Amin Najafi, J. Phys.: Conf. Ser 510, 012025(IOP),(2014).
Timings:
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Abstract:
Controlling the phase behavior of protein solution is important for diverse biological applications and fundamental studies in soft matter. Recent experi- ments have reported a lower critical solution temper- ature (LCST) phase behavior of aqueous solutions of a protein induced by multivalent ions, where upon heating the protein-salt solution phase separates[1]. This LCST behavior has been suggested to be en- tropy driven. In this work, we use all-atom molec- ular dynamics (MD) simulation along with the two phase thermodynamics (2PT)[2, 3] method for en- tropy calculation to decipher the molecular mecha- nism of this process. Our simulation results indicate two key steps that can help in explaining the LCST behavior. The first step is the cations binding to the protein. This requires release of tightly bound wa- ter molecules from the first solvation shell of cations as well as partial desolvation of the protein’s surface residues, which are indeed entropy driven. We show that this entropic driving force increases with tem- perature. In second step the bound cations attract other proteins present in solution, whose binding is again entropy driven, resulting in LCST behavior. We have carried out series of simulations using va- riety of cations, both monovalent (Na + ) and multiva- lent (Ca 2+ , Mg 2+ and Y 3+ ), at various temperatures ranging from 283 to 323 K, which suggest in general multivalent cations binding to any negatively charged surfaces is driven by entropy. These findings have di- rect implications for tuning the phase behavior of soft matter systems, such as reentrant condensation[4] and protein crystallization[5, 6].
Corresponding author: maiti@iisc.ac.in
- O. Matsarskaia, M. K. Braun, F. Roosen-Runge, M. Wolf, F. Zhang, R. Roth, and F. Schreiber, J. Phys. Chem. B 120, 7731 (2016).
- S.-T. Lin, M. Blanco, and W. A. Goddard III, J. Chem. Phys. 119, 11792 (2003).
- S.-T. Lin, P. K. Maiti, and W. A. Goddard III, J. Phys. Chem. B 114, 8191 (2010).
- F. Zhang, M. Skoda, R. Jacobs, S. Zorn, R. A. Mar- tin, C. Martin, G. Clark, S. Weggler, A. Hildebrandt, O. Kohlbacher, et al., Phys. Rev. Lett. 101, 148101 (2008).
- F. Zhang, G. Zocher, A. Sauter, T. Stehle, and F. Schreiber, J. Appl. Crystallogr. 44, 755 (2011).
- F. Zhang, R. Roth, M. Wolf, F. Roosen-Runge, M. W. Skoda, R. M. Jacobs, M. Stzucki, and F. Schreiber, Soft Matter 8, 1313 (2012).
Timings:
2. Department of Physics, Bangalore University, Bangalore-560056, India
Abstract:
An optical trap can trap micron sized objects when it is passed through a high numerical aperture objective[1].The optical tweezer consist of a single laser beam focused to a diffraction limited spot (typ- ically about λ/2, λ being the wavelength of the laser beam used).We optically trap a gram-positive bac- terium Bacillus subtilis- in an optical trap and study the flagellar rotation. Bacillus subtilis is a non- pathogenic bacterium which uses flagella rotation to move in a liquid environment [2]. The rotation of the flagella in an anticlockwise direction constitutes a run sequence and in a clockwise direction constitutes a tumble sequence. The rotating movement of bac- terium flagellum has an important role in cell motility and chemotaxis. B.subtilis flagellum consists of three architectural domains: the basal body, the hook and the filament. The filament is a helical structure made up of repeated units of protein flagellin. The hook is a distinct structure located at the base of the fila- ment and also attached to the basal body. The basal body is located inside the cell envelope. The motor in- cluded in the basal body contains two functional enti- ties; the rotor and the proton conducting stator. The proton-motive force generates a torque at the rotor interface in the basal body. This torque is imparted to the filament through the hook, causing the flagel- lum to rotate [3]. In order to balance this torque, the cell body of the bacterium rotates in opposite direc- tion (the cell rotates clockwise during run sequence (as shown in fig1) and anticlockwise during tumble sequence). When the bacterium is trapped in an op- tical trap, we observe the rotational motion of the cell body and are recorded by a high frame rate cam- era. The trajectory of the bacterium is obtained by video analysis and the data is processed to obtain the power spectrum of the trajectory ( fig 2). The power spectrum consists of two peaks, the larger peak corre- sponds to cell body rotation frequency and the smaller peak corresponds to flagella rotation frequency. This experiment helps us to determine the propulsion co- efficicents of the motile bacterium in low Reynolds number, which are useful in determining forces and torques exerted on the flagellum [4, 5]. Previously, several experiments are performed to determine the torque exerted on the flagellum of the bacterium by attaching beads to the hook of the flagellum to get the torque-speed relations [6]. We can consider this experiment as a non- contact way of determining the torque exerted on the flagellum without attaching any other external geometries to the bacterium by using a simple optical trap and can further be applied to study the torque-speed relations at different environmental conditions.
Ashwini V Bhat acknowledges a DST-INSPIRE fel- lowship. The experiment set up was enabled through a previous DST (Nanoscience and Technology Initia- tive) project
Corresponding author: sasp@uohyd.ac.in
- A Ashkin, J M Dzeidzic, J E Bjorkholm and S Chu Opt. Lett. 11(5) 288-90 (1986)
- S B Guttenplan, S Shaw, and D B Kearns Mol. Micro- biology 87(1) 211-29 (2013)
- C Diethmaier, R Chawla, A Canzoneri, D B Kearns ,P P Lele and D Dubnau Mol. Micro. 106(3), 367-80 (2017)
- E M Purcell Proc. Natl. Aca. Sci. USA. 94 11307 (1997)
- S Chattopadhyay, R Moldovan, C Yeung and X L Wu PNAS 103 13712-17 (2006)
- N Terahara, Y Noguchi, S Nakamura, N Kami-ike, M Ito, K Namba and T Minamino Scientific Reports 7 46081 (2017)
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2. Department of Physics, Bangalore University, Bangalore – 560050
asharath@gmail.com
Abstract:
A human Red Blood Cell (RBC) has a biconcave structure with the central crater region or the dimple region of thickness about 1 micron and the peripheral region or rim region of thickness of about 2 microns. The cell membrane of an RBC is highly deformable which allows it to sometimes squeeze through capillaries much smaller than itself and deliver oxygen throughout the body. Thus studies on the mechanical properties of the RBC have garnered sufficient interest in recent times. However, there is a paucity of studies that focus on the variation of membrane elasticity across the two prominent regions of the human RBC. This study investigates mechanical properties of RBC using atomic force microscopy (AFM) with the aim to understand the variation of the cell membrane stiffness at different regions of the cell membrane under the influence of Bovine serum albumin (BSA). Bovine serum albumin is a serum albumin protein derived from cows. BSA can be used to alter the membrane stiffness of RBCs [1] and thus mimic cells found in different pathological conditions. The objective of this study is to quantify a) the variation of membrane stiffness across the two regions and b) the changes in the membrane stiffness of the two regions.
The variation of cell stiffness of RBC at different regions of the cell is understood by performing local force spectroscopy on the sample. Force spectroscopy studies have been carried out in three different regions of the cell membrane: Rim region, dimple region and intermediate (region between the other two) and corresponding force distance curves are obtained. Elasticity modulus of the sample is obtained using Hertz model. It is observed that there is a considerable amount of variation in the stiffness of membrane at different regions of the membrane for the same BSA concentration. This non- uniformity is found to be significantly increasing for different concentrations of BSA. We are currently trying to study these variations in a detailed manner.
Acknowledgements
Authors would like to thank Department of Science and Technology (DST), Government of India for a grant under PURSE project which made this work possible.
References
- Rekha. S, et al. “Flow of Human Red Blood Cells with altered cell membrane stiffness through narrow channels” [submitted to Nature Scientific Reports and under consideration].
- Praveen, Parthasarathi, et al. "Effect of Bovine Serum Albumin on Red Blood Cell Optical Anisotropy Probed Through the Optomechanical Response in an Optical Trap."Macromolecular Symposia. Vol. 376. No. 1. 2017
- C. C. Lien et al., "Study on the Young’s Modulus of Red Blood Cells Using Atomic Force Microscope Applied Mechanics and Materials, Vol. 627, pp. 197-201, 2014
- Musielak, M. "Red blood cell- deformability measurement: review of techniques."Clinical hemorheology and microcirculation 42.1 (2009): 47-64.
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Animal movements on solid substrates involve com- mon mechanical principles emerging from elas- ticity of tissues. We unravel the mechanics governing the somersault of Hydra, one of the earliest multi-cellular organisms to have evolved substratum movement. We measured the local mechanical properties and discov- ered a specific variation in Youngs modulus of tissues along the body column. Using simulations, we demon- strate that this variation facilitates somersault by ef- ficient energy trans- fer between body parts. The per- turbation of observed gradient in elasticity completely hinders the somersault.
We would like to thank Drs Sudhakaran Prab- hakaran and Sanjay Sane for useful comments on the manuscript. We thank Yashodeep Matange for help with animations and Dr Arpita Roychoudhury for dis- cussion.
Corresponding author: apratim@iiserpune.ac.in
- A. A. Biewener, Science 250, 1097 (1990).
- R. M. Alexander, Principles of animal locomotion (Princeton University Press, 2003).
- L. Ristroph, J. C. Liao, and J. Zhang, Phys. Rev. Lett. 114, 018102 (2015).
- M. Saadat, F. E. Fish, A. G. Domel, V. Di Santo, G. V. Lauder, and H. Haj-Hariri, Phys. Rev. Fluids 2, 083102 (2017)
- J. Gray, Journal of experimental biology 10, 88 (1933).
- H. R. Bode, L. W. Gee, and M. A. Chow, Develop- mental biology 139, 231 (1990).
- H. R. Bode, Journal of cell science 109, 1155 (1996).
- B. Galliot, Current opinion in genetics and develop- ment 10, 629 (2000).
- B. J. Gemmell, S. P. Colin, J. H. Costello, and J. O. Dabiri, Nature communications 6, 879 (2015).
- S. Han, E. Taralova, C. Dupre, and R. Yuste, eLife 7, e32605 (2018).
- S. Shostak, N. Patel, and A. Burnett, Developmental bi- ology 12, 434 (1965).
- A. Trembley.
- H. M. Fox, Journal of Zoology 117, 365 (1947).
- J. Howard, Mechanics of Motor protein and the Cytoskeleton (Sinauer Adssociates, Sunderlan, Mas- sachusettes) (2001).
- M. P. Sarras, D. Meador, and X. Zhang, Developmen- tal biology 148, 495 (1991).
- A. J. Engler, S. Sen, H. L. Sweeney, and D. E. Discher, Cell 126, 677 (2006).
- R. C. Siegel, S. R. Pinnell, and G. R. Martin, Biochem- istry 9, 4486 (1970).
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2. Present address: School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, KY16 9SS, Scotland, United Kingdom.
2. International Centre for Materials Science, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India.
Abstract:
The mechanisms through which deeply supercooled liquids crystallize without large scale particle diffu- sion remains poorly understood. Recent numerical studies [1, 2, 3] have uncovered that crystal nucle- ation follows bursts of cooperative rearrangements of large number of particles termed avalanches. Never- theless, such avalanche events are yet to be observed in experimental systems. Here, by using confocal video microscopy we study devitrification of monodisperse dense PNIPAM soft sphere colloidal suspensions be- low the mode-coupling transition temperature. We observe intermittent collective displacements of parti- cles some of which results in the for- mation of crystal nuclei. Further the increase of free volume around the crystallites allows growth to also proceed via particle swapping loops and string like particle motions at the crystal-liquid interfaces. Our work provides a rare in- sight into the dynamics of particle motion that result in the devitrification of deeply supercooled liquids.
Corresponding author: divyagkanaka@gmail.com
- E. Zaccarelli et al., Crystallization of Hard-Sphere Glasses, Phys. Rev. Lett. 103, 135704 (2009)..
- Eduardo Sanz et al., Avalanches mediate crystal- lization in a hard-sphere glass., Proc. Natl. Acad. Sci. U.S.A. 111, 75-80 (2014)
- Taiki Yanagishima, John Russo and Hajime Tanaka., Common mechanism of thermodynamic and mechan- ical origin for ageing and crystallization of glasses, Nat. Commun. 8, 15954(2017).
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Abstract:
The study of the dynamics of supercooled liquids and glass transition is one of the most active field in mod- ern condensed matter physics. There are many as- pects which are studied and one of the interesting ar- eas of investigation is to find the relation between dy- namics and structure of glass-forming liquids. In a recent work [1] from our group, it was shown that the structure has the information of the dynamical transi- tion temperature. The dynamics of the system at the pair level was described by independent particles in an external field. The field had the information of the interaction between the particles. It was shown that only structure at pair level is required to describe the field. Using mean first passage time formalism it was shown that for multiple systems the dynamics predicts the dynamical transition temperature. Thus, the for- mulated theory was successful in differentiating the dynamics of two systems having very similar struc- ture ( one where the particles interact via Lennard Jones potential and the other where they interact via the WCA potential ) . Although in a similar theory [2, 3] developed by K.Schweizer and later applied [4] by Bertheir and Tarjus it was found that the two sys- tems appear quite similar.
In this work we will analyze why two theories which appear quite similar provide different results. The present work does not attempt to develop a better theoretical framework to study the full dynamics of a supercooled liquid. We employ both the theories to generate their respective results and will compare them in an equitable way.
The basic differences between the two models are in our model we started with a Fokker Planck equation of a binary system and obtained the mean first pas- sage time dynamics on the potential energy landscape. In Scheweizers model they started with the Langevin equation on the Free energy surface of a monatomic system and obtained the dynamics given by Kramers theory. Note that, we can recast any Langevin equa- tion onto a Fokker Planck equation and vice versa. We can also go from mean first passage time (MFPT) dynamics to Kramers dynamics. Thus, the main dif- ference between the two models are ours is the dynam- ics in the potential energy surface of a binary system and Schweizers is that on the free energy surface of a monatomic system.
It is an ongoing work. However, our preliminary stud- ies indicate that although Schweizer’s theory predicts that the dynamics of two systems are not profoundly different; but when analyzed properly we find the dy- namical transition temperatures of the two systems are different.
Corresponding author: mb.sarika@ncl.res.in
- M. K. Nandi, A. Banerjee, C. Dasgupta, S.M.Bhattacharyya. Role of the Pair Correlation Function in the Dynamical Transition Predicted by Mode Coupling Theory, Phys. Rev. Let., 119, 265502 (2017).
- K. S. Schweizer, J. Chem. Phys. 123, 244501 (2005).
- K. S. Schweizer and E. J. Saltzman, J. Chem. Phys. 119, 1181 (2003).
- L. Berthier, G. Tarjus, Eur. Phys. J. E 34, 96 (2011).
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We study numerically the ordering kinetics in a system where the amount of randomness can be gradually tuned. We show that, upon increasing such features, the behavior changes in a radical way. Small randomness does not prevent the system from a complete ordering, but this occurs in an extremely (logarithmically) slow manner. However, large randomness destroys complete ordering, a feature denoted as frustration, and the evolution is comparatively faster (algebraic). Our study shows a precise correspondence between the kind of developing order, complete versus frustrated, and the speed of evolution. Also, we presented an interpretation in terms of the different nature of phase space.
Corresponding author corberi@sa.infn.it
- F. Corberi, M. Kumar, S. Puri, and E. Lippiello, Phys. Rev. E 95, 062136 (2017).
- F. Corberi, E. Lippiello, R. Burioni, A. Vezzani, and M. Zannetti, Phys. Rev. E 91, 062122 (2015).
- F. Corberi, E. Lippiello, and M. Zannetti, J. Stat. Mech. P10001 (2015).
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2. International Centre for Materials Science, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
Abstract:
The statics and dynamics of a crystal residing on flat space is fundamentally different from those residing on curved space[1]. Intuition however suggests that spa- tial curvature should play a less influential role in the dynamics of disordered systems. Recent simulations however find that glass forming liquid on the surface of a 4D hypersphere freezes via a sharp transition into fully icosahedral structure on curving 3D space[2] and a monoatomic liquid on the hyperbolic plane exhibits increase in fragility with increasing curvature[3]. Ex- perimental studies that have investigated the role of spatial curvature on dynamics of supercooled liquid are scarce. We have developed a model binary col- loidal system residing on surface of a 3D sphere to understand the role of curvature on the dynamics of supercooled liquid. We used fast confocal microscopy to probe dynamics at the single particle level. In this poster, we will highlight recent findings on role of spa- tial curvature on the behaviour of dynamical hetero- geneities on approaching mode coupling glass transi- tion.
Corresponding author navneet22may@gmail.com
- William T. M. Irvine, Mark J. Bowick and Paul M. Chaikin, Fractionalization of interstitials in curved colloidal crystals, Nature Materials 11, 948 951, 2012.
- Francesco Turci, Gilles Tarjus and C. Patrick Roy-all, From Glass Formation to Icosahedral Ordering by Curving Three-Dimensional Space, Physical Review Letters 118, 215501, 2017.
- Franois Sausset, Gilles Tarjus, and Pascal Viot, Tun-ing the Fragility of a Glass-Forming Liquid by Curving Space, Physical Review Letters 101, 155701, 2008.
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Rich structural complexity of biomembranes arises from the chemical diversity of its constituents. This high complexity inevitably gives rise to degeneracy of great biological relevance. Degeneracy refers to struc- turally different species that perform same or differ- ent function according to the constraints imposed [1]. Here we focus on degeneracy in lateral organization of the membrane which plays a key role in processes such as signal transduction, pathogen intake and assembly of protein complexes.
Variety of lateral organization on the membrane surface occur due to preferential segregation and clustering of certain types of lipids and proteins owing to their differential inter and intra-molecular interactions. In this work, we explore the molecular- origin and degeneracy in the variety of organization using tools from simple statistical mechanics the- ories. We develop a physics-based Hamiltonian for membrane organization using long atomistic trajectories on systems that exhibit liquid-ordered and liquid-disordered (Lo/Ld) coexistence. Re- cently, Lyman’s group at Delaware carried out multiple long microseconds timescales all-atom (AA) simulations with carefully chosen lipid com- positions to reproduce a variety of phases [2, 3]. The three systems with their fractional composi- tions are (i) DPPC/DOPC/Chol (0.37/0.36/0.27) (ii) PSM/DOPC/Chol (0.43/0.38/0.19) (iii) PSM/POPC/Chol (0.47/0.32/0.21). These sys- tems have very different molecular-level substructures and unique Lo/Ld interface boundaries.
We evolve the Hamiltonian using Monte Carlo (MC) algorithm to recapitulate the lateral organization in the above-mentioned AA systems. The interaction potential is written as a function of the degree of non- affinity in topological rearrangement of the lipids (χ 2 ). The configuration of lattice sites is evolved while keep- ing the probability distribution of χ 2 (unique to the three systems) in the corresponding AA system con- served. The final configurations of the evolved states are mapped to AA equilibrium configurations [4, 5] and their energy values are reported. On evolving a given system with the Hamiltonian of another system, our preliminary calculations indicate that the lateral organization from the given Hamiltonian is captured with reduced probability for the new system and with a higher energy penalty. This provides us with an early indication of degeneracy in membrane organiza- tion between different composition.
The authors thank Edward Lyman (University of Delaware, USA) for sharing the AA simulation tra- jectories run on Anton computer at Piittsburg Super- computing Center (PSC) which was generously made available by D.E. Shaw Research. AS would like to thank IISc Bangalore for the start-up grant and the Department of Science and Technology, India for the HPC grant(MBU/DSTO/ASR/1809/2018). SS and AS thank Dr. Madusmita Tripathy for her insights into lattice model.
Corresponding author: anand@iisc.ac.in
- Edelman G. M., and Gally J. A, PNAS, 98, 1376313768 (2001).
- Sodt, A. J., R. W. Pastor, and E. Lyman, Biophysical journal, 109, 948955 (2015).
- Sodt, A. J., M. L. Sandar, K. Gawrisch, R. W. Pas-tor, and E. Lyman, Journal of the American Chemical Society, 136, 725732 (2014).
- Sadeghi. S., Muller M. and Vink R. L.C, Biophysical Journal, 107, 1591-1600 (2014) , pp. 666–999.
- Hakobyan D. and Heuer A., Journal of Chemical Physics, 146, 064305 (2017)
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Abstract:
Active particles belong to a class of non-equilibrium systems that constantly convert energy into mo- tion, resulting in a continuous dynamic reorganiza- tion of the constituents. A fascinating variety of non- equilibrium phenomena like swarming, lane forma- tion, giant density fluctuations, clustering, vortices, etc. has been revealed by a number of synthetic and biological systems. Theoretical models of these sys- tems, apart from the aforementioned novelties, have also been known to show equilibrium-like phenom- ena such as condensation, phase transition, crystal- lization etc. Recent research in the field has been towards explaining such behavior in terms of equiv- alent thermodynamic quantities. We explore prop- erties such as the states of phase coexistence and mechanical pressure[1], interfacial tension[2], chemi- cal potential[3], entropy generation and power dissipa- tion in these out-of-equilibrium systems. Our results show that the coexisting bulk states not only depend on bulk properties but also on the interfacial proper- ties even though the coexisting states are in mechan- ical and diffusive equilibrium[3]. Our findings relate to conclusions of previous studies which associate the stationary state with strong entropy production at the interfaces[4].
In this study we further explore the effect of an ex- ternal potential that is localized at the interface of a phase-separated system of Active Brownian Particles (ABPs). In particular, we apply a sawtooth-shaped potential (also known as a Ratchet potential) which is asymmetric. It has been observed in earlier studies that these kinds of setups can induce rectification of the particles[5]. In the case of arbitrarily large bulk regions enclosed by walls, the steady-state densities are dependent on the ratchet potential[6].
We perform numerical calculations for a system of non-interacting as well as interacting ABPs either by directly solving the Smoluchowski equation or per- forming explicit particle based Brownian dynamics simulations. Our observations indicate that the dif- ference in densities of the bulk regions depends on the parameters of the ratchet potential. For the Active ideal-gas, we establish a power-law dependence with respect to the degree of activity, height of the ratchet potential and the asymmetry. For the interacting sys- tem the preliminary results also indicate such a trend with respect to ‘effective height’ of the ratchet where the effective temperature of the particles is enhanced due to the presence of activity.
These results suggest that unlike equilibrium systems, the interfacial contributions play a major role in active systems to the extent that bulk properties such as the density depends on the arbitrarily far interface.
Corresponding author: s.paliwal@uu.nl
- V. Prymidis, S. Paliwal, M. Dijkstra, L.Filion, J. Chem. Phys. 145, 124904 (2016)
- S. Paliwal, V. Prymidis, L. Filion and M. Dijkstra, J. Chem. Phys. 147, 084902 (2017)
- S. Paliwal, J. Rodenburg, R. v. Roij, M. Dijkstra, New J. Phys. 20, 015003 (2018)
- C. Nardini, . Fodor, E. Tjhung, F. v. Wijland, J. Tailleur, and M. E. Cates Phys. Rev. X 7, 021007 (2017)
- A. B.-Quan and L. F.-Guo, Soft Matter, 13, 2536 (2017)
- L. Angelani, A. Constanzo, and R. D. Leonardo, EPL 96, 68002 (2011).
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Abstract:
Self propelled particles (SPPs), usually called active matters, are ubiquitous in living systems. They span a strikingly wide range of length scales - from the mi- cron sized cell cytoskeleton [1] and bacterial colonies [2] to much larger (meter to hundreds of meter) animal groups, such as flocks of birds, fish schools, swarms of insects, etc [3, 4]. These particles propel themselves by converting chemical energy to mechanical one, which is continually dissipated to the medium. The steady flow of energy keeps the system out of equilibrium and a novel nonequilibrium steady state (NESS) emerges. The steady state manifests itself by exhibiting rich collective phenomena, e.g., self-assemblies and pat- tern formations, otherwise impossible in equilibrium. Recently, there is a surge of interest in search of a suitable statistical mechanics framework which could describe macroscopic properties of the SPPs in terms of an intensive thermodynamic variable, such as chem- ical potential [5], pressure [6] or effective temperature [7]. However, a complete framework is still lacking.
We study, in the context of the SPPs, whether a general thermodynamic structure could enable one to unify fascinatingly broad-ranging phenomena in the systems of SPPs, directly connecting microscopic fluc- tuations to the macroscopic properties in such sys- tems. Previously additivity has been successfully used in nonequilibrium mass-transport processes for calcu- lating mass distributions and characterizing macro- scopic properties in terms of equilibrium-like chemi- cal potentials [9]. Here, we would like to address the broad question whether an equilibrium-like additivity property can be used to obtain large deviation prob- ability of the density fluctuations in systems of SPPs in general [8].
We study particle-number fluctuations in systems of interacting SPPs with random self-propulsion veloci- ties in a set-up of fluctuating hydrodynamics. Using an additivity property and a consequent fluctuation- response relation, we formulate a thermodynamic the- ory which captures remarkably well the broad fea- tures of nonequilibrium phase transition from a ho- mogeneous fluid phase to an inhomogeneous phase of coexisting gas and liquid, observed in the past. We validate the theory by analytically calculating subsys- tem particle number distributions and then compar- ing them with simulations in a microscopic model of active Brownian particles (ABPs) consisting of repul- sive disks with random self-propulsion velocities. Our analysis provides useful insights into the earlier re- sults, e.g., motility induced phase separation (MIPS) in SPPs. Moreover, our analysis suggests that, on the mean-field level, a broad class of SPPs could belong to the Ising universality.
We extend the formalism [11] to other active parti- cle systems like Vicsek model (VM) and two variants [12, 13] of it consisting of point polar particles with alignment interaction. There we compute subsystem particle-number distributions in the disordered fluid- like phase using additivity property and compare the number distributions with those obtained from simu- lations of such systems. We find quite good agreement between theory and simulations. Our theory captures well the non-Gaussian feature of the distribution.
Corresponding author: sub-hodip.chakraborti@bose.res.in, smishra.phy@iitbhu.ac.in, punyabrata.pradhan@bose.res.in
- Julicher F, Kruse K, Prost J, Joanny J-F. Phys. Rep.449, 328 (2007).
- C. Dombrowski et. al., Phys. Rev. Lett. 93, 098103 (2004).
- T. Feder, Phys. Today 60, 28 (2007); C. Feare, The Starling (Oxford University Press, Oxford, 1984)
- E. Rauch, M. Millonas, and D. Chialvo, Phys. Lett. A 207, 185 (1995).
- J. Tailleur and M. Cates, Phys. Rev. Lett. 100, 218103 (2008).
- A. P. Solon, Y. Fily, A. Baskaran, M. E. Cates, Y. Kafri, M. Kardar and J. Tailleur, Nat. Phys. (2015).
- D. Levis and L. Berthier, EPL 111, 60006 (2015).
- S. Chakraborti, S. Mishra, and P. Pradhan, Phys. Rev. E 93 052606 (2016).
- S. Chatterjee, P. Pradhan and P. K. Mohanty, Phys. Rev. Lett. 112, 030601 (2014).
- A. Das, S. Chatterjee, P. Pradhan, and P. K. Mo-hanty, Phys. Rev. E 92, 052107 (2015).
- Additivity and number fluctuations in Vicsek models, S. Chakraborti, S. Mishra, and P. Pradhan (to be submitted)
- T. Vicsek, A. Cziro, E. Ben-Jacob, I. Cohen, and O.Shochet, Phys. Rev. Lett. 75, 1226 (1995).
- G. Gregoire and H. Chate, Phys. Rev. Lett. 92, 025702 (2004).
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Abstract:
In vivo DNA organization at large length scales (≈ 100nm) is highly debated and polymer models have proved useful to understand the principles of DNA organization. We showed that ≈ 2% cross-links at specific points in a ring polymer can lead to a dis- tinct spatial organization of the polymer. The specific pairs of cross-linked monomers were extracted from contact maps of bacterial DNA. We are able to pre- dict the structure of 2 DNAs (E. coli and Caulobac- ter crescentus) using Monte Carlo simulations of the bead-spring polymer with cross- links at these special positions. Simulations with cross-links at random po- sitions along the chain show that the organization of the polymer is different in nature from the previous case. We provided some direct and some indirect ex- perimental validation for our predicted organization of DNA-polymers and this was published in [1, 2].
We have now systematically investigated (a) the role of changing excluded volume of the beads, which in turn affects chain crossing (b) the role of the solvent quality (alternatively this could be interpreted effec- tive attractive interactions between adjacent segments of chains mediated by suitable proteins) (c) the role of confining walls in the organization of the DNA- polymer. We find that the confinement plays the most crucial role in the organization of the DNA polymer, and we are able to make significant improvements in the match of theoretical predictions with experimental data.
Corresponding author: tejal.agarwal@students.iiserpune.ac.in
- T. Agarwal, G. P. Manjunath, F. Habib, P. L. Vad- davalli and A. Chatterji, J. Phys.: Condens. Matter 30, 034003 (2018).
- T. Agarwal, G. P. Manjunath, F. Habib and A. Chat- terji, EPL 121, 18004 (2018).
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