arxiv: 2605.01470 · v1 · submitted 2026-05-02 · ❄️ cond-mat.soft · cond-mat.stat-mech· physics.comp-ph

Recognition: unknown

Colloidal layer deposition with a controllable number of layers and compositional order

Aashima Aashima, Akshaya Kumar Jena, Bortolo Matteo Mognetti, Pritam Kumar Jana

Authors on Pith no claims yet

Pith reviewed 2026-05-09 17:58 UTC · model grok-4.3

classification ❄️ cond-mat.soft cond-mat.stat-mechphysics.comp-ph

keywords colloidal self-assemblyDNA-mediated interactionslayered aggregatescompositional orderreaction kineticsreaction-diffusion simulationfinite-thickness crystallites

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The pith

DNA-decorated colloids and surfaces self-assemble into crystallites with controlled layer count and alternating composition

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

The paper shows how attaching multiple DNA oligomers to colloids and a surface triggers localized self-assembly of binary colloidal crystallites that stop at a chosen number of layers. Equilibrium rules set the final thickness while tuned reaction rates between the DNA strands prevent same-type particles from binding and force them onto separate planes. Theory and reaction-diffusion simulations that include multibody effects are used to confirm the design works. A reader would care because this gives a programmable route to build ordered layered materials from particles without external templates or continuous forcing.

Core claim

What carries the argument

Multiple DNA oligomers with specific interactions attached to colloids and surface, triggering a localized reaction chain whose equilibrium sets aggregate thickness and whose kinetics enforce compositional order by limiting same-type binding.

Load-bearing premise

That DNA oligomers can be designed and attached so the intended specific bindings dominate without significant cross-reactivity or off-target effects, and that the reaction-diffusion model captures the actual multibody colloidal behavior.

What would settle it

An experiment or simulation showing aggregates whose thickness varies independently of equilibrium conditions or where same-type colloids occupy the same plane would falsify the claimed control.

Figures

Figures reproduced from arXiv: 2605.01470 by Aashima Aashima, Akshaya Kumar Jena, Bortolo Matteo Mognetti, Pritam Kumar Jana.

**Figure 1.** Figure 1: The model. (a) Illustration of a binary system comprising colloids (A and B) functionalized with two pairs of ligands (a1, a2 and b1, b2) in the presence of a surface functionalized with a single type of ligand (b1). (b) Schematic representation of ligands, consisting of a hydrophobic tag (anchoring the DNA to supported lipid bilayers), a rigid double-stranded DNA spacer, and a sticky end composed of three… view at source ↗

**Figure 2.** Figure 2: Kinetic vs Equilibrium Interactions. Effective, kinetic interactions (black circles) and equilibrium interactions (red squares) for a single particle near the surface (a, b), and a particle near another A-type particle bound to the surface (c, d). A-type particles bind the surface (a) but do not bind surface-bound A particles (c). Instead, B-type particles bind surface-bound A particles (d) and are repelle… view at source ↗

**Figure 3.** Figure 3: Colloidal layer deposition with a controllable number of layers and compositional order. Multi-particle reaction-diffusion simulations result in the self-assembly of crystals made of a controllable number of stacked, same-type colloid planes. The number of planes is controlled by NL (NL = 50, 75, and 100 in a, b, and c) and the chemical potential (ρid = 10−7 , 10−6 , and 10−4 in d, e, and f). In the top a… view at source ↗

**Figure 4.** Figure 4: Evolution of the number of complexes. (a) Average number of two- (b1a1 bridges) and three- (a1a2b1) strand complexes (n (2) ps and n (3) ps , respectively), formed between A-type colloids and the surface as a function of time. (b,c) Bottom view of the steady configurations. The color map highlights the number of (b) two- and (c) three-strand complexes featured by colloids in contact with the surface. We s… view at source ↗

**Figure 5.** Figure 5: Number of complexes found at different layers. The figure reports the average number of different complexes featured by colloids belonging to a given layer identified by the colloid-surface distance (rS). (a) Number of loops (n l , circles) and free strand (n f , squares). (b) Two-strand bridges formed by a and b ligands (circles), and by two a ligands (squares). (c) Three-strand complexes featuring two a… view at source ↗

**Figure 6.** Figure 6: Self-assembly is limited by reaction kinetics. We report the number of particles in the aggregate as a function of time for different values of τ0 (Eqs. 2, 3). This parameter controls the reaction timescales without affecting the equilibrium states. Increasing τ0 leads to larger aggregates. We set ρS = 0.28L −2 , NL = 75, β∆G0 = −20, β∆GT = −2, and ρid = 10−5 . To check if the previous considerations appl… view at source ↗

**Figure 7.** Figure 7: Number of particles vs simulation time for two different NL. We set ρid = 10−5 , ρS = 0.28L −2 , β∆G0 = −20, and β∆GT = −2 (as in Main Fig. 3a and c). xix view at source ↗

**Figure 8.** Figure 8: Number of particles vs simulation time for different chemical potentials µ (µ ∼ kBT log ρid ). We set ρS = 0.28L −2 , β∆G0 = −20, and β∆GT = −2. (a) (b) (c) view at source ↗

**Figure 9.** Figure 9: Same as in Main Fig. 5 but with view at source ↗

**Figure 10.** Figure 10: Same as in Main Fig. 5 but with view at source ↗

**Figure 11.** Figure 11: Number of particles vs simulation time for different ∆GT . We set ρid = 10−5 , ρS = 0.28L −2 , β∆G0 = −20, and NL = 75. B Configurational Entropies view at source ↗

**Figure 12.** Figure 12: Complexes’ Configurational Entropies. (a) The configurational volumes available to complexes play a crucial role in determining the forces between the particles and the reaction equilibrium constants. The configuration volumes of bridges (b) and loops/free strands (c) are calculated as the volume available to the sticky ends. We assume that the motility of the complexes (ligands, loops, and bridges) is si… view at source ↗

read the original abstract

We design a system with a binary suspension of colloids and a surface that triggers the self-assembly of crystallites with a finite thickness. The proposed design allows controlling the number of layers forming the aggregate and constrains the two types of particles to lie on different planes. These functionalities are achieved by decorating the colloids and the surface with multiple DNA oligomers featuring specific interactions. The surface triggers a chain of reactions between DNA oligomers, leading to localized self-assembly. Equilibrium principles control the thickness of the aggregates. Instead, compositional order is achieved by engineering the reaction kinetics between DNA oligomers in a way that limits interactions between colloids of the same type. We validate our design using theory and reaction-diffusion simulation algorithms, which capture the multibody nature of the interactions. This work demonstrates how engineering the kinetics provides a new avenue for controlling the morphology of aggregates assembled by DNA.

Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, simulated authors' rebuttal, and a circularity audit. Tearing a paper down is the easy half of reading it; the pith above is the substance, this is the friction.

Desk Editor's Note private letter to a colleague

The paper offers a DNA-colloid design that tries to set layer thickness by equilibrium while using kinetics for compositional order, but the two controls are probably coupled through the same sequence parameters.

read the letter

The main takeaway is a concrete proposal for binary DNA-decorated colloids that assemble into finite-thickness layers on a triggering surface, with the two particle types forced onto alternate planes. Equilibrium affinities are meant to fix the stack height while reaction rates are engineered to block same-type sticking. They back this with theory plus reaction-diffusion simulations that include multibody effects and surface localization via chained DNA reactions. That combination of localization, thickness control, and order enforcement is the new piece relative to earlier DNA-colloid work. The design itself is laid out clearly enough that a reader can see how the surface starts the process and how the kinetic barrier is supposed to act. The simulations are the right tool for checking whether the intended separation actually produces the morphology. The soft spot is the claimed independence of equilibrium and kinetics. DNA on-rates, off-rates, and free energies are tied to the same sequence choices, so tuning to suppress A-A or B-B binding will shift the binding strengths that set layer number. The paper asserts the simulations validate the design, but it needs to show the specific parameter sets and demonstrate that thickness remains stable when the kinetic modifications are applied. If the model simply uses the same DNA parameters for both regimes, the separation is not independently tested. Cross-reactivity and off-target binding are also assumed to be negligible, which is reasonable for a design paper but still requires at least a sensitivity check. This is for groups working on programmable colloidal assembly or DNA nanotechnology who want ideas for ordered aggregates. A reader building bottom-up materials would pick up the surface-trigger and kinetic-ordering tricks. The work is coherent on its own terms and shows clear thinking about the controls, so it deserves a serious referee even though the decoupling needs tighter evidence.

Referee Report

2 major / 2 minor

Summary. The manuscript proposes a design for a binary colloidal suspension and functionalized surface decorated with multiple DNA oligomers that triggers localized self-assembly into crystallites of finite, controllable thickness with compositional order (particles of different types constrained to distinct planes). Thickness is asserted to be set by equilibrium binding principles, while compositional order is imposed by kinetic engineering that suppresses same-type colloid interactions; the design is validated through theory and reaction-diffusion simulations that incorporate multibody interactions.

Significance. If the equilibrium-kinetics separation can be realized without feedback, the approach offers a route to morphology control in DNA-mediated colloidal assembly that goes beyond purely thermodynamic designs, with potential applications in layered materials. The explicit use of reaction-diffusion simulations to capture multibody effects is a positive methodological choice, though the absence of quantitative error analysis, specific parameter values, or direct comparisons to equilibrium-only cases in the validation limits the strength of the supporting evidence.

major comments (2)

[Design and validation sections] The central design claim requires decoupling equilibrium control of thickness from kinetic control of order, but DNA sequence design inherently links on-rates, off-rates, and equilibrium constants (K_eq = k_on/k_off). No derivation or parameter scan is provided showing that sequences can be chosen to suppress A-A/B-B kinetics while preserving the surface-particle and inter-layer affinities needed for finite stacking. This appears in the design description and validation sections.
[Validation section] The abstract and validation statement assert that theory and reaction-diffusion simulations confirm the design, yet no quantitative metrics (e.g., layer-number histograms, order parameters, or comparison of simulated vs. predicted thickness) or parameter values are referenced. Without these, it is impossible to assess whether the simulations actually demonstrate independent control or merely reproduce the input assumptions.

minor comments (2)

Notation for the distinct DNA oligomers (e.g., labels for surface vs. particle strands) should be introduced with a table or explicit definitions early in the manuscript to improve readability.
The reaction-diffusion model description would benefit from a brief statement of the diffusion coefficients and reaction rate constants used, even if they are illustrative.

Simulated Author's Rebuttal

2 responses · 0 unresolved

We thank the referee for their constructive and detailed comments on our manuscript. We address each major comment below and will revise the manuscript to incorporate additional details and quantitative validation as suggested.

read point-by-point responses

Referee: [Design and validation sections] The central design claim requires decoupling equilibrium control of thickness from kinetic control of order, but DNA sequence design inherently links on-rates, off-rates, and equilibrium constants (K_eq = k_on/k_off). No derivation or parameter scan is provided showing that sequences can be chosen to suppress A-A/B-B kinetics while preserving the surface-particle and inter-layer affinities needed for finite stacking. This appears in the design description and validation sections.

Authors: We agree that for any given hybridization reaction the on-rate, off-rate and equilibrium constant are linked. However, our design uses multiple orthogonal DNA sequences assigned to distinct interaction types (surface-A, A-B, B-surface, etc.). For A-A and B-B pairs we select sequences with minimal or no complementarity, rendering their k_on and K_eq negligibly small and thereby suppressing same-type interactions. The sequences for the required surface-particle and hetero inter-layer bindings are chosen independently to maintain strong complementarity and the affinities needed for finite stacking. Equilibrium thus governs layer number via the hetero-binding energies, while the absence of same-type binding enforces compositional order. We will add to the revised manuscript a short derivation of the binding-energy conditions together with example sequence choices and a parameter scan confirming that finite thickness and order can be achieved simultaneously. revision: yes
Referee: [Validation section] The abstract and validation statement assert that theory and reaction-diffusion simulations confirm the design, yet no quantitative metrics (e.g., layer-number histograms, order parameters, or comparison of simulated vs. predicted thickness) or parameter values are referenced. Without these, it is impossible to assess whether the simulations actually demonstrate independent control or merely reproduce the input assumptions.

Authors: We acknowledge that the validation section presents results qualitatively and does not include explicit quantitative metrics, tabulated parameters, or comparisons to equilibrium-only cases. In the revised manuscript we will add: (i) histograms of assembled layer numbers, (ii) compositional order parameters (e.g., layer-resolved type fractions), (iii) a table of all simulation parameters, and (iv) a direct comparison of simulated average thickness against the equilibrium-theory prediction. We will also include equilibrium-only control simulations to demonstrate the necessity of the kinetic suppression. These additions will allow quantitative assessment of independent control. revision: yes

Circularity Check

0 steps flagged

No circularity: design claims rest on independent engineering choices, not self-referential fits or citations

full rationale

The paper presents a colloidal design using DNA oligomers where thickness is controlled by equilibrium binding affinities and compositional order by separate kinetic engineering to suppress same-type interactions. No equations, fitted parameters, or derivation steps are exhibited that reduce either claim to a quantity defined by the result itself. Validation via reaction-diffusion simulations is asserted to capture multibody effects without evidence that the model parameters are constructed from the target morphology. No self-citation load-bearing steps or uniqueness theorems imported from prior author work appear in the provided text. The separation of equilibrium and kinetics is framed as a design feature rather than a tautological prediction.

Axiom & Free-Parameter Ledger

0 free parameters · 1 axioms · 0 invented entities

Based solely on the abstract, the design rests on standard assumptions of DNA hybridization specificity and colloidal interaction models; no explicit free parameters or new entities are named.

axioms (1)

domain assumption DNA oligomers can be engineered to exhibit the required binding affinities and kinetic rates without significant cross-reactivity
Invoked to achieve both equilibrium thickness control and kinetic compositional ordering.

pith-pipeline@v0.9.0 · 5460 in / 1273 out tokens · 38346 ms · 2026-05-09T17:58:41.411859+00:00 · methodology

discussion (0)

Reference graph

Works this paper leans on

62 extracted references

[1]

A.; Letsinger, R

Mirkin, C. A.; Letsinger, R. L.; Mucic, R. C.; Storhoff, J. J. A DNA -based method for rationally assembling nanoparticles into macroscopic materials. Nature 1996, 382, 607--609

1996
[2]

P.; Johnsson, K

Alivisatos, A. P.; Johnsson, K. P.; Peng, X.; Wilson, T. E.; Loweth, C. J.; Bruchez, M. P.; Schultz, P. G. Organization of 'nanocrystal molecules' using DNA . Nature 1996, 382, 609--611

1996
[3]

R.; Seeman, N

Jones, M. R.; Seeman, N. C.; Mirkin, C. A. Programmable materials and the nature of the DNA bond. Science 2015, 347, 1260901

2015
[4]

A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics

SantaLucia, J. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc.\ Natl.\ Acad.\ Sci.\ U.\ S.\ A. 1998, 95, 1460--1465

1998
[5]

E.; Porubsky, N

Fornace, M. E.; Porubsky, N. J.; Pierce, N. A. A unified dynamic programming framework for the analysis of interacting nucleic acid strands: enhanced models, scalability, and speed. ACS Synthetic Biology 2020, 9, 2665--2678

2020
[6]

H.; Eiser, E.; Foffi, G

Varrato, F.; Di Michele, L.; Belushkin, M.; Dorsaz, N.; Nathan, S. H.; Eiser, E.; Foffi, G. Arrested demixing opens route to bigels. Proc.\ Natl.\ Acad.\ Sci.\ U.\ S.\ A. 2012, 109, 19155--19160

2012
[7]

L.; Wang, T.; Emamy, H.; Li, H.; Yager, K

Liu, W.; Tagawa, M.; Xin, H. L.; Wang, T.; Emamy, H.; Li, H.; Yager, K. G.; Starr, F. W.; Tkachenko, A. V.; Gang, O. Diamond family of nanoparticle superlattices. Science 2016, 351, 582--586

2016
[8]

C.; McGinley, J

Wang, Y.; Jenkins, I. C.; McGinley, J. T.; Sinno, T.; Crocker, J. C. Colloidal crystals with diamond symmetry at optical lengthscales. Nat.\ Commun. 2017, 8, 14173

2017
[9]

Ducrot, \'E .; He, M.; Yi, G.-R.; Pine, D. J. Colloidal alloys with preassembled clusters and spheres. Nat.\ Mater. 2017, 16, 652

2017
[10]

Table of Elements

Macfarlane, R. J.; O'Brien, M. N.; Petrosko, S. H.; Mirkin, C. A. Nucleic Acid‐Modified Nanostructures as Programmable Atom Equivalents: Forging a New “Table of Elements”. Angew.\ Chem., Int.\ Ed. 52, 5688--5698
[11]

M.; van der Lelie, D.; Gang, O

Nykypanchuk, D.; Maye, M. M.; van der Lelie, D.; Gang, O. DNA -guided crystallization of colloidal nanoparticles. Nature 2008, 451, 549--552

2008
[12]

Y.; Lytton-Jean, A

Park, S. Y.; Lytton-Jean, A. K. R.; Lee, B.; Weigand, S.; Schatz, G. C.; Mirkin, C. A. DNA -programmable nanoparticle crystallization. Nature 2008, 451, 553--556

2008
[13]

Preparation Techniques, Design Strategies of Responsive Photonic Crystals and Their Typical Applications in the Field of Sensing

Ye, R.; Yang, R.; Hu, L.; Li, Z.; Luo, Z.; Chen, X. Preparation Techniques, Design Strategies of Responsive Photonic Crystals and Their Typical Applications in the Field of Sensing. Crystals 2026, 16, 232

2026
[14]

D.; Tkachenko, A

Halverson, J. D.; Tkachenko, A. V. DNA-programmed mesoscopic architecture. Phys.\ Rev.\ E 2013, 87, 062310

2013
[15]

Patra, N.; Tkachenko, A. V. Layer-by-layer assembly of patchy particles as a route to nontrivial structures. Phys.\ Rev.\ E 2017, 96, 022601

2017
[16]

K.; Mognetti, B

Jana, P. K.; Mognetti, B. M. Surface-triggered cascade reactions between DNA linkers direct the self-assembly of colloidal crystals of controllable thickness. Nanoscale 2019, 11, 5450--5459

2019
[17]

A.; Holmes-Cerfon, M

Marbach, S.; Zheng, J. A.; Holmes-Cerfon, M. The nanocaterpillar's random walk: diffusion with ligand--receptor contacts. Soft Matter 2022, 18, 3130--3146

2022
[18]

Lowensohn, J.; Stevens, L.; Goldstein, D.; Mognetti, B. M. Sliding across a surface: Particles with fixed and mobile ligands. The Journal of Chemical Physics 2022, 156

2022
[19]

Phase-transition-like behaviors of sequence-selective dynamic bonds

Dai, X.; Wang, Y.; Wei, W.; Jiao, Z.; Chen, W.; Cheng, L.; Yan, L.-T. Phase-transition-like behaviors of sequence-selective dynamic bonds. Proceedings of the National Academy of Sciences 2026, 123, e2514117123

2026
[20]

S.; Weck, M.; Pine, D

Wang, Y.; Wang, Y.; Zheng, X.; Ducrot, \'E .; Yodh, J. S.; Weck, M.; Pine, D. J. Crystallization of DNA-coated colloids. Nature communications 2015, 6, 7253

2015
[21]

L.; Kim, A

Biancaniello, P. L.; Kim, A. J.; Crocker, J. C. Colloidal interactions and self-assembly using DNA hybridization. Physical review letters 2005, 94, 058302

2005
[22]

Proceedings of the National Academy of Sciences 2020, 117, 5617--5623

Zhou, X.; Yao, D.; Hua, W.; Huang, N.; Chen, X.; Li, L.; He, M.; Zhang, Y.; Guo, Y.; Xiao, S.; others Programming colloidal bonding using DNA strand-displacement circuitry. Proceedings of the National Academy of Sciences 2020, 117, 5617--5623

2020
[23]

E.; Seyforth, H.; Jacobs, W

Hensley, A.; Videb k, T. E.; Seyforth, H.; Jacobs, W. M.; Rogers, W. B. Macroscopic photonic single crystals via seeded growth of DNA-coated colloids. Nature communications 2023, 14, 4237

2023
[24]

Y.; Winfree, E

Zhang, D. Y.; Winfree, E. Control of DNA strand displacement kinetics using toehold exchange. Journal of the American Chemical Society 2009, 131, 17303--17314

2009
[25]

Parolini, L.; Kotar, J.; Di Michele, L.; Mognetti, B. M. Controlling self-assembly kinetics of DNA-functionalized liposomes using toehold exchange mechanism. ACS nano 2016, 10, 2392--2398

2016
[26]

B.; Manoharan, V

Rogers, W. B.; Manoharan, V. N. Programming colloidal phase transitions with DNA strand displacement. Science 2015, 347, 639--642

2015
[27]

K.; Mognetti, B

Jana, P. K.; Mognetti, B. M. Self-assembly of finite-sized colloidal aggregates. Soft matter 2020, 16, 5915--5924

2020
[28]

K.; Bruylants, G.; Cicuta, P.; Mognetti, B

Lanfranco, R.; Jana, P. K.; Bruylants, G.; Cicuta, P.; Mognetti, B. M.; Di Michele, L. Adaptable DNA interactions regulate surface-triggered self-assembly. Nanoscale 2020, 12, 18616--18620

2020
[29]

Robust self-replication of combinatorial information via crystal growth and scission

Schulman, R.; Yurke, B.; Winfree, E. Robust self-replication of combinatorial information via crystal growth and scission. Proceedings of the national academy of sciences 2012, 109, 6405--6410

2012
[30]

D.; Schulman, R.; Rothemund, P

Barish, R. D.; Schulman, R.; Rothemund, P. W.; Winfree, E. An information-bearing seed for nucleating algorithmic self-assembly. Proceedings of the National Academy of Sciences 2009, 106, 6054--6059

2009
[31]

G.; O’Brien, J.; Winfree, E.; Murugan, A

Evans, C. G.; O’Brien, J.; Winfree, E.; Murugan, A. Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly. Nature 2024, 625, 500--507

2024
[32]

S.; Elghanian, R.; Thomas, A

Thaxton, C. S.; Elghanian, R.; Thomas, A. D.; Stoeva, S. I.; Lee, J.-S.; Smith, N. D.; Schaeffer, A. J.; Klocker, H.; Horninger, W.; Bartsch, G.; Mirkin, C. A. Nanoparticle-based bio-barcode assay redefines ``undetectable''PSA and biochemical recurrence after radical prostatectomy. Proc.\ Natl.\ Acad.\ Sci.\ U.\ S.\ A. 2009, 106, 18437--18442

2009
[33]

Chapman, R.; Lin, Y.; Burnapp, M.; Bentham, A.; Hillier, D.; Zabron, A.; Khan, S.; Tyreman, M.; Stevens, M. M. Multivalent Nanoparticle Networks Enable Point-of-Care Detection of Human Phospholipase-A2 in Serum. ACS Nano 2015, 9, 2565--2573, PMID: 25756526

2015
[34]

J.; Frenkel, D

Martinez-Veracoechea, F. J.; Frenkel, D. Designing super selectivity in multivalent nano-particle binding. Proceedings of the National Academy of Sciences 2011, 108, 10963--10968

2011
[35]

A.; Tkachenko, A

Licata, N. A.; Tkachenko, A. V. Kinetic limitations of cooperativity-based drug delivery systems. Physical review letters 2008, 100, 158102

2008
[36]

Self-assembly of DNA origami for nanofabrication, biosensing, drug delivery, and computational storage

He, Z.; Shi, K.; Li, J.; Chao, J. Self-assembly of DNA origami for nanofabrication, biosensing, drug delivery, and computational storage. Iscience 2023, 26

2023
[37]

Advances in programmable DNA nanostructures enabling stimuli-responsive drug delivery and multimodal biosensing

Hong, Y.; Ma, W.; Wang, M.; Wang, H.-H. Advances in programmable DNA nanostructures enabling stimuli-responsive drug delivery and multimodal biosensing. RSC Chemical Biology 2025, 6, 1366--1385

2025
[38]

van der Meulen, S. A. J.; Leunissen, M. E. Solid Colloids with Surface-Mobile DNA Linkers. J. Am. Chem. Soc. 2013, 135, 15129--15134

2013
[39]

W.; Chakraborty, I.; Kraft, D

Rinaldin, M.; Verweij, R. W.; Chakraborty, I.; Kraft, D. J. Colloid supported lipid bilayers for self-assembly. Soft Matter 2019,

2019
[40]

A.; Vanderlick, T

Beales, P. A.; Vanderlick, T. K. Specific Binding of Different Vesicle Populations by the Hybridization of Membrane-Anchored DNA . J. Phys. Chem. A 2007, 111, 12372--12380

2007
[41]

T.; Fellermann, H.; Eggenberger Hotz, P.; Hanczyc, M

Hadorn, M.; Boenzli, E.; S rensen, K. T.; Fellermann, H.; Eggenberger Hotz, P.; Hanczyc, M. M. Specific and reversible DNA -directed self-assembly of oil-in-water emulsion droplets. Proc.\ Natl.\ Acad.\ Sci.\ U.\ S.\ A. 2012, 109, 20320--20325

2012
[42]

M.; Kotar, J.; Eiser, E.; Cicuta, P.; Di Michele, L

Parolini, L.; Mognetti, B. M.; Kotar, J.; Eiser, E.; Cicuta, P.; Di Michele, L. Volume and porosity thermal regulation in lipid mesophases by coupling mobile ligands to soft membranes. Nat.\ Commun. 2015, 6, 5948

2015
[43]

M.; Frenkel, D

Angioletti-Uberti, S.; Varilly, P.; Mognetti, B. M.; Frenkel, D. Mobile linkers on DNA-coated colloids: valency without patches. Phys.\ Rev.\ Lett. 2014, 113, 128303--128306

2014
[44]

M.; Cicuta, P.; Di Michele, L

Mognetti, B. M.; Cicuta, P.; Di Michele, L. Programmable interactions with biomimetic DNA linkers at fluid membranes and interfaces. Reports on progress in physics 2019, 82, 116601

2019
[45]

J.; Kotar, J.; Parolini, L.; S ari \'c , A.; Cicuta, P.; Di Michele, L.; Mognetti, B

Bachmann, S. J.; Kotar, J.; Parolini, L.; S ari \'c , A.; Cicuta, P.; Di Michele, L.; Mognetti, B. M. Melting transition in lipid vesicles functionalised by mobile DNA linkers. Soft Matter 2016, 12, 7804--7817

2016
[46]

Sciortino, F.; Zhang, Y.; Gang, O.; Kumar, S. K. Combinatorial-entropy-driven aggregation in DNA-grafted nanoparticles. ACS nano 2020, 14, 5628--5635

2020
[47]

A.; Mahmoudabadi, G.; Milam, V

Baker, B. A.; Mahmoudabadi, G.; Milam, V. T. Strand displacement in DNA-based materials systems. Soft Matter 2013, 9, 11160--11172

2013
[48]

K.; Milam, V

Tison, C. K.; Milam, V. T. Programming the kinetics and extent of colloidal disassembly using a DNA trigger. Soft Matter 2010, 6, 4446--4453

2010
[49]

C.; Brujic, J.; Chaikin, P

Zhang, Y.; McMullen, A.; Pontani, L.-L.; He, X.; Sha, R.; Seeman, N. C.; Brujic, J.; Chaikin, P. M. Sequential self-assembly of DNA functionalized droplets. Nat.\ Commun. 2017, 8, 21

2017
[50]

Designing 3D multicomponent self-assembling systems with signal-passing building blocks

Evans, J.; S ulc, P. Designing 3D multicomponent self-assembling systems with signal-passing building blocks. The Journal of Chemical Physics 2024, 160

2024
[51]

D.; Tkachenko, A

Halverson, J. D.; Tkachenko, A. V. Sequential programmable self-assembly: Role of cooperative interactions. The Journal of chemical physics 2016, 144

2016
[52]

S.; Petitzon, M.; Mognetti, B

Bachmann, J. S.; Petitzon, M.; Mognetti, B. M. Bond formation kinetics affects self-assembly directed by ligand-receptor interactions. Soft Matter 2016, 12, 9585--9592

2016
[53]

Ranganathan, S.; Shakhnovich, E. I. Dynamic metastable long-living droplets formed by sticker-spacer proteins. Elife 2020, 9, e56159

2020
[54]

Gillespie, D. T. Exact stochastic simulation of coupled chemical reactions. The journal of physical chemistry 1977, 81, 2340--2361

1977
[55]

E.; S ulc, P.; Schaeffer, J

Srinivas, N.; Ouldridge, T. E.; S ulc, P.; Schaeffer, J. M.; Yurke, B.; Louis, A. A.; Doye, J. P.; Winfree, E. On the biophysics and kinetics of toehold-mediated DNA strand displacement. Nucleic acids research 2013, 41, 10641--10658

2013
[56]

L.; Dehmelt, F

Ho, D.; Zimmermann, J. L.; Dehmelt, F. A.; Steinbach, U.; Erdmann, M.; Severin, P.; Falter, K.; Gaub, H. E. Force-driven separation of short double-stranded DNA. Biophysical journal 2009, 97, 3158--3167

2009
[57]

Mitra, G.; Chang, C.; McMullen, A.; Puchall, D.; Brujic, J.; Hocky, G. M. A coarse-grained simulation model for colloidal self-assembly via explicit mobile binders. Soft Matter 2023, 19, 4223--4236

2023
[58]

P.; Tildesley, D

Allen, M. P.; Tildesley, D. J. Computer simulation of liquids; Oxford university press, 2017

2017
[59]

Propagation of large concentration changes in reversible protein-binding networks

Maslov, S.; Ispolatov, I. Propagation of large concentration changes in reversible protein-binding networks. Proceedings of the National Academy of Sciences 2007, 104, 13655--13660

2007
[60]

J.; Parolini, L.; Mognetti, B

Di Michele, L.; Bachmann, S. J.; Parolini, L.; Mognetti, B. M. Communication: free energy of ligand-receptor systems forming multimeric complexes. The Journal of Chemical Physics 2016, 144

2016
[61]

Understanding molecular simulation: from algorithms to applications; elsevier, 2023

Frenkel, D.; Smit, B. Understanding molecular simulation: from algorithms to applications; elsevier, 2023

2023
[62]

E.; Sha, R.; Tkachenko, A

Dreyfus, R.; Leunissen, M. E.; Sha, R.; Tkachenko, A. V.; Seeman, N. C.; Pine, D. J.; Chaikin, P. M. Simple Quantitative Model for the Reversible Association of DNA Coated Colloids. Phys. Rev. Lett. 2009, 102, 048301 mcitethebibliography document

2009